bone.wiki - User contributions [en]

Scanco Administration

2021-06-23T14:45:15Z

Yingzhu: /* USB Device Usage with Scanco Backup/Archive Software */

=OpenVMS=

==OpenVMS References==
*[[Media:OpenVMS Users Manual.PDF| OpenVMS User Manual]]
*[[Media:Vmsfaq.pdf| OpenVMS FAQ]]

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==Unix related==
*[[Media:Vms-unix-commands.pdf| OpenVMS Commands with UNIX equivalents]]

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===Unix filenames on VMS with multiple '.'===

The directory names would have been cvs-1.11.21.dir on Linux. However VMS doesn't allow more than 1 . in the name. If you enter

<pre>$ set process/parse=extended</pre>

in a terminal you'll be able to access these files. You could consider renaming them i.e. cvs-1_11_21.dir.

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===Unix command line basics===
====Twelve Essential Commands====

These are the commands which you have to know in order to be basically functional with a shell (command line).

{|
|-valign="top"
|width="80pt"| <tt>ls</tt>
| List directory contents.

<tt>ls -l</tt> long listing with dates and permissions

<tt>ls -a</tt> list all, including hidden files (hidden files start with a period)

|-valign="top"
| <tt>cd</tt>
| Change directory.

<tt>cd -</tt> change to previous directory

<tt>cd ~</tt> change to home directory

<tt>cd ..</tt> change to parent directory

|-valign="top"
| <tt>pwd</tt>
| Print current (working) directory.
|-valign="top"
| <tt>cp</tt>
| Copy file(s).

<tt>cp -r somedir somedest</tt> Copy recursively (directory and all contents)

|-valign="top"
| <tt>mv</tt>
| Move (or rename) a file (or directory)
|-valign="top"
| <tt>rm</tt>
| Delete (remove) a file.

<tt>rm -r somedir</tt> Delete recursively (directory and all contents)

<tt>rm -ri somedir</tt> Delete recursively, but prompt before each removal

<tt>rm -rf somedir</tt> Delete recursively, never prompt

|-valign="top"
| <tt>mkdir</tt>
| Create directory.
|-valign="top"
| <tt>rmdir</tt>
| Remove (empty) directory.
|-valign="top"
| <tt>cat</tt>
| Print file contents (to console).
|-valign="top"
| <tt>less</tt>
| Scroll through file contents, one page at a time. SPACEBAR to advance a page, B to go back a page, Q to quit, /pattern to search for pattern
|-valign="top"
| <tt>man</tt>
| Get help on <tt>command</tt>. (eg. <tt>man ls</tt> for help on <tt>ls</tt>). You move around in man as you do with less: SPACEBAR is forward a page, and so on.
|-valign="top"
| <tt>exit</tt>
| Close shell (i.e. the terminal). If this is your login shell, you will log out.
|}

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====File names with spaces====

Spaces on the command line separate arguments. Therefore file names containing spaces require special treatment to avoid being interpreted as two separate files. There are a couple of methods. You can use quotes:

cp "file name with spaces" file_name_without_spaces

You can also use the backslash, which indicates that any special significance is to be removed from the following character. Thus a space, instead of being the delimiter for arguments on a command line, is to be interpreted as a regular character.

cp file\ name\ with\ spaces file_name_without_spaces

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====Copying and pasting====

Copying and pasting in a terminal is generally done with the middle mouse button. Just mark the text you want to copy with the mouse, holding down the left mouse button in the usual way. Then move the cursor (which is different than the mouse pointer - move the cursor with arrow keys typically) to where you want to insert and click the middle mouse button (on a wheel mouse the middle button is the wheel).

Tip: You can double-click to mark a whole work, or triple-click to mark a whole line. Remember - you haven't only marked it, you've put it in the clipboard.

Note: This applies to X11, for example on Linux. If using OS-X, just use Option-C and Option-V as usual.

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====Recalling previous commands====

You can scroll though your previous commands (command history) by using the UP and DOWN arrow keys.

A more advanced trick is to use CTRL-R, which is particularly useful when you want to recall a command you used some time ago. Hit CTRL-R and then start typing some fragment of the command you're searching for. The prompt will automatically update to show you the most recent match to the fragment you've typed so far. If you want the matching command previous to the one shown, hit CTRL-R again. Once you've got the previous command you're looking for, hit ENTER to run it again, or start editing it.

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====Be lazy: use TAB to minimize typing====

Some commands and especially some file names can be pretty long. Don't want to type it all? Type the first few letters, then hit TAB. The shell will fill in the rest, as far as there is a unique completion (either command or filename). If there is not a unique completion to the end, you might have to type another character or two and then hit TAB again.

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====Keyboard Shortcuts====

Here are some common command line keyboard shortcuts. Some of these are bash-specific shortcuts, so not all of them will work on all systems.

Note: If you're using OS-X, a number of the editing shortcuts below work in ALL programs in OS-X. (With the sad exception of Microsoft Office, which overrides the system-wide key bindings.)

{|
|+ Table 1. Common editing key bindings
|-
|width="80pt"| <tt>CTRL-A</tt> || Move to the end of the line.
|-
| <tt>CTRL-E</tt> || Move to the beginning of the line.
|-
| <tt>CTRL-F</tt> || Move forward one character.
|-
| <tt>CTRL-B</tt> || Move backward one character.
|-
| <tt>ALT-F</tt> || Move forward one word.
|-
| <tt>ALT-B</tt> || Move backward one word.
|-
| <tt>CTRL-D</tt> || Delete one character forward.
|-
| <tt>CTRL-H</tt> || Delete one character backward.
|-
| <tt>ALT-D</tt> || Delete one word forward.
|-
| <tt>CTRL-W</tt> || Delete one word backwards.
|-
| <tt>CTRL-K</tt> || Delete (Kill) everything from the cursor forwards (to the end of the line).
|-
| <tt>CTRL-U</tt> || Delete everything from the cursor backwards (to the beginning of the line).
|-
| <tt>CTRL-T</tt> || Transpose two characters.
|-
| <tt>ALT-T</tt> || Transpose two words.
|-
| <tt>ESC .</tt> || Insert the last argument (word) from the previous command.
|-
| <tt>CTRL-X-X</tt> || Move between end of line and current cursor position
|}

{|
|+ Table 2. Common control key bindings
|width="80pt"| <tt>CTRL-C</tt> || Terminate the current program, or sometimes cancel some operation.
|-
| <tt>CTRL-\</tt> || Seriously kill the current program! Use only after <tt>CTRL-C</tt> has failed.
|-
| <tt>CTRL-D</tt> || End-of-file. This is often used to signal the end of input, or to exit a program.
|-
| <tt>CTRL-G</tt> || Cancel the current operation. An occasionally useful command to get yourself out of things.
|-
| <tt>CTRL-L</tt> || Redraw the console. Mostly useful if some program running in the background spews a lot of stuff onto your terminal.
|-
| <tt>CTRL-Q</tt> || The only time you need this is if you accidently hit <tt>CTRL-S</tt>. In that case the console is locked until you hit CTRL-Q to unlock it. Apparently once a long long time ago this was actually a useful feature.
|-
| <tt>CTRL-R</tt> || Recall command containing characters. After hitting <tt>CTRL-R</tt>, type the fragment you want to search for. If it returns a command which isn't the one one want, hit <tt>CTRL-R</tt> again to cycle through matches.
|-
| <tt>CTRL-Z</tt> || Suspend the current program and put it in the background. This is very useful once you figure out how it works. Refer to the section on putting jobs in the background.
|}

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====Using scp to copy files between computers====

scp is a secure copy command that works bewteen computers. Typically any computer that supports ssh also supports scp. You must have an actual user account on the target computer, so for example you typically won't be able to scp to mike.kin .

scp works just like the cp command, with a few extra decorations:

scp eric@mighty-mac.kin.ucalgary.ca:Documents/important_file.txt .

In this example the file I want to copy is on the computer mighty-mac.kin.ucalgary.ca, and I used eric@ to specify my user name. You can leave off the user name if it is the same on both computers. The period as the destination is just standard Unix short-hand for the current directory. You can use the -r flag to copy whole directories. For example:

scp -r calculations mighty-mac.kin.ucalgary.ca:Documents/Projects

In this example calculations is a directory containing many files, and possibly subdirectories. This example copies files to mighty-mac instead of from it.

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====Running long calculations====

Here are some useful tips for running long jobs.

=====Getting the prompt back after starting a job=====

Use & at the end of the command. This puts the job in the background. For example:

./myjob someargs &

To see all your background jobs (the ones started in the current shell), enter:

jobs

To bring one of these to the foreground, use:

fg %n

where <tt>n</tt> is the job number (yes it needs a <tt>%</tt> in front of it). To move it to the background again, hit CTRL-Z. This however doesn't just move the job to the background, it suspends it. To get it running again, use

bg %n

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=====Keeping a job running after you log out=====

Use nohup. For example, suppose you want to run <tt>./myjob 20</tt>. In this case, you could use:

nohup nice ./myjob 20 &> output &

There are several things to note here:

* The <tt>&</tt> at the end of the command line is there so you get the command prompt back immediately (see the previous section).
* We have redirected the output to a file out_file with <tt>&> output</tt>. If you don't do this, any output to STDIN (normally the console) will automatically go into a file called <tt>nohup.out</tt>.
* We've niced the job to reduce it's execution priority. This is courteous if you're a multiuser system.

If you want to see what's in nohup.out (or whatever you called it) at any time, you can do the usual

cat nohup.out

Here's another potentially more useful command:

tail -f nohup.out

tail shows you the last few lines of the files. In addition, the -f flag ("follow") means that as lines get added to the file, they are displayed on the screen. This looks just like when you run the program without nohup, except when you hit CTRL-C, the program keeps on running in the background.

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=====Finding out if any of your jobs are still running=====

This command will show all jobs that belong to user "eric":

ps -u eric

Another useful command is "top", which will show interactively which processes are using the most processor cycles.

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=====Terminating a job prematurely=====

If you decide that you want to kill the job before it completes, this is the command:

kill PID

where PID is the actual PID (a number) of the process. You find the PID with 'top' or 'ps -u eric' (replace eric by your user ID of course).

Occasionally a process will decline to terminate when you request it to. This is the more brutal, never-fails method to kill a job immediately:

kill -s KILL PID

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=====Suspending a long-running job and restarting it later=====

First find the PID (process ID) with top or with ps. For example, I might list all jobs belonging to me with:

ps -u eric

To stop the job, send it a STOP signal:

kill -s STOP PID

(replace PID with the actual PID number). It is now no longer running, but it still occupies memory (although the memory it uses will probably be swapped out to disk). When you want to resume execution, give it a CONT signal:

kill -s CONT PID

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==Graphical Applications==

===Calendar - Fix corruption===

Sometimes the calendar file can be corrupted, which is annoying every time you log onto the system.

When we login to a server through a workstation, there is a "File is not a Calendar Datafile." information message pops up.

This means that the calendar database got corrupted during an improper interruption such as a system crash due to a power outage.

To fix this, you will need to login to the Server through the Workstation

Once logged in:
cd xdefaults
dir *calendar*.dat /date

Delete the calendar file for the workstation, such as the following James workstation:
del decw$calendar_sc3401.dat

Once logged out and logged in again, you will be asked if you want to create a new calendar file.
Say "yes" there and a new calendar will open.

In the calendar window menu "options" -> "general" set the "start iconized" -> apply and "ok", then "options" -> "save settings".

So next time you log in, the calendar window will be minimized in the right lower corner.

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===Session Manager - Create a customized button===
The session manager part to enable the double-click on the AIM file:
Session Manager, 'Options', 'Menu', enter new item
SAP
with command:
<pre>
@decw$user_defaults:sap$vue
</pre>
Then move that menu point into 'Applications' menu.
Also:
'Options', 'File types', Create 'AIM' file type.
Move 'rename', 'copy', 'purge' etc. into menu, Select 'SAP', click on
'Change double click', and also move SAP into menu.

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===EVE Editor===

====Launch EVE editor====

On the command line
$ edit/display=decwindows/tpu fname.txt

Or to set it up permanently, edit <code>DISK1:[MICROCT]MICROCT_SETUP_USER.COM</code> to include

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====Configure EVE editor====

The following file, called <code>tpu.dat</code>, should be installed in <code>disk1:[microct.xdefaults]:</code>
<pre>
#
# DECTPU V3.1 1993-04-22 15:50 defaults
# CHANGED B.KOLLER 21-JUN-90
#
# Copyright (c) 1993 Digital Equipment Corporation. All rights reserved.
#
#
# The following are all the resource names that DECTPU supports.
#
Tpu.Tpu$MainWindow.Title: DECTPU Copyright © Digital Equipment Corporation 1992. All Rights Reserved.
Tpu.Tpu$MainWindow.ApplicationTitle: DECTPU
Tpu.Tpu$MainWindow.IconName: DECTPU
Tpu.Tpu$MainWindow.X: 610
Tpu.Tpu$MainWindow.Y: 0
#
# The following resource names are commented out so that users can specify
# *rows and *columns and have DECTPU obey those directives. If DECTPU finds
# finds no resource names governing the number of rows and columns it should
# have, it uses 24 rows and 80 columns.
#
#
Tpu.Tpu$MainWindow.Columns: 80
Tpu.Tpu$MainWindow.Rows: 56
*EVE_MENU_BAR*background: #ADADADADADAD
Tpu*XmScrollBar*background: #ADADADADADAD
Tpu*XmDialogShell*background: #ADADADADADAD
Tpu*XmMenuShell*background: #ADADADADADAD
*background: white
Tpu*condensedFont: OFF
Tpu*fontSetSelection: 0

# 0 = big font
# 1 = little font
# 2 = GS font (German Standard)
# 3 = Fine font (used only for non-latin 1 fonts?)
</pre>

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====EVE editor Commands====

* mark -> ctrl-space
* delete -> remove (delete)
* insert -> insert here (insert)
* learn -> ctrl-k (ctrl-r to stop)
* The right 'alt' key on the PC accesses the menu for EVE.

{| class="wikitable"
| copy
| <code><PF1><Remove></code> on VMS
|-
| paste
| <code><Insert Here></code> on VMS or <code> <ctrl><insert></code> on PC
|-
| cut
| <code><Remove> </code> on VMS or <code><delete> </code> on PC
|-
| learn
| <code><CTRL><K></code>
|-
| stop
| <code><CTRL><R> </code> (then give a key sequence such as <code><CTRL><Q></code>)
|-
| repeat
| <code><PF1><#><(CTRL-Q)> </code> (the <code>CTRL-Q </code> depends on the given key sequence).
|-
| find next
| <code><PF3></code>
|-
| enter search string
| <code><PF1><PF3></code>
|-
| replace string
| <code><PF1><S></code>
|-
| margins
| Mouse click bottom of window type: <code>set right 999</code>
|-
| kill line
| <code><PF4></code>
|-
| kill word
| - (minus key on number pad)
|-
| advance next line
| <code>0</code> (zero on number pad)
|-
| select text
| <code><CTRL><SPACE></code>
|}

*To avoid having the EVE editor automatically create multiple lines from a long input sequence set the margins [FORMAT - SET MARGINS] to some high number eg. 500.

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====Use Commands Remotely with XWin32====

Default key settings:

{| class="wikitable"
| remove (cut) and append to previous paste buffer
| <code>9</code> (nine on number pad)
|-
| paste
| <code><insert></code>
|-
| learn
| <code><CTRL><K></code>
|-
| stop
| <code><CTRL><R></code> (then give a key sequence such as <code><CTRL><Q></code>)
|-
| repeat
| <code><CTRL>-Q</code> or given key sequence
|-
| kill word
| - (minus key on number pad)
|-
| advance next line
| <code>0</code> (zero on number pad)
|-
| go to end of line
| <code>2</code> (two on number pad) or <code><CTRL><E></code>
|-
| go to start of line
| <code><backspace> or <CTRL><H></code>
|-
| go to start of word
| <code>1</code> (one on number pad)
|-
| delete line to left of cursor
| <code><CTRL></code>
|-
| turn on/off select text
| <code><CTRL><SPACE> or .</code> (on number pad)
|-
| select all text
| <code><CTRL><O></code>
|-
| turn on/off overstrike
| <code><CTRL><A></code>
|-
| save and exit
| <code><CTRL><Z></code>
|-
| enter command
| <code><CTRL></code>
|}

You may find it useful to define keys. For example, define keys to cut, copy and paste:

*To Cut <code><CTRL><X></code>:
:<code><CTRL></code> (enter command)
:Command: <code>define key=Ctrl/x cut</code>

*To Copy <code><CTRL><C></code>:
:<code><CTRL></code> (enter command)
:Command: <code>define key=Ctrl/c copy</code>

*To Paste <code><CTRL><V></code>:
:<code><CTRL></code> (enter command)
:Command: <code>define key=Ctrl/v paste</code>

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====Use terminal based editor (EVE)====
<pre>
$ edit file.txt
</pre>
If you are using this from a remote terminal, you will need to initiate a vt100 terminal.
<pre>
$ set term /vt100
</pre>
Some useful commands:
:* ctrl-z -> exit with save
:* ctrl-y -> kill without saving
:* do-key, then type 'quit' or 'exit' (what is the do key on a remote terminal?)
:* PF2 -> shows special keypad functions
:* GoldKey -> PF1

====Use EVE editor Remotely====
For remote sessions, once used $ EVE to start the text editor, press Ctrl-B to bring up a command line at the bottom of the screen.

*Command: @eveconfig

This will set backspace to delete normally.
*Ctrl-X cut
*Ctrl-C copy
*Ctrl-V paste
*Ctrl-S save file
*Ctrl-L learn command
*Ctrl-F find next
*Ctrl-Q quit
*Ctrl-O open
*Ctrl-space to select

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===Scout Views===
====View scout views in two locations====
Go to scout view directory
<pre>
XtremeCT side:
$ cd DISK1:[MICROCT.DATA.SCOUTS]

VivaCT side:
$ cd ADISK1:[VIVACT.DATA.SCOUTS]</pre>

Use the program ximage
<pre>$ x asdf.SCV</pre>

For XtremeCT users, 2 sets of scout views are saved. Scout views can be viewed from the main scouts directory (above) and in the data directory under specific patient and measurement numbers. For example using patient #: 2795 and meas#:9933:
$ cd DISK2:[MICROCT.DATA.00002795.00009933]
$ x C00008848.SCV

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====Reuse old scout views====
Reference SCV files are not overwritten. When you Save a new reference within the scout view Dialog, it writes a new version that is read by the measurement program.

If you want to return to an old scout view reference, you will have to manipulate files manually.

Typically all the scouts are accessible here:
DISK1:[MICROCT.DATA.SCOUTS]0000PPPPSS.SCV

PPPP being the patient number, and SS the Site Code number [i.e. 20,21,38,39 = RL, RR, TL, TR].

Assuming you have only version;1 and ;2 what you can do is to rename/delete version;2, so that it is not read anymore by the measurement program.
Or copy version;1 as version;3, but this is rather messy.

Note: Do not look in the measurement directories. There are copies of the SCV files, but those are not the one called by the measurement program.

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==File Operations==

===Copy and Move===
====Copy files between accounts/users====

As user <code>system</code> you can copy files between accounts (e.g., microct and devel). There is no need to set user/priv=bypass as this is set by default as user system.

If you want to copy between two users (i.e. normal users, not calibration or system), then you can only write on the user directories for which you are logged in. So, if you want
to copy files from account xtremect2 to microct, you need to log into microct account and copy the file from xtremect2 to microct

If you want to use the backup command for copying multiple subdirectories with
the three dots (e.g., <code>disk2:[microct.data.00000034...]</code>) then you HAVE to put an <code>/owner=devel</code> at the end:

<pre>
$ backup/log disk2:[microct.data.00000034...] -
disk2:[devel.data.00000034...]/own=devel
</pre>

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====Move a directory on the same device====

You can simply use the rename command to move a directory on the same device, but you need to set DELETE protection for the file owner for this to work
$ set prot=o:rwed <dir>.dir
$ ren <dir>.dir new:[parent.directory]
$ set prot=o:rwe new:[parent.directory]<dir>.dir

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====Move a whole directory structure with BACKUP command====

Sometimes we want to move entire directories. For example, moving a measurement directory from DISK2 to DISK6, or moving a project to another disk.

Here is how to move a project:
$ BACKUP DISK2:[MICROCT.PROJECTS...] DISK3:[MICROCT.PROJECTS...]/VERIFY

Note the use of <code>...</code> in both places.

If you move a data measurement, you could do it as follows:
$ BACKUP DISK2:[XTREMECT2.DATA...] DISK6:[XTREMECT2.DATA...]/LOG/VERIFY

In both cases, you can add a <code>/DELETE</code> command to so that it deletes after the move is completed and verified.
$ BACKUP/VERIFY/DELETE DISK2:[XTREMECT2.DATA...] DISK6:[XTREMECT2.DATA...]/LOG/VERIFY

Alternatively, you can simply check that the move was successful, and then delete the original files:
$ delete disk2:[microctt.projects...]*.*;*
$ dl disk2:[microctt.projects...]*.dir ! A for all; do until sub-dirs are gone

Note that I've misspelled "microctt" on purpose as these commands are VERY dangerous. You could wipe out a lot of data by accident. Be careful!

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====Fix corrupted VMS files when moved to or from a PC====

We start by getting good file format/attributes from a good aim/isq/gobj, etc.

$ ana/rms/fdl/out=correct.fdl good.aim

Then we edit the file correct.fdl, leaving only 5 lines:
RECORD
BLOCK_SPAN yes
CARRIAGE_CONTROL none
FORMAT fixed
SIZE 512

Now we have to set the file attributes of the affected aim (isq, gobi) file:

$ set file/attr=lrl=514 bad.aim ! Yes, 514
$ set file/attr=lrl=514 *.AIM ! do a bunch at a time

Finally we create a fixed file

$ convert/fdl=correct.fdl/trunc bad.aim converted.aim

This process discards the superfluous 2 bytes, usually caused by transferring to/from a PC.

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===Delete===

====Delete older versions of files====
Use the PURGE command.[[Image:Bones2.jpg|20px]] Warning: Extreme caution!
<pre>
$ PURGE !Removes older versions of all files in the directory! CAREFUL!!!!
$ PURGE myfile.aim !Removes older versions of myfile.aim.
$ PURGE /KEEP=3 !Removes all but the three most recent versions of all files.
$ HELP PURGE !More information on the PURGE command.
</pre>

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====Undelete Files====

The Disk/File Utility (DFU) will allow you to restore files that have been deleted, however, you will only be able to do so if the disk space hasn't been overwritten. This means that unless all scanning and access to the disk is stopped, you likely only have a couple of hours at most to undelete the files. 
 
Login as the system user and start the disk file utility program, DFU. 
<pre>
$ dfu
DFU> undelete diskX: /file=myfile OR undelete filepath/filename
</pre>
 
For example, suppose we want to restore an RSQ (C0001234.RSQ) that was deleted from the BH data disk (disk2): 
<pre>
DFU> undelete disk2:/file=C0001234.RSQ
</pre>
If the file can be undeleted successfully (i.e., without corruption), then you will be asked if you wish to restore the file. Type "y" or "n". 
When done restoring desired files, to get out of dfu:
<pre>
DFU> exit
$ logout
</pre>
 
*The undelete function will lock access to the disk while it searches for a file and until you respond "y" or "n" to restoring it. This means that all programs and commands trying to access the disk (i.e., by other people using the system) will appear to freeze momentarily until the disk is unlocked.
*If you search for a specific file, the lock period will be very short (maybe 15-30 seconds). If you search for files in general (e.g., *.RSQ), the lock period will be longer (maybe 5 to 10 minutes).
*You cannot search specific locations for files (i.e., a folder on a disk).
*Files are restored to their original location on disk.
*More information on DFU can be found here: http://digiater.nl/dfu.html

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====Delete a directory/file====
Use the DL command (this calls the script $ @SCOM:DL.COM), but first remove all files from the directory.
[[Image:Bones2.jpg|20px]] Warning: Extreme caution!
<pre>
$ DEL [.subdir...]*.*;* !Deletes all files in subdir. CAREFUL!!!
$ DL subdir.dir; !Deletes subdir.dir with confirmation.
$ DL disk:[dir.subdir...]*.dir !* for all; do until subdirs are gone.
</pre>

Use the DELETE command, but first remove all files from the directory and set file protections to enable deletion of the directory.
<pre>
$ SET FILE/PROT=O:RWED [.subdir...]*.*;* !Changes protections so you can delete the files. O is short for OWNER and RWED refers to Read, Write, Edit, Delete.
$ DEL [.subdir...]*.*;* !Deletes all files in subdir. CAREFUL!!!
$ SET FILE/PROTECTION=O:RWED subdir.dir !Changes protections so you can delete the subdirectory subdir.dir.
$ DEL subdir.dir; !Deletes the subdirectory.
</pre>

If the file cannot be deleted to due a permission error
<pre>
$ purge 12_RAD_FX.AIM
%PURGE-W-FILNOTPUR, error deleting DISK4:[BONELAB.PROJECTS.MULTILOAD.CAMOS]12_RAD_FX.AIM;1
-RMS-E-FLK, file currently locked by another user
</pre>
Do the following:
<pre>
$ set ho 0 ! log in as calibration
$ spb
$ del DISK4:[BONELAB.PROJECTS.MULTILOAD.CAMOS]12_RAD_FX.AIM;1
$ logout
</pre>

If that still doesn't work, then maybe you need to kill a process first:
<pre>
$ show device disk4 /file ! shows all the files currently involved in a process
$ set ho 0 ! log in as 'system'
$ stop /id=2081F1EC
$ del DISK4:[BONELAB.PROJECTS.MULTILOAD.CAMOS]12_RAD_FX.AIM;1
$ logout
</pre>

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===Authorizations===

====Can not access a Projects directory====
In principal, all Scanco user accounts (even including the calibration ones) should have read and write access to the Projects directories. While it (denied reading or writing access to a Project folder) did happen for a reason (used different accounts to create a file or a subfolder within a Projects folder), you could let lab administrator know and carefully run the following command to overwrite the authority, or switch to microct or xtremct2 account to perform as a walkaround.

<pre>
$ set file/prot=(g:rwe,o:rwe) disk4:[bonelab.projects.danielle...]*.*;*
</pre>

To avoid this happening again, make use always using the same account consistently to create all files and subfolders within their Project folder.

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==Administrative Commands==

===Query commands===
====Check licenses on VMS system====

This can be used to see what educational licenses (and other licenses) are currently on the system:

<pre>
$ SHOW LICENSE
</pre>

To apply for an educational license go to http://www.openvmsedu.com

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====Check MAC address of VMS system====
You can check them using the command
$ mcr lancp sh dev/char
For example, the result on percy.kin.ucalgary.ca gives

Device Characteristics EIA0:
Value Characteristic
----- --------------
1500 Device buffer size
Normal Controller mode
External Internal loopback mode
00-02-A5-20-29-99 Hardware LAN address
Multicast address list
CSMA/CD Communication medium
FF-FF-FF-FF-FF-FF Current LAN address
128 Minimum receive buffers
256 Maximum receive buffers
Yes Full duplex enable
Yes Full duplex operational
TwistedPair Line media type
100 Line speed (mbps)
Disabled/No Failset Logical LAN state
0 Failover priority

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===Update commands===

====Change hosts====
<pre>
$ mcr latcp show service * ! and if it shows you SCTHIN:
$ set host scthin ! or
$ set host scthin/lat
</pre>

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====Update OpenVMS Licenses====
This needs to be done on all the Calgary workstations, XtremeCT, vivaCT40/uCT35, and uCT100. 
Request licenses from HP:
*School Identification (for U of C): 855803-9502
*License type: OpenVMS VAX/Alpha (uCT100: OpenVMW Integrity) Layered Products? (Or try others)
*Member of DSPP or AlicanceONE: No
*Do you use a VAX or Alpha Emulator: No

On every workstation, you need to check which licenses are loaded and update those with a termination date.
<pre>
$ show license

Active licenses on node SCEVA3:

------- Product ID -------- ---- Rating ----- -- Version --
Product Producer Units PCL Activ Version Release Termination
C DEC 0 0 100 0.0 (none) 1-OCT-2012
CMS DEC 0 0 100 0.0 (none) 1-OCT-2012
CXX-V DEC 0 0 100 0.0 (none) 1-OCT-2012
FORTRAN DEC 0 0 100 0.0 (none) 1-OCT-2012
LSE DEC 0 0 100 0.0 (none) 1-OCT-2012
MMS DEC 0 0 100 0.0 (none) 1-OCT-2012
VMSCLUSTER DEC 0 0 100 0.0 (none) 1-OCT-2012
OPENVMS-I64-FOE HP 4 1 0 0.0 (none) (none)
</pre>

*HP will provide you with a script file ([[media:Openvms_license_update_hp.docx |'''Example script from HP''' ]]) containing a large number of licenses.
*Modify the script to contain only the relevant licenses and load the licenses ([[Media:Openvms_license_update.docx |'''Example modified script''']]).
*Login as user: system
*Re-check the licenses on the workstation to ensure that the termination date has been updated.
*The date after expiry, if cannot log in, then there is a problem with the VMS Cluster license, which was installed by Scanco. Contact Mark Blanchard (mblanchard@scanco.ch) about this problem.

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====Understanding how to set default parameters with OpenVMS====

Here is how the files all hang together...

LOGIN.COM is called automatically during login and calls
::MICROCT_SETUP.COM, which sets the scanner ID, data device, etc. This file calls
::::MICROCT_SETUP_COMMON.COM to create general settings. This file is located in DISK0:[MICROCT_COMMON] and calls
::::::MICROCT_FE.COM, if present, to setup the environment for Bert's FE program
::::::MICROCT_SETUP_SITE_SPECIFIC.COM to create local settings for all accounts (e.g. ICALC)
::::::MICROCT_SETUP_COMMON_*.COM, if present, typically to create application-specific settings for all accounts
::::::MICROCT_SETUP_GROUP_*.COM, if present, to create local settings for specific groups (e.g. group 3401)
::MICROCT_SETUP_USER.COM to create user-specific settings.

Note that the $UM designation is the MAIN directory, and the location of the binary files. To see a list:

$ dir DISK0:[MICROCT_COMMON.MAIN]

This is where you'll find IPL_SCANCO_FE.EXE, IPL_SCANCO_M.EXE, etc.

Lots of stuff here:

Directory DISK0:[MICROCT_COMMON]

3309.DIR;1 DATABASE.DIR;1 DEMO.DIR;1 EVAL.DIR;1
MAIN.DIR;1 TEMPLATES.DIR;1 TIPS.DIR;1 UIL.DIR;1
UTIL.DIR;1 WWW.DIR;1

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====Edit Symbol====

=====Edit SCANCO_SUBMIT_COMMAND=====

*Check the current setting:
<pre>
$ show sym *submit*
</pre>

In directory <code>DISK2:[MICROCT]MICROCT_SETUP_USER.COM</code> add the following line:
<pre>
$ SCANCO_SUBMIT_COMMAND :== SUBMIT/NOPRINT/QUE=SYS$SLOW /NOTIFY/LOG=SYS$SCRATCH:
</pre>
Then end session and log in again. Definition of the symbol in the
<code>MICRO_SETUP_USER.COM</code> supersedes the standard setting.

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=====Edit AIX=====

[[Image:Bones2.jpg|20px]] Warning: Extreme caution! Explicit permission for this change or similar changes must be obtained from Dr. Steven Boyd.

Log in as user calibration (Xtremect: calibration; VivaCT40: calib5019; uCT35: calib2339), the password is the same as for the system user.
Set priviledges to bypass.
$ set proc/priv=bypass
Or
$ spb
Change to the MICROCT_COMMANDS directory.
$ cdc
$ sea *.com aix
$ eve microct_setup_common.com
Edit the file which is called <code>MICROCT_SETUP_COMMON.COM</code>

''Another example'': To make the backspace/insert keys work properly, edit the <code>login.com</code> and insert the line
<pre>
$ set terminal/insert
</pre>
Anywhere suitable.

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====Setup Time====
=====Change system date and time=====
The OpenVMS system should adjust for daylight savings, however, this is currently incorrect for the alpha systems. The alpha systems will need to be manually moved forward in March and moved back in April. To do this, you will need to login as system
<pre>
$ set host 0
user: system
password:
$ show time
$ set time=dd-mmm-yyyy:hh:mm:ss/cluster !/cluster to change the time on all computers at once
$ set time=01-APR-2012:18:00/cluster !Example: Set the system to April 1, 2012, 6 pm.
</pre>

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=====Set time zone=====
As user system:

$ @sys$startup:utc$time_setup
Choose "CANADA" from the menu.
Choose "MOUNTAIN" from the menu.

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=====Disable Distributed Time Synchronization Service (DTSS)=====
DTSS will automatically adjust the clocks for daylight savings (i.e., 2am to 1am on the 2nd Sunday in March, 2am to 3am on the 1st Sunday in November). As user system:

$ mcr ncl disable dtss
$ mcr ncl delete dtss
$ eve sys$startup:sylogicals.com

Add line to disable DTSS
$ DEFINE/SYSTEM/EXEC NET$DISABLE_DTSS TRUE
Save and exit.
Now re-set the time zone.

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=====Configure Network Time Protocol (NTP) server to synchronize clocks=====
*NTP must be configured for each node (computer). Login as user system.
NTP can only synchronize the system clock if the error is less than 1000 seconds.

Synchronize the system clock to UofC's NTP server (ensures time is correct to within 1000s):

$ mcr sys$system:tcpip$ntpdate ntp.cpsc.ucalgary.ca

Enable NTP:

$ cd sys$startup
$ @tcpip$config
3 - Server components
12 - NTP
1 – Enable service on this node
E – Exit menu
E – Exit configuration procedure
N – don’t start service

Create the NTP configuration file:

$ sys$sysroot:[tcpip$ntp]
$ copy/log tcpip$ntp.template tcpip$ntp.conf
$ eve tcpip$ntp.conf

Comment out existing peer and server entries (# for comments).
Add entries for local servers.
server ntp.cpsc.ucalgary.ca
server ntp1.cpsc.ucalgary.ca
Save and exit.

Start NTP:

$ @sys$startup:tcpip$ntp_startup

Check the log:

$ type/cont/int=1 sys$sysroot:[tcpip$ntp]tcpip$ntp_run.log

Sample log file:

$ Set NoOn
$ VERIFY = F$VERIFY(F$TRNLNM("SYLOGIN_VERIFY"))
11 Apr 09:22:34 ntp[547708872]: ntpd version = 4.1.0
11 Apr 09:22:34 ntp[547708872]: precision = 976 usec
11 Apr 09:22:34 ntp[547708872]: drift file 'SYS$SPECIFIC:[TCPIP$NTP]TCPIP$NTP.DRIFT' does not exist: no such file or directory
11 Apr 09:22:34 ntp[547708872]: will attempt to create drift file

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====Setup Email====
=====Setup email server=====
The SMTP protocol is not enabled by default. If you use <code>tcpip$config</code> you can switch on the mail server under Client Components. As system:

$ set host 0
user: system
password:
$ @SYS$MANAGER:TCPIP$CONFIG
Or
$ @tcpip$config
-> 2 (client components)
-> 6 (SMTP)
-> 2 (Enable & Start services)

*Select option 2 (client components) from the menu.
*Select option 6 (SMTP) from the next menu to enable and start it.

Since your smtp server is not registered anywhere, it can be that emails sent from this server will be filtered out as spam on the way to your mailbox. In that case you would need a so called MX record for your mail server. Contact UofC IT to resolve this issue.

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=====Send an email=====
Example: Send an email without an attachment.
$ mail sys$scratch:email_message.txt/subject="email subject" "hbuie@ucalgary.ca,mkan@ucalgary.ca"

Example: Send an email with an attachment.
$ MIME :== $MIME.EXE
$ MIME MIME> NEW /NOEDIT sys$scratch:file.txt
MIME> ADD /TEXT thisattached.txt
MIME> ADD /BINARY thatattached.zip
MIME> ADD /MESSAGE this_is_written.txt
MIME> SAVE
MIME> EXIT
$ MAIL /SUBJECT="MIME-encoded Message" - sys$scratch:file.txt "hbuie@ucalgary.ca,mkan@ucalgary.ca"
$
*MIME> ADD /TEXT *.txt does not work

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===Action commands===
====Send a message to terminals====
<pre>
$ reply /all "Merry Christmas to Bone Imaging Lab!"

Reply received on SCEVA2 from user XTREMECT2 at _SCEVA2$FTA8473: 09:21:58
Merry Christmas to Bone Imaging Lab!

4 terminals have been notified on SCEVA2.
$
1 terminal has been notified on SCSRV2.
$
1 terminal has been notified on SC3309.
$
3 terminals have been notified on SCEVA1.
$
</pre>

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====<code>mcr</code> vs <code>run</code> command====

The command <code>mcr</code> is the same as <code>run</code>, but only with mcr you can hand over 'in-line' parameters to an .exe file:

<pre>$ run ut:ctheader.exe c000124.isq</pre>
does not work, but you have to say
<pre>$ mcr ut:ctheader.exe c000124.isq</pre>

But funnily if you define a symbol in <code>microct_setup_user.com</code> (or <code>login.com</code>),

<pre>$ ctheader :== $ut:ctheader.exe</pre>

with just neither run nor mcr, but the 'funny' $ sign, then you can also hand over the ISQ name in-line.

Small detail with big effect...

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====File Do All (fda) - apply a command to a set of files====

<code>$ fda ctheader dk0:[microct.data.0001234...]*.isq </code>

to see the header of all isq files of sample 1234 (the three dots ... means all subdirectories)

Or:

<code>$ fda aix dk0:[microct.data.0001234.00005678]*.aim</code>

to see the processing log of all aim files of scan 5678

Wildcard "*" means multiple characters, "%" is for ONE character:

<code>$ fda aix dk0:[microct.data...]C%%%%%%%.aim</code>

(yes, 7 %'s)

to show the aim header of the gray-scale c0000135.aim (etc) files only, and NOT from the _seg.aims also.

[[Image:Bones2.jpg|20px]] Warning: CAUTION! Always test the wildcard expression first with

<code>$ dir dk0:[xxx...]*.aim </code>

The 'file do all' fda command can even be combined with a pipe, or an /output qualifier:

<code>$ pipe fda aix dk0:[microct...]*.aim | search sys$pipe "Slope" </code>

will show you all "Slopes" in a row. (but you may not see which slope belongs to which aim file anymore...)

or:

<code>$ fda/output=sys$scratch:all_headers.log aix dk0:[microct...]*.aim</code>

will write all the output into the .log file - which you can then either edit, or
<code>$ search sys$scratch:all_headers.log "String"</code>

or whatever you want.

Another example with output:

<pre>$ pipe fda type *.log | search sys$pipe "BV/TV" /output=BVTV.txt</pre>

"fda" is our self-written script, so you may have to try-n-error a bit...

<code>$ fda command file_wildcard [Optional: further parameters]</code>

If the command consists of multiple words with spaces inbetween (e.g. mcr ut:xxx.exe), then enclose the command in double-quotes

<code>$ fda "mcr ut:uct_ext_header_display" dk0:[microct...]*.isq 8</code>

Grab more than one line using pipe and search command:

<code>$ pipe fda aix *.aim | search sys$pipe "dim", "pos", "name"</code>

*The further parameters may not contain wildcards - so unfortunately, the fda can NOT be used to 'adaptively' rename a whole bunch of files.

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====Make commands available to all users with symbols or paths====

DCL$PATH is one way to do that, WE don't use it...
<pre>
$ def dcl$path disk1:[microct.main],disk1:[microct.util]
</pre>
then, if you type
<code>
$ uct_t
</code>
it will first try to

<code>
$ @uct_t.com
</code>
and then
<code>
$ r uct_t.exe
</code>

however, we usually define it by giving full path:

<pre>
$ progx :== $disk1:[microct.main]progx.exe
$ com_proc_x :== @disk1:[microct.main]procedure.com
</pre>

then, you can just type the shortcut ('symbol' in VMS language)

We use the 'cd' to set the default path, you may also use this in your command procedure:

<code>proc.com</code>:

<pre>
$ cd 'p1'
$ dir *.*/size

$ define COM disk1:[microct.commands]
$ p :== @COM:PROC.COM
</pre>

these both go into <code>login.com</code>, but see the Wiki entry above to confirm exactly where...

then, you can just type:

<pre>
$ p disk4:[microct.data.0000007.000009]*.ISQ
</pre>

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====Stopping disconnected sessions====

As <code>system</code> user you can check if there are any disconnected sessions, with <code>$ show user/full</code>:

<pre>
$ sh user/full
OpenVMS User Processes at 5-JUN-2021 03:14:06.45
Total number of users = 2, number of processes = 7

Username Process Name PID Terminal
MICROCT DECW$MWM 00000EA4 MBA6597: (disconnected)
MICROCT DECW$SESSION 00000EA2
MICROCT VUE$MICROCT_3 00000EA6 MBA6601: (disconnected)
MICROCT VUE$MICROCT_4 00000EA7 (subprocess of 00000EA2)
MICROCT VUE$MICROCT_5 0000289E (subprocess of 00000EA2)
MICROCT _FTA24: 00012284 FTA24:
SYSTEM _FTA30: 000129DC FTA30:
</pre>

and kill any as follows:
<pre>
$ stop/id=00000EA4
$ stop/id=00000EA6
</pre>

There may also be FTP connections that aren't closed properly. You can check for open FTP connection with this:

<pre>
$ sh sys/proc=tcpip$ftp*
OpenVMS V8.3-1H1 on node SC4209 5-JUN-2021 03:12:53.14 Uptime 73 13:39:10
Pid Process Name State Pri I/O CPU Page flts Pages
00000426 TCPIP$FTP_1 LEF 9 786428 0 00:00:12.51 1089 751 N
000129E0 TCPIP$FTPC00046 HIB 4 106 0 00:00:00.03 431 353 N
</pre>

and again kill any with:

<pre>
$ stop/id=000129E0
</pre>

But DO NOT kill the <code>TCPIP$FTP_1</code> as this is the actual FTP server process.

Remember, in a cluster there will almost always be other open sessions which have their DECW$SM.LOG files locked. You don't need to delete them all!

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=Calibration and QC=

==System Updates==
{| class="wikitable"
|-
! scope="row"| XtremeCT II
|
*22-OCT-2020: Calibration Update
*01-OCT-2020: Calibration Update
*31-JUL-2020: Pixel Correction
*21-FEB-2019: New X-ray source, Recalibration
*25-JAN-2018: Calibration Update
*28-APR-2016: Calibration Update
*07-APR-2015: Calibration Update
*04-NOV-2014: Calibration Update
*21-MAY-2014: New Daily QC Phantom (Scanco concluded minimal differences from previous)
|-
! scope="row"| XtremeCT I
|
|-
! scope="row"| vivaCT80
|
*20-OCT-2020: Filter changer replaced, Recalibration
|-
! scope="row"| vivaCT40
|
*20-OCT-2020: New x-ray source, Recalibration
*09-NOV-2010: Recalibration (70KV energy only)
*01-NOV-2010: New x-ray source, Pixel Correction, Recalibration
|-
! scope="row"| µCT35
|
*20-OCT-2020: New x-ray source, Recalibration
*15-JUN-2011: Recalibration
*21-MAR-2011: Recalibration
*10-FEB-2011: Recalibration
*26-NOV-2010: Pixel Correction
*29-OCT-2010: Recalibration
|}

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==Calibration and Conversion==
===Attenuation measured by µCT===
A micro-CT 3D image of an object is basically a 3D map of local x-ray absorption in the object. The reconstruction from multiple angular views provides information on how much x-ray absorption is happening within each cubic voxel element of the scanned volume.

It is important to understand what is meant by “density” in a µCT image. The reconstructed grey-scale intensity of each image voxel does not relate directly to mass density alone, thus do not expect it to correspond with measurements of weight per volume, e.g. g.cm-3. The primary entity that is measured is x-ray absorption, defined as the x-ray linear attenuation coefficient in units of
1/distance, specifically, 1/cm. This is determined both by mass density and x-ray mass attenuation coefficient which is determined by the elemental composition of the material. The x-ray linear attenuation coefficients of typical material is shown blow.

[[File:Mu_comparison.JPG|thumb|center|600px|X-ray linear attenuation coefficient µ of typical material (image curtesy of Dr. Ying Zhu)]]

The images we obtain from the scanner are in a special scanner manufacturer format called AIM files. Each voxel in these images contains a scaled linear attenuation value (mu-value) to save disk space.

{| class="wikitable"
|-
! scope="col"| Symbol
! scope="col"| Name
! scope="col"| Unit
! scope="col"| Value Range
! scope='col'| Meaning or Comments
|-
! scope="row"| µ
| x-ray linear attenuation coefficient
| 1/cm
| µ > 0
| A constant that describes the fraction of attenuated incident photons in a monoenergetic beam per unit thickness of a material
|-
! scope="row"| mu_value
| linear attenuation in Scanco images
| 1/cm
| -8～8 typically
| mu value represented in Scanco images
|-
! scope="row"| pixel_Scanco
| pixel intensity value in Scanco images
| -
| −32768～32767
| Original format of Scanco images in 16-bit signed
|-
! scope="row"| pixel_uint
| pixel intensity value in converted Scanco images
| -
| 0～65535
| Converted format of Scanco images in 16-bit unsigned, using the same slope (unscaled) but an updated intercept
|}

<pre>
pixel_Scanco = mu-value * scaling_factor
</pre>

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===Calibration by BMD===
When we know that the x-ray absorption of a material is dominated by one specific material, then we can relate the measured x-ray linear attenuation coefficient (mu_value) to the mass density of that material. The calibration of [[Scanco_User_Instructions#Descriptive_Statistics_.28Mean.2C_Median.2C_SD.29_of_Calibrated_Voxel_Values| '''Bone Mineral Density (BMD)''']] is an example of this. We assume that the x-ray attenuation within mineralized tissues such as bone, dentine and enamel is dominated by, and can be approximated as, the x-ray attenuation of the mineral compound calcium hydroxyapatite (CaHA) which has the formula Ca5(PO4)3(OH).

Then we obtain “phantoms” with two or more known mass concentrations of CaHA. By linking these mass concentrations of CaHA with measured mu_value in the micro-CT images, we can establish calibration linking the two quantities, allowing us to infer from the micro-CT measured linear attenuation coefficient (mu_value) in a mineralized tissue, to the density of CaHA in mg.cm-3.

*The assumption of linear correlation between the two quantities is based on a well-applied beam hardening correction and the phantoms' diameter matching with the size of bone within the sample.

*This calibration system could be used to calibrate measurement of other substances apart from CaHA and bone, where x-ray absorption is known to be dominated by a certain substance and phantoms can be prepared with known concentrations of that substance.

{| class="wikitable"
|-
! scope="col"| Symbol
! scope="col"| Name
! scope="col"| Unit
! scope="col"| Value Range
! scope='col'| Meaning or Comments
|-
! scope="row"| BMD
| Bone Mineral Density
| mg HA/ccm
| 0～3000
| Volumetric density of calcium hydroxyapatite (CaHA) in a biological tissue in terms of mg/cm^3
|-
! scope="row"| BMD_value
| Bone Mineral Density in Scanco images
| mg HA/ccm
| -1500～3000 typically
| BMD value in Scanco images
|}

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===Conversion between Attenuation and Bone Density===
<pre>
BMD_value = mu-value * slope + intercept

mu-value = (BMD_value – intercept) / slope

pixel_Scanco = scaling_factor * (BMD_value – intercept) / slope

</pre>

For example, to convert mu_value of 1.7923 (1/cm) to BMD (mg HA/ccm):
<pre>
BMD_value = 1.7923 * 3.67162994e+02 + -2.06399002e+02 = 451.667 (mg HA/ccm)
</pre>

For example, to convert the lower threshold of 125 mg HA/ccm that is in the IPL script to pixel intensity in Scanco images:
<pre>
pixel_Scanco = 4096 * (125 - -2.06399002e+02) / 3.67162994e+02 = 3697
</pre>

*You could get the scaling_factor, intercept and slope values from the AIM header of your scan by using aix -l command:
[[File:Aix.JPG|400px]]

*Reference: [[Media:Jbmr.141.pdf|Bouxsein ML, Boyd SK, Christiansen BA, Guldberg RE, Jepsen KJ, Müller R, Guidelines for assessment of bone microstructure in rodents using micro-computed tomography. J Bone Miner Res. 25(7): 1468-86. 2010.]]

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===Convert CT numbers to mg HA/ccm / Houndsfield units (HU)===

The two byte numbers (short) can be converted to mu values by first dividing by mu_scaling which is probably 4096 (uCT35, vivaCT40) or 8192 (XtremeCT).

Houndsfield units (HU)

Here is the conversion formula from mu (lin.att. in 1/cm, our original, 'physical' image numbers) to HU:

<pre>HU(pixel) = -1000 + mu(pixel) * 1000/mu(water)</pre>

so the mu(water) is the 'constant' that is needed for this conversion of any pixel value mu(pixel) to HU of that pixel.

divide the 2-byte numbers in our dicom/aim/isq files by 4096 to get mu. (4096 --> 'mu_scaling' in our headers). E.g. you see
gray-scale number 8192 in our files --> mu = 2 [1/cm].

A reasonable result for the uCT35 is:

<pre>HU = (CT / 4096) * 1718.19 - 1000</pre>

and that means 1000/mu(water) = 1718.19 --> mu(water) = 0.58299 which is a reasonable number.

mg HA/ccm

<pre>
mg HA/ccm = (AIM/mu_scaling) * slope + intercept
mg HA/ccm = (AIM/4096) * 295.494 - 189.695 ! vivaCT40
mg HA/ccm = (AIM/4096) * 256.51 - 172.99 ! uCT35
mg HA/ccm = (AIM/8192) * 1402.549 - 340.953 ! XtremeCT
</pre>

These numbers are available in the AIM header, or the ISQ header (<code>$ run ut:ctheader</code>).

To look up slope, intercept and mu_scaling, check either the AIM header
<pre>$ aix C1234567.AIM</pre>
or
<pre>$ run ut:uct_update_calibration</pre>
and look at a record, and you'll find slope and intercept and mu-water.

<pre>
vivaCT40
!----------------------------------------------------------------------
Mu_Scaling 4096
Calibration Data 55 kVp, 200mg HA wedge, 4096 scaling
Calib. default unit type 2 (Density)
Density: unit mg HA/ccm
Density: slope 2.95493988e+02
Density: intercept -1.89695007e+02
HU: mu water 0.58200
!----------------------------------------------------------------------
</pre>
<pre>
XtremeCT
!-------------------------------------------------------------------------------
Mu_Scaling 8192
Calibration Data 60kVp, BH: 200 mg HA/ccm, Scaling 8192
Calib. default unit type 2 (Density)
Density: unit mg HA/ccm
Density: slope 1.40254895e+03
Density: intercept -3.40953003e+02
HU: mu water 0.23900
!-------------------------------------------------------------------------------
</pre>

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===Calibration FAQ===
====Change brightness scaling====
*Refer to [[Media:Mu-scaling.pdf|'''Change the brightness scaling''']].

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====Update a scan after pixel correction====
Contact Lab personnel with system-level priviledges to perform
<pre>
$ set host 0
! Username: calib2339 (µCT35)
! Username: calib5019 (vivaCT40)
$ spb ! set priviledge bypass to write in other user accounts
$ run ut:pixel_corr_apply

PIXEL_CORR_APPLY Version 1.5
Scanner ID from UCTD:UCT_SCANNER_2339.DAT : 2339 !2339 for µCT 35, 5019 for vivaCT 40
Is this Scanner ID correct ? [?]: y
Give RSQ-Filename (leave empty to exit) []: DISK4:[BONELAB.DATA.00005283.00011668]C0005128.RSQ
...
...
Copy .RSQ to _CORRECTED.RSQ befor correction ? [?]: y

$ logout
</pre>

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====Update calibration in ISQ====
If DICOM files are converted to ISQ with IPL and then used for patient evaluation, the calibration data in the ISQ header needs to be present and correct. If this information is missing, utilizing upat_list to extract the values will say 'Error: Density calibration not valid'. In order to add calibration data to an ISQ file, do the following as user calibration:
<pre>
$set proc/priv=bypass ! gain read/write access to the files
$mcr ut:uct_ext_header_add_calib ! provide ISQ file name and header type (I chose [2])
</pre>

If you need to adjust the calibration of a file, without changing the system calibration data, copy the calibration database into a different directory, e.g. sys$scratch. Then, add a new calibration record to this temporary calibration database. This way your new, temporary values will not show up in the scan program.

$ copy uctd:uct_calibration_3401.dat sys$scratch:

Define the following logical in a terminal MAKE SURE TO DO THIS!!!!

$ def UCT_CALIBRATION_DATABASE sys$scratch:uct_calibration_3401.dat

Run uct_update_calibration and click trough the current calibration record (always enter).

$ r ut:UCT_UPDATE_CALIBRATION.EXE
select current calibration record
enter...

$ r ut:UCT_UPDATE_CALIBRATION.EXE

Then select the last number (New Record), copy all values from above, change slope and intercept.

Then use

$ mcr ut:uct_ext_header_add_calib

for ISQ and RSQ.

At the end, close the terminal!

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==Quality Control (QC)==
===Scope===
*Only Authorized XCT and µCT Operators are permitted to perform QC scans, including both scan acquisition and analysis.
*Authorization is a formal process. If you are not sure whether you have or should have authorization, speak to Dr. Boyd or Dr. Hallgrimsson or the MoJo Operations Manager.
*Authorized XCT and µCT Operators are responsible for ensuring a QC schedule is maintained.
*Only the manufacturer can calibrate the scanner! QC only checks the calibration.

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===Overview===
*Micro-CT systems cannot directly measure the density of a material, however, the density is linearly correlated to the x-ray absorption (assuming a proper beam-hardening correction is applied), which can be measured by micro-CT. Density is therefore determined by measuring a reference material of known density (i.e., a phantom) to define a conversion function to relate x-ray absorption to density. Quality control of density and structural measurements for the micro-CT systems is achieved through weekly checks of phantom values to their reference values and recalibrating the system (i.e., defining a new conversion function) as necessary.

*Performing QC is essential to the:
# Safety of our study participants and lab members
# Validity of our research data

[[File:QC_phantom.jpg|thumb|center|600px|Scanco Medical quality control phantom (a) and its CT scans of the density QC1 (b) and the structural QC2 (c)]]

*Reference: Koller B, Laib A (2007) Calibration of micro-CT data for quantifying bone mineral and biomaterial density and microarchitecture. In: Advanced bioimaging technologies in assessment of the quality of bone and scaffold materials: techniques and applications. Springer, pp 79-84.

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===Density QC1===
QC1 measures the density of 5 different rods of known hydroxyapatite (HA) densities within the QC phantom: approximately 0, 100, 200, 400, and 800 mg HA/cm3. This tests 3 things:

# That the scanner’s last calibration is still valid. This is done by comparing daily QC values to an acceptable range.
# The presence of drifts and shifts in the calibration. This is done by plotting daily QC results over time and using Shewart’s Controls to mathematically look for drifts and shifts. (Shewart’s Controls replaces visual assessment.)
# The correct functioning of scanner hardware and electrical components. This is done by visual inspection for image artifacts.

*QC1 is checked daily or 3 times a week on XtremeCT scanners whenever used and weekly on microCT scanners.

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===Structural QC2===
QC2 measures the volume of 3 fine aluminum rods within the QC phantom (Al rod volume measurement). This tests for:

# Alignment of the gantry (or stability of architectural parameters)
# The correct functioning of scanner hardware and electrical components. This is done by visual inspection for image artifacts.

*QC2 is checked weekly on both XtremeCT and microCT scanners.

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===QC Scan Instructions===
*XtremeCT QC Scan Instructions: Boyd Drive:\02 - Operations\01 - Scanner QC, Specifications, & Maintenance\QC Workflows\QC 001.2 - XCT Quality Control.docx
*[[Media:Calibration-instructions-for-uct35.pdf |µCT35 QC Instructions]] or [[Media:uCT35_Calibration.pdf|µCT35 QC another Instructions]]
*[[Media:Calibration-instructions-for-vivact40.pdf |VivaCT40 QC Instructions]] or [[Media:VivaCT40_Calibration.pdf| VivaCT40 QC another Instructions]]

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===Print out QC reports===
After running a QC1 or QC2 analysis, the results are output to:
*DISK4:[BONELAB.PROJECTS.QC] for XtremeCT QC results
*DISK3:[MICROCT.PROJECTS.CALIBRATION] for microCT QC results performed by BH lab
:*login with microct account
*DISK5:[BONELAB.PROJECTS.CALIBRATION] for microCT QC results performed by Bone Imaging lab
:*RESULTS_QC1_UCT35.TXT;2
:*RESULTS_QC1_VIVACT.TXT;4
:*RESULTS_QC2_UCT35.TXT;2
:*RESULTS_QC2_VIVACT.TXT;2

As usual as [[Scanco_User_Instructions#Print_out_report_sheets|'''print out report sheets''']], you use
$ upat_list
When it asks for a template, you can select for a graphical report
template = UU:UCT_EVAL_PHANTOM_SCANCO.PS
or for a text output
template = UU:UCT_3D_LIST.TXT

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===System Stability and Precision===
System Stability and Precision here is based on the QC measurement, QC1 for density variations and QC2 for structure variations.
{| class="wikitable"
|-
! scope="col"| System Stability and Precision
! scope="col"| XtremeCT
! scope="col"| vivaCT40
! scope="col"| µCT35
|-
! scope="row"| Long Term Precision
|
*QC1: ± 8mg HA/cm3
*QC2: ± 2.0%
|
*QC1: ± 0.4%
*QC2: ± 0.7%
(Ref term: 26-NOV-2010 to 8-APR-2011)
|
*QC1: ± 1.0%
*QC2: ± 1.6%
(Ref term: 26-NOV-2010 to 8-APR-2011)
|-
! scope="row"| Short Term Precision
|
*QC1: ± 8mg HA/cm3
*QC2: ± 2.0%
|
*QC1: ± 0.4%
*QC2: ± 0.9%
(Ref term: 4-MAR-2011 to 8-APR-2011)
|
*QC1: ± 1.0%
*QC2: ± 0.7%
(Ref term: 6-MAR-2011 to 8-APR-2011)
|}

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===QC FAQ===
====Determine calibration drift for microCT QC1====
The microCT QC1 analyses provide an estimate of the calibration drift by considering 'mean5' values. Use <code>$ uct_list</code> and make sure to use UU:UCT_3D_MEANS.TXT as the template. Then give the measurement numbers of the QC1 measurements (or all of them and remove what's not needed later).

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====Update QC1 contours====
If the QC contours don't line up on the phantom, then the contours need to be updated on the system. Normally this should not happen unless the phantom has become loose - if this is the case, re-fix it.

1. Login as user system. Do not use the <code>$ set host 0 </code> command since you will not be able to open windows for program. 
2. Run the login script for the user that does the QC scans so that Scanco logicals point to that scan database.
$ @adisk1:[microct]login.com on the XtremeCT cluster
$ @adisk1:[microct]login.com on the vivaCT cluster
$ @disk1:[microct]login.com on the µCT100 cluster

3. Run the evaluation program.
$ uct_evaluation
4. Load the most recent QC scan and locate the contours. File-->Load Gobj... Filter: <code>uctd:*.GOBJ</code>. Locate the contours for the phantom: <code> UCT_PHANTOM_KP_HA_XXXX_Y.GOBJ </code> where XXXX corresponds with the scanner ID (XtremeCT 3309, vivaCT 5019, µCT35 2339, µCT100 6002) and Y corresponds with the rod number (1-5 and results mean1 - mean5. 

5. Adjust the contours to centre on the rods.
Load a contour.
Move the contour on the first slice to be centred on the rod.
Copy the contour.
Delete the contours on slices 2 to the end.
Paste the contour on the last slice.
Morph between the two contours.
Save the contours. They should be saved to (A)DISK0:[000000.MICROCT_COMMON.DATABASE].
6. Perform a new QC scan as the standard (i.e., microct) user. Check that the contours line up for the evaluation. Evaluate and check the results.

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====Update Gobj for QC1 Analysis====
Refer to [[Media:Fix_QC1_gobj.pdf| '''Fix QC1 Gobj''' ]] for instructions.

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====Update XtremeCT QC1 calibration====
This procedure needs to be done for each beam hardening correction (e.g., QC1 with 200 mg HA/cm3, QC1 with 1200 mg HA/cm3) and for each scan energy.

1. Perform 3 back-to-back QC1 scans, which ensures the x-ray tube is very warm. 
2. Evaluate the last QC1 scan. 
3. After the evaluation is done, determine parameters for the new calibration
<pre>
$ uct_calib_phantom
UCT_CALIB_PHANTOM Version V1.0

Reading UCTD:UCT_CALIB_PHANTOM_KP_HA_3309.TXT
Phantom Type in file: 6
Phantom Number in file: 304
Voltage in file: 0
No of Materials in file: 1
With each, no of steps: 5
and mus: 1.000000
No. of Cylinders: 5
Measurement No. (0 to Stop) [0]: 11404

Mus: 0.2382 0.3163 0.3823 0.5358 0.8112
*****************************************************
Calibration: Slope Intercept: 1398.628 -339.819
Enter in Calibration Records if wished.
*****************************************************
Measurement No. (0 to Stop) [0]:
End of program
$
</pre>

4. Save the above screen output in a file called CALIB_3309_YYYY-MM-DD.TXT.

5. Now update the calibration. For most settings, you will use the default value by pressing return. You need to choose the correct calibration record, the one that corresponds with the energy and beam hardening correction used in the QC1 scans you did. Next, you need to update the slope, intercept, and mu water values to those determined in step 3 (copy and paste values to avoid typos). The new values should be similar to the old ones. Finally, if you have not made any mistakes, then save the record.
<pre>
$ run ut:uct_update_calibration
UCT_UPDATE_CALIBRATION V2.5

IDX Calib/Rec. Description
1 1/42 60kVp, BH: 200 mg HA/ccm, Scaling 8192
2 2/43 60kVp, BH: 1200 mg HA/ccm, Scaling 4096
3 3/0 New Record
Choose Calibration Record (IDX): [2]: 1
Valid Flag [1]:
Scanner-ID [3309]:
Energy [V] [59400]:
Intensity [µA] [0]:
Description [60kVp, BH: 200 mg HA/ccm, Scaling 8192]:

Antiring Enable [0]:

Beamhardening Enable [1]:
Beamhardening Coeff file [MICROCT_COMMON:[DATABASE]UCT_BH_COEFF_60KV_0200HA_3309.TXT;5]:
Beamhardening Checksum [0]:
CCD_CORR: Read to mem: 500 bytes to correct 1 pixels (588 bytes allocated)

Default unit type (1=µ, 2=mg, 3=HU, 4=Custom) [2]:
µ Enable [1]:
µ-scaling [8192]:

Density Enable [1]:
Density units [mg HA/ccm]:
Density Slope [1402.549]: 1398.628
Density Intercept [-340.953]: -339.819

HU Enable [1]:
µ of water [0.239]: 0.2382

CUSTOM Enable [0]:

HW Filter Code [0]:
HW Filter Description []:

Save Record ? [Y]: Y
End of program
$
</pre>

6. Save the above screen output in a file called CALIB_3309_YYYY-MM-DD_ENTERED.TXT. Send both text files to support@scanco.ch for them to archive.

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====Update microCT QC1 calibration====
Refer to [[Media:QC1_Calibration_Update.pdf|'''QC1 Calibration Update''']] for instructions for the VivaCT40 and uCT35.

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====Update a scan with new calibration or BHC====
If the QC1 range was out of range but it was not possible to update the system calibration before scanning, you can update the scan with the new density calibration (i.e., slope and intercept). It is also possible to change the beam hardening correction that is applied (e.g., from 200 mg HA/cm3 to 1200 mg HA/cm3).

{| class="wikitable"
|-
! scope="col"| Type of Update ||RSQ||ISQ||AIM
|-
|QC1 was out of range, need new slope and intercept
(e.g., after updating the system calibration)
|Yes||Yes||No, Create New
|-
|Change beam hardening correction type
(e.g., 200 mg HA/cm3 to 1200 mg HA/cm3)
|Yes||No, Reconstruct||No, Create New
|}

Use the UCT_EXT_HEADER_ADD_CALIB program to update an RSQ and, if appropriate, repeat for the ISQ.
*Use default values for all prompts except those commented after !.
<pre>
$ mcr ut:uct_ext_header_add_calib

UCT_EXT_HEADER_ADD_CALIB V 1.1
Raw-Data-File []: !give the name of the RSQ/ISQ with full path if not in that directory

Reading Raw Data ...
IDX Calib Description
1 1 45 kVp, 200mg HA wedge, 4096 scaling
2 2 55 kVp, 200mg HA wedge, 4096 scaling
3 3 70 kVp, 200mg HA wedge, 4096 scaling
4 4 General, non-bone-density-calibrated scan, scale 4096
5 5 45 kVp, BH: 1200 mg HA/ccm, Scaling 4096
6 6 55 kVp, BH: 1200 mg HA/ccm, Scaling 4096
7 7 70 kVp, BH: 1200 mg HA/ccm, Scaling 4096

Calibration Record No [0]: !specify the new calibration, e.g. 6

Calibration No. 6
Description 55 kVp, BH: 1200 mg HA/ccm, Scaling 4096
Scanner-ID 5019
Energy [V] 55000
Antiring Enable 0
Beamhardening Enable 1
Beamhardening Coeff file UCTD:UCT_BH_COEFF_55KV_1200HA_5019.TXT
Default unit type (1=µ, 2=mg, 3=HU, 4=Custom) 2
Same type already found. Setting old to invalid
SUCCESS: calib hext written
updating header...
SUCCESS: Header successfully updated.

Calib record indicates that BH-Corr is usually applied.
Info: There is a BH-Corr corr already in hext.
Add another BH-Corr from file again? (Y/N) [N]: Y
</pre>

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====Update a scan with new QC1 calibration====
Refer to [[Media:Update_Scan_with_new_QC1.pdf|'''Update Scan with new QC1''']] for instructions.

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====Fix: un-centered QC1 Gobj====
The contour for the QC1 scan is not centered on the on hydroxyapatite rod, which will result in erroneous low density values.

This can occur for a couple of reasons:
*The metal spindle has come loose on the phantom, in which case re-glue it and update the contours
*The slot on the phantom's spindle was not correctly aligned
*For the vivaCT 40, the sample bed was not pushed to the right before locking it in place
[[File:Phantom_not_pushed_right.jpg|600px]]

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====Fix: rods in QC2 images====
The QC2 scan has aluminum rods AND hydroxyapatite rods. This happens because the slot on the phantom's spindle was not correctly aligned and the phantom positioning is off slightly. Adjust the phantom and re-scan.

[[File:Phantom_spindle_not_in_right.jpg|600px]]

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=Scanning=

==Scanner User Manual==
For XtremeCTs:

* [[Media:Scanco - Manual_XtremeCTII_2.5.pdf |XtremeCT II User's Guide V2.5]]
* [[Media:XtremeCT User Guide XCT I.pdf |XtremeCT I User's Guide V6.4]]

For microCTs:
* [[Media:Manual_vivaCT_80.pdf |VivaCT80 User's Guide V1.5]]
* [[Media:scanco-manual-vivact40.pdf |VivaCT40 User's Guide V4.05]]
* [[Media:Scanco-manual-uct35.pdf |MicroCT35 User's Guide V4.05]]

==Scanco's FAQ==
Navigate to the manufacturer [http://www.scanco.ch/index.php?id=customer_login Scanco Medical FAQ].

* Username: users@scanco.ch
* Password: basser5dorf

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==Scan==
===Scan SOP===
====Image Quality====
*Refer to [[Media:Scanco-faq-image-quality.pdf|'''Image Quality: Resolution vs. Noise''']] by Scanco Medical.

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====Optimize Control File Settings====
*Refer to [[Media:ControlFileSettingsUserMeeting2014Final.pdf|'''Optimize Control File Settings''']] with regards to resolution, contrast and scan time.

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====Scan materials of different densities====
*Refer to [[Media:UM_HongKong_DifferentDensityMaterials.pdf|'''Scan materials of different densities''']].

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====Optimize Scan for Soft and Adipose Tissue Separability====
*Refer to [[Media:Scanco-faq-adipose-vs-soft-tissue.pdf|'''Scan Protocol Optimization for Soft and Adipose Tissue Separability''']].

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====Measure multiple samples in one scan====

This quite often happens when you want to scan 6 rat bones, for example, but using our six-gun sample holder you scan them in one go. But, you want to analyse them separately, so you have to import the ISQ multiple times as new MEASUREMENTS into each SAMPLE.

There are two options: manual and auto. Read this entire HowTo before proceeding. There is significant potential for mistakes!

<pre>
$ @com:import_manual.com

P1: Measurement Number to duplicate
P2: New Sample Number from Database
P3: New Start Letter of ISQ file
P4: Optional: Operator Number
P5: Optional: Controlfile Number
</pre>

So:

<pre>$ @com:import_manual.com 1234 342 D</pre>

will copy the ISQ from measurement 1234, import it into the database to sample 342, give some feedback lines with 'old' and the new samplename, CHECK IT, and at the end it gives the feedback line on the terminal which you take with the mouse and drop to rename the data over to the new location.

IMPORTANT: BE VERY SURE NOT TO MIX UP MEASUREMENT AND SAMPLE NUMBER !!!

This distiction needs to be VERY clear in your mind! Of course, you can duplicate one scan and give it to the same samplenumber again (e.g. to evaluate different parts of the same sample, and each has its database
entry).

Please build up some system so you see immediately that the right meas. goes to the right sample. E.g. all four bones in one scan have the same part in the name, distinct from other 4 bones. If there is any trace of a doubt later on that somebody MAY have messed up the samples in this duplication step, you'll most probably have to start from scratch again...

Of course, I'll have to make you aware that Scanco declines all responsibility - this program is NOT in the normal user-friendly, quite fool-proof Scanco controlbox, but it's up to you to use it carefully, and not on Friday night when you're sleepy and mistakenly mix up sample and meas. numbers...

The new startletter I built in so you always know which one was the 'original' measurement (which has an RSQ), and which are the duplicated ones.

Backup
And the organization of how you know which duplicated scan is which part is
completely up to you - as well as how you want to handle the backup - our
software allows you to back-up each duplicated scan (but this might be an
overkill, since it's the same ISQ always) so you may choose to delete the
duplicated ISQ by hand in the session manager (only keep the 'original' ISQ), and only backup the .gobj, .aim and _seg.aim etc. (but then you will need to know not to get scared if you retrieve a scan, and the ISQ is missing...) (Or you just 'move to trash' the duplicated scans to nicely delete them with the backup program if you want to remove them completely (but you still have the 3D results in the evaluation database))

Autosubmit

<pre>$ import_autosubmit.com</pre>

Please use the manual one for a while. Then, if you feel comfortable, use the autosubmit one (which also does the last command automatically, the renaming of the isq to the new location.) Because it goes into a batch que, you can quickly submit all duplications, and do not have to wait for the whole file-copying like in the manual one.

One thing you should check there:
$ show que sys$fast/full

This needs to be one single queue (/job_limit=1). In a clustered enviroment,
this might be a '/generic=' que that then gives the jobs to multiple queues in the cluster. This is NOT good. If this is the case, please edit the autosubmit script, and replace sys$fast in the following line at the end by ONE of the generic fast queues, e.g. SC4240_FAST or whatever the name is (preferrable the one computer where also the data disk DK0 is sitting:

<pre>
$!
$ SUBMIT/NOPRINT/QUE=SYS$FAST/DELETE/NOTIFY/LOG=SYS$SCRATCH: 'COMMANDFILE'
$!
</pre>

(Reason: if multiple uct_imports would run at exactly totally the very same time, both jobs might get the same new measurement number... bad...)

I also suggest to add the following line to your login.com

<pre>$ dupl*icate :== @com:import_autosubmit.com</pre>

then you can just start it with

<pre>$ dupl 1234 342 D</pre>

And I also recommend to put into login.com:

<pre>
$ check_dup :== search sys$scratch:import*.log """ name:""
</pre>

(yes, with all these double-quotes)

Then use it to check the feedback that the right scans were given to the right samples.

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===Scan FAQ===
====Unlock a locked controlfile====
If you accidentally locked a controlfile, it is possible to unlock it so that it can again be modified.

Login as the calibration user (Xtremect: calibration; VivaCT40: calib5019; uCT35: calib2339), the password is the same as for the system user, Set priviledges to bypass.
$ spb

Set the controlfile database to the microct, or other, user where the controlfile is locked.
*The file is usually located on (a)disk1:[username.database] and may be accessible using the uctd logical.
*The database file contains the scanner ID (e.g., 3309 for the XtremeCT, note there's no SC before 3309).
$ def uct_controlfiles_database adisk1:[microct.database]uct_controlfiles_3309.dat
$ run ut:uct_upd_controlfiles

Choose the controlfile.Use T and F to indicate true and false.
*YOU MUST SAY YES TO UPDATE CTRL-FILE! There is a bug so do this even if you make a mistake.

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====Warning: Selected operator is not an operator CODE: 24====
You must enter an operator name in the micro-CT control panel.
*You only need to enter the beginning part of your operator name (e.g., Bo for Bone Imaging Lab) or your operator number.
*You can also press "Edit..." and then press the "Find..." and press "OK" to show a list of all the operators that have been registered.

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====Warning: Error assigning IO-channel for UCT_ACQ_LINE, device already allocated to another user CODE: 2112====
Only one person can be given control of the scanner at any time. Most likely the scanning program is already open. Check the minimized icons on the desktop.

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====Error: ROT (M1) end switch detected, Motor stopped CODE: 3031====
We're not sure why motor errors occur occasionally. The solution is to exit the scanning program and turn off the scanner (the switch is on the side of the machine). Wait 30 seconds. Turn the scanner on again. Re-start the scanning program. Wait for the scanner to warm up (20 min).

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====Error: Acquisition error, Buffer overrun CODE: 1005====
This error occurs if the computer hooked up to the scanner is overloaded and does not accept the stream of CT data quickly enough. Check that no large calculations are running interactively (e.g., loading a large dataset into the 3D viewer while the scan is running). If you happen to be there at the very exact second when the buffer overrun happens, do the following:
<pre>
$ show user/node/full !check how many users/processes there are
$ monitor system/int=1 !check the process that is using the most cpu and page file quota
</pre>
Advise lab personal of the problem. If nobody is around, put the output of the above commands into a text document, stop the queues for the computer, and repeat the scan.
<pre>
$ stop/que/next sc5019_fast !for the vivaCT 40
$ stop/que/next sc5019_slow !for the vivaCT 40

$ stop/que/next sceva2_fast !for the µCT35
$ stop/que/next sceva2_slow !for the µCT35
</pre>
When finished, restart the queues that you stopped by <code>$ start/que queue_name </code>.

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====Error: Shutter fail safety test timeout CODE: 2101====
This happens if the scanning program has accidentally be left on overnight and the shutter fail safe test cannot be performed. Ensure that uct_tomography is closed at the end of the day and the scanner computer is logged out at the end of the day to avoid this error.

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====Error: Input error detected, Z protection detected CODE: 4001====
This means the big plate that you can see through the gantry has moved or been touched, activating one of the Z protection switches. This can happen during positioning a patient for a tibia scan if the person's leg isn't pushed into the scanner straight. The cast can potentially touch the plates and cause this error.

In the rare case where this error occurs spontaneously during or at the end of a scan, or during a precalibration, one of the switches may have become activated due to the position of the Z plate. To determine the position(s) this error is triggered, do the following:
<pre>
$ set host 0 Username: calibration Password:

$ sdl
$ spb
$ run um:ccd_2d
</pre>
The Scanco test programs will open. First click on the Reset Z button (upper left corner). Then move the Z slider all the way to the right and hit move. If the Z-protection error appears, record exactly which Z position triggers the error (should be a red number on the left hand side of the slider). When you are done with this test, hit Reset Z again, wait until the motor comes to a complete stop (max. 15 seconds), close the software and in the same terminal by <code>$ logout </code>.

Contact Scanco regarding this error and provide the details from running the ccd program. They will provide further instructions on how to proceed and fix the problem.

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====Fatal: CCD frame timeout, HOTLink reframing CODE: 1007====
Take a screenshot of the error message and email Scanco immediately. Message indicates that X-ray tube is arcing. Try and warm up the X-ray tube again, and notify Scanco if there is any abnormal activity and whether the tube was able to warm up.

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====Fatal: Invalid Scanner ID CODE: 24====
You have logged in with the incorrect user name. End the session and login with the correct user name (vivaCT 40: vivact or invivo; µCT 35: microct or invitro).

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====Fatal: Unable to create shared memory, global page table full CODE: 196====
The temporary fix is to reboot the system. But before you restart, if you have system access, do the following and save the output to a text to send to Scanco.
<pre>
$ set host 0
Username: system
Password:

$ search sys$system:agen$feedback.dat gblpages
$ write sys$output f$getsyi("contig_gblpages")
$ write sys$output f$getsyi("free_gblsects")
</pre>

==Reconstruction==

===Standard Reconstruction===
Scans are automatically submitted for reconstruction, so manual submission is usually only necessary if there was a problem during reconstruction (e.g., a power failure).

*To reconstruct all slices from the RSQ, first delete or rename the old ISQ.
*To reconstruct a selection of slices, a valid ISQ must exist. There is an offset of 1 slice when designating slice selection.
'''General Usage for Interactive Reconstruction''':
<pre>
$ uct_reconstruction P1 P2 P3

P1: RSQ Filename
P2: Slice number (A – all, start:finish)
P3: Log file of batch job
</pre>
'''General Usage for Non-interactive Reconstruction''':
$ submit/noprint/que=sys$slow um:uct_reconstruction.com/params=(DISK2:MICROCT.DATA.00000610.00002449]C000####.RSQ , a)
*Normally jobs are submitted to sys$slow queue instead of running them interactively.

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====Reconstruct a selection of slices====
Here are examples of how to reconstruct a single RSQ file: C0007655.RSQ, sample 4111 and measurement 9899. 
To reconstruct slices 101 to 201 and submit the job to the sys$slow queue:
<pre>
$ submit/noprint/que=sys$slow um:uct_reconstruction.com /log=sys$scratch:reco4111.log/para=(dk0:[microct.data.00004111.00009899]C0007655.rsq, 100:200, sys$scratch:reco4111.log)
</pre>
*The command must be all on one line (or use hyphen), and it wants the 3 parameters: filename, slices, and log.file name

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====Reconstruct all slices====
To reconstruct all slices, use “a” for all slices and submit the job to the sys$slow queue:
<pre>
$ delete C0007655.ISQ;*
$ submit/noprint/que=sys$slow um:uct_reconstruction.com/log=sys$scratch:reco4111.log/para=(dk0:[microct.data.00004111.00009899]C0007655.rsq, a, sys$scratch:reco4111.log)
</pre>
*The .log filename is up to you, as long as it's the same at both places.
*Give full pathname for RSQ file.

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====Reconstruct multiple files====
For multiple files, create a script and submit the job to the sys$slow queue. For example,
<pre>
$ cd sys$scratch
$ eve reco_all.com
</pre>
Or open editor (command 'Edit'), put the following lines in the file and save it as .e.g sys$scratch:reco_all.com:
<pre>
$ uct_reconstruction dk0:[microct.data.00004111.00009899]C0007655.rsq a
$ uct_reconstruction dk0:[microct.data.00004111.00009900]C0007656.rsq a
$ uct_reconstruction dk0:[microct.data.00004111.00009001]C0007657.rsq a
$ exit
</pre>
Save the script and exit the text editor, then submit the job (e.g. to sys$slow):
<pre>
$ submit/noprint/que=sys$slow/log=sys$scratch:reco4111.log sys$scratch:reco_all.com
All the files will be reconstructed as a single job, with one log file.
</pre>

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====Batch reconstruction on XtremeCT2====
The reconstruction software available for the XT2 supports the /batch syntax that replaces reco_all.com.
You can split a manual reconstruction into several jobs using

$ uct_reconstruction DK0:[XTREMECT2.DATA.00001234.00005678]D0123456.RSQ a/batch=16

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====Update to uct_reconstruction V6.2-5, March 2019====

As of March 2019, we should only use uct_reconstruction v6.2-5 on xtremect2.
For studies with baseline and follow-up scans overlapping this time, the old version (V6.2-2) can still be accessed using
<pre>
$ uct_old_recon
</pre>
Changing reconstruction versions can lead to small systematic differences in the result parameters of a trabecular bone analysis. The old version should only be accessed by those who absolutely need to use it. (Scanco recommends re-reconstructing all measurements of a study with version 6.2-5 instead).

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=== Rotated Reconstruction (about z-axis)===
#Use the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] to measure the angle for the rotated reconstruction.
#*To start the program type <code>$ uct_evaluation </code> in a DEC terminal, or use the graph button.
#*Load your sample and select the angle measurement button.
#*Drag the ends and the intersection of the green lines to measure the desired rotation angle.
#:[[File:Angle meas.preview.jpg|600px]]
#Rotate and reconstruct
#*Use <code>$ @com:reco_all </code> to reconstruct all slices.
#*Use <code>$ @com:uct_reconstruction_angle </code> to reconstruct selected slices from an RSQ.
#Use the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] to check the sample after the rotated reconstruction:
#:[[File:Rotated_reconstruction.preview.jpg|600px]]

*'''General Usage''':
<pre>
$ @com:reco_all.com P1 P2 P3

P1: Angle in degrees
P2: Sample number
P3: Measurement number

$ @com:uct_reconstruction_angle.com P1 P2 P3 P4 P5

P1: RSQ Filename
P2: Slice number (A – all, start:finish)
P3: Log file of batch job
P4: Delete log file (true/false)
P5: Angle in degrees
</pre>
*The angle of rotation uses the right-hand rule: a counterclockwise rotation is positive and a clockwise rotation is negative.
*The angle of rotation uses a single decimal place.
*By default the reconstruction jobs will be placed in the sceva3_slow queue.
*Both functions are executed from the measurement directory.

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====Reconstruct all slices====
The following examples are for a 19.1 degree counterclockwise rotation of sample 6876, measurement 15417, C0005086.RSQ.
<pre>
$ @com:reco_all.com 19.1 6876 15417
</pre>
*Delete the ISQ file from the measurement directory.

====Reconstruct a selection of slices====
*A valid ISQ must exist.
*There is an offset of 1 slice when designating slice selection.

To reconstruct slices 36 to 41:
<pre>
$ @com:uct_reconstruction_angle.com DK0:MICROCT.DATA.00006876.00015417]C0005086.RSQ 35:40 sys$scratch:reco610.log true 19.1
$ @com:uct_reconstruction_angle.com DK0:MICROCT.DATA.00006876.00015417]C0005086.RSQ 35:40 "" "" 19.1
</pre>
*"" is used as a null input for optional parameters.

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===Other Reconstruction===

====Reconstruct at a new voxel size====
See a script in:
DISK1:[XTREMECT2.EVAL]UPDATE_HEADER.COM

This script includes the following type of information:
$ r ut:updh_voxelsize.exe
DK0:[XTREMECT2.DATA.00000010.00000050]D0000068.RSQ
122
82000
1706
$ r ut:updh_voxelsize.exe
DK0:[XTREMECT2.DATA.00000011.00000054]D0000072.RSQ
122
82000
1706

This is what one would do in a terminal. The only requirement is that this <code>updh_voxelsize.exe</code> cannot be executed as the normal user.
Prior to that, one has to log as calibration, and do:
$ set proc/priv=bypass

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==Manipulate RSQ==

===View RSQ projections and flat field===

It can be very useful to examine the projections that are contained in the RSQ file, as well as to see the flat field correction frames.

In the session manager, double click the RSQ file and the program ximage will open. Or, type:
$ sh sym x
X == "$UM:XIMAGE.EXE"
$ x D0000018.RSQ
Then switch to xz view and go to the second slice (in this order). Then you should see a frame of the none attenuated beam (nothing in the beam, or Scanco calls it the I0 frame). If it is a multi stack measurement then there will be several copys of this frame in this image.

In an RSQ you have for each slice of the detector one dark current line and then the full intensity line followed form the radiographs taken under the different angles (sinogram). In the x direction is the detector line, in the y direction is the rotation angle (except dark and I0) and in the z direction is the z-direction of the scanner. If you switch the view to xz, then you can see the frames as acquired by the detector (or stacked frames all taken under the same rotation angle). Frame 1 is then the dark image and Frame 2 is the full intensity image.

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===Convert RSQ to AIM===
<pre>
$ ipl
ipl> rsq_to_aim in YP_IGFAMOTION_003_6.RSQ
-pos [0 0 0] >
-dim [-1 -1 -1] >
-convert_to_pro [false] > true
-sinogram_not_frames [true] > true
-div_unsigned_by_2 [false] > true

ipl> write
-name [internal_name] > in
-filename [default_file_name] > YP_IGFAMOTION_003_6_rsq.aim
-compress_type [bin] > none
-version_020 [true] >
</pre>

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===Convert RSQ to PSQ===
First, in the terminal turn on the 'advanced questions' mode
<pre>
$ define uct_reconstruction_calibration true
</pre>
Second use the reconstruction EXE to convert RSQ to PSQ
<pre>
$ run UCT_RECONSTRUCTION.EXE
raw file: DISK3:[MICROCT.PROJECTS.YVES.LANDMARK.RAW]filename.RSQ

Give slice number, or 'a' for all
hit return a few times

Write Projection [N]: -> say y and it writes the PSQ and continues with reco
Say p if it shall just produce PSQ and NOT continue with reco!
</pre>
Beam hardening correction can be turned off by doing
<pre>
$ DEFINE UCT_RECONSTRUCTION_CALIBRATION TRUE
$ define uct_disable_bh_correction true
$ deass UCT_BEAMHARD_POWER
$ deass UCT_BEAMHARD_factor
</pre>
and then run <code>uct_reconstruction</code>

The RSQ contains the RAW projection data. The PSQ represents tilted parallel beam projections:

[[Image:CB-Rebinned.gif]]

The rebinning process reduces the number of projections from 836 (1 bright field, 1 dark field and 834 projections spaced at 0.24 deg/proj, spanning 200.16 deg) to 750 (spanning 180 deg) with a resolution of 0.24 deg. In addition to the geometric changes, intensities are adjusted ln(I/I0) and beam hardening correction is applied. After converting a PSQ to AIM with IPL, an image can be reconstructed with Matlab's iradon(), note that only the central slice will be geometrically 'correct', but differences in other slices are small (Circumference of calibration phantom differs less than 1%). in the final reconstruction these effects are accounted for reducing the number of z-slices from 124 (acquired) to 110 in the reconstructed image.

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===Measure RSQ motion artifact===
Based on RSQ data, in-plane translation and rotation, and longitudinal translation can be determined.

The RSQ is first converted to a tilted parallel-beam sinogram. Motion is measured using the bonelab_measuremotion command in the Calgary extension of IPL installed on percy. Copy the motion scripts available in <code>DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]</code> to your COM directory. Here is how they work:

* RSQ_TO_PSQ.COM;1 - (optional) convert RSQ to PSQ, PSQ gets created in the same directory as RSQ. Usage:

<code>$ @rsq_to_psq.com DK0:[BRUNO.DATA.00000162.00009479]C0008921.RSQ</code>

* IPL_MEASUREMOTION.COM;2 - Takes a PSQ and measures motion using Calgary IPL on percy

<pre>
$! example of how to submit a motion measurement
$ SUBMIT/NOPRINT/QUE=SYS$FAST /LOG=SYS$SCRATCH: -
DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]IPL_MEASUREMOTION.COM -
/PARAM=(DISK3:[MICROCT.PROJECTS.DEVEL.RECO_TEST.RAW]PHANTOM_NOMOTION.PSQ) -
/LOG=DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]MEASUREMOTION.LOG
</pre>

Results are save in <code>MEASUREMOTION.LOG</code> and the following section contains all information:
<pre>
/bonelab_measure_motion
-input org
Motion:
Translation = 2.135364
Rotation = 0.024216
Index = 3.694660
Translation weight = 0.943156
Rotation weight = 69.403737
Z_motion = 2.274551

Use the line below with search.
Translation,Rotation,Index,Trans_weight,Rot_weight,Z_motion
2.135364,0.024216,3.694660,0.943156,69.403737,2.274551

Use the line below for DB entry (Index*100).
db_motion_index=369.466034
</pre>

In-plane translation is '''Translation''', in-plane rotation is '''Rotation''' and longitudinal translation is '''Z_motion'''. '''Index''' is the total in-plane motion as used in the IEEE ISBI 2009 paper by linear combination using the weights, not used any more, now we use in-plane translation only. '''db_motion_index''' is the motion index value multiplied by 100 and that could be written to the patient database. Multiplication by 100 is necessary since the motion field in the database is integer only.

For more background on the algorithm look at ''Pauchard Y., et al, Measuring patient motion in HR-pQCT, IEEE ISBI 2009'', and ''Pauchard Y., et.al., Automated quantification of three-dimensional subject motion to monitor image quality in high-resolution peripheral quantitative computed tomography, Phys Med Biol. vol. 56, pp 6523-6543, 2011''. '''IMPORTANT''': The IPL implementation has not been validated against the Matlab implementation used in these publications. Motion Values can be different. Values can be automatically extracted as described below.

* RSQ_MEASUREMOTION.COM;10 - The full deal: creates PSQ and measures motion all in the same directory as the RSQ.
<code>
@DISK3:[MICROCT.PROJECTS.RESCAN.COM]RSQ_MEASUREMOTION.COM DISK3:[MICROCT.PROJECTS.RESCAN.RAW]M0003508.RSQ;1
</code>

Make sure to adjust the line:
<code>$ SCRIPTFILE := DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]IPL_MEASUREMOTION.COM</code>
to the location of your <code>IPL_MEASUREMOTION.COM</code>.

The results are stored in the same directory as the RSQ in <RSQname>MOTION.LOG and can be extracted into motion_all.txt by running the search command:
<pre>search/output=motion_all.txt/window(0,1)/match=OR *motion.log "Translation,","Patient Name "</pre>

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===Update RSQ's Center Information===
<pre>
$ set host 0
username: calibration
password:
$ spb or $ set proc/priv=bypass
$ run [.util]updh_center
Raw-Data-File: enter location of raw data (with directory if necessary)
Center X: [15430]: enter new center value (e.g. 15415)
Press return for all other options.
</pre>

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===Determine RSQ's Centre Calibration Values===
<pre>
$ define uct_reconstruction_calibration true ! Note: do not mistype... or the calibration program will not run
</pre>
In the SAME terminal:
<pre>$ uct_reconstruction dk0:[microct.data.00004026.00004576]c0001344.rsq
Slice-Nr. [0...919] (Neg. to stop): 100
Center [207]: here enter a new number
</pre>
Hit return a few more times to use default values for other options.
<pre>
XtremeCT check these values, that they do not change:
Maximal possible Scan-Distance (mm) = 125.9520
Cropped adjusted Scan-Distance (mm) = 125.9520
See that it does not change, e.g. drop to 124 mm or such...
</pre>
Then do that again, $ uct_reconstruction ....rsq 100 (for the first time, for each file/scan).

Double click on ISQ. slide to slice 101 (!) (100+1, since terminal zero based) compare with image in e.g. slice 100 or 99 (disregard funny half image shift...)

Should already look nicer.

Then try out with e.g. center 230 or so, with e.g. slice 101 (thus slice 102 in Ximage). (now, only one run is necessary)
<pre>
compare against image with center e.g. 200.
continue at libitum until you find the best center, the crispest image.
</pre>
Usually the centre is determined to within about 3 to 5 points (which is 0.3 to 0.5 pixels), so e.g. test 225 and 230, and maybe 228.

Write down your favourite.

If you cannot decide: let Andres know which ISQ slice was reco-ed with which center (in 'Ximage' slice numbers), and I can check - but since remote Ximage is SOOO slow, thanks for only pointing out a few options, I cannot check 20 settings...

Then continue with next diameter scan (the first time for each scan, reco twice again)

The different diameter centers should be a steady function, so all the new center values should be increasing as diameter decreases.

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===Modify RSQ's BHC for in-air scans===
This is necessary because the beam-hardening correction factor assumes scans were done in soft tissue. It is necessary to choose calibrations of 1200 or 700, instead of the default 200.

Currently, the XtremeCT has options for 200 (standard) or 1200 calibration (in air).

To do this, log in as users <code>calibration</code> and then:

<pre>
$ set proc/priv=bypass ! as user calibration; modification of MICROCT user data
$ run ut:UCT_EXT_HEADER_ADD_CALIB.EXE
> Raw-Data-File []: DISK2:[MICROCT.DATA.00000401.00001495]C0001404.RSQ
> ...
> Add another BH-Corr from file again? (Y/N) [N]: ! Enter yes (UCTD:UCT_BH_COEFF_60KV_1200HA_3309.TXT)
</pre>

Then, delete the old ISQ. It must be deleted or else the header information will not be changed. Finally, reconstruct the new ISQ and analyze...

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==Manipulate ISQ==

===Read an ISQ header===
You can either read using the standard tool

$ ctheader C0014141.ISQ
$ sh sym ctheader
CTHEADER == "$UT:CTHEADER.EXE"

Or, use the extended header tool to show the calibration data

$ run ut:uct_ext_header_display.exe

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===Import ISQ===
When you import, please note that the sample number AND measurement number are updated, so meas 10907 is now 10908.

Suppose you have a sample 3000, meas 10000, C0001234.isq, and want to import this into sample 3001, this is what I would do:

To make a copy of the scan (i.e., keep it in sample 3000 and make another copy in 3001)
<pre>
$ cd *3000*10000
$ copy C0001234.isq D0001234.isq, also copy any other files you want imported (RSQ, GOBJs, etc)
$ import

UCT_IMPORT V1.2

---------------

ISQ-file []: D0001234.ISQ

Sample number [0]: 3001

Change File Header name [Y]: Y

Optional: Operator Measurement [0]: 1 (1 = bonelab)

Site 20 Radius L

Optional: Controlfile Nr. [0]: (change if desired)

Execute Rename Command [Y]: Y
</pre>

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==Image Artifacts==
===Ring Artifact===
*Refer to [[Media:Microct_ring_correction.pdf|'''MicroCT Ring Correction''']].

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===Partial Volume Effect===
*Refer to [[Media:Partial_Volume_Effect.pdf|'''Partial Volume Effect''']].

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===Beam Hardening Correction (BHC)===

====Use the right BHC====
*Refer to [[Media:Beam_hardening_correction.pdf|'''Use the right beam hardening correction''']].

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====Understand Scanco BHC====
If you see lines like 'CCD_CORR: Expand BH-corr to1536' etc. etc.:

then we do a polynomial correction:
<pre>
$ dir uctd:*bh_coeff*.txt
</pre>
and you see a file with the scanner ID.

<pre>
--> $ type uctd:UCT_BH_COEFF_60KV_0200HA_3309.TXT

-->
! Function 9 is Addpolynom
Function: 9 A
0: 3 0.00000000 -0.38599902 0.30870225 -0.06162301
--> 0: for all pixels. 3 --> 3rd degree polynom, with factors:
x^0 = 0
x^1 = -0.38...
x^2 = 0.308...
x^3 = -0.061...
</pre>

This polynom is added to the PROJECTION value (not the raw counts).

the BH-corr is doing a 'linearization', e.g. see

http://iospress.metapress.com/content/twcxb9jfk8knhpq2/

for more info.

The values in the middle of the scan are amplified more - not just because of their position, but because the object is thicker there, thus the projection values are higher, thus the correction term is higher.

NOTE : Linearisation, as used by Scanco, will compensate 'soft-tissue' beam hardening (inside of water phantom appears LESS dense). Bone related beam hardening, e.g. soft tissue near skull appearing MORE dense, will NOT generally be compensated. See Kak and Slaney 'Principles of computerized tomogprahic imaging' and Joseph and Spital J Comp Assist Tomo 1978 vol 2 for more information.

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=Evaluation=

==Analysis Topics==

===Cortical thickness analysis in standard evaluation===

!!Note - with ipl v5.42 this should be changed to <code>/dt_cortical_thickness</code>

Use the IPL command <code>/dt_cortex_obj_param</code> to measure cortical thickness using direct methods.

When extracting the results from the database using <code>uct_list</code>, specify the <code>UCT_3D_LIST_W_CTH.TXT</code> template in directory <code>DISK0:[MICROCT_COMMMON.UIL]</code>.

<pre>
$ uct_list
UCT_LIST.EXE Version V5.1
Template-File [UCT_3D_LIST_SHEET]: DISK0:[MICROCT_COMMON.UIL]UCT_3D_LIST_W_CTH.TXT
</pre>

UCT_3D_LIST_W_CTH.TXT is now the default template as of March 2009.

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===Cortical porosity and finite element analysis on XtremeCT===

* This procedure is broken down into 3 separate components
* All Scripts mentioned be copied directly from DISK3:[MICROCT.PROJECTS.KYLE.SCRIPTS]
* Files should be copied from data to projects prior to running analysis (see bonelab procedures.doc on sodor)

1. Autocontour the image 
2. Calculate and extract cortical measurements 
3. Create FE files and run FE 

====Autocontour====
* The main autocontour script is located in the ue: directory, this should NOT be modified!
* The procedure is executed using a "hijack" script [[Media:HIJACK_AUTOCONTOUR.TXT|'''HIJACK_AUTOCONTOUR.TXT''']], but the filename must be changed to .COM or found in the directory mentioned above.
* Files should already have a _SEG.AIM created and should be in the same directory as the raw .AIM file.

* You then create a SUBMIT.COM script as you would for other files. For example:
$ QQ = "SUBMIT/NOPRINT/QUE=SCEVAL_FAST/LOG=SYS$SCRATCH com:HIJACK_AUTOCONTOUR.COM"
$ 'QQ' /PARA=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.MODELS]'''FILENAME'''.AIM

* This command will then create various files for examination and further analysis. These include:
** FILENAME_COMBI.AIM - shows cortical, trabecular, and pores all in different colors
** FILENAME_COMBIPO.AIM - shows only the cortex with porosity as different color
** FILENAME_CRTXFILL.AIM - gives sold mask of cortex, porosity filled (can be used to calculate Ct.Th)
** FILENAME_CRTXPO.AIM - shows only the pores
** FILENAME_TRAB.GOBJ - gobj of trabecular region
** FILENAME_CRTX.GOBJ - gobj of cortical region
** FILENAME_AUTO2.GOBJ - gobj of whole bone region

* Further technical details and references can be found in the following publications:
** Buie, H., Campbell, G., Klinck, R., MacNeil, J., & Boyd, S. (2007). Automatic segmentation of cortical and trabecular compartments based on a dual threshold technique for in vivo micro-CT bone analysis. Bone, 41(4), 505-515.
** K.K. Nishiyama, Macdonald, H., Buie, H., Hanley, D., & Boyd, S. (2010). Postmenopausal Women With Osteopenia Have Higher Cortical Porosity and Thinner Cortices at the Distal Radius and Tibia Than Women With Normal aBMD: An In Vivo HR-pQCT Study. Journal of Bone and Mineral Research, 25(4), 882-890.

====Evaluate Cortex====

*This Step 2 method of doing the cortical analysis is no longer used now that we have the IPL_UPAT_CALGARY_EVAL_XT1.COM or XT2.COM version. The problem with this approach is that it is a Frankenstein of the standard analysis and the advanced analysis. The cortical bone assessment is correct, but the trabecular compartment from the standard analysis is not a perfect match. Instead, we should be using the GOBJs described in IPL_UPAT_CALGARY_EVAL_XT1.COM so that we have a perfect mix.

Nevertheless, we keep this information here for now for posterity.

*After the autocontour is computed we used to call IPL_EVAL_CORTEX.COM that will calculate the cortical parameters:
**Cortical porosity (%)
**Direct cortical thickness (mm)
**Cortical density (mg HA/ccm)

This WAS called as the following:
$ QQ = "SUBMIT/NOPRINT/QUE=SCEVAL_FAST/LOG=SYS$SCRATCH com:IPL_EVAL_CORTEX.COM"
$ 'QQ' /PARA=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.MODELS]'''FILENAME.AIM''' -
/LOG=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.LOG]'''FILENAME'''_EVAL_CRTX.LOG

* The results of this script are outputed into individual log files for each file being evaluated.
* To extract these results into one file use:
$ search/output=output_results_filename.txt *EVAL_CRTX.LOG "!% ov/tv","!> C.Th","!% mean_unit"
*A learn command in the eve editor can be used to extract the specific results desired:
**!% ov/tv is the amount of bone in the cortex (ie. 1- ov/tv = cortical porosity)
**!> C.Th is the direct cortical thickness in mm
**!% mean_unit is the cortical density in mg HA/ccm

====Create and run FE models====

*The most current common FE model to run is a homogeneous model where all elements have the same material properties and the cortex and trabecular regions are labeled separately in order to determine the percentage of load carried by each region.
*The other option is to create a model where the material properties are scaled based on the density values and scripts for this can be found in the COM directory.

*The script IPL_FEM_HOMOGEMOUS_LS.COM will use files created by the autocontour and appropriately label the cortex and trabecular regions as well as remove any disconnected pieces of bone.
$ QQ = "SUBMIT/NOPRINT/QUE=SCEVAL_FAST/LOG=SYS$SCRATCH com:IPL_FEM_HOMOGENOUS_LS.COM"
$ 'QQ' /PARA=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.MODELS]'''FILENAME'''.AIM

*Files will now be created with the suffix _HOM_LS.AIM and can be moved to Mighty-Mac or Mavis for FE analysis. You will require user accounts for these computers and can contact Eric or Steve. If using FTP be sure to transfer the files in binary mode (further documentation on this can be found in this Wiki)

*[[Media:2009-10-15_FEM_Tutorial.pdf|'''FEM tutorial main steps''']] to submit the FE files with a detailed manual is recommended for first time users.
*This is now out of date, but is kept here because it still contains useful information about preparing AIM files and post-processing.
*For running the FE itself, please refer to the current manual at [[FAIM Finite Element Solver]].

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===Cortical midshaft analysis with moment of inertia calculation===

This explains what happens when you type

<pre>
$ midshaft ! or
$ eval_midshaft
</pre>

Draw a rough contour around your slices: open the Contouring Sub-window, double-click on the big image, and it automatically finds the best contour. Then click on 'Selection' 'Forwards', then 'Iterate Forwards'.

Then 'cancel' the contouring sub-window, and start the 3D evaluation. Make sure you have already set the correct threshold, sigma, support in file
<pre>DISK2:[MICROCT.EVAL]IPL_FIXED_BATCH_MIDSHAFT.COM</pre>

When you type

<pre>$ show queue</pre>

you should find a job called UCT_EVALUATION_MIDSHAFT and a SYS$SCRATCH:*_MIDSHAFT_*.LOG

The IPL_FIXED_BATCH_MIDSHAFT.COM by default does not calculate the direct measurement results because you must have many more than 20 slices for these to be valid. You can uncomment these parts of the file if you contoured the whole stack (i.e., stack thickness is >> than cortex thickness).

TILDE: Note that you will see lots of tildes (~) on the result sheets. This is to tell you that, if the measurements were trabecular bone, those values would only be approximate. But now for the cortex, they are actually correct! (see below for more explanation about this) I would now use the tildes to check the 'excel' table that the operator has taken the correct script for the trab. or cort. evaluations for the respective measurements!

So what's the advantage of all this? Now, also VOX-TV is correct! So VOX-TV is the whole area, VOX-BV the doughnut, so TV - BV is the marrow area! And still, TRI-Tb.Th is the cortical thickness (TRI-TV is NOT correct, because the .gobj feature was turned off).

I say 'area' above: depending on how many slices one individual scan has,
VOX-BV (and VOX-TV) might be different for different scans, so you will HAVE to
convert the volumes to area again:

<pre>
volume equals area times height
--> Bone Area = VOX-BV / height = BV / (dim.z * el_size_mm.z)
</pre>

and same for Total area, of course :-)

POROSITY: If you want porosity of the bone itself draw two contours: one around, counter-clockwise, on on the inside, clock-wise (thus a 'negative', excluding contour). Now, TV will be just that ring area, BV will be the bone within that ring area, and BV/TV will be 1 - porosity, thus BV/TV 94% means 6% porosity.

METAPHYSIS: Application of this script to metaphysis scan (with trab. in middle):

<pre>
$ midshaft
</pre>

Draw one contour around the cortex, and in the same slices, a NEGATIVE contour on
the inside (CW contour) to exclude the trabecular bone. You may potentially work with the BP (break-point) system to be able to morph the negative contours, even though there is already an 'outer' contour around the bone in every slice.

Start 3D eval, read out the data-base with <code>$ uct_list</code>.

NOTE: You CANNOT give the .gobj a special name such as c0001234_cortex.gobj if you are using the automatic evaluation button on UCT_EVALUATION. Only after the eval (or midshaft eval) has finished, you may copy it to a more meaningful name, but all of the evaluations are just taking the STANDARD gobj name!

Afterwards (after renaming or copying the _seg.aim to _cortex.aim, and .gobj to _cortex.gobj), you may want to start the very normal eval with normal (inner) contours to evaluate the trabecular compartement.

<pre>
Remember: the values in our 3D result database then are OVERWRITTEN.
</pre>

If you have a large study, I would recommend to run the $ midshaft for ALL
samples, <code>$ uct_list</code> to e.g. <code>sys$scratch:mystudy_cortex.txt</code>,
rename/copy gobj and seg for all, and THEN run the trabecular evaluation for all samples. <code>$ uct_list</code> and you have two nice complete excel sheets.

NOTE ON PLATE MODEL: More explanations of why the plate model is correct

Assume a ring (cortex).

<pre>
Area = thickness * 'middle line'.
'middle line' = average of outer and inner circumference
--> 'middle line' = 0.5 * 'bone surface'

--> thickness = bone volume * 2 / bone surface.
</pre>

And this is nothing else but the 'plate model' formula for Tb.Th!

NORMAL TRABECULAR EVALUATION? And why not just run the 'normal trabecular eval'? Because in the 'normal' TRI calculation, we are EXCLUDING all surfaces that are created artificially by a gobj line that cuts through a trabecula.

However, for the midshaft, this means the whole outer (or even inner, if also
inner contour is there) is SUPPRESSED, because it is touching the gobj line. So
this is where that midshaft script comes in: it turns off that suppression.

MORE EXPLANATIONS: Why the direct DT-Tb.Th* is NOT correct for a scan with
just 12 slices.

If we fill the structure with spheres, those spheres should be bounded by the
width of the cortex, not just by the fact that we only have 12 slices (and even more so, we are always doing 'aim box' suppression with the spheres) if a sphere touches the boundary of the aim box, it is suppressed!

So this is quite crucial for Tb.Sp and Tb.N. To get meaningful Tb.Sp, you would
need a LOT of slices. Also, then, you cannot have the inner contour - otherwise
the negative inner contour will delete the Tb.Sp. spheres.

If you have enough slices, you may opt to turn the <code>/dt_object</code> on again in the
midshaft script (second half). Then DT-Tb.Th* and TRI-Tb.Th just have a slightly different behaviour if there are little pores within the cortex:

<pre>
TRI: the little pore just adds a little BS, thus the influence is not that big.
DT: the little pore cuts the thickness sphere in half, thus at that location, the thickness is halved.
</pre>

MEAN1 and MEAN2: The script is also calculating Mean1 and Mean2 now.

<pre>
Mean1: 'apparent' density, average over whole TV
Mean2: 'tissue' density: average over what was segmented as bone only.
</pre>

These mean values will be in mg HA/ccm if you have the calibration option for bone density installed (and activated for those scans). Remember: the bone has to have some soft-tissue (or equivalent) on the inside, and preferably also on the outside then.

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===Joint Thickness Measurements===
*Sample script to search histogram files for results: [[Media:Summarize_Joint_Th_Measurements.pdf|Summarize Joint Th Measurements]]

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===Scanco Joint Space Width (JSW) analysis===
The scripts published in [https://doi.org/10.21037/qims.2019.12.11 Stok et al. 2020], and released by Scanco, are available for XCT1 and XCT2.

On XCT2 they have been installed as Tasks #112 to #116.

Instructions to run this analysis are available here [[Media:ESD_Joint_Space_Width_v2.3.pdf]].

The full citation for this work is:
<pre>
Stok KS, Burghardt AJ, Boutroy S, Peters MPH, Manske SL, Stadelmann V, Vilayphiou N, van den Bergh JP, Geusens P, Li X, Marotte H, van Rietbergen B, Boyd SK, Barnabe C; SPECTRA Collaboration. Consensus approach for 3D joint space width of metacarpophalangeal joints of rheumatoid arthritis patients using high-resolution peripheral quantitative computed tomography. Quant Imaging Med Surg. 2020 Feb;10(2):314-325. doi: 10.21037/qims.2019.12.11. PMID: 32190559; PMCID: PMC7063288.
</pre>

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==UCT_EVALUATION==

===UCT_EVALUATION SOP===
====Start 3D evaluation from terminal for XtremeCT II====

Logged into the terminal as "xtremect2" you can see the evaluation scripts in <code>IDISK1:[XTREMECT2.EVAL]</code>

The morphological evaluation: Control file #25. It basically runs auto contouring (#23) and then the morphological analysis.
* <code>UCT_EVALUATION_V6_XT2_DT61.COM</code>
* <code>IPLV6_EVAL_CORT.COM</code>
* <code>IPLV6_EVAL_TRAB.COM</code>
* <code>IPLV6_EVAL_TOTAL.COM</code>

* <code>UCT_3D_LIST_CORT_XT2.TXT</code>
* <code>UCT_3D_LIST_TRAB_XT2.TXT</code>
* <code>UCT_3D_LIST_TOTAL_XT2.TXT</code>

Contouring scripts:
* <code>IPLV6_AUTOK.COM</code>: Creates automatically the standard GOBJ. Control file #22.
* <code>IPL_AUTOK_CTTB.COM</code>: Creates automatically the CORT, TRAB and PORE.GOBJ (previously CRTXPO). Control file #23.
* <code>IPLV6_AUTOK_CTTB_CORR.COM</code>: Creates automatically the CORT and PORE.GOBJ, after manual correction on the TRAB.GOBJ. Control file #24.

Laplace- Hamming scripts:
* <code>IPLV6_UPAT_EVAL_LH61_XT1DB.COM</code>
* <code>IPLV6_UPAT_EVAL_LH82_XT1DB.COM</code>

Results will be generated in the <code>IDISK2:[XTREMECT2.RESULTS]</code> directory, in the same way as they are generated for the cortical analysis on XtremeCT I, i.e. using the uct database and appended text files.

Laplace Hamming evaluations will generate results in the upat_list database. The direct measurements will be stored in the uct_list database.

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====Symbols for XtremeCT II vs XtremeCT I====
<code>microct</code> account you get

"MICROCT_BIN" = "DISK1:[MICROCT.]" (LNM$PROCESS_TABLE)
= "DISK0:[MICROCT_COMMON.3309.]"
= "DISK0:[MICROCT_COMMON.]"

for <code>xtremect2</code>

"MICROCT_BIN" = "DISK1:[XTREMECT2.]" (LNM$PROCESS_TABLE)
= "DISK0:[MICROCT_COMMON.]"

So 3309 has its own directory where the software versions for the two scanners are different, e.g.

xtremect: DISK0:[MICROCT_COMMON.][MAIN]IPL_SCANCO_M.EXE
microct: DISK0:[MICROCT_COMMON.3309.][MAIN]IPL_SCANCO_M.EXE

We have defined some symbols for the different ipl versions:

IPL
IPLREG
IPLFE
IPL_BATCH
IPLREG_BATCH
IPLFE_BATCH

In the scripts you can directly use these symbols instead of ipl_scanco_prog (old style).

IPL and IPL_BATCH are different for the two scanners because the newest version is not officially released for XT1.
IPL of the microct account (XT1) cannot read data of the xtremect2 account (XT2). The other way around it works.

IPLREG and IPLREG_BATCH point to <code>$DISK1:[XTREMECT2.MAIN]IPL_SCANCO_REGIS_V107.EXE</code> for both accounts.

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====Start 3D evaluation from terminal for microCTs====

[[Image:Bones2.jpg|20px]] Warning:Do not change <code>uct_evaulation_v4.com</code> and <code>ipl_fixed_batch_v4.com</code> in .eval, but only work on your own file (i.e., eval_steve).

First, an explanation of how the normal evaluation runs by hitting the 'Start 3d' button.
<pre>$ scanco_submit_command ue:uct_evaluation_v4.com/para=(xxx,yyy,zzz,…)</pre>
There are 8 parameters:
*P1: number of print outs of our results sheet
*P2: the ISQ filename
*P3-5: start x (pos x), y, z
*P6-8: dim x, y, z
The parameters p3-p8 come from the white bounding box. The problem is that when you start from the terminal you do not have these. This problem can be overcome by using the <code>isq_to_aim_gobjbox.exe</code> and then give the relevant parameters. You can
<code>$ run um: isq_to_aim_gobjbox.exe </code>
to see what it's asking for.
By using gobjbox you do not need p3-p8. Therefore you can start the evaluation by giving:
<pre>$ scanco_submit_command ue:uct_evaluation_special_josh.com –
/para=(1,dk0:[microct.data.0000275.0000245]c0000332.ISQ)</pre>
*You can make <code>uct_evaluation_special_josh.com</code> such that there is no need for P1 (change p2 to p1 in the script, etc).
*Alternatively to using the gobjbox you could use the normal isq_to_aim, but hard code the dim and pos.
*Then call whatever IPL files you want to call. Look into <code>fixed_batch_v4</code> to see how we turn on the database always on the first line of every IPL part, and how we calculate parameters.

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====Temporarily change evaluation for UCT_EVALUATION====

In a terminal window, we need to redefine the logical that determines which
3D evaluation is associated with the <code>UCT_EVALUATION</code> tool.

For example, typing <code>VOI</code> runs the <code>UCT_EVALUATION</code> tool
by executing <code>UE:UCT_EVALUATION_VOI.COM</code>

Type
<pre>$ show logical UCT_EVALUATION</pre>
and then you can redefine this to point to another evaluation script.
<pre>$ define UCT_EVALUATION UE:UCT_EVALUATION_CUTOUT.COM</pre>

This is only redefined in the particular terminal you are using, and it
will reset to its default in a new terminal. It will also not work if you
try to submit the job to a queue. It only works interactively.

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====Assign special evaluation to UCT_EVALUATION====

'''Warning''': This is for advanced users ONLY. Do not attempt this without contacting Steve!

This will show how to set up <code>$ eval_kyle</code>:
It is easy to set up multiple .COM files for the 3D evalulation tool, one such set-up is already prepared on your computer:
<pre>
$ eval_special
</pre>
will do something similar to <code>$ voi</code> where the normal contour program opens, but if you start the 3D eval, the special script <code>um:uct_evaluation_special.com</code> is called (associated with eval_special), which then in turn calls <code>ipl_fixed_batch_special.com</code>, where you can specify your own set of thresholds, etc.

So it is a daisy chain of files which we will need to follow to set up a special <code>xxx_kyle.com</code> script, and where ever we encounter <code>_special.com</code>, we copy and change it to <code>_kyle.com</code>.

So to set up <code>$ eval_kyle</code> you will need to do the following:

*1. Edit <code>disk1:[microct]microct_setup_user.com</code> (double-click on file), please be careful here, it's very important! (and I hope you have done your 'weekly full backup' regularly, so you could always retrieve a good version of login.com...)

*2. Then, towards to bottom and duplicate the line
<code>$ eval_special :== @com:eval_var.com um:uct_evaluation_special.com</code>
and change duplicate to
<code>$ eval_kyle :== @com:eval_var.com um:uct_evaluation_kyle.com</code>

This will make this command <code>eval_kyle</code> available after you login freshly. Save and Exit.

*3. Then go to <code>disk1:[microct.eval]</code> and copy the file <code>uct_evaluation_special.com</code> to the name <code>uct_evaluation_kyle.com</code> ('Commands', 'Copy ...', BUT CLICK ON THE THREE DOTS and give new output name.
If you do not see the <code>eval_special:</code> go to terminal, <code>$ dir ue:*special*.com</code> and take it from the <code>microct_common</code> directory)

*4. Edit the <code>_kyle.com</code> file: at the top, change <code>ipl_......_special.com</code> to <code>_kyle.com</code>

*5. Copy <code>ipl_fixed_batch_special.com</code> to <code>ipl_fixed_batch_kyle.com</code>

*6. Edit <code>ipl_fixed_batch_kyle.com</code> to your liking. If you want <code>$ eval_kyle</code> to not perform the full evaluation, but only something akin to <code>voi</code>, then, in the steps above, copy <code>uct_eval_voi.com</code> to <code>uct_evaluation_kyle.com</code>, and <code>ipl_voi.com</code> to <code>ipl_fixed_batch_kyle.com</code> (thus you take the <code>voi</code> script as template for the <code>_kyle</code> script).

*7. Then open a new terminal ('applications', 'decterm'), <code>$ eval_kyle</code> should work now!

'''Notes''': When you start the 3D eval, then
<code>$ que</code>
will show you your batch job with your name on it now!

And now a few more explanations how the whole thing works: in all eval programs, hitting 'Start 3d' just submits the logical <code>uct_evaluation</code>, <code>$ show log uct_evaluation</code> shows you that by default, this points to <code>ue:uct_evaluation_v4.com</code>.

Those little <code>voi</code> and <code>eval_steve</code> scripts then just temporarily redefine this logical so that a different script is submitted when you <code>'start 3d eval'</code>.

About the '''corelut eval''': Then we start a whole different eval program: the <code>.exe_corelut</code>. So, if you set up a <code>eval_steve_c</code> (or whatever you want to call it): Produce a <code>eval_var_c.com</code> in the directory commands (maybe copy from microct_common to [microct.commands]), and there, on the last line, instead of starting
<code>$ uct_evaluation</code>
(the normal program), replace by
<code>$ evalc</code>
which starts the <code>.exe_corelut</code> - and because the <code>eval_var.com</code> has over-ridden the <code>uct_evaluation</code> logical just before, then you are starting different script upon starting 3d eval.
NB: we have a logical AND a symbol called <code>uct_evalution</code>. Sorry for confusion. Symbol <code>uct_evaluation</code> starts normal <code>eval</code> program, so this is what you replace by symbol <code>evalc</code> now).

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===UCT_EVALUATION FAQ===
====Warning: Not all required GOBJ files found, Continue anyway?====
This occurs when the chosen evaluation script is looking for a contour file, but can't find it.
*To see what contours the script is looking for go to "File" then "Save GOBJ As...". You can now see the list of required gobj files.
*For some scripts, it may not be necessary to supply a gobj and you can continue with the evaluation without it. For example, the "3D Segmentation of VOI, 1 solid object" applies the contour to isolate the region of interest, however, this may not be necessary if the object of interest can be extracted from thresholding.
[[File:Save_gobj_as.jpg|400px]]

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====Warning: Attempt to access non-existent record CODE: 36====
The scan is most likely still in the process of being reconstructed. Try to access the scan again in a few hours.

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====Error: Insufficient logical unit numbers CODE: 1409716====
Exit the evaluation program and restart it.

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====Error: Process quota exceeded====

[[Image:Process_quota_error.JPG|300px]]

When running UCT_EVALUATION from a dec terminal, an error when starting an evaluation may occur if there are to many dec terminals opened.
*The easy fix for this is to open the terminals from the applications menu in the [[Scanco_User_Instructions#Session_Manager|'''session manager''']] instead of using the dec command.
*Alternatively you can set up a new login script and add <code>/DETACH</code> to the dec definition
<pre>
$ DEC == "CREATE/TERMINAL=DECTERM/DETACH".
</pre>
An example script can be found here @DISK5:[BONELAB.PROJECTS.BUIE]SETUP.COM.

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====Bug: UCT_EVALUATION v6 in customizing EVAL scripts====

<pre>$ run um:uct_k_v6</pre>

The new evaluation tool v6 should be used in place of the older v5. Please see the Documents section of this wiki for a manual on its use.

Known bugs:

When you are producing your own EVAL scripts, and want to call your own ipl file
or such:

The 'EVAL:' keyword in the scripts has the filenames of the
uct_evaluation_v6.com, then the ipl_v6_xxxx.com, then additional filenames (such
as the _prs.com to print and the 3dresults_append.com)

Now, if you are in BASIC mode in the modify window, and you change any of the 3
filename fields, the last of the additional filenames is 'dropped'... ooops...

So please go to Advanced mode and check the long 'EVAL:' keyword that all wished
files are still in the list, otherwise add the last again (most of the time,
that's the useful _3dresult_append.com script...)

Will correct that of course in the next version.

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====Not work: Left mouse button====
When the left mouse button doesn't work in the µCT evaluation program:
*Turn off caps lock.
*For remote sessions, turn of the Num Lock key (this will also allow you to use Ctrl-C and Ctrl-V to copy and paste contours).

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====Not work: Remove and insert keys====

The remove and insert buttons on the keyboard don't work in the µCT evaluation program:
*Turn off caps lock.

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==Evaluation FAQ==

===Customize your evaluation script===
The basic procedure is to create your customized evaluation script is:
#Clear the database of existing results
#Do your evaluation
#Extract the results
#Paste results into excel template.
You could repeat as necessary to evaluate a measurement multiple times and write out the results to a file.
*You must submit all jobs to a single queue!!!

'''1) Start ipl and clear the database of existing results.'''
<pre>
$ IPL_BATCH

/db_clear_eval
-input "IPL_AIM

..
</pre>

'''2) Insert your IPL evaluation.'''

'''3) Extract the results.'''
<pre>$@com:extract_results.com P1 P2</pre>
*P1 is the aim file (including path) and P2 is the result file (including path)

Example:
<pre>
$@com:extract_results.com DISK5:[BONELAB.PROJECTS.BUIE]MYAIM.AIM DISK5:[BONELAB.PROJECTS.BUIE]MYRESULTS.TXT
</pre>
*P2 should be the same for all samples in your project so that results are compiled into a single file.

'''4) Paste results into excel template.'''
*Refer to the [[Media:Extract_Results_Template.xlsx |'''Excel Extract Results Template''']].
*Open your results text file and copy and paste the contents into cell A2. There's no need to use paste special since the sheet is protected.

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===Create your own IPL script===

To make a script that would submit a job to the queue with the command as follows:
<pre>
$ @um:ipl_eval_only.com 'aim_file' 'gobj_file' 'p1' 0
</pre>

you need to create your own IPL file would be translated to the following command:
<pre>
$ submit /noprint /que=sys$slow ue:IPL_VOI_JOSH_M.COM
- /log=sys$scratch:test.log /para=('aim_file','gobj_file','seg_file')
</pre>
The IPL file would look something like this…
<pre>
$ if p1 .EQS. ""
$ THEN
$ write sys$output "Give DK0:[xxx]C0001234_SEG.aim on the line."
$ write sys$output "Or: "
$ write sys$output "Type $ scanco_submit_command um:ipl_eval_autostart/para=(dk0:[xxx]c00123_seg.aim) "
$ exit
$ endif
$
$ gobj_file = p1-F$PARSE(p1,,,"VERSION")-"_SEG.AIM" + ".GOBJ"
$ aim_file = p1-F$PARSE(p1,,,"VERSION")-"_SEG.AIM" + ".AIM"
$
$!
$ @um:ipl_eval_only.com 'aim_file' 'gobj_file' 'p1' 0
$ exit
</pre>

Some more handy IPL sequences are:
<pre>
$ INPUT = F$SEARCH("UCT_MEASUREMENT_DATA:[*.*''P1']*.RSQ",1)
</pre>

and then you just need to give meas. number as P1 (and maybe slice range as p2),
<pre>
$ if p2 .eqs. "" then p2 := A
</pre>
OR, some nice starts are:
<pre>
$ IF P3 .EQS. ""
$ THEN
$ WRITE SYS$OUTPUT "P1: Measurement Number to duplicate"
$ WRITE SYS$OUTPUT "P2: New Sample Number from Database"
$ WRITE SYS$OUTPUT "P3: New Start Letter of ISQ file"
$ WRITE SYS$OUTPUT "P4: Optional: Operator Number"
$ WRITE SYS$OUTPUT "P5: Optional: Controlfile Number"
$ EXIT
$ ENDIF
</pre>
where you say which parameters HAVE to be there (up to p3), and which ones are optional.

All together, the script may look like this:
<pre>
$ IF P1 .EQS. ""
$ THEN
$ WRITE SYS$OUTPUT "P1: Measurement Number to reco"
$ WRITE SYS$OUTPUT "P2: Optional: Slice number N or Range M:N. Auto:All"
$ WRITE SYS$OUTPUT "P3: Optional: Queue. Auto: sys$slow"
$ EXIT
$ ENDIF
$ if p2 .eqs. "" then p2 := A
$ if p3 .eqs. "" then p3 := SYS$SLOW
$ slices = p2
$ quename = p3
$ INPUT = F$SEARCH("UCT_MEASUREMENT_DATA:[*.*''P1']*.RSQ",1)
$ INPUT = INPUT - F$PARSE(INPUT,,,"VERSION")
$ logfile = "sys$scratch:RECO_" + f$PARSE(input,,,"NAME") + ".LOG"
$ submit/noprint/queue='quename' uct_reconstruction_file -
/para=('input','slices','logfile')
$ exit
</pre>
Note that <code>uct_reconstruction_file</code> is a logical that points to <code>um:uct_reconstruction.com</code>.

Logicals are preferred in scripts to make them more universal.

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===Run Scanco cut and match function (on Percy)===

;At DATA DISK:
Run<code>$ upat_list</code>
*mode 1, list mode.
*Select patients and site, etc.
*Select the appropriate template file, e.g. <code>UE:UPAT_TEMPL_CUTMATCH_AUTO_PATTB_CT.TXT</code>
*Output to a file, then run that file.

;At PROJECT DISK:
If you have moved the files to the project directory and renamed them, you can generate a script from:
<pre>
$ @UE:SEARCH_PROJECTS_CUTMATCH.COM
-P1 = filename with device and directory
-P2 = site (RR, RL, TR, TL)
-P3 = output filename
</pre>
For example, if we run:
<pre>
$ @UE:SEARCH_PROJECTS_CUTMATCH.COM DISK3:[MICROCT.PROJECTS.GRACE]GRACE_01_00MTH_RR.AIM RR MYFILE.COM
</pre>
The script will search <code>DISK3:[MICROCT.PROJECTS.GRACE]</code> for files in the form <code>G*RR*.AIM</code> with the same
length as <code>GRACE_01_00MTH_RR</code>, then check sample numbers to determine if the file is a follow-up scan.
*Upat_list is called to obtain position and dimension data for matching slices.
*The output file <code>DISK3:[MICROCT.PROJECTS.GRACE]MYFILE.COM</code> is created to submit and run the cut and match.

Before running, open the file and add <code>$ exit</code> at the end.
<pre>$ @DISK3:[MICROCT.PROJECTS.GRACE]MYFILE.COM</pre>

For multiple files, do something like the following.
<pre>
$ @UE:SEARCH_PROJECTS_CUTMATCH.COM DISK3:[MICROCT.PROJECTS.GRACE]GRACE_01_00MTH_RR.AIM RR MYFILE.COM
$ @UE:SEARCH_PROJECTS_CUTMATCH.COM DISK3:[MICROCT.PROJECTS.GRACE]GRACE_02_00MTH_RR.AIM RR MYFILE.COM
</pre>
Open MYFILE.COM and add <code>$ exit</code> at the end.
<pre>$ @MYFILE.COM</pre>

*The script assumes all follow-ups are provided.
*If follow-up scans are missing, it will be necessary to modify the output file so that the position and dimension data matches the files or update the <code>SEARCH_PROJECTS_CUTMATCH.COM</code> script.

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==IPL FAQ==
===Submit a job to the queue===

<pre>
$ submit/noprint /que=sys$slow ipl_voi_josh_m.com /log=sys$scratch:test.log
</pre>

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===Rotate with turn3d / turn2d===

The turn3d function can be used to perform a single rotation about any axis in 3d. The turnaxis_angle input is the angle between the x, y, and z axes and the line about which the rotation will be performed. The turnangle input is the amount to be rotated about the specified line. To use this function to perform three sequential rotations about the image's original x, y, and z axes requires compensation for the previous rotations.

To rotate an image from the axial view in the z plane to the sagittal view in the z plane:

<pre>
$ipl
/turn3d
-input             in
-output          out
-turnaxis_angles 90 0 90
-turnangle 90
-img_interpol_option 0
</pre>

No interpolation is necessary as this is "pure reformatting" (turning +-90 or 180 degrees around x,y or z axis)

For knee images, to put the femur above the tibia, you further add the step:

<pre>
/turn2d
-input out
-output happyFemur
-turnangle 270
-turnpoint_global_not_local true
-turnpoint -1 -1
-img_interpol_option 0
</pre>

Refer to [[Media:turn3d.pdf |'''turn3d.pdf''']] for further instructions.

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===Noise removal by component labeling===
*Refer to [[Media:ComponentLabeling.pdf|'''Noise removal by using component labeling''']]

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===Create MSQ image and view===

This is based on marching cubes. See <code>IPL_UPAT_EVAL.COM</code> for an example as per below:

<pre>
/read seg C0000214_SEG.AIM

/sup_divide ! careful of the order of inputs here
-input seg
-suppos_pixels_local -1 -1 -1
-supdim_numbers 1 2 1
-subdim_pixels -1 -1 -1
-testoff_pixels 0 0 0

/sub_pick
-input seg
-output segsub
-subpos_numbers 0 1 0

/tri
-input segsub
-output tri
-gobj_filename none
-peel_iter 0
-ip_sigma 0.8
-ip_support 1
-ip_threshold 40
-nr_ave_iter 2
-size_image 512 512
-scale_image 0.800000
-edges false
-nr_views 1 ! Important

/msq_from_aim
-aim_name tri
-msq_filename C0000123_3D.MSQ
</pre>

Then, use <code>UCT_3D</code> to view it. If you click on "animations" it will give you the option to read the MSQ file.

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===db_scanco_activate associate evaluation database===

When <code>/db_scanco_activate</code> is used in the IPL files, the correct association with the evaluation database is through the Index Patient and Index Measurement in the AIM header.

<pre>
Index Patient 3095
Index Measurement 5962
!-------------------------------------------------------------------------------
</pre>

Using IPL
<pre>
$ ipl
$ read in xxx.aim
$ examine in log
$ db true {activates database}
$ dt_object {at end "writing results to database for measurement 1234"}
</pre>

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===dicom_to_aim bug in IPL v5.03===

In IPL, use the /dicom_to_aim function. There is a bug in pre IPL v5.03 which requires that a small AIM be read in before doing the DCM conversion.
<pre>
ipl> read in tmp.aim
ipl> dicom_to_aim
-aim_name [in] >
-dicom_filename [default_file_name] > 4F65038B3986.DCM
-multifile [false] > true
ipl> write in MYFILE.AIM
</pre>

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===Understand "New" DT functions in IPL v5.42===

This applies to:
<pre>/distance_map /dt_ow_thickness /dt_number
/dt_thickness /dt_spacing /dt_cortical_thickness
</pre>

XT1 (old dt) and XT2 (new dt) use 0.5 for assign_epsilon and 0.9 for
ridge_epsilon.

µCT uses 1.8 for assign_epsilon and 0.9 for ridge_epsilon (old dt).

Therefore I recommend to take 0.9 and 1.8 also for the new dt functions
for µCT/vivaCT measurements.

The <code>suppress_boundary</code> feature is new and works as follows:

0: The ridges and spheres are calculated on the full seg AIM, also
outside the gobj. At the end the gobj is applied.

1: The ridges that are on the AIM boundary are not used for the
calculation of the maximal spheres.

2: The ridges are calculated on the full seg aim but then the gobj is
applied to the ridges. This means that at the end there are only spheres
that have the center inside the structure (gobj). The maximal sphere
filling algorithm still accounts for the structure outside the gobj, but
only uses center points inside the gobj.

<code>dt_thickness</code> for example can be used in two different ways in a script:

1) cut out aim - apply threshold - apply gobj - dt_thickness
This way the suppress_boundary options do influence the results
because there are no ridges outside the gobj anyway.

2) cut out aim - apply threshold - dt_thickness (with corresponding gobj)
This calculates the dt on the full aim first and applies then the
gobj and suppress options.

If you examine for example trabecular bone only on a small area bounded
by a gobj then the most accurate way to calculate the dt is to cut out a
much larger area (still containing trabecular bone) and use way 2) above
with suppress_boundary 0.

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===Develop new IPL commands in C===
*Refer to [[Media:IPL programming.doc|'''A short manual on how to develop new IPL commands in C'''.]]

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=Results=

==Extract Results==

===UPAT_LIST command===

*Refer to Scanco specification document on using the [[Media:Specification_upat_print_list_V2.0.pdf | '''Upat_print_list V2.0''']] on XCT2.
*Refer to [[Media:Using_upat.docx |'''Using upat_list Additional Notes''']].

upat_list (version 1.9 on XCT1) is identical to 2.0 except:

:* there is no option for using group codes

:* there is no option for using evaluation types

For all of the available parameters for generating results using upat_list command:
$ upat_list -h

Program: upat_print_list V1.9
Use the following modes to run upat_print_list:
upat_print_list -list for export to spreadsheet, default mode
upat_print_list -print for PostScript output
upat_print_list -show for text output
upat_print_list -advanced to access advanced options interactively
Standard Command-Line Arguments:
-b=<pat_nr> First patient, default = 1
-e=<pat_nr> Last patient
In list & show modes, default = last patient in database
In print mode, default = first patient
-s=<site_code> Site code
In list & show modes, RL RR R* TL TR T* CU *, default = *
In print mode, RL RR TL TR CU, default = RL
-mb=<date> Begin of measurement period, default = 1st measurement date
-me=<date> End of measurement period, default = current date
Dates must be given in VMS format, e.g. 01-JAN-2000
-f=<#_followups> Maximum number of follow-ups to match, default = 19
-t=<file_name> Name of template file
In list mode, default = UPAT_LIST_SHEET
In print mode, default = UPAT_EVAL_SHEETxx
In show mode, default = UPAT_SINGLE
-o=<file_name> Name of output file (in SYS$SCRATCH by default)
In list & print modes, stored in SYS$SCRATCH
In show mode, written to SYS$OUTPUT
-c=<number> Number of Print copies if in print mode. default = 1
-v=<level> Verbosity from 0 (silent) to 2 (verbose), default = 1
-h Print this help and exit
Advanced Command-Line Arguments:
-et=<eval_type> Type code of evaluation, default = 2
-eb=<date> Begin of evaluation period, default = 1st measurement date
-ee=<date> End of evaluation period, default = current date
-tb=<date> Begin of matching period, default = 1st measurement date
-te=<date> End of matching period, default = current date
Dates must be given in VMS format, e.g. 01-JAN-2000
-sk=<#_to_skip> Number of measurements to skip, default = 0
-m=<meas_list> Numbered List of measurements to take, e.g. 0,1,2,5,8
-nomatch Do not match follow up measurement, just take all slices
-sb Begin of Slice Range in % to be evaluated
-se End of Slice Range in % to be evaluated
-q Only take evaluations with quality better than (and including) this.
If positive number: all scans of better quality (incl. this) as well as all non-graded scans are taken.
If negative number: non-graded scans are NOT taken.
-qs Only take Structural evaluations with quality better than (and including) this.
Thus: between -qd and -q: only Density results are printed.
Parameter is disregarded if -qs >= -q.
-ut=<unit_type> 0->default unit, 1->linatt, 2->mg HA/ccm, 3->HU, default = 0
-cd=<density> Value of compact density to use, default = 1200.000000
If no command line arguments are specified, upat_print_list runs interactively.

Note that using "TB" and "TE", you can pull out exact measurements in the specified date range, while using "MB" and "ME", all you get is the latest measurement no matter what date range provided.

For results of all time points for a single site and sample # without matching to Baseline, use:
I.e. the common region will be 100% for all measurements.
$ upat_list -nomatch

From these options, you can write out your own command (vs. using prompts) to give you the specifics you are looking for.

By specifying the CAMOS template of “UPAT_EVAL_CAMOS.PS”, you will get the “Camos” report style. For example:
$ upat_list -nomatch -b=1000 -e=1000 -s=TL -tb=01-MAY-2000 -te=01-AUG-2018 -t=DISK1:[MICROCT.COMMANDS]UPAT_EVAL_CAMOS.PS -c=0 -o=sys$scratch:upat_pat_1000_tl_camos.ps

Note that there are actually many kinds of report templates. These can be found via:
$ dir UU:*.PS

“SCUSA” is a short form for Scanco USA templates. I.e. templates that fit on an 8.5” X 11” page.

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===Extract followup data without slice matching===
Use:
<pre>
$ upat_list -advanced
</pre>
*Choose 'disable slice matching:' -> y.

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===Extract patient results on a slice-by-slice basis===

There is an executable that was specially installed by Andres. Run it as user <code>microct</code>:

<pre>
$ RUN ut:UPAT_EXPORT_MEASUREMENT.EXE
</pre>

Choose from "Style: 0 = default, 1 = raw". Default gives standard patient parameters.

This gives you the .txt file in scratch containing the morphological parameters determined for each slice.

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===UCT_LIST Extract results===

Assuming you've used the <code>SCANCO_SUBMIT_COMMAND</code> to initialize your evaluations (either manually or through the <code>uct_evaluation</code> tool) then you can get all of your results stored into a text file that can be easily imported in Excel.
<pre>$ uct_list</pre>
The output text file will be stored in <code>sys$scratch</code> and you can ftp this to a PC so that it can be imported into excel and further analysis can be performed.

Importing into Excel requires setting a deliminator based on the space.

Customizing the <code>uct_list</code> output.

The default list template is set by the logical <code>UCT_3D_LIST_SHEET</code> which is normally
set to point to <code>UU:UCT_3D_LIST.TXT</code>. See the templates by

<pre>$ dir uu:*.txt</pre>

Almost all the available keywords are in <code>UCT_3D_LIST.TXT</code> enclosed
by \\ and //.

Only when you use the 'show directly on screen mode':
<pre>$ uct_list 1234</pre>
then you need to do this to override the default output:
<pre>
$ def/user uct_3d_single_sheet my-template_file.txt
$ uct_list 1234
</pre>

Some example format files are:
<pre>
UCT_3D_LIST.TXT
UCT_3D_SINGLE.TXT
UCT_3D_LIST_W_CRH.TXT
UCT_3D_MEANS.TXT --> Use this to get the 5 mean values (i.e., calibration)
</pre>

A summary of all the available keywords is available in <code>UU:UCT_3D_SINGLE_SHEET.TXT</code>
<pre>
Name :\\UCTMEASFILENAME//
Sample-Name :\\SAMPLENAME//
Sample-Nr :\\SAMPLENUMBER//
Meas-Nr :\\UCTMEASNR//
Date of Birth :\\SAMPLEDOB//
Sample-Remarks :\\SAMPLEREM//
Meas-Remarks :\\UCTMEASREM//
Meas-NrofSlices :\\UCTMEASNUMSLI//
Direct: -------------------------------------------------------------------
TV : \\VOX_TV//
BV : \\VOX_BV//
BV/TV : \\VOX_BV_TV//
Conn.Dens.: \\UCT_CONN//
SMI : \\MC_SMI//
Tb.N* : \\DT_N//
Tb.Th* : \\DT_TH//
Tb.Sp* : \\DT_SP//
Tb.1/N.SD*: \\DT_N_SD//
Tb.Th.SD* : \\DT_TH_SD//
Tb.Sp.SD* : \\DT_SP_SD//
Lin.Att.1 : \\UCT_MU0// +-\\UCT_MU0_SD//
Lin.Att.2 : \\UCT_MU1// +-\\UCT_MU1_SD//
Lin.Att.3 : \\UCT_MU2// +-\\UCT_MU2_SD//
Lin.Att.4 : \\UCT_MU3// +-\\UCT_MU3_SD//
Lin.Att.5 : \\UCT_MU4// +-\\UCT_MU4_SD//
TRI (Plate Model): --------------------------------------------------------
TV : \\MC_TV//
BV : \\MC_BV//
BS : \\MC_BS//
BV/TV : \\MC_BV_TV//
BS/BV : \\MC_BS_BV//
Tb.Th : \\MC_TH//
Tb.Sp : \\MC_SP//
Tb.N : \\MC_N//
Anisotropy: --------------------------------------------------------------
|H1| : \\MC_H1// H1x: \\MC_H1X// H1y: \\MC_H1Y// H1z: \\MC_H1Z//
|H2| : \\MC_H2// H2x: \\MC_H2X// H2y: \\MC_H2Y// H2z: \\MC_H2Z//
|H3| : \\MC_H3// H3x: \\MC_H3X// H3y: \\MC_H3Y// H3z: \\MC_H3Z//
DA : \\MC_DA//
Dim X : \\VOX_DX//
Dim Y : \\VOX_DY//
Dim Z : \\VOX_DZ//
Pos X : \\VOX_PX//
Pos Y : \\VOX_PY//
Pos Z : \\VOX_PZ//
El-Siz X : \\VOX_ELSX//
El-Siz Y : \\VOX_ELSY//
El-Siz Z : \\VOX_ELSZ//
</pre>

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===Tabulate LOG results from 3D evaluations===

Only use this if you have not used the standard <code>uct_evaluation</code> tool to generate your 3D evaluations (in which case see the HowTo related to the 3D database).
You can tabulate the LOG files:
<pre>$ search xxxx.log "ov "</pre>
Or whatever you want to search for can be stored in a text file
<pre>$ search/output=sys$scratch:ov.txt xxxx.log "ov "</pre>
To search more than one log file, and get the output into one single file:
<pre>$ fda/output=xxx.txt search *.log "ov "</pre>

The fda means 'file do all' and is a script made by Scanco to do one command (search) on a wildcard of files (*.log). Then put all the ov.txt, tv.txt, name.txt etc. files into excel.
Josh has made a .com file that does a similar job as described above.

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===Compile evaluation LOGs into one file===

Call the <code>UE:UCT_EVALUATION_V4_3D_RESULT.COM</code> with the same construction
as <code>$ eval_special</code>. If you need help with this, see the HowTo on this
Wiki site (HowTo: Assign special 3D evaluation to the UCT_EVALUATION tool).

Edit <code>UE:UCT_EVALUATION_V4_3D_RESULT.COM</code> file to call a specific ipl
script as you wish.

When you run the evaluation, you will have three new files created:

:*Two files in the measurement directory (on DK0!) (one with each eval 3D results in its own file, and one <code>APPENDED_ALL.TXT</code> file)
:*Then in sys$scratch, you will have one <code>SYS$SCRATCH:UCT_LIST_ALL_3D_RESULTS.LOG</code> file with ALL 3D evaluations of all measurements.

Note: You may need to edit the <code>SCANCO_SUBMIT_COMMAND</code> to specify a single queue (i.e., /que=sceval$fast)

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==Database==

===Examine patient databases===
This is for advanced users only!

There are two patient databases that get updated every time an evaluation is performed. Below is the name of the database, and the method used to check database values:
<pre>
$ show logical UPAT_EVAL_DATABASE
$ run disk1:[calibration.util]upat_export_measurement.exe ! as microct
</pre>
<pre>
$ show logical UPAT_SLICE_DATABASE
$ set host 0 ! login as user calibration
$ @disk1:[microct]login.com
$ spb
$ run DISK1:[CALIBRATION.UTIL]UPAT_GET_DB_INFO.EXE ! enter '1' to list records
</pre>

In the slice database every evaluation is recorded, but only one is currently active at a time.

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===Manipulate scan sequence===

Upat_list reports the baseline scan and then the percentage change of follow-up scans from the baseline scan. The order of scans in upat_list is determined from the measurement number (not the measurement date). In the case you need to manipulate the baseline and follow-up sequence, you will need to:

[[Image:Bones2.jpg|20px]] Warning: Use this with caution, and as little as possible!! even if the operation is reversible. Database manipulation is sensitive after all.

1. Log in as the "calibration" user (beware which calibration account to use for the different scanners).

How to proceed in the terminal:
$ SPB
$ @DISK1:[MICROCT]LOGIN.COM or $ @DISK1:[XTREMECT2]LOGIN.COM !! don't miss that line, otherwise you would modify the CALIBRATION databases

2. Use the following command to modify the measurement number:

$ RUN DISK1:[CALIBRATION.UTIL]UCT_CORRECT_SAMPLE_FIRST.EXE !! To redefine the very first measurement in the sequence

:* I do mean "First" measurement in the sequence, and not "baseline" measurement. You may have 2 baseline scans, one for radius and one for the tibia, but only one of them is the very "first in the sequence".

$ RUN DISK1:[CALIBRATION.UTIL]UCT_CORRECT_MEAS_PREV_NEXT.EXE !! To redefine the follow-up sequence beyond the first measure

:* The PREV_NEXT utility is a bit tricky to use, as for each measurement you will have to define its "chronological" previous and its next. It is not related to any anatomical site: one might think for example of defining the Radius follow-up sequence for example. It is not the case. The PREV_NEXT sequence will alternate between different anatomical sites, that is how it should be.

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===Add placeholders for missing follow-up scans===
If there is NO scan at a certain time point in a series (i.e. patient did not show up), the program ut:upat_create_meas_placehoder.exe and upat_create_eval_placeholder can insert fake records, so the slice matching and timepoints/visits are still all in order.

The attached file describes how to create an manage placeholders in the case of missing follow-up visits in longitudinal studies. [[Media:SOP_Create_Placeholders_draft.pdf|'''SOP Create Placeholders''']]

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===Disable a database measurement===

It is not possible to delete an evaluation from the database, but it can be disabled.

NOTE: QC results are stored in the UCT database, and there is no tool to disable a UCT database result.

Log in as the normal user (e.g. XTREMECT2). Then in a terminal you may use this simple utility program:
$ RUN UT:UPAT_CORRECT_VALID_FLAG

See below a typical prompt to deactivate an entry:
<pre>
UPAT_CORRECT_VALID_FLAG V2.0

Measurement No. (0 to stop): 1
Evaluation type [2]: 5
Group code [0]: 0

Found evaluation 57 for patient 4: ID003

Value for valid flag (0=invalid, 1=valid) [1]: 0
Value for placeholder flag (0=write results, 1=placeholder) [0]: 0

Measurement No. (0 to stop): 0
</pre>

You can always re-activate the entry, by switching the valid flag from 0 to 1.

Or, to make a scan invalid, you can also login as calibration user.

Point to microct user

$ @DISK1:[MICROCT]LOGIN.COM

Set priviledges to bypass.

$ SPB

Run Correction File
$ run DISK1:[CALIBRATION.UTIL]UPAT_CORRECT_VALID_FLAG.EXE

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===Disable a uct_list database measurement===
You cannot really disable data in the UCT_LIST output. What you can do using IPL is to clear the complete result entry for a given measurement, for example:

$ ipl
/read
-name in
-filename default_file_name
/db_scanco_activate
-write true
/db_clear_eval
-input in

Then UCT_LIST might still report the "disabled" measurement, leaving only the few first meta-data columns non empty. The rest would be cleared.

I must bring your attention to the fact that this sequence is used a lot on XtremeCT I scripts, for the cortical porosity for example.
This means that on XT-I, the UCT_LIST content is highly unstable, as it was used back then while UPAT_LIST was not able to handle those results.
In the future, when new applications come they may delete/overwrite the UCT_LIST entry for a measurement.
That is the rationale for using the TXT output in the RESULTS directory, that at least keeps track of past analyses.
As long as you have a single application on XT-II going through UCT_LIST, calling results on demand with it is fine. Later it might come complicated.

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===Troubleshoot UPAT database===

If there is an error ('inconsistent key change or duplicate key!') in the log file during 'upat_filldb', this is likely caused by too many servers doing UPAT evaluations:

Basically, the UPAT database can not be accessed by 2 evaluation jobs "at the same time", and works on a "1st arrived 1st served" basis. It is actually one reason to have only 1 evaluation at a time running on a single workstation (the usual setup).
In your case (and in mine as well), when you have several workstations clustered together, you can technically run several evaluation jobs at the same time which will eventually access the very same database.
So what happens is that a 1st job executes the /upat_fill_db, and accesses the database for a short amount of time.
During this time, any unfortunate evaluation job trying to access the database will end up in the exact same error as you reported, as their access to the database is restricted. Even though the time window is short, this kind of thing is unavoidable in setup such as ours, and when lots of evaluation are started at the same time.
Here you have no other choice than restarting the evaluation job, in order to update the database (or ultimately you could write a small script just to run the /upat_fill_db command, but I do not think it makes sense).

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===Redirect to a temporary database===

We need to temporarily redefine the logicals UPAT_EVAL_DATABASE and UPAT_SLICE_DATABASE. Normally, the definition is

<pre>
UPAT_EVAL_DATABASE = UCTD:UPAT_EVAL_CALGARY.DAT
UPAT_SLICE_DATABASE = UCTD:UPAT_SLICE_CALGARY.DAT
</pre>

Typically, we submit our jobs to the queue with an IPL script, so within the script we'll have to redefine the name of the database by adding lines such as
<pre>
$ def UPAT_EVAL_DATABASE SYS$SCRATCH:TEMP_UPAT_EVAL_CALGARY.DAT
$ def UPAT_SLICE_DATABASE SYS$SCRATCH:TEMP_UPAT_SLICE_CALGARY.DAT
</pre>
so that the results from the IPL evaluation are redirected to this temporary database.

Then, we need to extract the results from the database. These results are provided on a slice by slice basis (at least with the UPAT data). As user <code>microct</code> in a terminal window, we will again need to redefine the database and then run the program that translates the results to a text file:

<pre>
$ def UPAT_EVAL_DATABASE SYS$SCRATCH:TEMP_UPAT_EVAL_CALGARY.DAT
$ def UPAT_SLICE_DATABASE SYS$SCRATCH:TEMP_UPAT_SLICE_CALGARY.DAT
$ run disk1:[calibration.util]upat_export_measurement.exe ! give the measurement number and output file
</pre>

Or extract the results from the temporary database with:

<pre>
$ def UPAT_EVAL_DATABASE SYS$SCRATCH:TEMP_UPAT_EVAL_CALGARY.DAT
$ def UPAT_SLICE_DATABASE SYS$SCRATCH:TEMP_UPAT_SLICE_CALGARY.DAT

$ def UCT_MEASUREMENT_DATABASE SYS$SCRATCH:UCT_MEASUREMENTS_TORONTOXT.DAT ! only necessary if data came from another system
$ def UCT_SAMPLE_DATABASE SYS$SCRATCH:UCT_SAMPLES_TORONTOXT.DAT ! only necessary if data came from another system

$ upat_list ! choose option [3]show, give the patient number and output file, e.g. sys$scratch:myvalues.txt
</pre>

For an example IPL script that redirects to a temporary database, see Percy:
<pre>
DISK1:[MICROCT.COMMANDS]IPL_UPAT_EVAL_AIMINPUT.COM
</pre>

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===Import from a foreign database===
IF MEASUREMENTS COME FROM A TOTALLY DIFFERENT DATABASE (such as Toronto's XCT):

You will need to redefine the logicals UCT_MEASUREMENT_DATABASE and UCT_SAMPLE_DATABASE
<pre>
def UCT_MEASUREMENT_DATABASE SYS$SCRATCH:UCT_MEASUREMENTS_TORONTOXT.DAT
def UCT_SAMPLE_DATABASE SYS$SCRATCH:UCT_SAMPLES_TORONTOXT.DAT
</pre>

However, it is quite possible that you won't have a copy of the foreign MEASUREMENT and SAMPLE databases. If this is the case, then you must import the ISQ files into our own database. Then, by setting
<pre>
$ define UCT_EVALUATION_DATABASE SYS$SCRATCH:TEMP_EVALUATIONS_CALGARY.DAT
</pre>
you could redirect the results to a temporary database (but normally, if you already imported the data, why not use our own database now).

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===Duplicate as new import to database===

You will need to copy ISQ and GOBJ files to a new designated location. This is done when a screening study is completed to look for potential subjects and then a main longitudinal study is completed under a different study name. 

1. Make a new patient/subject ID 
2. Make a copy of the ISQ. For example: 
<pre>
$ copy DISK2:[microct.DATA.00002584.00008992]*.isq -
DISK2:[microct.DATA.00002696.00009345]*.isq
</pre>
3. Import ISQ into new patient/subject ID number by typing:
<pre>
$ import
</pre>
4. Follow the prompts for the ISQ file names, changing of control file # etc. 
5. Check the data directory to see if ISQ and GOBJ files have been copied properly 
2. In uct_evaluation, open new .ISQ and copied .GOBJ and re-run the evaluation to create .AIM, _SEG.AIM, _CORTEX.AIM, _LHTH_DTH.AIM 
 
3. Copy Scout Views so scanning program will load baseline scout view for followup scans In DISK1:[MICROCT.DATA.SCOUTS], you'll see two series of scout views: one series with the PATIENT # followed by 020 or 021 or 038 or 039, the site code (radius or tibia, left or right respectively) 
Copy the old patient scouts to the new patient #s
For example (using the same old and new #s as above): 
<pre>
$ copy DISK1:[MICROCT.DATA.SCOUTS]00002584021.SCV -
DISK1:[MICROCT.DATA.SCOUTS]00002696021.SCV
</pre>

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===Recover a disappeared due to import===
If you need duplicate a measurement in both the original and new directories, but you forgot copying the measurement before importing as a new. The original measurement will be automatically removed from the original directory. This can be fixed! You will need to copy the measurement back and then fix the header information, as the header will no longer match the original directory.

1. Manually copy all of the associated files for the measurement from the new directory to the original directory:
<pre>
$copy DISK2:[xtremect2.data.00001234.00001234]*.*;* DISK2:[xtremect2.data.00004321.00004321] /log
</pre>
2. Change the header information of the measurement files to those of the original directory. To do this, you will need special software. The use of this software is RESTRICTED. Users must seek special permission to use the software from Steve, Ying, or Anne BEFORE using. Once you have permission, the software can be found here: DISK1:[MICROCT.COMMANDS.FORBIDDEN].

3. Run the software:<pre>
$r [software]
</pre>
4. The software will ask for:
a) the ISQ file
b) the new sample # you would like to give it (i.e. the original directory sample #)
c) the new measurement # you would like to give it (i.e. the original directory measurement #)
c) the new sample name you would like to give it (i.e. the original Study ID)

You can view the header information for a file by using the command:
<pre>
$ctheader [ISQ file]
</pre>

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===Move to fix wrong Study_ID/Sample_No===

Situation: One study participate was assigned in followup scans multiple Study_ID or multiple Sample_No under the same Study_ID.
Action: To correct this mistake and update the database correctly, you get to

1. Return/Restore the RSQ from tape to measurement disk using Move (not Copy) in uct_backup program, otherwise the new location won't have its RAW backup record and thus have no idea where its RSQ was located.

2. When there is no original ISQ in the measurement disk, you will have to reconstruct a new ISQ from this RSQ. If there is an original ISQ there, then skip this step.

3. Import ISQ into a new designated location (correct Study_ID and Sample_No with new Measurement_No).
$ import
Follow the prompts for the ISQ file names, changing of control file # or site # if needed. This action will import RSQ, Gobj and all the files in the folder to the new location.

A reminder is that without an ISQ ready by importing a RSQ only will produce wrong slice no. and site location in the database as shown in the uct_backup.

4. If the ISQ is newly reconstructed (original ISQ could skip this step), the database will show the new reconstruction date & time (not the original scan date & time) as the scan records in the uct_backup. To correct this,

$run ut:uct_correct_meas_measdate

1) To see the original scan date & time: run this command and follow the prompt and input the original measurement No. as the Index, but don't change this by copying and pasting it back in Messdatum/Zeit.

2) To set the new scan date & time: run this command again and input the new measurement No. as the Index, copy & paste the original scan date & time got from 1) in Messdatum/Zeit.

This way will update the database as shown in the uct_backup with the original scan date & time with newly reconstructed ISQ in the correct Study_ID and Sample_No.

5. Backup/Move the RSQ at the new location to tape, so that the new record will have full information of both RAW and IMA.

6. Even though ISQ, RSQ, GOBJ and all other files have been moved over to the new location, you will still need to re-run the evaluation (in uct_evaluation, open ISQ and GOBJ) to create .AIM, _SEG.AIM, _CORTEX.AIM, _LHTH_DTH.AIM ect.

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===Move to fix wrong account used for scanning===

Xtremect2 (on disk2) and xt2recalib (on disk6) accounts share the same databases. However, the definition of DK0 is account specific, ie. the scans are stored on different disks. So when scanning under Xtremect2 account instead of Xt2recalib account, to correct the wrong measurement location you will need to:

#Create the patient directory on disk6:[xtremect2.data], if needed;
#Create the same measurement directory on disk6:[xtremect2.data];
#Create a save set of the measurement folder on disk2:[xtremect2.data] with the isq, rsq, rad and scv files included;
#Unzip the save set in the measurement directory on disk6:[xtremect2.data];
#Delete the measurement directory on disk2:[xtremect2.data] using delete command in the terminal. Caution: Do NOT use the backup program.

[[Image:Bones2.jpg|20px]] Warning: This procedure is specific to this situation between Xtremect2 and Xt2recalib accounts, Microct and Xt1recalib accounts, and vice versa, but not applicable between any other accounts!

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===Update database after RSQ/ISQ restoration===

If you are restoring RSQ or ISQ files from tape (or other source) it might be preferable to do your analysis without resetting the database info.

The database is specific to the user. So, we have to modify the database for <code>microct</code>, and be careful not to modify the <code>calibration</code> (or other users) database. However, we still need to have permissions from <code>calibration</code> in order to do the modification.

When we restore an ISQ or RSQ to disk, the database needs to be updated to ensure it finds it. We have to change the database back to say it's on disk. To do this we need to log in as user <code>calibration</code>.

<pre>
$ set host 0
login as calibXXXX where XXXX is the scanner id (5019 for VivaCT or 2339 for uCT35) or calib3309 or calib3401 (for the XtremeCT and XtremeCTII system, respectively).
password from Steve

$ @ADISK1:[BONELAB]microct_setup_XXXX.com ! XXXX=scanner id, sets the logicals to point to bonelab data for SB group
or
$ @ADISK1:[VIVACT]LOGIN.COM ! sets the logicals to point to microct data for BH group
or
$ @DISK1:[MICROCT]LOGIN.COM ! sets the logicals to point to microct data on the XtremeCT system
or
$ @IDISK1:[XTREMECT2]MICROCT_SETUP.COM ! sets the logicals to point to xtremect2 data on the XtremeCT2 system

$ set proc/priv=bypass or $ spb
$ run DISK1:[CALIBRATION.UTIL]UCT_CORRECT_DIR ! make sure to include the full path to the executable as shown here.
$ run DISK1:[CALIBRATION.UTIL]UCT_CORRECT_MEAS_DIR.EXE ! on xtremect2 system, use this program
</pre>

Note: Only change those items which have to be changed (e.g. just hit RETURN for RAW fields if you only want to change the IMA location. Also, when specifying the directories, use DK0, not DISK2.

<pre>
$ run ut:UCT_CORRECT_DIR.EXE
</pre>

<pre>
Measurement Nr.: 1234
MeasNr. 1234
PatientNr: 268
RAW: RAW004
TP0:00001234_RAW
IMA: IMA002
TP0:00001234_IMA
</pre>

<pre>
RAW-Label: [ RAW004 ]

RAW-Dir : [ TP0:00001234_RAW ]

IMA-Label: [ IMA002 ] DISK
IMA-Dir : [ TP0:00001234_IMA ] DK0:[microct.data.00000456.00001234]

Measurement Nr.: 0
End of program
</pre>

The IMA-label does not matter on disk - but we have to write something to get rid of the IMA002, so 'DISK' makes sense.

Using the standard backup/archiving program, you can archive (MOVE TO) that IMA again to a tape, but use a DIFFERENT TAPE than where the first instance of this scan is on.

Background: Tapes just write file after file, without any directory structure or hierarchy, so the program will always find the first instance (the old dataset) if you try to read it again from that tape.

Note One other option is to change the permissions of UCT_CORRECT_DIR.EXE so that user <code>microct</code> can use it directly. To do this, log in as users <code>calibration</code> and then:

<pre>
$ set proc/priv=bypass ! as user calibration
$ set prot=g:re ut:uct_correct_dir.exe
$ run disk1:[calibration.util]uct_correct_dir ! as user microct
</pre>

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==Other FAQ==

===View Sample info===
<pre>
$ mcr um:uct_info 1234
</pre>
will show you sample-name and date-of-birth of sample-number 1234
<pre>
$ mcr um:uct_info -m 1234
</pre>
will give you some (stupid) info about meas 1234

'''Note:''' If you use this function all the time, put the following into <code>microct_setup_user.com</code>
<pre>
$ uct_info :== $um:uct_info
</pre>
and then the usage info will even be correct.

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===List measurements for data and backup location===

*To generate a list of measurements that are registered in the database, to determine where backups are stored, or if the data is still on disk:

::<code>$ write_info</code>

*Ask you for a range of measurement numbers or sample names.
*Create a <code> sys$scratch:info.txt</code> file.

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===Anonymize patient name and DOB===

Here is the link to [[Media:SOP_Anonymize_patient_name_dob.pdf | Scanco's SOP]] to change a long list of patient's name and/or DOB to de-identify the data.

This does not affect the headers of past RSQ, ISQ or AIM files.

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===Fix a wrong scan site code===

This is done if accidentally scanned using the wrong control file.
For example scan site RR is scanned mistakenly under RL, or TL scanned by mistake using the control file for TR ect.

To see our site codes, e.g. 20 = RL, 21 = RR etc using

<pre>$ show log *eval*</pre>

;Scenario 1:

If the correction commands (uct_correct_meas_site and updh_site) are already in your account (which is the case for the xtremect2 and xt2recalib accounts on the XtremeCT cluster)

$ cd util
$ dir *site*

and you see two programs (uct_correct_meas_site and updh_site). Set priviledge to bypass first

$ spb

$ run uct_correct_meas_site

and enter the meas. number to be corrected and then enter in the correct site code (20 = RL, 21 = RR, 38 = TL, 39 = TR).
*This modifies the database, so the correct site is displayed in the eval program.
*Enter meas. number 0 to exit program.

Then we must also correct the ISQ and RSQ files (has to be restored from tape if not on disk):

$ run updh_site !'updh' = update header</pre>

*Enter the full (i.e. pathname included) ISQ or RSQ filename. For DISK6 data should use DISK6:[xtremect2.data....].
*Then enter the correct site number.

;Scenario 2:

Normally the correction commands (uct_correct_meas_site and updh_site ect.) are only provided in a calibration account to prevent from misusage. We have to login as user calibration to make the change.

$ set host 0
$ username: [enter calibration account, e.g. calib3401]

Then we use the same steps in Scenario 1 to change the site code in both database and ISQ and RSQ files.
*Make sure to <code>logout</code> from user calibration afterwards.

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===Fix for results fail to print/list/show after evaluation===

There are a number of reasons the results may not print:

====Incorrect first measurement number====
When sample information (such as patient name, DOB, remark) is changed DURING scanning, this can over write the 1st Scan measurement number, resulting in the evaluation sheet not being printed, and data not shown when running upat_list. For example, this happens when:

1) open sample program, enter name, hit save, leave program open

2) start scan (which would write correct record with 1st meas. in sample database)

3) in sample program: then only enter DOB, and hit 'save' again in the sample program --> it 'overwrites' the 1st meas. with an empty string again.

If you want to enter DOB after the scan has started, you HAVE to 'Find...' and re-load that patient first (so it correctly loads the 1st meas. entry also). It is best to just not use the sample management program whilst scanning is taking place.

However, if you do encounter this problem, use the following to fix (shown using patient 668 as an example. 1st scan measurement number was 2672):
<pre>
$ set host 0
calibration
xxxxx

$ spb
$ @[microct]microct_setup
$ run [calibration.util]uct_correct_first
$ r UCT_CORRECT_FIRST

Patient Nr.: 668
SampleNr.: 668
First: 0

2672

Patient Nr.:
</pre>
and continue with next non-working patient, give patient number 0 to exit.

$ logout

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====Evaluation completed with results not written to database====
If the first measurement number and DOB are correct... check the .log file of the evaluation... However, if there is no upat*.log file available for that scan, use:

upat_list -v=2 and you will see (for eg sample 594):

<pre>
Found sample 594, CAMOS_0018
Found measurement 2536 made 19-MAR-2007 12:52:58.48
Measurement site RL found in list at index 0
Measurement 2536 within measurement period
ERROR finding evaluation for measurement 2536

No valid evaluation found for measurement 2536
</pre>

So it seems the 3D upat eval never wrote anything to the database for that scan. In this case, you can run:

<pre>
$ @ue:ipl_upat_eval_again_quick.com
</pre>
and let it run for the missing data.
'''NOTE''' it will only need the aim files and gobj files that you still have in your 'models' directory.

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====Incorrect sequence of measurement numbers====
Finally, if none of these options work... check the order of measurement numbers: especially if an import has occured, first check the first measurement number is correct (as above). Then run sys$Scratch:uct_correct_prev_next.exe and correct the order of the measurements: The database keeps a 'daisy' chain of meas. numbers, each meas. knows which one was the previous meas and the next meas.

0 means: no prev. meas (or no next meas) So corrected the order for you like this:

<pre>
$ r UCT_CORRECT_prev_next

Measurement No. (0 to stop) [0]: 2821
MeasNo.: 2821 PatientNo: 723

Previous [0]: <-- leave 0
Next [0]: 2828 <-- give next meas number
Measurement No. (0 to stop) [2828]:
MeasNo.: 2828 PatientNo: 723

Previous [0]: 2821 <-- give prev. meas number
Next [0]: <-- leave 0 for very last meas.

</pre>
Please note: the series of meas. numbers per patient is NOT separate per meas. site, thus radius and tibia meas. are linking to each other. '''Do not mess up!'''

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=Data Management=
==Lab’s Data Responsibility==
*Weekly
#Clean up sys$scratch directory and only keep last week's data.
#Archive RSQ to corresponding tapes.
#*RSQ from temporary tests and non-project (not a formally established project) will NOT be archived unless specifically notified to lab personal.
#Database backup to disks.
*Monthly
#Database backup to corresponding tapes.
#Archive QC RSQ to corresponding tapes.
#Delete QC IMA and only keep last week's data.
*6-monthly
#System backup to corresponding tapes when prompted.
*Yearly
#Data Disk clean up when usage is over 90%.
#*Temporary tests and non-project RSQ and IMA data will be deleted during check up.
#Project Disk clean up when usage is over 90%.
#Winston backups clean up.
*Whenever requested
#Projects backup to Winston server and restoration.
#Projects archive to HOG server and restoration.

[[File:BoneLabDataManagement.JPG|800px]]

[[Image:Bones2.jpg|20px]] Warning: STRONGLY URGE TO DO THE WEEKLY and MONHTLY BACKUP. Two users DID experience disk crashes before, and without the weekly backup, you may still have all scans on the data disk, but without the databases you cannot tell which scans belong the which sample.

*Refer to [[Media:Microct_management.pdf|'''XtremeCT Micro-CT Management SOP''']] or [[Media:Microct_management.docx|'''its Word format''']] for references.

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==HP Server and Disk Array==
===HP References===
*[[Media:Hp-quick-specs-msa30.pdf|'''MSA30 Disk Array Quick Specs''']]
*[[Media:Hp-integrity-rx2620-sceva2-user-service-guide.pdf|'''Integrity RX2620 User Guide''']]
*[[Media:Hp-integrity-rx2660-sceva3-user-service-guide.pdf|'''Integrity RX2660 User Guide''']]

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===HP FAQ===
====Change disk description for $ disks====
Login as the system user and change to the system commands directory.

$ cd scom
$ eve show_disks.com

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==Tape==
[[Image:Bones2.jpg|20px]] Warning: While the tape is running and writing to it, DO NOT LOG OUT, DO NOT INTERRUPT THE PROGRAM! This would make that tape unusable from this point on - you could still read from that tape up to this point, but could not add more scans to this tape.

===Tape Label Convention===
Tape labels are 6 characters in length. For the Bone Imaging Lab projects, the first three letters indicate if the tape is for raw (RAW) or image (IMA) data, and the last three digits are for the tape number.

<pre>
RAW040 = RAW date, tape #040
IMA001 = IMAGE data, tape #001
</pre>

Alternatively, the first two characters may be set to a PI's initials, the third character indicates if the tape is for raw (R) or image (I) data, and the last three digits are for the tape number.

<pre>
SBR040 = Steve Boyd RAW, tape #040 
SBI001 = Steve Boyd IMA, tape #001 
BHR006 = Benedikt Hallgrimsson RAW, tape #006 
BHI017 = Benedikt Hallgrimsson IMA, tape #017 
FJR012 = Frank Jirik RAW, tape #012 
FJI003 = Frank Jirik IMA, tape #003 
</pre>

CaMos raw data is backed up with the following naming:
<pre>
CAMOS1 = CaMos RAW, tape #1
</pre>

When a tape becomes full, start (initialize) a new tape, increasing the tape number by one so that each tape label is unique.

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===Initialize a New Tape===
Put a new tape into the tape drive, then press "Initialize", this will format (erase) everything on the tape. When prompted for a label for the tape, follow the [[Scanco_Administration#Tape_Label_Convention|'''Tape Label Convention''']]. The tape can now be mounted for use. 

[[File:Uct_backup_pic02.jpg|400px]]

===Full Tape===
A tape automatically ejects during a backup procedure if it becomes full.
*Remove the tape and write protect it (orange indicator will be displayed).
*Exit the disk-utility program.
:*Hit <code>ctrl/c</code> to interrupt the program if needed.
*Start a new instance of the program.
*[[Scanco_Administration#Initialize_a_New_Tape|'''Initialize a New Tape''']].
*Backup any remaining files.

[[File:Uct_backup_pic03.jpg]]

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===Tape Drive Setup on XCT cluster===
Both the old and new tape drives are connected to SC3309 (XCT1) and powered on. You do not need to power off one to use another.

New tape in new drive <--> microct, xtremect2, xt2recalib, calib3401, calib3309

:*The 'new' Ultrium 3000 tape drive is for the new tapes and the default tape drive for all other accounts (microct, xtremect2, xt2recalib, calib3309, calib3401).
:*Use the following command to use the old SDLT tape drive no matter which account on the command line:
<pre>
$ uct_backup_sdlt
</pre>

Old tape in old drive <--> xt1recalib

:*The 'old' SDLT tape drive is for the old tapes. You have to log into the default xt1recalib account to recognize this tape drive.
:*Restoring from old tapes in xt1recalib account will restore your data to DISK6:[MICROCT.DATA].
:*By default, xt1recalib account can only see old tape drive, not the new tape drive.
:*Use the following command to use the new tape drive no matter which account on the command line:
<pre>
$ uct_backup_sas
</pre>

*With either of the above commands, you must not "submit" the tape usage jobs to the queue (i.e., cannot run a batch backup from a script), but only run them interactively in the
software. Any job in the queue will use the default tape drive again.

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===Extract from Tape===

====Scripts to Extract from Tape====
Generally, all files on the tape can be extracted, or only specific files.
To extract all files on a tape, for example, a tape received from a collaborator, insert the tape into the drive and do the following:
$ cd ur
$ create/dir [.collaborator]
$ create/dir [.collaborator.com]
$ create/dir [.collaborator.log]
$ create/dir [.collaborator.models]
$ cd ur collaborator models
$ backup/log tp0:*.sav []/by=parent ! be sure you are the user (i.e. 'microct' or 'xtremect2') that has permission
$ backup/log tp0:*.sav DISK4:[BONELAB.PROJECTS.FRAMINGHAM.MODELS...]/by=parent ! The "..." keeps the directory structure. The /by=parent ensures owner of the files is same as parent directory

This will save all the files on the tape to the current directory. Alternatively, if you only want a certain file extracted from the tape, such as an RSQ file, do essentially the same as per above, except with a different final command:
$ backup/log tp0:*.sav/select=*.rsq []/by=parent

The <code>/by=parent</code> part of the command is a qualified for the file owner, and it makes the files that are copied the same owner as the parent directory (nothing to do with how directories are structured). The <code>[...]</code> generates sub-directories.

A custom script is required when extracting data from tape from another micro-CT system or to extract the data to a central location (e.g., a user's directory).
*The script is then submitted to the backup queue of the workstation the tape drive is connected to (i.e., SCEVA3_BACKUP)
*Some example scripts are provided below.

*Extract image data for three scans to a custom folder, maintaining the sample and measurement directory structure:
<pre>
$ mount/foreign tp0
$ backup/log tp0:00001234_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie...]
$ backup/log tp0:00001245_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie...]
$ backup/log tp0:00001238_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie...]
$ dismount tp0
</pre>

*Extract segmented AIM files for three scans to a custom folder without the original directory structure:
<pre>
$ mount/foreign tp0
$ backup/log tp0:00001234_IMA.sav/select=[microct.data...]*seg.aim disk3:[microct.projects.buie]
$ backup/log tp0:00001245_IMA.sav/select=[microct.data...]*seg.aim disk3:[microct.projects.buie]
$ backup/log tp0:00001238_IMA.sav/select=[microct.data...]*seg.aim disk3:[microct.projects.buie]
$ dismount tp0
</pre>

*Extract segmented AIM files for all scans on tape to a custom folder:
<pre>
$ mount/foreign tp0
$ backup/log tp0:*_IMA.sav/select=[microct.data...]*seg.aim disk3:[microct.projects.buie]
$ dismount tp0
</pre>

*Extract raw data for three scans to a custom folder, without the original directory structure:
<pre>
$ mount/foreign tp0
$ backup/log tp0:00001234_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie]
$ backup/log tp0:00001245_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie]
$ backup/log tp0:00001238_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie]
$ dismount tp0
</pre>

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===Tape FAQ===
====Error: Can't mount tape, Medium offline====
This can happen if a tape is interrupted during use (e.g., due to a power failure or system restart while the tape drive is in operation).

#Use the manual eject button to remove the tape from the drive.
#Turn off the tape drive, the switch is on the back of the drive.
#Shutdown the whole micro-CT system.
#Turn on the tape drive.
#Startup the micro-CT system, starting with the server.
#Try to mount the same tape again.

If the above does not work then either the tape or the tape drive is damaged. To determine if it is the drive, take a brand new tape and try to initialize it. Do not use a tape with data on it in the drive unless you are certain the drive is okay.

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====Error: positioning====
This can have two reasons usually:

#The tape is just faulty. Try with a fresh tape.
#A previous tape write operation was interrupted (e.g., a user did an 'End Session', the power went out, or the eject button was pressed on the tape drive, which killed the backup program). In this case the drive did not write the very important 'End of Tape' marker, and now, the tape drive cannot find the current place where it can start adding new data.
*Solution: either take a fresh tape, or if there were only a few scans are on the 'bad' tape, 'Move to Hard Disk' of ALL the scans on that tape, check that the scans have been retrieved well, then initialize that tape again (which will erase everything on the tape!) and archive those scans again.
*IMPORTANT: never interrupt the tape drive while it is running!

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====Error: parity====
Either tape or the tape drive is faulty. Take a fresh tape (potentially from a new batch of tapes), and see if the error persists.
*If yes: have the tape drive repaired.
*Further things to check: for DLT and SDLT tape drives: is the terminator ('dead end') connected on the second SCSI port in the back of the tape drive.

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====Fix: non-responsive tape drive====
This can occur if the user ejects the tape with the little button (and not with the recommended "dismount" button in the uct_backup program). This can also occur if a tape is mounted immediately after one is dismounted. You get the same error for both cases, "medium offline".

:*Check all that all cables are connected.

:*Check that the number on the back of the drive says "5" (use +/- to adjust if necessary)

:*Check that the top connector has a cable connecting to the computer and the bottom one has a terminator.

:*Try turning the tape drive on and off again.

:*Log in as user <code>system</code> (you will need a password from Steve):
<pre>
$ mcr sysman io auto/sele=mk
$ @sys$startup:scanco_setup_devices.com

$ show device tp0
</pre>

If it's online again, then great. If not, then the last resort is to reboot the entire system. If this doesn't work, then shut down the system (see user manual for proper steps) and eject the tape. You may need to turn the computer back on before it will eject. The tape drive should be turned on first (no tape), then the server, and any other computers. Check that the drive is online ($ show device mk). If it is, then test the drive by initializing, mounting and dismounting a brand new tape. If the drive is not online, do not insert any tapes or they will likely get stuck. Log in as system and re-try the command lines shown above.

NOTE: See "Fix a stubborn tape drive" elsewhere in this wiki.

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====Fix: stubborn tape drive====
If the drive cannot be mounted, or it is not visible with
<pre>
$ show device tp0
</pre>
then something went wrong. For example, the server computer was booted while the tape was turned off. It then does not load the driver.

You can 'force load' it - but this will disconnect the scanner for a moment, so only do it while no scan is running:

as user <code>system</code>, on sc3309:
<pre>
$ mcr sysman io auto

$ show dev tp0
</pre>

and you should see it now (otherwise turn on the tape drive, and do again)

Then you'll also have to make it available to all users:
<pre>
$ @sys$startup:scanco_setup_devices.com
</pre>

NOTE: See "Fix a non-responsive tape drive" elsewhere in this wiki.

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====SDLT320 Tape and Tape Drive FAQ====
Please refer to [[Media:Hp-faq-sdlt320-tape-drive-and-sdlt-tapes.pdf|'''SDLT320 Tape and Tape Drive FAQ''']] for details.

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==USB Drive==

===Use a USB drive===
Connect USB to VMS system and format.

Transfer files from the terminal after plugging in the USB device
$ show device dna
Usually the device is dna1 or dna2
$ mount /over=id dna2
$ create/dir dna2:[microct]
$ copy dk0:[microct]
or
$ backup/log dk0:[
and then
$ dismount dna2

Transfer files back again

$ mount /over=id dna2
$ dir dna2:[microct]
$ copy dna2:[microct]myfile.txt disk1:[microct.data.00000702.00001234]

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===USB Device Usage with Scanco Backup/Archive Software===

For illustrated help on USB device usage on Itanium systems, please refer to [[Media:Scanco_TD387_USB_Device_Usage.pdf ‎ | '''Scanco_TD387_USB_Device_Usage.pdf ‎''' ]]

====Initialize procedure====
If an external USB device is to be used to archive measurement data, the USB device must be initialized by Open-
VMS. The data will not be accessible from any other operating system.

- Attach the USB device to the front USB port of the Itanium rx2660.
(note: Itanium rx2620 only supports USB1.1, which will have a very slow transfer rate)

- Open the Scanco backup/archive software.

- Select the correct USB device with the arrow buttons in the “USB Device” section.

- Use the “Initialize<” button in the “USB Device” section to initialize the USB device.

- Confirm the Warning message. Note: All data currently on the device will be erased!

- Enter a six-character label

The USB device will be initialized and mounted.

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====Archive procedure====

- Attach an OpenVMS formatted USB device to the front USB port of the Itanium.
(note: Itanium rx2620 only supports USB1, which will have a very slow transfer rate)

- Open the Scanco backup/archive software.

- Select the correct USB device with the arrow buttons in the “USB Device” section.

- Use the “Mount” button in the “USB Device” section to mount the USB device.

The device label of the mounted USB device will be shown in the “USB Device” section.

- Select the measurement data to be archived.

- Select “Move To:” and “USB/VMS” and click “Start<” to archive the selected data to the USB device.

After the move procedure, the new current location of the measurement data will be shown next to the files path.

- “Dismount” the USB device when done with archiving.

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====Manual file copy procedure====
An OpenVMS formatted USB device can also be mounted and used for file storage using commands in a DECterm.

- Attach an OpenVMS formatted USB device to the front USB port of the Itanium.
(note: Itanium rx2620 only supports USB1, which will have a very slow transfer rate)

- List available devices. The last shown device is usually the attached USB device; dna12 in this example.
$ show device dna

- Mount the USB device using the correct device name
$ mount /over=id dna12

- Create a root directory. Ignore any messages if the directory already exists.
$ create /dir dna12:[microct]

- Copy any wished files to the USB device
$ copy {source files} dna12:[microct] /log

- Dismount the USB device
$ dismount dna12

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====Exporting Files / FAT file system====
If an external USB device is to be used to export measurement data to a Windows or MAC OS, the USB device must be formatted as FAT file system.

- Attach the USB device to the front USB port of the Itanium.
(note: Itanium rx2620 only supports USB1, which will have a very slow transfer rate)

- Open the Scanco backup/archive software.

- Do not “Initialize<” or “Mount” the USB device !

- Select the measurement data to be copied to the USB device, may be even sub-select the wished file type
(TIF files in the example below).

- Select “Copy To:” and “USB/FAT” and click “Start<” to copy the selected data to the USB device.

Once the USB device is connected to Windows or MAC OS, it will show a ZIP file named like the copied measurement
number. This ZIP file contains the same directory structure like the data disk on OpenVMS:

data\sample number\measurement number

In the lowest sub-directory are the copied files, as selected in the backup/archive software (TIF files in this example).

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===Problems with connected USB devices===

Sometimes USB configurations can be problematic, in which case log in as "system" on the server and run

$ dir/date SYS$SYSROOT:[SYSEXE]USB$UCM_DEVICES.DAT

to see whether a file was created recently. If one has, delete that file and reboot the server.

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==CDROM==
===Mount a CDROM===

Device could be <code>dqa0</code> or <code>dqb0</code>. I'm not sure which works:
<pre>
$ mount/foreign dqa0:
</pre>
OR
<pre>
$ mount/override=id dqa0:
</pre>
Then
<pre>
$ dismount dqa0:
</pre>

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==Saveset and Zip files==

===Saveset===

====Saveset Naming Convention====
The Scanco backup program stores raw (RAW) and image (IMA) data as save sets (SAV).
*RAW save sets contain RSQ files and IMA savesets contain all other file types.
*The saveset filename is composed of the 8-digit measurement number plus "_RAW.SAV" for raw data and "_IMA.SAV" for image data.
*For example, the data for a scan with measurement number 1234 would be stored as:
<pre>
00001234_RAW.SAV ? RSQ
00001234_IMA.SAV ? all other files, ISQ, AIM, GOBJ, TXT, SCV, etc.
</pre>

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====Create and Unpack Saveset====
Savesets are OpenVMS backup files, similar to a zip. Use the backup command.
<pre>
$ BACKUP/LOG disk3:[microct.projects.buie...] disk3:[microct.projects]buie2012.sav/sav
!Creates a saveset file of disk3:[microct.projects.buie].
!The ... after the folder indicates to include all subfolders and files.
$ BACKUP/LOG mysaveset.sav/sav disk3:[microct.projects.buie]
!Unpacks the whole saveset to disk3:[microct.projects.buie]
$ BACKUP/LOG mysaveset.sav/sav disk3:[microct.projects.buie...]
!The ... at the end of the output location indicates to unpack the saveset and maintain the original directory structure.
$ BACKUP/LOG mysaveset.sav/sav/select=*.aim disk3:[microct.projects.buie]
!The select flag is used to indicate extraction of only aim file types.
$ BACKUP/LOG mysaveset.sav/sav/select=[microct.data...] disk3:[microct.projects.buie]
!The select flag is used to indicate extraction of the folder data and all subfolders and files.
$ HELP BACKUP !More information on the backup command.
</pre>

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====View Saveset Contents====
To view contents of a saveset (SAV) on disk:
<pre>
$ backup/list upat_print_list_nomatch.sav/sav
</pre>

To view the savesets (SAV) on a tape:
<pre>
$ mount/ov=id tp0:
$ dir/date tp0:*.*
$ dismount tp0:
</pre>

To view contents of a saveset (SAV) on a tape:
<pre>
$ mount/foreign tp0:
$ backup/list tp0:*.* ! OR, backup/list tp0:*.SAV
or
$ backup/list=results.txt tp0:*.* ! save output in results.txt
$ dismount tp0:
</pre>

An idea to get the results of the backup/list into a text file: Run the procedure in a submitted script and save the resulting log file with all the output.

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====Extract a single file from SaveSet====

In a large SaveSet, sometimes we only want one file extracted, not the whole archive extracted. This can be done with

$ backup /log /select=myfile.txt mysaveset.sav /sav disk1:[microct.scratch]

or [] as destination will put the file in the current directory.

This can take a while as it looks through all the saveset. Once it logs that the file has been restored, you may interrupt with F6. Else it goes on looking through the rest of the saveset.

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====Transfer Saveset from microCT to XtremeCT====

You can create a SAV set of your project on the VivaCT and transfer it to the Xtreme system, or vice-versa.
First, create the SAV set using the command:
<pre>
For example:
$ BACKUP/LOG DISK3:[MICROCT.PROJECTS.SB.MYPROJECT...]*.*;* -
SYS$SCRATCH:MYPROJECT.SAV/SAV
</pre>
This creates the MYPROJECT.SAV file in the scratch directory. Now zip the file:
<pre>
$ cd sys$scratch
$ zip "-V" MYPROJECT.ZIP MYPROJECT.SAV (NOTE: must use quotes and a capital V!!!!)
</pre>
FTP the .ZIP file to SODOR ( in binary mode!!!), and then FTP it off onto your destination system (Viva or Xtreme). See the appropriate HowTo for FTP instructions. Once you've FTP'd it, unzip the file:
<pre>
$ unzip MYPROJECT.ZIP
</pre>
Finally, unpack the contents of the .SAV file:
<pre>
$ BACKUP/LOG MYPROJECT.SAV/SAV DISK3:[MICROCT.PROJECTS.MYPROJECT] <--- or whatever destination directory
</pre>
NOTE: transferring a .SAV directly from VMS to VMS should work, but not via any third operating system (like SODOR) - so zipping is always the safe way to make sure it works.

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===Zip===

====Zip and Unzip files====
Use the zip program to add files to a zip archive.
<pre>
$ ZIP myzip.zip myfile.txt;1 !Adds myfile.txt to myzip.zip.
$ ZIP "-V" myzip.zip myfile.txt;1 !Adds myfile.txt;1 to myzip.zip. The "-V" maintains the OpenVMS version number.
$ ZIP "-V" myzip.zip [.subdir...]*.*;* !Adds all files within subdir to myzip.zip, maintaining their version number.
$ ZIP !Displays the help for the zip command.
</pre>

Use the unzip program to unzip an archive.
<pre>
$ UNZIP "-V" myzip.zip !Extracts myzip.zip, maintaining the OpenVMS structure.
$ UNZIP !Displays the help for the unzip command.
</pre>

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====Transfer Zip between Scanco systems====

Files must be zipped before transfer by e-mail or ftp because important attributes will be lost in the transfer otherwise.

To transfer files from system A to B, do the following.

On system A:
<pre>
$ zip "-V" for_calgary.zip uctd:UCT_SAMPLES_TORONTOXT.DAT ! for each filename
$ zip "-V" for_calgary.zip uctd:UCT_MEASUREMENTS_TORONTOXT.DAT
</pre>
This will add both files to the same zip file.

Note: "-V" is very important, it must be capital V!

Transfer the file by e-mail, or by ftp.

On system B:
<pre>
$ unzip -j for_calgary.zip ! to unzip on your end them (-j to 'junk' the original file path)
</pre>

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====Unpack Zip sent by Scanco====
In the .zip file, you'll find a .sav file. Unzip the .zip just by saying

<pre>$ unzip xxxx.zip</pre>

Then:

<pre>$ backup/log xxxx.sav/sav disk3:[steve.devel.temp]</pre>

and it will unpack everything into <code>disk3:[steve.devel.temp]</code>

Or:

<pre>$ backup/list xxxx.sav/sav</pre>

and you see what's in the .sav.

Then:

<pre>$ backup/log xxx.sav/sav/sel=[andres.uct.ipl_for_cust...] disk3:[steve.devel.cipl...]</pre>

and it will create the same diretory tree in steve.devel.cipl as it was when I
packed it into the .sav.

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==Backup and Archive==

===UI Procedures===

====µCT Disk-Utility====
The µCT Disk-Utility Program is used to archive and restore scan data. To start the program type <code>$ uct_backup</code> in a DEC terminal, or use the disk button.

[[File:Uct_backup.jpg|40px]]
*The backup captures both the programs and databases.
*A little helper terminal comes up and gives feedback of every file backed up.
[[File:Uct_backup_pic01.jpg|600px]]

Two possible ways to use <code>UCT_BACKUP</code>:
:* COPY TO -> this does not update the database.
:* MOVE TO -> this updates the database.

Scenario 1:
<pre>
1. Use UCT_BACKUP to 'move' the RSQ to 'tape'
2. Use UCT_BACKUP to 'move' the ISQ to 'garbage'
3. Use UCT_BACKUP to 'move' the remainder (AIM/GOBJ) to 'tape'
</pre>
*At operation 3, the measurement directory will be deleted from the measurement disk.
*The directory will automatically be restored if you restore your data from tape.

Scenario 2:
<pre>
1. Use UCT_BACKUP to 'move' the RSQ to 'tape'
2. Use UCT_BACKUP to 'move' the ISQ to 'garbage'
3. Move all the GOBJ/AIM/etc to a project directory.
4. Generate a .SAV file and put on the IMA tape.
</pre>
*You will have to delete the measurement directories (using UCT_BACKUP if you like).
*The disadvantage of this scenario is that the image data cannot be restored using UCT_BACKUP.

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====Raw Data Backup====
*Ideally 1-2 week after scanning.
*RSQ files are backed up onto RAW tapes (see [[Scanco_Administration#Tape_Label_Convention|'''Tape Label Convention''']]). Put the most recent RAW tape into the tape drive, then press "Mount".
*Show "Current (with RAW)", use the file filter (Measurement: ) to search for your files (e.g., CAMOS) and press enter or press "Update List".
*Select all the files to backup by highlighting them using the left mouse button and ctrl to select individual files or shift to select a range.
*Highlight RAW, choose "Move To" and "Tape". Press "Start...".
*When the backup is complete press "Dismount" to eject the tape.
*If the tape auto-ejected without pressing "Dismount" then the tape is full (see [[Scanco_Administration#Full_Tape|'''Full Tape''']]).
*If you select multiple files, be sure they all need to be backed up, otherwise you will get an error.
:[[File:Uct_backup_pic04.jpg|500px]]

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====Image Data Backup====
*Ideally 1-2 months after scanning, after contouring, onsite analysis and copied image data to project disk.

#'''Delete ISQ After Evaluation'''
#*ISQ files are normally deleted after completing your evaluation since they are very large files and can be reconstructed from the RSQ file.
#*Show "Current (on Disk)", type the beginning of your sample name (e.g., CAMOS) in the file filter and press enter or press "Update List".
#*Select all the files for which you have completed the evaluation (there will be a + sign next to any scan that has been evaluated). #*Highlight IMA, choose "Move To" and "Trash".
#*[[File:Important.JPG|20px]] After you choose the trash symbol, you will now be given the option to select specific file types, choose "Select" and "ISQ". Press "Start...".
#*Only choose one file type to delete at a time. The wildcard (*) indicate all files other than "ISQ" and "AIM" files.
#:[[File:Uct_backup_pic05.jpg|500px]]
#: 
#'''Backup IMAGE Data'''
#*AIM, GOBJ and other evaluation files are backed up onto IMA tapes (see [[Scanco_Administration#Tape_Label_Convention|'''Tape Label Convention''']]).
#*Put the most recent IMA tape into the tape drive, then press "Mount".
#*Show "Current (on Disk)", type in the beginning of your sample names (e.g., CAMOS) in the file filter and press enter or press "Update List".
#*Select all the files to backup by highlighting them using the left mouse button and ctrl to select individual files or shift to select a range.
#*Highlight IMA, choose "Move To" and "Tape". Press "Start...".
#*When the backup is complete press "Dismount" to eject the tape.
#*If the tape auto-ejected without pressing "Dismount" then the tape is full (see [[Scanco_Administration#Full_Tape|'''Full Tape''']]).
#:[[File:Uct_backup_pic06.jpg|500px]]

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====Use 'Script...' button====
Usually, you will start the move/copy by clicking on <code>'Start...'</code> button. The <code>'Script...'</code> button is for advanced users.

*Use of the 'Script...' button will generate a script <code>sys$scratch:archive.com</code>, that you may submit it in batch mode later (e.g. over night) by typing: <pre>$ scanco_submit_command sys$scratch:archive.com/after=23:59</pre>
*In a multi-computer cluster setup, you may want to specify the exact queue name of the computer that has the tape hooked up by giving e.g. <code>/que=sceval_fast</code>.
*Insert a tape, but do NOT mount the tape in the normal program. If necessary: if it's a new tape, [[Scanco_Administration#Initialize_a_New_Tape|'''initialize''']] it as usual.
*The batch job will be started one minute before midnight in the example above. <code>$ show entry</code> will show you that it is holding until then.
*See <code>$ help submit /after</code> and <code>$ help dcl_tips date_time example</code> for more help on this.
*Sample script file (archive.com) restoring the RSQs of measurements 6452 and 6580:
<pre>
$ MOUNT/FOREIGN TP0:
$ UCT_BACKUP_BATCH
ALL
RAW
COPY
DISK
! Meas: SB_BUIE_EX_CTRL_PH_01 (6452)
MEAS
6452
EXECUTE
! Meas: SB_BUIE_EX_CTRL_PH_01 (6580)
MEAS
6580
EXECUTE
EXIT
$ DISMOUNT TP0:
$ EXIT
</pre>

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====Database Backup====

The database (DB) backup should be performed for each user on the system. It should not be performed as user 'calibration' or some derivative. In the case of the XtremeCT2 and XtremeCT cluster, both the 'microct' and 'xtremect2' user accounts must be used to backup their respective DB.

By performing the DB backup, the warning dialog that appears when logging into the system should go away.

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====Operating System (OS) Backup====
If the following error-message appears on the screen then you can click OK to continue your work.

MESSAGE: No recent OS Backup found!
Please perform OS backup (DISK0) in privileged account!
%RMS-W-FNF file not found.
CODE: 268534416
Facility RTL

This message means that no operating system (OS) backup has been performed within the last 6 months. Please perform an OS backup as soon as possible by following the steps below:

1. Make sure there are no scans in progress and that the que is halted from all activity.

2. Log in to the calibration account: Since we have two scanners on the same system, login as either "calib3401" or "calib3309", depending if you need to backup the XtremeCT2 or XtremeCT, respectively. For microCT clusters, (best to do this on SCEVA3) using the username calib5019 and the password (ask Steve for this).

3. Type in the DECterm window:
$ set proc/priv=bypass
Or Set priviledge to bypass by <code>$ spb</code>
$ r um:uct_b Or $ uct_backup

4. You will now see 2 additional buttons on the bottom left that is not seen when logged in as microct user. Push either the button "OS Backup to Disk DK0" or mount the specific OS backup tape and push the "OS Backup to Tape" button.
* A system backup to tape and to DK0 should both be performed.

5. Check the command line & queue to ensure that the backup is being carried out. If you submit the job as 'batch mode' the backup is submitted to SYS$BACKUP queue and allows you to close the backup program and 'end session' without interrupting a running backup. Check with 'show queue' to see the backup job on the queue.

6. Exit the Backup Program and log out of the calibration account.

After a successful OS backup the message above will not appear for the next six months.

Alternatively a system backup can be completed using the command line, without using the uct_backup program. The instructions from Scanco can be found here. The advantage to this method is that you will be able to name the specific backup save set.

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===Using Scripts for Backup/Archive===

====Project Backup/Archive====
*Refer to [[Media:Microct_project_backup.pdf|'''Project Backup SOP''']] or [[Media:Microct_project_backup.docx|''' its Word format''']] for reference.

=====Backup Project=====
Regularly backup projects on a monthly basis using command <code>$ @com:BACKUP_PROJECT.COM</code>
*The script is submitted to the queue and upon completion the log is emailed to the user.
*a SAVset (an OpenVMS file type similar to a zip file), a project info file and a file list are created in DISK5:[BONELAB.PROJECTS.BACKUP] for the microCTs and DISK4:[BONELAB.PROJECTS.ARCHIVE.ARCHIVE] for the XtremeCTs.
*The saveset along with two TXT files created will be automatically SFTP to Winston:\\Backups\backup\
*After the transfer, the saveset file on disk are deleted, leaving only two TXT files on the project disk.
*Only keep the two most recent backups for each project, A or B version name appended on the project name:
:*Backup version "_A" for odd months (Jan, Mar, May, Jul, Sep, Nov), e.g. YZHU_A_OTHER_2017-01-12.SAV
:*Backup version "_B" for even months (Feb, Apr, Jun, Aug, Oct, Dec), e.g. YZHU_B_OTHER_2020-04-08.SAV
*The user MUST verify that the backup completed successfully.
*SAVsets greater than 250 GB cannot be transferred by automatic SFTP, use interactive/manual SFTP instead to transfer to Winston.
*If you are backing up a very large project, please check the server disk space before starting the backup.

<pre>
$ @com:BACKUP_PROJECT.COM
===========================================================
BACKUP PROJECT TOOL V1.2 (XtremeCT)
P1:LOCATION DISK4:[BONELAB.PROJECTS.DUNCAN]
P2:TYPE 1=MOUSE,2=RAT,3=HUMAN,4=OTHER
P3:PROJECT CAMOS
P4:PERSON Ying Zhu
P5:DESCRIPTION A monthly backup
P6:EMAIL me@ucalgary.ca
P7:SFTP y,n
P8:START y,n
</pre>

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=====Restore Project=====
In the commands directory (com) is a BACKUP_RESTORE.COM script which will automatically generate a script to restore a user's project.
*The saveset file has to be moved to Winston:\\Backups\archive folder to be restored.
*The user will be asked if they wish to restore to the original location, or to a new location.
*The script is submitted to the queue and the log from the restore job is emailed to the user.
*The user MUST verify that the job completed successfully.
<pre>
$ @COM:BACKUP_RESTORE.COM
</pre>

=====Delete Project=====
In the commands directory (com) is a BACKUP_DELETE.COM script which will automatically generate a script to delete all the files and subdirectories of a specified path.
*The command script is opened so that the user can check the files to be removed to go ahead.
*You will need to manually delete the root project directory after it's empty.
<pre>
$ @COM:BACKUP_DELETE.COM
</pre>

=====Known Bugs in Project Tools=====
*Long file name won't work (28 letters work but not 32 letters).
*if the user specifies too long a file name, the Project Backup Scripts will fail with the following error:
RMS-E-CRE, ACP file create failed
SYSTEM-W-BADFILENAME, bad file name syntax

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=====Archive Project Saveset to Tape=====
Projects should be stored safely onto a backup tape once complete.

Summary

The following steps summarize the process:
:* Archive the project directory to the tape (detailed instructions below).
:* Change tape to "read only" to protect contents
:* Check tape saveset to ensure proper backup
:* Write name of tape on the project LOG sheet
:* Copy project LOG sheet and bring to Bone Imaging Laboratory "completed" project book
:* Bring copy of tape to the Bone Imaging Laboratory for safe keeping
:* Delete the contents of the project from the disk

In the project, there should be the regular set of directories including DOC, COM, MODELS, LOG. Once the project is stored to tape, ensure that the log sheet for that project include a note stating which tape it was backed up to. Take a photocopy of the log sheet and add it to our Bone Imaging Laboratory project book for COMPLETED projects.

In the following example, a project titled BERN is backed up onto tape. Ideally, the name of the SAV file on tape is the same as the project (i.e., BERN). Note that SAV files must have names with no more than 13 characters (including the .SAV)!

The following example backs the BERN project/directory onto tape IMA001. For large projects and/or critical projects, it is advisable to dedicate an entire tape. The three dots (...) indicate that ALL subfolders of DK0:[MICROCT.PROJECTS.BERN] will be included.

<pre>
$ mount/foreign tp0:

$ backup/log dk0:[microct.projects.bern...]*.*;* tp0:proj_bern.sav - ! writes a saveset to tape
/block=65534 /label=IMA001 -
/media_format=nocompaction ! NEVER use the /rewind option here

$ backup/log tp0:*.sav/select=*.isq DISK4:[BONELAB.PROJECTS.TBONE.ISQ_FROM_TAPE...]/by=parent ! extracts all ISQ files from the tape

$ dismount tp0:
$ dismount tp0: /nounload ! same as previous command, but does not eject the tape (i.e. if you want to read the tape once more)
</pre>

Note that the <code>/rewind</code> option should never be used for backup as it instructs the tape drive to rewind after backup is complete causing a major risk of over writing.

Sometimes it might be handy to exclude certain files. For example, to exclude RSQ files: <code>/excl=*.rsq</code>

A good reference for backup commands and ideas are available in the <code>UM:UCT_MOVE_FILES.COM</code> script which is used by the <code>UCT_BACKUP</code> program. See also the <code>help backup</code> instructions:
<pre>
$ help backup
</pre>

To view the contents of a tape to ensure you've successfully stored your project use the following commands (further details in "HowTo: View save set (SAV) contents"):

To just view if the saveset is on tape (but not its contents):
<pre>
$ mount/ov=id tp0:
$ dir/date tp0:*.*
$ dismount tp0:
</pre>

Note: you can also save the saveset list in a text file using the /output qualifier.

To view the files within a saveset on tape, and save the results in a file called <code>results.txt</code>:
<pre>
$ mount/foreign tp0:
$ backup/list=results.txt tp0:*.*
$ dismount tp0:
</pre>

To delete a set of directories, use the <code>dl</code> command.
<pre>
$ cd ur BERN
$ del *.*;* ! Deletes ALL files in a directory
$ dl *.dir;* ! Will only delete empty directories (not nested directories)
</pre>

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=====Extract Project Saveset from Tape=====
To restore a project, you have two choices:
*1. Login as user <code>calibration</code> and then go to the projects directory. From there:
<pre>
$ spb (bypass priv)
$ backup/log tp0:proj_davison.sav/rewind [*...]
</pre>
This puts all the files back in their original directory structure.

*2. As user <code>microct</code>
<pre>
$ mount/foreign tp0:

$ backup/log tp0:proj_davison.sav/rewind/select=[microct.projects.davison...]
disk2:[microct.projects.davison...]

OR

$ backup/log tp0:*.*/rewind disk3:[microct.projects.vitamink.models]
</pre>
Make sure to write the same path in the /select as the output (except for the
actual disk2 portion). Alternatively, you could unpack it into a slightly different root
directory (i.e., TMP) by changing the output path.

The three dots infers to use the same paths in the saveset as the file structure put onto disk.

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====Scripts to Backup RAW and IMA====
A script can be output from the backup tool to backup and restore data using the backup program.
*When restoring data using this method, choose the COPY to DISK option. The data will be restored to its original location on the data disk.
*You must manually submit the script to the backup queue.
*The command procedures are written to SYS$SCRATCH:ARCHIVE.COM.
*Here is the sample script for backing up RAW data:
<pre>
$ MOUNT/FOREIGN TP0:
$ UCT_BACKUP_BATCH
ALL
RAW
MOVE
TAPE
! Meas: ATHLETE_126 (10565)
MEAS
10565
EXECUTE
! Meas: ATHLETE_126 (10566)
MEAS
10566
EXECUTE
! Meas: ATHLETE_126 (10567)
MEAS
10567
EXECUTE
EXIT
$ DISMOUNT TP0:
$ EXIT
</pre>
*Here is the sample script for backing up IMA data:
<pre>
$ MOUNT/FOREIGN TP0:
$ UCT_BACKUP_BATCH
ALL
IMA
MOVE
TAPE
! Meas: ATHLETE_126 (10565)
MEAS
10565
EXECUTE
! Meas: ATHLETE_126 (10566)
MEAS
10566
EXECUTE
! Meas: ATHLETE_126 (10567)
MEAS
10567
EXECUTE
EXIT
$ DISMOUNT TP0:
$ EXI
</pre>

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====Disk Usage information====
<pre>
$ @COM:DISK_MOUNTIES.COM !Give data disk usage information on an account.
$ eve sys$scratch:disk_mounties_output_summary.txt
</pre>

The template file for summarizing the disk mounties results: [[Media:BoneLab_Data_Disc_Usage.xlsx|'''BoneLab_Data_Disc_Usage.xlsx''']]

To look at the RSQs in the database
<pre>
$ dir/siz dk0:[microct.data...]*.rsq
</pre>
the three dots means all subdirectories.

Other useful commands:

<code>$ ctheader xxxxxx.isq</code>

or

<code>$ ctheader xxxxxx.rsq</code>

shows you header.
<pre>
$ fda command file-wildcard
</pre>
does a 'file do all' of the command on all the given wildcard filenames.
<pre>
$ pipe xxxx | search sys$pipe "patient"
</pre>
is the pipe command in VMS.

So all three combined:
<pre>
$ pipe fda ctheader dk0:[microct.data...]*.rsq | search sys$pipe "patient name"
</pre>
or any other field you want to search for!

If you have a more complex program to run (e.g. with an argument), use the double quotes as follows:
<pre>
pipe fda "aix -l" *.AIM | search sys$pipe "Patient Name"
</pre>

'''Other ideas''':

<pre>$ write_info</pre>

gives you a file <code>sys$scratch:info.txt</code> with info in it (leave defaults to get all samples ever scanned, otherwise 'zoom' in on some samples.)

Check out the <code>search</code> command:
<pre>
$ help search
</pre>
and <code>/match=and</code>
or <code>/match=or</code>

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====Disk Backup====
In the commands directory (com) is a BACKUPDISK script which will automatically generate scripts to backup all the directories on the projects disk.
*As the backup requires significant amounts of space, please check the server disk space before starting the backup.
*Each directory is saved as a separate save set (an OpenVMS file type similar to a zip file) on Winston://Bonelab/Backup/.

<pre>
$ @COM:BACKUPDISK
</pre>

*Refer to [[Media:Microct_disk_backup.pdf|'''Disk Backup SOP''']] or [[Media:Microct_disk_backup.docx|''' its Word format''']] for reference.

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=Process, Printer and System=

==Processes and Jobs==

===Manage jobs in the queue===
Use the DELETE/ENTRY and SET ENTRY commands to manage a batch job.

<pre>
$ SH QUE !Get process info
$ SH QUE /all/by_job_status=executing !Get all executing process info
$ SHOW ENTRY 1131 /full !Get full process info of entry 1131
$ SE 1311 !Get full process info of entry 1131

$ DELETE /ENTRY=251 !Deletes batch job number 251.

$ SET ENTRY 251/PRIORITY=50 !Changes the priority of batch job number 251.
!Default priority is 100 for all jobs, max is 200.
$ SET ENTRY 251/REQUEUE=SCEVAL_FAST !Moves to queue sceval_fast.
!The job cannot be executing to do this, has to be in pending status.
$ SET ENTRY 251/AFTER=TOMORROW !Holds entry 251 until the following day (midnight).

$ HELP SET ENTRY !More information on the SET ENTRY command.
</pre>

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===Control processors # on multi-processor machines===

For example, on the itanium there are two processors. By default, only one takes reconstruction jobs. The other is left for so that evaluations can take place without competing for the CPU.

But if a bottleneck is the reconstruction, it can be switched as user <code>system</code>:

<pre>
$ set que sceva2_slow/job=2
</pre>

so that it will do two reconstruction jobs simultaneously.

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===Create a new queue===
This may be useful to separate jobs for a project. The following will create a queue called BUIE$FAST, which will submit jobs to SCEVAL_FAST and SC3309_FAST.

$ initialize/queue/GENERIC=(SCEVAL_FAST,SC3309_FAST)/OWNER=[SYSTEM] -
/PROTECTION=(S:M,O:D,G:R,W:S)/BATCH/START BUIE$FAST

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===Clear out all entries in a queue===
First create a dummy queue, then merge (i.e., move) all the entries from the queue to be cleared into it, then delete the dummy queue.

Example: Clear out the printer queue.
$ stop/reset printer1
$ initialize/que dummy
$ assign/merge dummy printer1
$ delete/que dummy

Example: Clear out a batch queue, e.g., sys$fast.
$ initialize/que/batch dummy
$ assign/merge dummy sys$fast
$ delete/que dummy

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===Stop and restart queues===
There are three methods. First the nice method.

1. As for the printer queue, a normal user can stop and start other queues.

<pre>
$ stop/que/reset sceval_slow
$ start sceval_slow
</pre>

This kills the current process running. If you want to let the current process complete before stopping the queue, use:
<pre>
$ stop/que/next sceval_slow
</pre>

2. Use the web browser Mozilla.

:*Open mozilla
:*'batch queues'

:*Resize the window so it occupies the right half of the screen

:*Click on 'delete job' once with the MIDDLE mouse button, this will open a new window on the right half of the screen. Ensure the two windows do not overlap, if they do resize the window which contains the batch queues list. Once window locations are correct MIDDLE click on the rest of the jobs which you wish to delete (click on 'Delete Job' in the batch queue list). The reason for locating the widows is because each successive click on 'Delete Job' will open a new window and you don't want it to cover the batch queues list.

:*Then Exit from mozilla, this will delete all the open windows, it may take a bit if you are deleting lots.

3. Now the harsh method.

[[Image:Bones2.jpg|20px]] Warning: Extreme caution! Explicit permission for this change or similar changes must be obtained from Dr. Steven Boyd.

Completely remove the queue and re-generate, as user <code>system</code>

<pre>
$ stop/queue/reset sc3309_slow
$ delete/queue sc3309_slow
</pre>

Then you must restart the queue. To learn how to do this refer to:
<pre>
$ eve sys$startup:dcps_hpljet_ip.com
</pre>

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===Kill hunging processes===

Sometimes jobs need to be stopped manually, such as when FTP or TCPIP is hung. This is done as follows:

Checked processes with
$ show sys
where the FTP jobs are running. Doing it as system with these commands would show all the FTP jobs on all nodes:
$ mcr sysman
SYSMAN> set env /cluster
SYSMAN> do pipe sh sys|sear sys$pipe ftpc
It showed that they all were running on SCEVA1 only. So I logged in there and using the IDs given at the list from above's command:
$ stop/id=29804056
...

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===Check CPU usage and kill a process===
Determine what process is using all the CPU (e.g., SYMBIONT, a print process) using the monitor command, then use the show system command to determin the Pid, which can be used to stop the process.

The print (SYMBIONT) process is known to consume excessive CPU when the clocks are advanced for daylight savings on the alpha systems.
<pre>
$ monitor process/topcpu
$ show system
OpenVMS V7.3-2 on node SCEVAL 6-APR-2009 12:42:22.82 Uptime 124 23:16:08
Pid Process Name State Pri I/O CPU Page flts Pages
20C00081 SWAPPER HIB 16 0 0 01:07:05.63 0 0
20C00087 CLUSTER_SERVER HIB 14 2218 0 00:00:00.54 63 77
20C00088 CONFIGURE HIB 10 23 0 00:00:00.02 54 20
20C00089 LANACP HIBO 13 -- swapped out -- 32
20C0008B FASTPATH_SERVER HIB 10 9 0 00:00:00.01 79 94
20C0008C IPCACP HIB 10 10 0 00:00:00.02 37 28
$ show process/all/id=Pid
$ set host 0
user: system
password:
$ stop/id=Pid
</pre>
*Process Name = BATCH_122 means entry 122 in the queue

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==Printer==

===Set up TCPIP printer queue on a VMS workstation===
$ stop/que/res hpljet
$ tcpip set nohost hpljet
$ tcpip set host "hpljet" /address= xxx.xxx.xxx.xxx
$ start hpljet

Note that many HP printers will not work with OpenVMS. Checking for compatibility is important.

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===Stop and restart the printer queue===

How to fix the printer queue when hung, not working or giving an error.
A full printer queue can seriously affect system performance.
Be sure that the queue is cleaned up from time to time.

<pre>$ show queue</pre>

to first find out the real name of your printer queue.
* Replace "hpljet" and "...dcps_hpljet..." by your own queue (i.e., PRINTER1 for XtremeCT) name below.
* First approach, as normal user <code>microct</code>:
<pre>
$ stop/queue/reset hpljet
$ start/queue hpljet
</pre>

If you need to release a job
$ set entry/release 123

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==System==

===Monitor System===
====Monitor system usage====

<pre>
$ monitor/interval=1 processes/topcpu
$ monitor/interval=1 system
$ show error
$ show system
$ @SCOM:SHOW_DISKS.COM (or simply $ DISKS)
</pre>

The command <code>show error</code> may indicate errors. One or two errors is OK.

To see what processes are running (specific to the machine, not cluster wide).

<pre>
$ show device disk2/file
$ show user /full
</pre>

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====Check status of OpenVMS system====

If when rebooting a VMS system there is a failure, sometimes a message can be repeated many times. The way to stop this repeating message is to press <code>ctrl-C</code> or <code>ctrl-P</code> to get to the <code>>>></code> prompt.

Then show some of the device information, either specifically

>>> show device py*
>>> show device dy*

or in general

>>> show device

which might show more than needed. The output of

>>> show bootdef_dev

can also be useful.

Once settings are all good, you can reboot the system with
>>> init
>>> set bootbios pyb0
>>> boot

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====Check disk status====
Login as the system user on the workstation connected to the disk array that you want to check.

$ run sys$system:msa$util.exe
MSA> set controller

Show the raid volumes (e.g., to check if it failed or is recovering).
MSA> show unit

Locate disks associated with a raid volume (e.g., unit0).
MSA> locate unit0

Accept a failed unit (e.g., unit0) - only for itanium workstations, which use a newer version of OpenVMS.
MSA> accept unit0

Show disk information.
MSA> show disks

Get information on MSA utility functions.
MSA> help

Exit the MSA utility.
MSA> exit

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====Check status of disk array====
To look at the disks in an MSA30 tower:
There are several options to check the status of the disks. One is, if it is installed, to use the command-line utility
<pre>$ mcr msa$util</pre>
as "system". Enter
<pre>
MSA> set controller
MSA> show unit
MSA> show disks
MSA> exit
</pre>

Another is to start the WBEM web interface, which shows the status of the hardware graphically.

It is possible to fix a disk array that hasn't booted by doing the following:

At the login prompt, type 'shutdown'. This will get you to the <code>>>></code> prompt.
There should be a RAID card, for example on Percy, named <code>pya0</code>. Try:
>>> show device
>>> set auto_action halt
>>> init
>>> run bios pya0
>>> set auto_action restart
>>> boot

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====Check disks status in enclosure====

Periodically connect to http://10.148.64.254/ (user name: manage, password same as system password) and check if there are any errors or warnings, like failed disks. You can easily see which disk has failed in the graphical view of "Physical" -> "Enclosure X"

Consider not all web browsers allow connection to this rather old web server. Firefox and Mozilla on the workstations do work fine.

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===Recover System===
====Consistently needs warm-up scanner - Shutter-failsave-Job====

If the scanner is consistently needing to warm-up on consecutive days, and was not powered off, this is likely due to the Shutter-failsave-Job disappearing from the 3309-Batch queue (for XT1). The job must be re-submitted.

The executing file is located in the CALIB3309 ($ um:submit_shutter_test.com) and the command to submit the job is:
<pre>
$ submit/after="tomorrow"/noprint/que=uct_measurement_queue um:submit_shutter_test.com
</pre>

You can check the status by typing:
<pre>
$ show que *3309_batch*/all
</pre>

This job tends to disappear now and then, perhaps because of an abrupt shutdown of the workstation or maybe when stop/pause/re-start the queue. Contact Scanco if this does not resolve.

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====Disk not mounted/unavailable, directory not found, volume not enabled====
Disk is not mounted or is unavailable. Error opening ...., directory not found, volume is not software enabled.
<pre>
%DIRECT-E-OPENIN, error opening DISK4:[MICROCT.PROJECTS]*.*;* as input
-RMS-E-DNF, directory not found
-SYSTEM-F-VOLINV, volume is not software enabled
</pre>
This can happen if communication is broken between workstations, causing the disk mount to time out. Check if this is by showing the devices, then dismount and remount the disk.
<pre>
$ show dev

Device Device Error Volume Free Trans Mnt
Name Status Count Label Space Count Cnt
SC3309$DKA100: Online 0
SC3309$DKD0: Mounted 0 ALPHASYS 3.18GB 642 2
SC3309$DKD1: Mounted 0 AUSER_01 42.84GB 4 2
SC3309$DKD2: Mounted 0 ADATA_01 173.00GB 4 2
SC3309$DKD3: Mounted 0 ADATA_02A 215.80GB 1 2
SC3309$DKD4: Mounted 0 ADATA_02B 215.85GB 1 2
SC3309$DKD5: Mounted 0 ADATA_02C 215.81GB 1 2
SC3309$DQA0: Online 0
SC3309$DQA1: Offline 1
SC3309$DQB0: Offline 1
SC3309$DQB1: Offline 1
SCEVAL$DKA0: Online 0
SCEVAL$DKA1500: Mounted 0 (remote mount) 1
SCEVAL$DKC0: MntVerifyTimeout 0 ADATA_03A 541.62GB 1 2
SCEVAL$DKC1: MntVerifyTimeout 0 ADATA_03B 541.38GB 1 2
SCEVAL$DKC2: MntVerifyTimeout 0 ADATA_03C 541.60GB 1 2
SCEVAL$DQA0: Online 0

$ set host 0
system

$ dismount SCEVAL$DKC0:
$ mount/cluster SCEVAL$DKC0: ADATA_03A
%MOUNT-I-MOUNTED, ADATA_03A mounted on _SCEVAL$DKC0:
$ mount/cluster SCEVAL$DKC1: ADATA_03B
%MOUNT-I-MOUNTED, ADATA_03B mounted on _SCEVAL$DKC1:
$ mount/cluster SCEVAL$DKC2: ADATA_03C
%MOUNT-I-MOUNTED, ADATA_03C mounted on _SCEVAL$DKC2:
$
</pre>

If this does not restore the disk, then shutdown the computer. At the blue screen...
<code>>>> init</code>
Wait for blue screen to return.
<code>>>> run bios pya0</code>
Press F2 at the prompt to accept potential data loss.
Wait for blue screen to return.
<code>>>></code>
Press power button to turn off.
Press power button to turn on.

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====Kill hanging program====

If a program is hunging, it may not be necessary to shut down the system and restart. For example, if the <code>uct_evaluation</code>
program is hung, do the following

<pre>
$ show dev/full microct_scsi

$ stop/id=<Owner process ID> (Replace the <> with the actual ID)

for example:

$ stop/id=2280091C
</pre>

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====Reset the display/GUI====
These commands will terminate the current login session and may restore a frozen or messed up screen. You will need to remotely access the problem workstation either from another micro-ct workstation or using a personal computer.

Use the set host command to connect to the problem workstation (e.g., thomas) using the node name (e.g., sc3309) or the IP address (e.g., thomas.kin.ucalgary.ca).

$ set host sc3309
login: system
password:

Issue the reset display command.
$ @sys$startup:decw$startup restart

At the prompt, type "y".

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====Restart screen server====

If the monitor fails to show the login prompt and displays a blank gray screen...telnet to the computer from another computer (e.g. a PC or so) and login as user system. Run the restart command:

<pre>
$set host gordon.ucalgary.ca. [or other computer name]
$username: system
$password: [system password]
$@sys$startup:decw$startup restart</pre>
confirm (answer "yes" at the prompt) and logout.
<pre>
$y
$logout</pre>

This will kill all programs on your screen, but it will leave all batch jobs running, so if you do a BATCH measurement, this will survive! (but interactive scan will be killed).

If you are restarting a monitor connected to a KVM box, unplug and re-plug in the box.

This command also helps when the mouse/keyboard freezes.

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====Restart Alpha stations====

[[Image:Bones2.jpg|20px]] Warning: Do not do this unless absolutely necessary.

For shutdown

At the login screen, type "shutdown"/no password and hit enter.
Then, you can turn the computer off at the prompt.

Then, you may turn the disk array off (unplug it as there is no power switch).

After you move the computer, power on the disk array and then the computer.

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====Slow/non-responsive computer====

This is usually caused by people logging in via SSH multiple times. The solution involves resetting the SSH/TCPIP daemon.

:*If you are local at the computer:

You will need to log in as user <code>system</code>. ONLY EXPERIENCED USERS SHOULD EVER LOG IN AS SYSTEM!

The system will be extremely slow (it will take 5 minutes just to get a log in prompt). This is expected.

<pre>
$ set host 0 ! user name 'system' and password
$
$ @sys$startup:tcpip$ssh_shutdown ! shutdown SSH
$
$ set host 0 ! user name 'system' and password
$
$ @sys$startup:tcpip$ssh_startup ! restart SSH
</pre>

Alternatively, you can reboot the system to reset the SSH. This is not an appropriate solution and it is solving the problem by hitting it with a jack hammer. Sometimes it is the only choice though.

:*If you are remotely logged in:

You will have to log in as user <code>system</code> and run a script called STOP_START_TCPIP.COM.

This works essentially the same as for the above method, except that since it would be impossible to restart SSH remotely once it is shut down, two separate scripts are called and submitted on SCEVAL_FAST (make sure the queue isn't clogged) separated by a 1 minute delay. The first script called is STOP_TCPIP.COM and the second is START_TCPIP.COM.

To execute this process, you must log in as system, go to the SYS$SCRATCH directory, and interactively execute the script:
<pre>
$ @STOP_START_TCPIP.COM
</pre>

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====Shutdown a workstation remotely====
If a workstation becomes unresponsive, it may be possible to shut it down remotely from another workstation or personal computer, which is preferable over doing a hard power off. These instructions were provided by Mark Blanchard.

'''1. Remote shutdown from another micro-ct workstation'''. MAY NOT WORK FOR CLUSTER SERVER

Login as the system user.

$ set host 0
user: system
password:

Start the system manager.
$ mcr sysman

Set the environment to the workstation to be shutdown (e.g., thomas) using its node name (e.g., sc3309).
SYSMAN>< set env/node=sc3309

Issue the shutdown command. Add a time delay, e.g., 5 min, if you want to give users time to disconnect and the automatic reboot flag if you want to restart.
SYSMAN> shutdown node /min=5 /automatic_reboot

*You need to remain logged into the session running the shutdown until the other node has been shutdown completely!!!

'''2. Remote shutdown from a personal computer'''.

Begin a remote session to the workstation and login as the system user.

Create a detached terminal.
$ create/terminal/detach

On the PC, port 6000 needs to be accessible to the micro-ct workstation and in the X-server's configuration (e.g., in file X0.hosts for Xming).

Issue the shutdown command.
$ shutdown

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====Slow computers - Change RAID battery for Itanium computers====

If computers become sluggish, particularly when saving data after a scan, have Scanco check the batteries in the RAID drive. The batteries in SCEVA3 were changed 2014-11-10. There are two batteries. Order the HP brand (should look like the ones in the image).
*Instructions to open the Itanium work station and access the PCI card: [[Media:HP_rx2660_PCI_card.pdf |'''Change PCI card''']].
*Instructions to change the batteries after accessing the PCI card: [[Media:HP_SA6402_Batteries.pdf |'''Change batteries''']].

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====Frozen computer - "bootstrap failure" on boot up====
The micro-CT computer is frozen or there is a "bootstrap failure" on boot up, This happens to the client computers (those connected to the scanners) when there is interruption in the network. The only option is to restart the computer.

====Crash of XtremeCT II workstation computer====

For a non-responsive monitor and/or a mouse and/or a keyboard of the XtremeCT II workstation (sometimes caused by a lost of connection to server, or an internet outage):

:*1. The first thing to do is to check system logs for any indication of the cause of the issue, if you have the "Administrator" user privilege.
:*2. The next thing to do is to soft-reboot by remote-login and using command line to reboot the workstation, if you have the "system" user privilege.
:*3. If no success, try hard-reboot by pressing the power button as indicated below.
:*4. If no success, try hard-reboot by unplugging both power cords as indicated below.
:*5. If still no success, contact Scanco immediately.
:*6. The last thing to do is to record the issue and any possible reasons.

1. Checking system logs:

:*1) Remotely log into the iLO (the management console of the workstation) using SSH as user "Administrator" with the system password.
Both user/pw are case sensitive. For XtremeCT II workstation (James) it is SSH to 10.148.64.231. For others, consult the network diagram.

A trick: This connection only succeeds through a MAC or PC (via putty) direct login, not through an OpenVMS or Scanco system.
$ ssh -l Administrator 10.148.64.231
:*2) Then you get to a MP> prompt here:

MP MAIN MENU:
CO: Console
VFP: Virtual Front Panel
CM: Command Menu
CL: Console Log
SL: Show Event Logs
HE: Main Help Menu
X: Exit Connection
[sc3401-mp]</> hpiLO->

:*3) Type in 'SL' to show event logs, then you could choose 'E' for system event:

[sc3401-mp]</> hpiLO-> SL
Event Log Viewer Menu:
Log Name Entries % Full Latest Timestamped Entry
-------------------------------------------------------------------------------
E - System Event 1661 58 % 13 Sep 2018 11:17:43
F - Forward Progress 20000 100 % 13 Sep 2018 11:17:43
I - iLO Event 500 100 % 18 Sep 2018 07:46:42
C - Clear SEL and FPL
L - Live Events

Enter menu item or [Ctrl-B] to Quit: E
Log Name Entries % Full Latest Timestamped Entry
-------------------------------------------------------------------------------
E - System Event 1661 58 % 13 Sep 2018 11:17:43
Event Log Navigation Help:
+ View next block (forward in time, e.g. from 3 to 4)
- View previous block (backward in time, e.g. from 3 to 2)
<CR> Continue to the next or previous block
D Dump the entire log
F First entry
L Last entry
J Jump to entry number
H View mode configuration - Hex
K View mode configuration - Keyword
T View mode configuration - Text
A Alert Level Filter options
U Alert Level Unfiltered
? Display this Help menu
Q Quit and return to the Event Log Viewer Menu
Ctrl-B Exit command, and return to the MP Main Menu

:*4) From here you can use - and + to go through the log history back and forth. Not all logs do make a lot of sense though, as they are mainly meant for HPE engineers.
:*5) When finished, use CTRL + b to get back to the main MP> prompt.
:*6) Use MP> co to get to the console, where you see at what stage the booting process is, in case it does not boot properly.
:*7) When finished, use CTRL + b to get back to the main MP> prompt.
:*8) Use MP> x to end the connection.

2. Soft-reboot by remote login:

If a workstation becomes unresponsive, it may be possible to shut it down remotely from another workstation or personal computer, which is preferable over doing a hard-reboot. These instructions were provided by Mark Blanchard.

:*2.A) Remote shutdown from another micro-ct workstation. MAY NOT WORK FOR CLUSTER SERVER

Login as the system user.
$ set host 0
user: system
password:

Start the system manager.
$ mcr sysman

Set the environment to the workstation to be shutdown (e.g., thomas) using its node name (e.g., sc3309).
SYSMAN>< set env/node=sc3309

Issue the shutdown command. Add a time delay, e.g., 5 min, if you want to give users time to disconnect and the automatic reboot flag if you want to restart.
SYSMAN> shutdown node /min=5 /automatic_reboot

You need to remain logged into the session running the shutdown until the other node has been shutdown completely!!!

:*2.B) Remote shutdown from a personal computer.
Begin a remote session to the workstation and login as the system user.

Create a detached terminal.
$ create/terminal/detach

On the PC, port 6000 needs to be accessible to the micro-ct workstation and in the X-server's configuration (e.g., in file X0.hosts for Xming).

Issue the shutdown command.
$ shutdown

3. Hard-reboot by power button:

:*1) Hold the power button until it turns yellow.
:*2) Wait a minutes or two, then press the power button only once and shortly. You will not see anything for a while. Pressing the power button again during this time will turn off the workstation again !
:*3) After about 10~15 min, the workstation would boot up properly.

4. Hard-reboot by unplugging both power cords:

:*1) Hard-reboot by unplugging both the power cords. This will reset the console and controllers.
:*2) Wait for 5~10 minutes, then press the power button only once and shortly. You will not see anything for a while. Pressing the power button again during this time will turn off the workstation again !
:*3) After about 10~15 min, the workstation would boot up properly.

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=Remote Access=

==For Scanco support==
===Send a terminal to a remote computer===

To send a terminal from XCT clusters to Scanco for maintenance, you need to know the ip address for the terminal location.
Such as For Mark Blanchard:

$ set display/create/transport=tcpip/node=193.72.60.24
$ create/terminal/detach

The cursor will disappear for a minute or so, and reappear with the $ prompt indicating sent already.

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==Access VMS filesystem==
===Access XtremeCT VMS filesystem on a Mac===

In finder, select Go --> Connect to Server

This opens up a window that allows you to enter a server address. Enter the following information:
<pre>smb://136.159.130.28</pre>

Click connect. If the internet connection is working, you will then be prompted to enter in login info:

<pre>
USERNAME: xtremect
PASSWORD: uct
</pre>

Select the volumes you want to mount.

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===View XtremeCT VMS filesystem from a Windows PC===

The HP program that allows the VMS file system to be viewed by a PC is called Pathworks (on the VMS system). The following information is needed to connect to the VMS system:

<pre>
USERNAME: xtremect
PASSWORD: uct
WORKGROUP: microct
</pre>

Then, in Windows explorer, while connected in the same network as the VMS station (i.e., .130) enter the following IP address for Thomas (SC3309):

<pre>\\136.159.130.28\</pre>

Alternatively, map the drive.
<pre>
Right click on my computer and choose map network drive.

Folder:
\\136.159.130.28\UCT_DATA1
or
\\136.159.130.28\UCT_DATA2

User name: xtremect@microct
Password: uct
</pre>

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===View VivaCT40/uCT35 VMS filesystem from a Windows PC===

The HP program that allows the VMS file system to be viewed by a PC is called Pathworks (on the VMS system). The following information is needed to connect to the VMS system:

<pre>
USERNAME: vct_40
PASSWORD: uct
WORKGROUP: microct
</pre>

Then, in Windows explorer, while connected in the same network as the VMS station enter the following IP address for SCEVAL:

<pre>\\136.159.74.140\</pre>

Alternatively, map the drive.
<pre>
Right click on my computer and choose map network drive.

Folder:
\\136.159.74.140\SB_DATA
or
\\136.159.74.140\SB_PROJ
or
\\136.159.74.140\BH_DATA
or
\\136.159.74.140\BH_PROJ

User name: vct_40@microct
Password: uct
</pre>

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===Map a Network Drive to the VMS filesystem from Windows===

To do this you must be on the same network as the OpenVMS system. For main campus and the XtremeCT, you will map the drive to Thomas (136.159.130.28), the workstation connected to the scanner.

<pre>
Right click on My Computer and choose Map Network Drive...

Folder: \\136.159.130.28\uct_data1 !FOR THE PROJECTS DISK

and/or

\\136.159.130.28\uct_data2 !FOR THE DATA DISK

User name: microct\xtremect
Password: uct
</pre>

Note: You must use the numerical IP address and not the host name (i.e. thomas.kin.ucalgary.ca).

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==Setup remote access FAQ==
===Access data remotely===
Refer to [[Media:Scanco-faq-accessing-data-remotely.pdf|'''Scanco tutorial on accessing your data remotely''']] for

*A quick refresher course on accessing files
**Web browser
**File sharing
**File transfer protocol (FTP)
*Network file system NFS
*Running Scanco programs remotely

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===Use Hummingbird Exceed for remote access===

*Screen definition
:Server visual = PseudoColor
:Window mode = multiple

*Keyboard input
:Primary = decemus
:Alternate = us

*EVE commands
:select = "end"
:cut = "delete"
:paste = "insert"

:move forward a word = CTRL + right_arrow
:move to start of document = CTRL + up_arrow
:move to end of document = CTRL + down_arrow

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===Use XWin32 for remote access===

Run XWin32. Run Putty and connect to sceval.ucalgary.ca. Use the terminal normally to run programs, which should open with XWin32.

Additional terminal windows can be opened with <code>$ dec</code>

If you try to connect from somewhere other than the university, you will probably get the following error when trying to open a window:

Xlib: connection to "sceval.ucalgary.ca:10.0" refused by server
Xlib: Can not connect to a host on a restricted network
X Toolkit Error: Cannot Open Display
%DWT-F-DWTABORT, xtoolkit fatal error

Type the following at the command prompt to direct the display:

$ set display/create/transport=tcpip/node=Your_IP_Address/server=0

You can find your IP address from: http://www.ip-adress.com/

If you're running XWin32 from off campus and behind a router, forward ports 6000 - 6010 TCP and 177 UDP to your computer.

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===Set up Putty with gold-key access===

Refer [http://bone.wiki/index.php?title=Scanco_User_Instructions#PuTTY_and_Xming '''PuTTY and Xming'''] to download putty.

Set 'keyboard' to Vt400, and 'initial state of numeric keyapad' to 'Application', and now the 'NumLock' key is the gold key (like PF1), and the editor can repeat stuff.

Then

<pre>$ set term/vt100</pre>

to enable the editor in the terminal.

And duplication of a line is:
<pre>
- (which would be PF4) to erase a line,
then twice "numlock, then -" (gold-PF4 is 'restore line')
</pre>

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===SSH tricks===
====RSA and DSA Authentication====

The main advantage of setting up RSA authentication is that you will no longer have to type your password each time you access a host with ssh. There are some technical reasons why RSA and DSA access is more secure than password access.

These instructions work on both Linux and OS-X.

# Create your public/private key pair on your local computer
#* At the command prompt type: ssh-keygen -t rsa
#* You will be asked to create a passphrase.
#* This will create the files .ssh/id_rsa and .ssh/id_rsa.pub . Once you have these files, you never have to repeat this step.
# Copy your public key contents into the .ssh/authorized_keys2 file on the remote server
#* You can email yourself the file .ssh/id_rsa.pub from the local computer.
#* Alternatively, you could do this: ssh username@remoteserver.com 'cat >> ~/.ssh/authorized_keys2' < /Users/Youruser/.ssh/id_rsa.pub

NOTES ABOUT KEYS
Remember, the "authorized_keys" file is a concatenation of public (id_rsa.pub) keys,
and the "id_rsa" is the private key.
Every user on every computer should only have ONE "id_rsa" file,
but can have multiple "id_rsa.pub" files concatenated into
their "authorized_keys" file.

=====SSH Agent=====

SSH-Agent is a tool to store your passphrase so you don't have type it every time.

On OS-X, it is integrated into the system Keychain - you will be asked once if it should remember your passphrase, and after that you don't have to worry about it.

Most Linux systems also have ssh-agent configured to start with every session. You may however have to do this once:
ssh-add ~/.ssh/ida_rsa

====SSH Tunneling====

This is an alternative to VPN through kinesiology. It may come in handy if for some reason VPN is not working.

If you're outside the university system and want to access, for example, svn on mike.kin, which is normally blocked by the university firewall, you can do that with ssh tunneling. Here is an example:

ssh eric@mighty-mac.kin.ucalgary.ca -L 2000:mike.kin.ucalgary.ca:443 -N

Here is what is going on:
* I want to access port 443 (which is https) on mike.kin.ucalgary.ca.
* I have an account on mighty-mac, so I'm using that server to create an ssh tunnel inside the university firewall. I could use any machine I had an account on inside the university system, even mike.kin.ucalgary.ca, the one I'm trying to get to (in fact, that would be best, but for purposes of demonstration I'm using a different machine).
* I'm mapping the local port 2000 to port 443 on mike. Anything I send to localhost:2000 will by sent by ssh or the ssh tunnel to mighty-mac, which will then send it on to port 443 on mike.
* 2000 is a random 4-digit port number. If by some fluke you happen to choose one that is in use, ssh will complain and you will have to try another port number.

Now I can fire up my browser and point it to

https://localhost:200/trac/

And what I get is the trac site on mike.

If I want to get the code, I can do this:

svn checkout https://localhost:2000/svn/numerics88/trunk trunk_tunnel

("trunk_tunnel" is just the directory name where it will end up. It can be named anything, but this will remind me that it only works when the tunnel is up.)

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==Physical connections==
===Connect to VMS station with a serial port cable===

To do this, you will need to connect from a PC using a PC-to-PC (NULL modem) serial cable, 9600 baud. Install PuTTY and connect with the 'serial' option. You will need to know the COM port that is used by the PC to connect the serial cable. You can do this by checking on the PC the [Hardware][Device] settings.

Typical login is "Admin" and password is usually same as the 'system' password.

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===Export VMS display to SUN or LINUX terminal===

<pre>
# - temple
$ - sceval
# xhost +temple.ucalgary.ca
# ssh -X microct@sceval.ucalgary.ca
$ set display /create /transport=tcpip /node=temple.ucalgary.ca
</pre>

NOTE: Do not use <code>xhost+</code>. Always specific exactly which computer is being
allowed X access.

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=Dose=

==Dose Calculations==

===XtremeCT radiation dose===
Some notes about radiation dose to help decide acceptable scanning protocols. These comments are based on scanning an adult (not children having significant red marrow at the scan region).

:*The annual dose limit for the hand for an occupational user is 500 mSv (as per the ICRP), and with the x-ray energy of our XtremeCT that translates to 500 mGy local dose per year. For non-occupational subjects, the limit is generally 10x lower (i.e., our volunteers should not have more than 50 mGy local dose per year).
:*Our scanner delivers a local dose of about 5.3 mGy per scan. However, if we have adjacent scans, there is some overlap due to the penumbra of the x-ray beam which results in about double the local dose (a conservative guess would be 10 mGy) for a ~1mm overlap region. Averaging over the whole scanned regions (overlap and non-overlap regions) we can say that the average delivered local dose is about 7-8 mGy. The local dose is not additive. If we're very conservative, and we take 10 mGy as the local dose, then we could theoretically scan a person 5 times before exceeding the 50 mGy limit based on a tenth of the occupational limit (500 mGy).

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===vivaCT CTDI dose===
====Dose calculation====

Assuming the following settings on the vivaCT for "high mode", we will calculate the CTDI dose.

2000 projections (360 degrees)
0.109 mA
200 ms IT

I calculate the time current value as:

0.109 mA * (0.200 + 0.012) S * 2000 proj= 46.22 mAs

The 0.012 is the integration time between projections.

Taking the proportion of the 68 mAs at 55 kV resulting in 720 mGy (see the document on example
dose calculation on this Wiki site), we have:

46.22 / 68 * 720 = 490 mGy

Since CTDI in air is approximately two times the weighted CTDI, and since our setup is more like in air, we get:

2 * 490 = 980 mGy per scan.

It's always a good idea to look at the time-current product in the control file to get an approximate estimate.

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====Dose chart and example====
*Refer to [[Media:VivaCT dose information-fyi.pdf|'''VivaCT CTDI Dose Calculation Example''']].

We have measured the following CT dose indices (CTDI).
:*CTDIw: Weighted CTDI (chart below)
:*CTDIair: CTDI in air (2 times CTDIw - calculate from chart below).

The detector was placed in the center of a 35 mm PMMA cylinder which was placed in the center of rotation.

<pre>
70kV 300ms 85uA Field of view 38.9mm 1000 Proj./180°: CTDI = 260 mGy
55kV 300ms 109uA Field of view 38.9mm 1000 Proj./180°: CTDI = 220 mGy
45kV 300ms 133uA Field of view 38.9mm 1000 Proj./180°: CTDI = 190 mGy

70kV 300ms 85uA Field of view 30.7mm 1000 Proj./180°: CTDI = 420 mGy
55kV 300ms 109uA Field of view 30.7mm 1000 Proj./180°: CTDI = 350 mGy
45kV 300ms 133uA Field of view 30.7mm 1000 Proj./180°: CTDI = 305 mGy

70kV 300ms 85uA Field of view 21.5mm 1000 Proj./180°: CTDI = 850 mGy
55kV 300ms 109uA Field of view 21.5mm 1000 Proj./180°: CTDI = 720 mGy
45kV 300ms 133uA Field of view 21.5mm 1000 Proj./180°: CTDI = 620 mGy
</pre>

high res = 1000 Proj./180°
medium = 500 Proj./180°
standard = 250 Proj./180°

The CTDI scales linear with the integration time (s), with the current (uA) and number of projections. If you have different settings there, it is easy to calculate the CTDI.

CTDI Definition:
<pre>
Integral from +50mm to -50mm of D(z)/NxT
</pre>
:*where D(z) is the dose profile along a line z which is perpendicular to the tomographic plane
:*N is the number of tomographic sections produced in a single rotation
:*T is the nominal tomographic section thickness

Example: How to estimate how much radiation would be incurred by a mouse scanned at 25
um resolution (medium resolution -- MR) at 55 kVp, 109 uA, 150 ms IT, for about 30 minutes?

If you take your settings you can calculate the CTDI. First thing you have to be aware is that the CTDI is something like the local dose but it takes the cone beam geometry and the not perfect collimation of the x-ray beam into account (The CTDI value is always higher than a local dose measurement with for example TLDs). It does not matter how many stacks you are scanning. The dose you have at one point which is within the volume you are scanning gets the same local dose if you are performing a 1 stack or a 4 stack measurement.

With the 55kVp/109uA HR with 300ms we have a value at the 30.7 mm position of 350 mGy. Because you have MR we can divide the values by a factor of 2; and because you have 150ms instead of 300ms there is an other factor of 2. You would get 87.5 mGy for the position 30.7 mm. Because of the cone beam the dose has a quadratic dependency to the diameter of the field of view. (30.7 mm/25 mm)2 = 1.5. The CTDI value for your settings is in the order of 87.5 mGy * 1.5 = 132 mGy.

Note that for in vivo measurements, we should multiply the result by a factor of two since we are doing the measurement in AIR, not WATER. The charts above are assuming the CTDI done in water.

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==Optimize Scan for Low Dose==
*Refer to [[Media:Scanco-faq-optimization-for-dose.pdf|'''Optimize Scan Protocols for Low Dose''']].

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File:Scanco TD387 USB Device Usage.pdf

2021-06-23T14:43:37Z

Yingzhu: Scanco USB Device Usage on Itanium Systems

Scanco USB Device Usage on Itanium Systems

Scanco User Instructions

2021-06-10T20:39:31Z

Yingzhu: /* Extract Results from XtremeCT Database using UPAT_LIST */

=OpenVMS Basics=
The micro-CT scanners in the lab are manufactured by [http://www.scanco.ch Scanco Medical] and most analyses are performed using their custom software. The micro-CT workstations run OpenVMS as its operating system and it is useful to learn some basic commands.

==OpenVMS Beginner's Reference==
OpenVMS (informally known as VMS) is a high-end computer server operating system with reliable, multitasking, real-time and batch processing. OpenVMS supports computer clustering via a LAN, enabling computers to share resources such as processors and disks to balance workload efficiently.

*[http://saf.bio.caltech.edu/vms_beginners_faq.html '''OpenVMS Beginner's FAQ''']

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==Session Manager==

The session manager automatically starts after a user logs in locally. For remote sessions, the session manager can be started with the command <code>$ vue </code>.

[[Image:SessionManager.jpg|600px]]

===Session===
Here you will find an option to "End Session", which you should do when you are finished using a workstation. You can click "Work in Progress..." when you have to leave in the middle of a session without logging out but showing a work in progress screen to other users to prevent interference.

===Views (directory shortcuts)===
The session manager is a graphical user interface that can be used to navigate directories (left side of session manager) and open files (right side of session manager). There are shortcuts to key directories under "Views". Single-click on a directory to list its subdirectories and files. Double-click on a file to open it.

===Commands and Utilities===
Under commands you will find tools such as copy, delete, and rename; however, it is much more practical to do these sorts of operations from a DEC terminal.

===Applications===
Under applications you can launch various applications including:
*DECterm: opens a DEC terminal
*MICROCT: opens the micro-ct control panel (buttons for Scanco Medical programs)
*Mozilla/Netscape: opens a web browser
*XV: opens a screen capture program

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==DEC Terminal and Digital Command Language (DCL)==
This is a DEC terminal: Commands issued in a DEC terminal are DCL commands.

[[Image:decterm.jpg|600px]]

===Copy and paste using the mouse in DEC terminal===
In the DEC terminal, you can highlight text by holding down and moving the mouse. Highlighted text can be pasted into applications or in the terminal using the middle mouse button. You can also highlight files in the Session Manager and paste the filename (with its full path) using the middle mouse button.

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===What is a symbol===
DCL can store information such as strings or integers in "symbols". DCL can also manipulate these symbols to create other symbols.
Symbols are primarily used to define short strings that replace long commands, perform certain calculations and replacements within DCL
procedures, hold status information.
<pre>
$ UR == "SET DEFAULT DISK4:[BONELAB.PROJECTS]" !A short hand to change locations to the project disk.
$ UR :== SET DEFAULT DISK4:[BONELAB.PROJECTS] !Another way to define the symbol without quotations.
$ x == 3 !Store the value 3 in the symbol x.
$ SHOW SYMBOL x !Displays the value of the specified symbol, x.
$ DELETE/SYMBOL/GLOBAL x !Deletes the specified symbol, x.
</pre>
Selected symbols on the Scanco system:
<pre>
$ UD !Changes to the data directory.
$ UR !Changes to the projects directory.
$ DISKS !Shows the current disk usage.
$ DEC !Opens a new DEC terminal.
$ EVE file.txt !Opens the file in the text editor.
$ AIX file.aim !Shows the processing log for an aim file.
$ AIX -L file.aim !The "-L" is used to show the full processing log.
$ QUE !Shows all entries in the queue.
$ GS file.ps or file.pdf !Opens *.ps and *.pdf files in GhostScript.
$ CTHEADER file.isq or file.rsq !Shows scan information for an *.isq or *.rsq file.
</pre>

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===What is a logical===
Logical names are strings, like symbols, but can be passed into programs whereas symbols can usually only be interpreted by the command line interpreter. For example, if the logical name UD was defined to be DISK2:[XTREMECT2.DATA] then UD: could be used as a substitute when entering the path to search for files from within a program.
<pre>
$ DEFINE UD DISK2:[XTREMECT2.DATA] !Defines a logical ud to point to the data directory.
$ DEFINE uct_default_isq myfile.isq !Defines the default isq file for Scanco Medical programs. The isq filename must contain the full path to the file to be evaluated, whereas the path can be left out if you just want to contour the scan.
</pre>
Selected logicals on the micro-CT system:
<pre>
COM !Logical pointing to the commands directory IDISK1:[XTREMECT2.COMMANDS]
UD !Logical pointing to the data directory DISK2:[XTREMECT2.DATA]
UD6 !Logical pointing to the data directory DISK6:[XTREMECT2.DATA]
UR !Logical pointing to the projects directory DISK4:[BONELAB.PROJECTS]
UE !Logical pointing to the evaluation script directory MICROCT_ROOT:[EVAL]
UU !Logical pointing to the templates directory MICROCT_ROOT:[UIL]
UCT_RESULTS !Logical pointing to the results directory MICROCT_USER:[RESULTS]
</pre>

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===Arithmetic operations===
{| class="wikitable"
|style="width: 10%"|Addition ||style="width: 5%;text-align:center;"| + ||The plus sign (+) adds two numbers.
|-
|style="width: 10%"|Subtraction ||style="width: 5%;text-align:center;"| - ||The minus sign (-) subtracts the second specified number from the first specified number.
|-
|style="width: 10%"|Multiplication ||style="width: 5%;text-align:center;"| * ||The asterisk (*) multiplies two numbers.
|-
|style="width: 10%"|Division ||style="width: 5%;text-align:center;"| / ||The slash (/) divides the first specified number by the second specified number. If a number does not divide evenly, the remainder is lost. No rounding takes place.
|}

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===Logical expressions===
{| class="wikitable" style="width: 100%;"
|style="width: 10%"|And||.AND.||The operator .AND. combines two logical values as follows
true .AND. true = true true .AND. false = false false .AND. true = false false .AND. false = false
|-
|style="width: 10%"|Or||.OR.||The operator .OR. combines two logical values as follows
true .OR. true = true true .OR. false = true false .OR. true = true false .OR. false = false
|-
|style="width: 10%"|Not||.NOT.||The operator .NOT. reverses the bit configuration of a logical value. A true value becomes false and a false value becomes true.
|}

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===Numeric comparisons===
{| class="wikitable"
|style="width: 15%"|Equal to||style="width: 5%;text-align:center;"|.EQ.||Compares one number to another for equality.
|-
|style="width: 15%"|Not equal||style="width: 5%;text-align:center;"|.NE.||Compares one number to another for inequality.
|-
|style="width: 15%"|Greater than||style="width: 5%;text-align:center;"|.GT.||Compares one number to another for a greater value in the first number.
|-
|style="width: 15%"|Greater than or equal to||style="width: 5%;text-align:center;"|.GE.||Compares one number to another for greater or equal value in the first number.
|-
|style="width: 15%"|Less than or equal to||style="width: 5%;text-align:center;"|.LE.||Compares one number to another for a lesser or equal value in the first number.
|-
|style="width: 15%"|Less than||style="width: 5%;text-align:center;"|.LT.||Compares one number to another for a lesser value in the first number.
|}

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===String comparisons===
The operators for string comparisons are the same as for numeric comparisons with an added "S" for string.
{| class="wikitable"
|style="width: 15%"|Equal to||style="width: 5%;text-align:center;"|.EQS.||Compares one character string to another for equality.
|-
|style="width: 15%"|Not equal||style="width: 5%;text-align:center;"|.NES.||Compares one character string to another for inequality.
|-
|style="width: 15%"|Greater than||style="width: 5%;text-align:center;"|.GTS.||Compares one character string to another for a greater value in the first specified string.
|-
|style="width: 15%"|Greater than or equal to||style="width: 5%;text-align:center;"|.GES.||Compares one character string to another for greater or equal value in the first specified string.
|-
|style="width: 15%"|Less than or equal to||style="width: 5%;text-align:center;"|.LES.||Compares one character string to another for a lesser or equal value in the first specified string.
|-
|style="width: 15%"|Less than||style="width: 5%;text-align:center;"|.LTS.||Compares one character string to another for a lesser value in the first specified string.
|}

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==DCL Programming Guide==
The OpenVMS systems allow for scripts to be written in a language called '''DCL (DIGITAL Command Language)'''. It was not designed to be more difficult than other scripting languages, but learning any new programming language comes with its learning curve.

*DCL has 243 commands, but most programs can be written with a base set of about 20 commands. The goal of this section is to provide a convenient reference for these commonly-used commands.

It is recommended to open a text editor, enter the whole series of commands, and then run them as a whole program. The terminal on OpenVMS is technically a DCL interpreter, so these commands could be typed in sequence into a terminal with the same result. Typing code interactively is helpful when testing a small code snippet in more detail.

===Your First DCL Script===
Ever since Kernighan and Ritchie wrote the book "The C Programming Language", it has been custom to start with a program that prints the text "Hello, world" to the screen. Open a text editor (for example "EVE") and enter the text below.
<pre>
$! My First DCL Script
$ mymessage = "Hello, world"
$ WRITE SYS$OUTPUT mymessage
$ EXIT
</pre>
Now save the file as HELLO1.COM, and run it using <pre>$ @HELLO1.COM</pre>

Several things are happening in the above program:
*'''Comment !''': The exclamation mark can appear anywhere on the line, and everything following the mark will be treated as a comment.
*'''Variable''': "mymessage" variable is populated with the string "Hello, world", which can be used in the rest of the script.
*'''Command''' "WRITE" send text to various places, in this case to "SYS$OUTPUT", that is to the standard output (i.e. screen).
*'''EXIT''' command tells the DCL interpreter that the script is done and we should exit.
*Commands in DCL are '''NOT case sensitive''', so the command "write sys$output mymessage" would produce the exact same result, but by convention we write commands in all uppercase.

*'''Special Comment !!''' automatically prints the contents of the comment to the screen/logfile. It is useful when you want to know what part of the script you are in.

===Basic Arithmetic===
The DCL language supports several types of data in variables. In the "Hello, world" example above, we saw how to store a string in a variable. We could have stored an integer, that is a positive or negative whole number, in the variable, and done some basic math.
*Refer to [[Scanco_User_Instructions#Arithmetic_operations|'''Arithmetic Operations''']], For example:
<pre>
$ i = 1
$ WRITE SYS$OUTPUT i+1
$ j = 3
$ k = j * (i + 1)
$ WRITE SYS$OUTPUT k
$ WRITE SYS$OUTPUT (k / 4)
$ WRITE SYS$OUTPUT 2 + 2 * 2
$ EXIT
will return:

2
6
1
6
</pre>
Two things are worth noting.
*Because we are limited to integers, division of 6 / 4 needs to return an integer (1.5 is not an integer); the value is truncated, which means rounding is always done toward zero.
*Order of operations is done in the "correct" order, and not left-to-right, so "2 + 2 * 2" is interpreted as "2 + (2 * 2)".

===Conditional Statements===
Sooner or later, you will want to run a program with some logic. The general syntax is:
<pre>
IF [condition]
THEN
[do something]
ELSE
[do something else]
ENDIF
</pre>
*The "ELSE" component is optional.
*If you need a very simple if..then with only one command, it can be written on one line without the "ENDIF":
<pre>
IF [condition] THEN [do something]
</pre>
*Refer to [[Scanco_User_Instructions#Numeric_comparisons|'''Numeric Comparisons''']], [[Scanco_User_Instructions#String_comparisons|'''String Comparisons''']] and [[Scanco_User_Instructions#Logical_expressions|''' Logical Expressions''']] for all possible logical operators (very similar to Fortran).

===Loops===
Most programming languages have 3 kinds of loops:
*Precondition Loops: Condition is tested at the beginning of the loop
*Postcondition Loops: Condition is tested after the loop has executed at least once
*Iterative Loops: A variable changes in a predetermined fashion each time the loop is called.

DCL has none of these. Instead, it has the concept of a "label" and the "GOTO" command. A loop in DCL would look like this:
<pre>
$ i = 1
$loop1:
$ IF i .GE. 10 THEN GOTO exitloop1
$ WRITE SYS$OUTPUT i
$ i = i + 1
$ GOTO loop1
$exitloop1:
$ EXIT
</pre>
This program will print the numbers from 1 to 10 in sequence.

===Subroutines===
Most programming languages allow to define a set of commands that can be called from various parts of the program.
*In DCL, the subroutine can be defined anywhere in the file (unlike C or Python, where the definition must precede the call).
<pre>
$ CALL mycustomsub Joe
$ CALL mycustomsub Mary
$ EXIT
$mycustomsub: SUBROUTINE
$ WRITE SYS$OUTPUT "Hello, ", P1, "!"
$ EXIT
$ ENDSUBROUTINE
</pre>

The first line calls a subroutine named "mycustomsub", which jumps execution to the 4th line. The parameters after the name of the function get copied over to local variables named "P1", "P2", "P3" etc. (in this example, only one parameter, but the maximum is 8) that are available to the subroutine. Note that the command "WRITE" accepts several arguments separated by commas, which get printed on one line.
*The subroutine should be terminated with the command "EXIT" followed by "ENDSUBROUTINE".
*Note that the parameters get passed literally to the subroutine, that is the subroutine gets the text "Joe", and not the contents of a variable named "Joe".
*To force symbol substitution, the parameter would need to be enclosed in single quotes.
<pre>
$ Joe = "Joe Smith"
$ Mary = "Mary Jane"
$ CALL mycustomsub 'Joe'
$ CALL mycustomsub 'Mary'
$ EXIT
$mycustomsub: SUBROUTINE
$ WRITE SYS$OUTPUT "Hello, ", P1, "!"
$ EXIT
$ ENDSUBROUTINE
</pre>

===Reading from files===
Sometimes you have a list of files (for example Micro-CT scans) that are to be processed in a certain way. The obvious way is to copy-paste the code several times, changing only the name of the file, but this is error-prone and inefficient.
*A better way is to put the list of models into a text file, and then call a subroutine on each model file. For example:
<pre>
$ CLOSE/NOLOG foo
$ OPEN/READ foo DISK3:[MICROCT.PROJECTS.OWOC.COM]MYLIST.TXT
$read_loop:
$ READ/END=done foo myline
$ CALL process_me 'myline'
$ GOTO read_loop
$done:
$ CLOSE/NOLOG foo
$ EXIT
$process_me: SUBROUTINE
$ scriptname = DISK3:[MICROCT.PROJECTS.OWOC.COM]MYSCRIPT.COM
$ SUBMIT/NOPRINT/QUE=SYS$FAST/PARAM='P1' 'scriptname'
$ EXIT
$ ENDSUBROUTINE
</pre>
*The first line closes the file handle, in case it was left open in a previous script.
*The second opens the file "MYLIST.TXT" for reading, and assigns the open file a handle named "foo".
*A loop reads the file line-by-line, calling a subroutine with the contents of each line.
*When the end of the file is reached, the file is closed and the script exits.

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==List of basic commands==
<pre>
$ VUE !Start the session manager. Press enter after to regain prompt.
$ DEC !Open a new DEC terminal
$ UCT !Open the micro-CT control panel.
$ UCT_SAMPLE !Start µCT Samples.
$ UCT_MEASUREMENT !Start µCT Tomography.
$ UCT_EVALUATION !Start µCT Evaluation Program.
$ UCT_3D !Start µCT Ray.
$ UCT_BACKUP !Start µCT Disk-Utility.
$ CD UD !Change location to the data directory.
$ CD UR !Change location to the projects directory.
$ CD SYS$SCRATCH !Change location to the scratch directory.
$ CD UCT_RESULTS !Change location to the results directory.
$ DIR UE !List files in the evaluation directory.
$ DIR UU !List files in the templates directory.
$ DIR COM !List files in the commands directory.
$ UCT_LIST !Extract results from the database.
$ AIX -L !View the header of an AIM file.
$ CTHEADER !View the header of an RSQ or ISQ file.
$ EVE !Start the text editor.
$ DISKS !Show the current disk usage (all hard drives).
$ LOGOUT !End a session. For remote sessions, logout from the main (initial) login terminal.
</pre>

===How to move to a different directory===
Use the SET DEFAULT command. You can use an absolute directory path or a relative directory path.
<pre>
$ SET DEFAULT disk:[dir.subdir] !Moves to specified path.
$ SET DEFAULT [.subdir] !Moves one level into subdirectory subdir.
</pre>

Use the CD (i.e., change directory) command (this calls the script $ @SCOM:CD.COM).
<pre>
$ CD subdir !Moves into subdirectory subdir.
$ CD subdir1 subdir2 !Moves into subdirectory subdir1, then into subdir2.
$ CD .. !Moves up one level (i.e., out of one directory).
</pre>

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===How to list the files in a directory===
Use the DIRECTORY command, which may be abbreviated to DIR.
<pre>
$ DIR !List everything in the current directory.
$ DIR disk:[dir.subdir] !Lists everything in the specified directory.
$ DIR disk:[dir.subdir...] !Lists everything in the specified directory and subdirectories.
$ DIR/COL=1 *.aim !Lists all files with the extension .aim in a single column.
$ DIR /VERSIONS=1 !Show only the newest version of each file in the directory.
$ DIR/SINCE=TODAY !Lists all files created today.
$ DIR [...*.aim] !The "..." indicates to do so recursively (i.e., counting all files in all subdirectories).
$ DIR/SIZE !Lists each file and its size.
$ dir/size/grand_total [.subdir...] !List the total size of all files in the SUBDIR directory.
$ HELP DIR !More information on the DIRECTORY command.
</pre>

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===How to copy files===
Use the COPY or BACKUP command.
<pre>
$ COPY file1.ext disk:[dir.subdir1]file2.ext !Make a copy of file1.ext to another location and call it file2.ext
$ COPY *.aim;* disk:[dir.subdir1] !Copy all .aim files (including all versions) to another location keeping the same name.
$ HELP COPY !More information on the COPY command.
</pre>
<pre>
$ BACKUP/VERIFY [.subdir1...]*.*;* [.subdir2...] !Copy entire directory SUBDIR1, including all subdirectories and files, into SUBDIR2.
$ BACKUP/VERIFY [.subdir1...]*.*;* []subdir1.sav/SAVE !Copy entire directory SUBDIR1, including all subdirectories and files, into a save set. The save set could be transferred and unpacked on another OpenVMS machine.
$ HELP BACKUP !More information on the BACKUP command.
</pre>

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===How to delete files===
Use the DELETE command, which may be abbreviated to DEL.
<pre>
$ DEL myfile.txt; !Delete the most recent version of myfile.txt.
$ DEL myfile.txt;* !Delete all versions of myfile.txt.
$ HELP DELETE !More information on the DELETE command.
</pre>
[[Image:Bones2.jpg|20px]] Warning: Extreme caution!
<pre>
$ DEL *.*;* !Delete everything in the current directory!
</pre>

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===How to create a directory===
Use the CREATE/DIR command.
<pre>
$ CREATE/DIR [.subdir] !Creates a subdirectory named subdir.dir in the current directory.
$ CREATE/DIR disk:[dir.subdir] !Creates the subdirectory subdir at the specified path.
</pre>

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===How to rename files and directories===
Use the RENAME command.
<pre>
$ SET FILE/PROTECTION=O:RWED olddir.dir !Sets protections so you can rename the directory.
$ RENAME oldfile.ext newfile.ext !Renames oldfile.ext to newfile.ext.
</pre>

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===How to check the queue===
Use the SHOW QUEUE command, which may be abbreviated to SH QUE.
<pre>
$ SHOW QUEUE !Shows all the queues, there are many!
$ SH QUE *FAST !Shows all queues whose names end with "fast", these are used for evaluations.
$ SH QUE *SLOW !Shows all queues whose names end with "slow", these are used for reconstructions.
$ SH QUE *FAST/ALL !By default you are only shown queue entries for the user you are logged in as. To show jobs for all users, use the /ALL qualifier.
$ SH QUE *FAST/BY=EXE/ALL !Show only jobs that are currently executing for all users.
</pre>

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===How to get queue information===
Use the SHOW ENTRY command to obtain information about batch jobs in the queues.
<pre>
$ SHOW ENTRY !Shows all the batch jobs for your user, there may be lots!
$ SHOW ENTRY 251 !Shows information for batch job number 251.
$ SHOW ENTRY 251/FULL !Shows detailed information for batch job number 251.
$ SHOW ENTRY/ALL !Shows all the batch jobs for all users.
</pre>

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=Micro-Computed Tomography (µCT) Basics=

==User Tutorials==
For Scanco MicroCT Systems and Software:
:*[[Media:Microct-v14.pdf | '''Scanco MicroCT Systems and Software''']]

For XtremeCT II and I:
:*[[Media:SOP Berlin V1.0.pdf | '''Scanco XtremeCT I SOP (Berlin)''']]
:*[[Media:XtremectIIB-v4-us.pdf | '''Scanco XtremeCT II Specs''']]

For MicroCT35, VivaCT40 and VivaCT80:
:*[[Media:ScancoMicro-CT_User_Policy_Guidelines_19052005.pdf| '''MicroCT User Policy & Guidelines''']]
:*[[Media:MicroCT_Starter_Package.pdf | '''MicroCT Starter Package''']] and its [[Media:Microctstarterpackagejun2012.docx| '''Word format''']].
:*[[Media:Scanco-training-uct35-and-vivact40.pdf | '''MicroCT Customer Training Guide''']]
:*[[Media:Vivact_80_v3-nomarks.pdf | '''VivaCT 80 Specifications''']]

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==Micro-CT Image Basics==
Computed tomography is a non-destructive x-ray imaging modality that enables three-dimensional (3D) virtual models of an object to be created, which can be subsequently visualized and analyzed. Micro-CT refers to CT in which the [http://www.scanco.ch/index.php?id=faq_general#c779 resolution] lies in the micro-scale, which is achieved with a high-resolution x-ray detector and a field of view that is much smaller than conventional CT. Structural detail provided by CT depends on differences in x-ray attenuation properties. Components with very different x-ray attenuation properties, for example air, soft tissue, and bone, can be differentiated in a CT scans whereas different types of soft tissues, for example muscle and cartilage, do not have sufficient differences in attenuation to be distinguish.

===Dark Field===
Detector response with x-rays off. Enables corrections of non-uniformities of the detector. Acquired automatically by the scanning software before each scan.

[[File:Dark_field_single.img_assist_custom-400x97.jpg|400px]]

===Bright Field===
Detector response with x-rays on but no sample. Enables corrections of non-uniformities of the x-ray beam. Acquired automatically by the scanning software before each scan.

[[File:Bright_field_single.jpg|400px]]

===Raw Projection===
A raw x-ray projection of a mouse leg. The darker regions correspond with higher x-ray attenuation. The discontinuities result from overlaps where the detector was shifted to acquire the large region of interest (3x2 detector frames in this example). Projections are acquired at many incremental rotations around the sample.

[[File:Raw_projection_notes.jpg|400px]]

===Sinogram===
The sinogram is a different representation of the projection data. The sinogram represents the attenuation values of one row of the detector at each rotational increment around the sample.

[[File:Sinogram.jpg|400px]]

===Attenuation Projection===
Accounting for the inhomogeneities of the detector and beam, we can calculate the x-ray attenuation caused by the sample. Bright regions correspond with higher attenuation.

[[File:Attenuation_projection.jpg|400px]]

===Reconstructed Image===
From the attenuation projections, the original structure can be calculate using filtered back projection.

*[https://youtu.be/DBLYSETYbe8 CT Back-projection Reconstruction]
*[https://youtu.be/NWeM35_KR2w CT Reconstruction of a Head]

[[File:Reconstruction_xy_yz_planes.jpg|400px]]

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==Image Data==
===Image Data Type===
====Binary Images====
Binary images are images whose pixels contain only two possible intensity values (off-on, or black-white B&W). The off or black value is usually 0 and the on or white value is usually 1 (1-bit pixel) or 255 (8-bit pixel). This type of image is commonly used as a multiplier to mask regions within another image.

====Grayscale Images====
Grayscale images represent intensities. Pixels range from least intense (black) to most intense (white). Pixel values usually range from 0 to 255 or are scaled to this range when displayed.

====Indexed Images====
An indexed image uses direct mapping of pixel values to colormap values. Instead of intensities, a pixel value within an indexed image relates to a color value within a color lookup table. An indexed image consists of a data matrix and a colormap matrix. The data matrix can be of class uint8, uint16, or double. The colormap matrix is an m-by-3 array of class double containing floating-point values in the range [0,1]. Each row of map specifies the red, green, and blue components of a single color. Since indexed images reference color tables composed of up to 256 colors, the data values of these images are usually scaled to range from 0 to 255.

====RGB Images====
Within the three-dimensional array of an RGB image, two of the dimensions specify the location of a pixel within an image. The other dimension specifies the color of each pixel. The color dimension always has a size of 3 and is composed of the red, green, and blue color bands (channels) of the image.

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===Image Data Pixel Values===
The image data type is determined by the pixel depth in bits per channel, or bit depth. Bit depth for each channel can be 8, 16, 32 or 64. The data may be signed, unsigned (u), floating-point (f), real or complex (c) for some arithmetic functions, where each channel value is represented by two numbers: real and imaginary part. All channels in an image must have the same data type.

{| class="wikitable"
|-
! scope="col"| Image Data Type
! scope="col"| Name
! scope="col"| Byte
! scope="col"| Value Range
! scope='col'| Comments
|-
! scope="row"| char
| 8-bit signed integer
| 1
| -128 ~ 127
| Scanco SEG.AIM, GOBJ
|-
! scope="row"| uchar
| 8-bit unsigned integer
| 1
| 0 ~ 255
|
|-
! scope="row"| int
| 16-bit signed integer
| 2
| −32768 ~ 32767
| Scanco grey-scaled images, ISQ, AIM
|-
! scope="row"| uint
| 16-bit unsigned integer
| 2
| 0 ~ 65535
| Converted format of Scanco grey-scaled images
|-
! scope="row"| long
| 32-bit signed integer
| 4
| −2^31 ~ 2^31 - 1
|
|-
! scope="row"| ulong
| 32-bit unsigned integer
| 4
| 0 ~ 2^32 - 1
|
|-
! scope="row"| float
| floating point
| 4
| ±3.40282347 E+38
| 32-bit single-precision with 6~7 significant digits
|-
! scope="row"| long64
| 64-bit signed integer
| 8
| −2^63 ~ 2^63 - 1
|
|-
! scope="row"| ulong64
| 64-bit unsigned integer
| 8
| 0 ~ 2^64 - 1
|
|-
! scope="row"| double
| double precision floating point
| 8
| ±1.79769313486231570 E+308
| 64-bit double-precision with 15~16 significant digits
|-
! scope="row"| complex
| floating point complex
| 8
| same as floating-point
| same as floating-point
|-
! scope="row"| dcomplex
| double precision complex
| 16
| same as double-precision
| same as double-precision
|}

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===Scanco Image File Types===

{| class="wikitable"
! scope="col"| Extension
! scope="col", style="width: 65%"| Description
! scope="col"| Creation
! scope="col"| Opens with
|-
! scope="row"| RSQ
| '''R'''aw '''S'''e'''Q'''uence data. This is the raw data collected after the scan. This file contains the bright and dark field corrections and the raw projections. || created with scan || $ x
|-
! scope="row"| ISQ
| '''I'''mage '''S'''e'''Q'''uence data. This is the reconstructed 3D image, which you see in the µCT Evaluation Program. || created from RSQ
| $ uct_evaluation
$ x
|-
! scope="row"| AIM
| '''A'''ny '''IM'''age data. This is a binary raw data format (16-bit signed data, little endian) 3D discretized data you see using the µCT Ray Program and used for the analysis. The AIM file is a volume of interest isolated from the ISQ file. || extracted from ISQ
|$ uct_3d
$ uct_evaluation
|-
! scope="row"| GOBJ
| '''G'''raphical '''OBJ'''ect data. These are the green contours in the µCT Evaluation Program, which are used to isolate regions of interest from an AIM file for analysis. || extracted from ISQ/AIM || $ uct_evaluation
|-
! scope="row"| SCV
| '''SC'''out '''V'''iew || created with scan || $ x
|-
! scope="row"| RAD
| Scout View || created with scan || $ x
|-
! scope="row"| RSW
| raw data (RSQ) || created with scan || $ x
|-
! scope="row"| IMA
| image data (AIM, ISQ, GOBJ)|| created from RSQ || $ uct_evaluation
|}
*Refer to [[Media:Aimpack_documentation.pdf|'''Scanco Aim Format''' ]] or its [[Media:Scanco_Aim_File_Format.doc|'''Doc Format''']] for its header info.

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==Scanco Medical Micro-CT Software==
In the bottom left hand corner of the micro-CT workstation desktop is the micro-CT control panel, from which the micro-CT programs can be launched. The standard operating procedure for scanning a samples involves proceeding through the programs in the control panel from left to right:
<pre>
$ UCT_SAMPLE !Samples: Registering a sample
$ UCT_MEASUREMENT !Tomography: Scanning
$ UCT_EVALUATION !Evaluation: Evaluating the scan
$ UCT_3D !Ray: Viewing the 3D scan
$ UCT_BACKUP !Disk-Utility: Archiving the data
</pre>
You must specify an operator in the control panel to use the scanning and evaluation programs.
* XtremeCT
[[File:XCTcontrol_panel.img_assist_custom-302x100.jpg|300px]]
* MicroCT35, VivaCT40 and VivaCT80
[[File:Uct35_control_panel.jpg|300px]]
[[File:VivaCT40_control_panel.jpg|300px]]
[[File:VivaCT80_control_panel.jpg|300px]]

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===µCT Samples===
The µCT-Samples program is used to register new samples to be scanned and update sample names (e.g., to correct a sample name). To start the program type <code>$ uct_sample</code> in a DEC terminal, or use the sample button.

[[File:Xtremect_button_samples.jpg|40px]]
[[File:Uct_sample_uct35.jpg|40px]]
[[File:Uct_sample_vivact40.jpg|40px]]

#'''Prepare Sample Names''' according to [[Scanco_User_Instructions#Sample_Name_Convention|'''Sample Name Convention''']]
#'''Register Sample Names'''
#*Create a new sample by clicking “New” and typing in your sample name where it says “Name.” “Save” the sample.
#*You are now given a sample number. Record the sample number on the log sheet.
#:[[File:Uct_sample_pic01.jpg|500px]]
#'''Create Additional Sample Names Using Copy and Paste'''
#*If you have many samples to register, you can copy and paste part of the sample name you just created. Highlight the part of the sample name you want to copy by holding down the left mouse button while dragging the mouse, then release the mouse button.
#:[[File:Uct_sample_pic02.jpg|500px]]
#*Paste the highlighted text into a DEC terminal by pressing the middle mouse button. Now highlight the text in the DEC term.
#:[[File:Uct_sample_pic03.jpg|300px]]
#*Go back to the µCT-sample window, click "New", and paste the information next to "Name" using the middle mouse button. Update the name as required and "Save."
#'''Add Additional Sample Details'''
#*When a patient comes in for their first scan, you need to update their sample with their date of birth, sex, and hand/foot dominance.
#*Use the "Find..." button to search for a sample that has already been registered. You can search by sample number or by project name (e.g., CAMOS).
#*Date of birth: DD/MMM/YYYY. Example: 14/JAN/1951
#*Remarks: include the sex and hand/foot dominance. Example: F-RHRF for female that is right hand dominant and right foot dominant

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===µCT Tomography===
The µCT-Tomography program is used to perform a scan.

NOTE: Only Authorized Operators are permitted to use uCT or XtremeCT scanners. For the XtremeCT scanners, this is a formal process. To inquire about authorization, speak to your supervisor. The below description is intended to provide general understanding of how scans are acquired. It is not a substitute for complete training.

To start the program type <code>$ uct_measurement</code> in a DEC terminal on the scanner computer (remote access does not allow this functionality), or use the scanner button. If you use the button, you must specify an operator prior to using the program.

[[File:Xtremect_button_scan.jpg|40px]]
[[File:Uct_measurement_uct35.jpg|40px]]
[[File:Uct_measurement_vivact40.jpg|40px]]
[[File:VivaCT80_scan.jpg|40px]]

[[File:Uct_tomography_pic00.jpg|600px]]

#'''Select Sample'''
#*When the µCT-Tomography program is first started, you will be prompted to enter the sample name or number of the specimen you are about to scan.
#*If you have not registered your sample, press "Cancel" to close the select sample box, then press "New..." in the measurement sample box to register a new sample (see [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT-Samples''']]).
#*Once you have entered your sample information, the measurement sample box will show details for that sample, including the sample name and scan (measurement) history.
#:[[File:Uct_tomography_pic01.jpg|400px]]
#*After your first scan you will need to press the "Other..." button to open the sample selection box and find your next sample.
#'''Select a Controlfile'''
#*The controlfile contains scan parameters such as the x-ray energy, current, and more (see [[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29 controlfiles |'''Controlfiles''']]).
#*Once the controlfile is setup, you need only to select it. If there are many controlfiles, you may want to search for yours using the file filter by entering part of the name or number in the white box and pressing enter; if you do this, you still must click on the controlfile so that it is highlighted in black as shown below.
#:[[File:Uct_tomography_pic02.jpg|400px]]
#'''Precalibrate'''
#*Calibrations are done before loading your patient/animal and scanning for quality control and to reduce the time the patient/animal is under preparation/anaesthesia. Start the calibration by pressing the "Precalibrate" button.
#:[[File:Uct_tomography_pic03.jpg|400px]]
#*Press "Start Calibration". The calibration will start with an "X-Ray Warmup", followed by "Measuring Dark" and "Measuring I0" and usually takes about 2-3 minutes to complete.
#:[[File:Precalibrate.jpg|300px]]
#*The precalibration is good for 15~20 min. The time remaining is shown on the "Precalibrate" button.
#:[[File:Uct_tomography_pic5.jpg|400px]]
#*The precalibrate option cannot be used with batch measurements, and it's not available for MicroCT35 which is not intended for invivo/live scan.
#'''Load and Position the Patient/Sample'''
#*Instruct the patient to remove any jewelry in the scan areas (wrist/ankle/knee/elbow ect). With the patient seated, put the wrist/ankle/knee/elbow into the appropriate cast. Different pads with different sizes can be used to fit the patient.
#*For invivo/invitro samples, prepare your sample in terms of orientation, immobilization, hydration ect.
#*After the precalibration is complete, you can now open the bore cover and insert the patient's wrist/ankle/knee/elbow or sample into the scanner. Gently move the wrist/ankle/knee/elbow or sample into the scanner until you can snap in the cast at the gantry. Check that the cast is positioned correctly and the patient/sample is comfortable.
#*Close the bore cover.
#'''Scout-View'''
#*A scout-view is similar to a 2D x-ray image and allows the user to set where to start and stop the scan.
#*After loading your sample, press the "Scout-View..." button to bring up the scout-view window.
#*The start position (top of the scanner) and end position (bottom of the scanner) can be modified to zoom in on the region of interest.
#*The angle of the scout view can also be changed to see the object in a different orientation.
#*Once pressed the "Scout-View" button but the scout view is found not in an appropriate position, press "Cancel", modify the start position, end position, or angle and press "Scout-View" again.
#:[[File:Scout_view_window.jpg|400px]]
#*Scout view image is displayed in the top right hand corner of the program and will start by showing the right half of the image, followed by the left half of the image.
#'''Set Reference Line and Launch a Scan'''
#*A reference line (solid green line) is placed to set the scan region (green block).
#*Press the "Reference-Line" button to show the reference line and default scan region over the scout view.
#*To change the number of slices to scan, move the reference line to the top of the scan region, then hold down the shift button while dragging the mouse to extend the scan region and press the left mouse button to set the reference line.
#*To centre the scan region between two reference lines, move the reference line to the top of the scan region, then hold down the alt key while dragging the mouse until the second green reference line is in place, then press the left mouse button to set while still holding down the alt key!
#:[[File:Uct_tomography_pic06.jpg|700px]]
#*For a single scan, select "OK", "Scan" and "Start Measurement". Record measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']].
#*For a batch scan which is only available on microCTs, select "Batch Measurement" and record the measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']]. You may now setup a new scan (select new sample and controlfile, perform scout, etc). When you have finished setting up all scans, press "Start Batch Scans." (See [[Scanco_User_Instructions&action=edit&section=48#Perform_Batch_Scans|'''Perform Batch Scans''']] for detailed instructions)
#'''Cancel or Reposition a Scan'''
#*If you need to interrupt a scan, press the cancel button and restart the scan or if you do not want to rescan then "unload" the scanner.
#*If you have not started a scan and need to reposition the patient, you also must "unload" the scanner.
#'''Remove Patient/Sample from Scanner'''
#*After the scanning is complete, open the bore cover and slide the patient's wrist/ankle/knee/elbow or sample out of the scanner. Release the cast by pushing down the cast release handle.

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===µCT Evaluation Program===
The µCT Evaluation Program is used to evaluate a scan. To start the program type <code>$ uct_evaluation</code> in a DEC terminal, or use the graph button. If you use the button, you must specify an operator prior to using the program.

[[File:Uct_evaluation.jpg|40px]]

'''SCREEN SHOT TO BE ADDED SHORTLY'''

#'''Find Your Sample'''
#:Enter the first part of your sample name in the file filter box and press enter. The samples are shown in the left hand box. The measurement box on the right shows scans for the selected sample (highlighted in black). Select a measurement and press "OK."
'''SCREEN SHOT TO BE ADDED SHORTLY'''
#'''Draw Contours (If Applicable)'''
#*Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
#*Contours must always be drawn COUNTER-CLOCKWISE!!!
#*[[Media:Contouring-tools.pdf |'''Contouring tools reference sheet''']]
#*For this sample, we are only interested in viewing the object in 3D and drew contours to isolate the bone and soft tissue from the sample tube.
#:[[File:Uct evaluation pic03.jpg|600px]]
#'''Evaluate'''
#*Scanco Medical provides several standard evaluation scripts. Open the 3D-Evaluation menu either using the "T..." button or from the top menu by going to "Tasks" and "Evaluation 3D...". If you set a default evaluation script in your scanning controlfile, it will be listed under "Task/Evaluation."
#:[[File:Uct_evaluation_pic04.jpg|400px]]
#*If you want to run a different evaluation press "Select...", highlight the evaluation script of interest, and press "OK".
#:[[File:Uct_evaluation_pic05.jpg|400px]]
#*When the 3D-Evaluation window is activated, a white box will appear on your reconstructed image. The white box is the region of interest that will be "cut out" of the full scan. If you have drawn contours, the white box will automatically be adjusted to fit the contours. Adjust the box if necessary by grabbing one of the white handles; use the left mouse button to move the box and the right mouse button to resize. The box can also be resized using the "VOI Start" and "Dimensions" in the 3D-Evaluation window.
#*For most evaluation scripts, you will be required to specify parameters for a Gaussian filter, to reduce noise, and a threshold, to isolate your object (e.g., bone) from the background. Check that the parameters used provide a good representation of your scanned sample by flipping back and forth between the segmented and grayscale image using the "Preview" and "Grayscale" buttons.
#:[[File:Uct_evaluation_pic06.jpg|400px]]
#*When you are satisfied with the segmentation parameters, press "Start Evaluation", which will submit the job to the queue.

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===µCT Ray===
The µCT Ray program is used to view scanned objects in 3D, create images, and create image sequences for animations. To start the program type <code>$ uct_3d</code> in a DEC terminal, or use the 3D object button.

[[File:Uct_3d.jpg|40px]]

'''SCREEN SHOT TO BE ADDED SHORTLY'''

#'''Select and Render Your Sample'''
#*'''Select:''' If you have used the default Scanco Medical scripts, then
#:*If your data is on the "data disk" and you can search for your files using the file filter to select a sample and measurement then press "OK". To open a new file, File --> Open.
#:*If your data is not in the standard location (e.g., it was copied to the projects disk), then use File --> Read and navigate to find the file to open.
#:*Alternatively you can start the program with a file to open <code>$ uct_3d myfile_seg.aim</code>
#: 
#*'''Rendering:'''
#:*Use a single click of the left mouse button to start or to stop rendering the sample.
#:*You can also use the "Start" and "Stop" buttons at the bottom of the options on the left.
#:*You must stop rendering to change viewing options on the left.
#: 
#*'''Change View:'''
#:*To adjust the view, move the "Rotation" and "Elevation" slider bars in the options on the left.
#:*The slider bar is located above its label.
#:[[File:Uct_3d_pic02.jpg|600px]]
#: 
#*'''Change Colours''' (Object and Background):
#:*From the top menu choose "Options" then "Object/Display Properties...".
#:*A segmented image typically only has two values, 0 (black, background) and 127 (white, object). To change the colour of the object only, we need to set the value 127 to a specific colour.
#:*In this example, the slider bar value "1" corresponds with the value 127 and we will set both slider bars to "1" so that we are adjusting values "127 ... 127", in other words, only value "127".
#:*Under "Surface" click on the "white box" to open the "Color Mixing" window.
#:*Choose the new colour for the object (e.g., orange) and press "OK."
#:*Close the "Object Properties" window or move it to the side.
#:*Now re-render the object with a single click of the left mouse button.
#:[[File:Uct_3d_pic03.jpg|300px]] [[File:Uct_3d_pic04.jpg|300px]]
#: 
#*'''Cutplane (left options) and Subdim (top menu):''' 
#:*The cutplane and subdim functions allow you to show a cross-section of your object.
#:*The subdim function tends to work better than the cutplane but is limited to axes of the scan.
#:[[File:Uct_3d_pic05.jpg|600px]]
#: 
#'''Print an Image to File'''
#*An image must be fully rendered in order to be saved.
#*From the top menu choose "File" then "Print". Set the print format to "TIFF" and the directory to "Scratch/Temp" (or another location using the "Specify in Filename" option).
#*Change the filename to something meaningful then press "OK."
#:[[File:Uct_3d_pic06.jpg|300px]]
#: 
#'''Auto-Print Images for an Animation'''
#*Creating an animation involves saving a sequence of rendered images, which can then be compiled into an animated GIF or other video format using various software packages (e.g., Photoshop, Quicktime Pro).
#*From the top menu choose "Options" and "Animation..." to open the Animation Settings window. Set the viewing parameters for the start of the animation, fully render the image, then press the "Get Settings A" button.
#*Set the parameters for the end of the animation, fully render the image, then press the "Get Settings B" button.
#*Set the number of frames you want, the higher the number frames, the smoother the animation will be, but also the larger the file size.
#*Now setup the auto-print feature. From the top menu choose "File", then "Print". Choose "TIFF" for the print format, and the "Scratch/Temp" for the directory (or use the "Specify in Filename"). Specify a filename prefix, to which numbers will be appended for the image sequence.
#*Activate the "Auto-Print" feature. Press "OK" then press the "Start Calculation" button on the Animation Settings window.
#*Do not interrupt the program while the frames are being rendered and saved. When the program is done rendering all the frames, transfer them to your computer to compile into an animation.
#:[[File:Uct_3d_pic07.jpg|200px]] [[File:Uct_3d_pic08.jpg|300px]]

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===XImage===
The XImage program is used to view the raw data (RSQ file) and scout view. To start the program type <code>$ run um:ximage</code> or <code>$ x </code>in a DEC terminal.

When loading an RSQ, the default view (XY plane) is of the sinogram.

[[File:Ximage_1.jpg|600px]]

To view the attenuations, choose the XZ plane. The first slice in this orientation is the dark field, the second slice is the bright field , and slices three and onward are the raw projections (attenuations).

[[File:Ximage_2.jpg|600px]]

To view the corrected projections, from the Evaluations menu, choose Projection Mode.

[[File:Ximage_3.jpg|400px]]

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=Scanning=
==Sample Name Convention==
*At the Bone Imaging Laboratory, all sample naming must conform to the following format
:'''PROJECT IDENTIFIER _ SAMPLE DETAILS'''
*In CAPITAL LETTERS (filenames are case sensitive, so this makes it easy to remember how you input your sample name)
*No special characters (spaces, /, %, etc.) as further evaluations will not work if spaces are present.
:Examples: CAMOS_771, TESTS_0001, TESTS_0002, TESTS_0003

==Register Samples for Scanning==
*Although samples can be registered immediately prior to a scan, it is much more efficient to register all your samples beforehand.
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT Samples''']] for instructional details.

==Log Sheets==
*Log sheets are used to record important information about scans that are performed, such as sample and measurement numbers ect.
*Log sheets are to remain in the lab. If you would like a copy of your log sheets, please make a photocopy or print two copies to record the scan information.
*Use the PDF file to print blank log sheets. Use the Excel file to make your own custom log sheet.

#Bone Lab for General Patients
#*[[Media:XCT_II_Log_(Studies).pdf|'''XCT II Log Sheet for Studies''']]
#*[[Media:XCT_II_Log_(Miscellaneous).pdf|'''XCT II Log Sheet for Miscellaneous''']]
#MicroCT Lab for General Non-Patients
#*[[Media:UCT_log_sheet_general.pdf|'''MicroCT Log Sheet for Studies (PDF)''']]
#*[[Media:UCT_log_sheet_general.xlsx|'''MicroCT Log Sheet for Studies (Excel)''']]

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==Patient Casts and Sample Holders==
===Patient Casts for XtremeCTs===
Regardless of what cast is used, the X-, Y-, and Z- dimensions remain the same:
*X=14cm
*Y=14cm
*Z=designated 20cm distance in the scanner

Standard Scanco Distal Radius Cast
*Used for distal radius scans of 1-3 stacks. Designed with the hand to be in a curved position. The field-of-view allows for scanning of approximately the most distal 1/4 of the forearm.
Standard Scanco Distal Tibia Cast
*Used for distal tibia scans of 1+ stacks. Designed with the foot to be in a flexed (upright) position. The field-of-view allows for scanning of approximately the most distal 1/4 of the tibia.
Standard Scanco Sample Holder
*This is a cylindrical tube with a cut-out window on the top.
*Allows for scanning small ex-vivo and other samples. The tube provides support for the sample during scanning.
*Also used for in-vivo scans of the hand along with a platform that conforms to the hand and slides into the tube.
Elbow Holder
*Used for scans of the elbow. Designed to support the forearm during scanning.
Knee Holder
*A long cylinder cast cut in half lengthwise and with a foot holder at the end. This cast is designed to slide over the gantry tongue, placing the leg further into the gantry, in order to scan at distances closer to the core of the body.
*Used for distal femur and proximal tibia (i.e. knee) scans.
*Used for mid-shaft tibia scans.
*Used for larger ex-vivo and other samples.

===Sample Holders and Scan SOP for microCTs===
====Ex Vivo Sample Holders====
*Ex vivo and inanimate samples are scanned in sample holder tubes. These tubes come in a variety of diameters. It is extremely important that the tube diameter corresponds to, or is smaller than, the field of view (FOV) set in your scanning control file.

*Biological tissues should be hydrated and wrapped in plastic wrap to prevent drying of the sample. Your sample should then be secured in the sample holder using foam to prevent it from shifting around during scanning, which would lead to poor image quality.

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=====Chemical Resistivity of Sample Holders=====
*White tube sample holders are made of PMMA (poly-methyl-methacrylate).
*Yellow tube samples holders are made of PEI (poly-ether-imide).
*Use the yellow tubes if you will need to disinfect the sample holder after scanning.

{| class="wikitable"
!colspan="3"|Thermal and chemical compatibility of sample holders
|-
! scope="col"| Properties
! scope="col"| White Tubes (PMMA)
! scope="col"| Yellow Tubes (PEI)
|-
! scope="row"| Max. Temperature
| +85°C
| +170°C
|-
! scope="row"| Sterilization Steam Autoclave
|non resistant
|resistant (138°C for 20 Min. at 1 bar)
|-
! scope="row"| Water
|resistant
|resistant
|-
! scope="row"| Inorganic Acids
|limited resistance
|resistant
|-
! scope="row"| Inorganic Bases
|non resistant
|limited resistance
|-
! scope="row"| Aldehydes (Formaldehyde)
|limited resistance only in diluted form
|resistant
|-
! scope="row"| Alcohols
|limited resistance
|resistant
|-
! scope="row"| Bleach
|non resistant
|resistant
|}

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=====Mounting of Sample Holders=====
[[File:Uct35_holder.jpg|thumb|right|100px|µCT35 setup]]
*The spindle (metal bit) of the sample holder has a slot, which must be aligned in the scanner or adapter plate.
*The sample holder sits vertically in the µCT35 while horizontally in the VivaCT80 and VivaCT40.
*For the vivaCT40, attach the adapter plate for the tube sample holders to one of the animal bed. The tube sample holders are held horizontally in the vivaCT 40.
:[[File:Vivact40_holder.jpg|thumb|none|700px|VivaCT40 setup]]

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=====Ex vivo rodent scanning SOP=====
*Refer to [[Media:Ex_vivo_scan_sop.pdf|'''Ex Vivo Rodent Scanning''']] for its scan SOP.
*Refer to [[Media:Ex_vivo_scan_sop.docx|'''Ex Vivo Rodent Scanning in docx''']] for its Word version.

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====In Vivo Sample Fixtures and Anesthetic System====
*[[Media:VivaCT40_Anaesthetic_System.pdf |'''Anaesthetic System''']] : You must receive training to use the anaesthetic system.
*[[Media:VivaCT40_Mouse_and_Rat_Tibia_Fixture.pdf |'''Mouse/Rat Tibia Fixture''']]
*[[Media:VivaCT40_Mouse_Lower_Body_Fixture.pdf|'''Mouse Lower Body Fixture''']]
*[[Media:VivaCT40_Mouse_Whole_Body_Tube.pdf|'''Mouse Whole Body Tube''']]

=====In vivo rodent scanning SOP=====
*Refer to [[Media:In_vivo_scan_sop.pdf|'''In vivo rodent scanning''']] for its scan SOP.
*Refer to [[Media:In_vivo_scan_sop.docx|'''In vivo rodent scanning in docx''']] for its Word version.

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====Align whole body device in FOV====

It's important to have your whole sample in the field of view for accurate density measurements.
* Refer to [[Media:wholebody.pdf |'''Align the device''']] for detailed instructions.

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==Scan Parameters (Controlfiles)==

:{| class="wikitable" style="text-align:center;"
|-
! scope="row"| Manufacturer
| colspan="5"|[http://www.scanco.ch '''Scanco Medical AG''']
| [https://www.zeiss.com/microscopy/int/products/x-ray-microscopy.html '''Carl Zeiss X-ray Microscopy''']
|-
! scope="col" rowspan="2"| Model
! scope="col"| XtremeCT II || XtremeCT I || VivaCT80 || VivaCT40 || µCT35 || Xradia 520 Versa
|-
|[[File:XtremeCT.jpg|150px]]
|[[File:XtremeCT.jpg|150px]]
|[[File:VivaCT80.jpg|120px]]
|[[File:VivaCT40.jpg|135px]]
|[[File:UCT35.JPG|150px]]
|[[File:Xradia-520-versa-small.jpg|160px]]
|-
! scope="row"| Application
|colspan="2"| Clinical studies for human extremities in vivo
Horizontal static patient setup
|colspan="2"| Preclinical in vivo animal studies
Horizontal static animal setup
|colspan="2"| High resolution ex vivo specimen scans
Vertical rotational sample setup
|-
! scope="row"| E (KVp)
| 68 || 60
|colspan="3"| 45, 55, 70
| 30 ~ 160
|-
! scope="row"| Power (W)
| 100 || 54
|colspan="3"| 4, 8
|4 ~ 10
|-
! scope="row"| Filter
| Fixed 0.2mm Cu + 1mm Al
(Equivalent 6.7mm Al)
| Fixed 0.1mm Cu + 0.6mm Al
| Default 0.5mm Al,
Air, 0.1mm Al, 0. mm Cu
| Fixed 0.5mm Al
| Fixed 0.5mm Al
| Air, LE1~LE6, HE1~HE6,
customizable filter
|-
! scope="row"| FOV (⌀ * L) (mm^2)
| 140 ⌀ * 200 L
| 126 ⌀ * 150 L
| 31.9 ~ 80 ⌀ * 145 L
| 21.5 ~ 38.9 ⌀ * 148 L
| 7.2 ~ 38 ⌀ * 140 L
(75 L standard)
| 90 ⌀ * 100 L
|-
! scope="row"| Image Matrix
| 4608*4608 ~ 512*512
| 3072*3072 ~ 512*512
| 4096*4096 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
|-
! scope="row"| Voxel Size (µm)
| Standard 60.7
(30.3 ~ 273.4)
| Standard 82.0
(41.0 ~ 246.0)
| 5 ~ 156
| 10.5 ~ 76
| 3.5 ~ 74
| 0.7 ~ 50
|-
! scope="row"| Sample Image
|[[File:XCT2_human_distal_femur.png|160px]]
human distal femur
|[[File:XCT1_human_distal_tibia.JPG|160px]]
human distal tibia
|[[File:VivaCT80_Rat_distal_femur.JPG|160px]]
rat distal femur
|[[File:Vivact40_in-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Uct35_ex-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Xradia_mouse_distal_femur.png|160px]]
mouse distal femur
|}

Controlfiles are used to specify the parameters for the scans. Once your controlfile is setup, you should not modify it over the course of your project.

[[File:XCT2 ControlFile.JPG|right|600px]]

*'''Control File Name''': Specify a meaningful name so that others can reuse yours.

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===General Settings===
*'''Holder Type''': Choose the used holder type for XtremeCT II from Standard Casts, Knee Cast and Elbow Cast. No option for XtremeCT I scanner. For microCTs, Choose the used sample holder type with the correct diameter.

*'''Mode of operation''': Default is continuous operation for all scanners. Gated operation mode is available for VivaCT80 and VivaCT40 scanners.

*'''Evaluation Script''': This sets the default evaluation script used for the analysis. You can manually select a different script from the evaluation program.

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===X-ray Settings===
*'''Tube Energy (KVp)''': Fixed energy for XtremeCTs while having 3 options for each of microCTs: Use the 70 KVp for most samples, use the 55 or 45 KVp for low density objects (e.g., soft tissue) or specimens with a diameter less than 20 mm. Lower energies provide better contrast while higher energies provide better signal to noise (SNR).

*'''Tube Current (µA)''': Fixed current for XtremeCTs while having 2 options for each of energy settings of each microCTs: Use the higher current except when the voxel size is set for the best resolution of the scanner. The higher current will yield better SNR but a larger spot size.

:{| class="wikitable" style="text-align:center;"
|-
! scope="col"|
! scope="col"| XtremeCT II
! scope="col"| XtremeCT I
! colspan="3"| vivaCT80，vivaCT40， µCT35
|-
! scope="row"| E (KVp)
| 68
| 60
| 70
| 55
| 45
|-
! scope="row"| I (µA)
| 1470
| 900
| 114, 57
| 145, 72
| 177, 88
|-
! scope="row"| Power (W)
| 100
| 54
|colspan="3"| 8, 4
|}

*'''Filter''': Fixed filter settings for all scanners except VivaCT 80 has 4 filter options.

*'''Calibration''': This sets the mu scaling factor, density and beam hardening correction used for the reconstruction. For standard patient scans use 200 mg HA/cm3. For ex vivo bone scans, use 1200 mg HA/cm3, for soft tissue use the plexi scaling, and for non-biological tissues use the aluminum scaling.

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===Scout-View Settings===
Normally you will want to enable this and here you can specify the default start and end position, and scout-view angle, which you may override for each scan.

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===CT Scan Settings===

*'''Resolution''': This setting includes the reconstruction matrix size (2048x2048, 1536x1536, 1024x1024, or 512x512) and the number of projections per 180°. The lower the resolution setting, the better the SNR and larger the voxel size.

*'''FOV / Diameter''': This field of view must fully contain the sample holder for accurate density measurements. Fixed FOV for XtremeCTs while having 5 options for each of microCTs: If you choose a smaller FOV than the sample holder, the scan may be aborted to prevent damage to the scanner. For the best resolution, you should choose the smallest holder that contains your sample.

*'''Voxel Size''': The nominal isotropic voxel size is determined by the FOV and the reconstruction matrix.

*'''Number of Slices''': You can specify a specific number of slices or image stacks to acquire (1x110 = 1 image stacks of 110 slices). The scan time increases with each image stack, therefore pay attention to the stack boundaries (e.g., 111 slices will take 2x longer to scan than 110 slices).

*'''Rel Position of First Slice''': This option enables you to offset the scan region from the reference line. This is useful for scanning a region a specific distance from the growth plate or centering the scan region around the reference line. If you disable the scout view, then the position is relative to the absolute 0 position of the scanner (top of the sample holder for the µCT35 and towards the back of the scanner for the vivaCT40).

*'''Integration Time''': The higher the integration time, the better the SNR and longer the scan time. Use 100 ms for patient scans and higher values for ex vivo scans of better image quality. To get the highest integration time, uncheck the "Continuous ROT" button. For standard microCT measurements, use ~400 ms for the µCT35 and ~200 ms for the vivaCT40. The maximum integration time is scanner-specific and limited to prevent saturation of its detector.

*'''Average Data''': This is often referred to as frame averaging and is used to improve a scan's SNR. Multiply the average data value by the integration time to calculate the effective integration time. Only use this if the integration time is maxed out.

*'''Measurement Time''': This is the estimated scan time without the time performing the scout view or warm-up of the scanner.

*'''CTDIvol''': Computed Tomography Dose Index (CTDI) is a standardized measure of radiation dose output of a CT scanner for scanner settings' comparison purposes only, and it represents the average absorbed dose along the longitudinal axis from a series of contiguous CT exposures. Volumetric CTDI is the ratio of the weighted-CTDI to the level of overlap between slices (pitch). CTDIvol has no consideration of real scan length and does not represent actual dose administered to the patient.
:[[File:CTDI.JPG|600px]]

*'''DLP''': Dose Length Product DLP = CTDIvol * Scan Length in unit of mGy-cm.

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====XtremeCT II Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 4608
| 2304
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 3000
| 900
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 140 mm
| 30.3
| 60.7
| 91.1
| 136.7
| 273.4
|-
! colspan="2"| Slices/Stack
| 338
| 168
| 112
| 74
| 37
|-
! colspan="2"| Stack Thickness (mm)
| 10.24
| 10.20
| 10.20
| 10.12
| 10.12
|-
! colspan="2"| Time/Stack (min, at 43 ms Integration Time)
| 8.1
| 2.0
| 2.0
| 1.4
| 0.7
|-
! colspan="2"| Time Current Product (mAs)
| 238
| 71
| 59
| 40
| 20
|-
! colspan="2"| CTDIvol (mGy)
| 37.4
| 11.2
| 9.3
| 6.4
| 3.2
|-
! colspan="2"| DLP (mGycm)
| 38.3
| 11.4
| 9.5
| 6.4
| 3.2
|}

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====XtremeCT I Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 3072
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 126 mm
| 41
| 82
| 123
| 246
|-
! colspan="2"| Slices/Stack
| 221
| 110
| 73
| 36
|-
! colspan="2"| Stack Thickness (mm)
| 9.06
| 9.02
| 8.98
| 8.86
|-
! colspan="2"| Time/Stack (min, at 100 ms Integration Time)
| 3.7
| 2.8
| 1.9
| 1.0
|-
! colspan="2"| Time Current Product (mAs)
| 114
| 86
| 57
| 29
|-
! colspan="2"| CTDIvol (mGy)
| 7.3
| 5.5
| 3.6
| 1.9
|}

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====VivaCT80 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 3072
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1500
| 1000
| 500
| 250
| 125
|-
! rowspan="6"| Voxel Size (µm)
! scope="row"| FOV/Diameter 31.9 mm
| 10.4
| 15.6
| 31.9
| 31.2
| 62.4
|-
! scope="row"| FOV/Diameter 35.9 mm
| 11.6
| 17.5
| 35
| 35
| 70.1
|-
! scope="row"| FOV/Diameter 39.9 mm
| 13
| 19.5
| 39
| 39
| 78
|-
! scope="row"| FOV/Diameter 49.8 mm
| 16.1
| 24.2
| 48.5
| 48.5
| 97.1
|-
! scope="row"| FOV/Diameter 63.9 mm
| 20.8
| 31.2
| 62.4
| 62.4
| 124.8
|-
! scope="row"| FOV/Diameter 79.9 mm
| 26
| 39
| 78
| 78
| 156
|-
! colspan="2"| Slices/Stack
| 333 ~ 328
| 222 ~ 219
| 111 ~ 109
| 111 ~ 109
| 55 ~ 54
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 14.9
| 10.0
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 73
| 48
| 24
| 12
| 6
|}

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====VivaCT40 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 21.5 mm
| 10.5
| 21
| 21
| 42
|-
! scope="row"| FOV/Diameter 25.6 mm
| 12.5
| 25
| 25
| 50
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 35.8 mm
| 17.5
| 35
| 35
| 70
|-
! scope="row"| FOV/Diameter 38.9 mm
| 19
| 38
| 38
| 76
|-
! colspan="2"| Slices/Stack
| 213
| 106
| 106
| 53
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 9.9
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 61
| 31
| 15
| 8
|}

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====µCT35 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 7.2 mm
| 3.5
| 7
| 7
| 14
|-
! scope="row"| FOV/Diameter 12.3 mm
| 6
| 12
| 12
| 24
|-
! scope="row"| FOV/Diameter 20.5 mm
| 10
| 20
| 20
| 40
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 37.9 mm
| 18.5
| 37
| 37
| 74
|-
! colspan="2"| Slices/Stack
| 232 ~ 235
| 116 ~ 117
| 116 ~ 117
| 58
|-
! colspan="2"| Time/Stack (min, at 400 ms Integration Time)
| 23.9
| 12.3
| 6.5
| 3.5
|-
! colspan="2"| Time Current Product (mAs)
| 119
| 60
| 30
| 15
|}

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===Advanced Settings===
*'''Number of Det-lines (for Scout-View)''': Defines how many lines on the detector shall be used during the Scout-View. Using all available lines provides faster Scout-Views but some faint horizontal lines might be seen between the stacks. Limit the number of lines to a small number to obtain Scout-Views without these artifacts but the time of the Scout-View will increase.

*'''Number of Det-lines (for CT-scan)''': Defines how many lines on the detector should be used. This number influences the number of slices within a stack. Limit the number of detection lines if you see residual cone beam artifacts.

*'''FOV/Scan Diameter''': Chose the diameter of the FOV. This action is cropping the area of the detector.

*'''Software binning''': factor of the pixels on the detector.

*'''Hardware binning''':

*'''Samples''': number of (possibly binned) pixels on the detector that are used for each slice (note: this number is given for the whole FOV).
*'''Proj/180°''': number of projections taken per 180° turn of the sample.

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===Reconstruction===

*After each image stack is acquired, it is automatically submitted to the queue (sys$slow) for reconstruction. The reconstruction for each image stack is split into four jobs to make efficient use of processors.
*The reconstruction time depends on the resolution setting, with low resolution scans reconstructing faster than high resolution scans. Normally scans are reconstructed within a day or two.
*It is possible to resubmit a scan for reconstruction (refer to [[Scanco_Administration#Reconstruction | '''Scanco Administration's Reconstruction''']]) for details. This may be necessary or desirable for several reasons:
#The sample did not reconstruct properly (e.g., due to a power failure)
#To reconstruct the object at an angle (e.g., so that the anterior surface of a bone is always in the same direction).
#A new beam hardening correction was applied to the sample
#The scaling was changed for the sample to change the brightness

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==Perform a Scan==
===Perform a Single Scan===
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] for instructional details.

===Perform Batch Scans===
*Batch scan mode is only available on microCT scanners.
*Batch scans can be setup for different regions of interest (ROI) within a sample or for different samples contained within a sample holder.

#'''Setup the First Scan'''
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] to use the "Other..." button to find your sample number, choose a controlfile, perform a scout view (a mouse's whole body in this example), use the reference line to setup the first scan region (mouse skull in this example).
#*To add a batch scan press the "Batch Measurement" button.
#:[[File:Batch_scan_01.preview.jpg|600px]]
#*An information window is displayed with the scan measurement number. Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']] then press "OK" to close the window. An entry is also added to the measurement history for the sample.
#:[[File:Batch_scan_02.preview.jpg|600px]]
#'''Setup the Next Scan'''
#*Using the "Other..." button, find your next sample number, choose a new control file (if desired).
#*If the next region of interest or sample is not in view of the current scout view, adjust the parameters of the scout view and obtain a new one.
#*Use the reference line to set a new scan region (upper limbs in this example).
#*To add a batch scan press the "Batch Measurement" button.
#*As the first scan, a measurement number is assigned for this new scan. Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']].
#:[[File:Batch_scan_03.preview.jpg|600px]]
#*Repeat this process until you have added all your scans.
#'''Start the Batch Scans'''
#:There are two ways to start a batch scan:
##Click the "Start Batch Scans" button: the program will automatically close so that control of the scanner can be allotted to the queue.
##Exit the scanning program.
#:[[File:Batch_scan_04.preview.jpg|600px]]
#'''Check the Queue'''
#*Batch jobs will be submitted to the SCEVA2_BATCH queue for µCT35 or SC5019_BATCH queue for vivaCT40.
#*Initially the jobs will show up as temporary (TMP) jobs:
#:[[File:Batch_scan_05.preview.jpg]]
#*After about 30 seconds, the sample number will show up in entrie names:
#:[[File:Batch_scan_06.preview.jpg]]
#'''Request an Email Notification'''
#*There is a script in the commands (com) directory that will put an entry into the batch queue to send an email. Run the script and input parameters (queue and email) as prompted.
#:[[File:Batch_scan_07.preview.jpg]]
#'''Cancel a Batch Scan'''
#*For errors made during batch scan setup, to cancel a scan in progress, or to cancel a pending scan.
#:[[File:Batch_scan_08.preview.jpg]]
#*If you cancel all the scans and the scanner door does not unlock automatically (µCT 35 only), then start the measurement program and the scanner will unload, unlocking the door.

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==Action on Image Artifacts==
===Rescan for===
*'''Motion Artifacts'''
*'''Sample Out of the Field of View'''

===Contact Scanco Medical for===
*'''Ring Artifacts''' (Bad Detector)
:*Ring artifacts are caused by a faulty detector pixel and show up in the reconstructed image as a full or partial white circle.
:*For uCT scanners: When noticed, please notify lab technicians who will contact Scanco Medical to perform a "Pixel Correction", which will correct this artifact for future scans and can be used to update previous scans. You should not rescan the sample if there is a ring artifact.
:*For XtremeCT scanners: A small number of rings artifacts are expected and acceptable. For a 168-slice scan, ring artifacts present in <5 slices total is acceptable. If you observe ring artifacts in a larger number of slices, notify a staff member. Do not repeat scans for ring artifacts. In most cases, it is also unnecessary to perform a correction to already acquired data.
<div><ul>
<li style="display: inline-block;"> [[File:Ring_artifact.jpg|thumb|none|350px|Image with Ring Artifact]] </li>
<li style="display: inline-block;"> [[File:Ring_artifact_corrected.jpg|thumb|none|350px|Same Image after with Detector Correction]]</li>
</ul></div>

*'''Bad Centre Calibration Values'''
*'''Defective Shutter Artifact'''

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=Evaluation=
==Evaluate a Scan==
*To evaluate a scan, refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.

===Open default ISQ===
You can load a defualt ISQ usig uct_evaluation program:

<pre>
$ def uct_default_isq DISK3:[MICROCT.PROJECTS.VALIDATION.MODELS]C0000123.ISQ ! or
$ def uct_default_isq DISK2:[MICROCT.DATA.00001234.00005678]C0003456.ISQ
$ uct_evaluation
</pre>

Hit <code>cancel</code> when asked files to load, and the file you just set as default will be loaded.

*Use the whole pathname for ISQ.
*If you don't import your data into the system, you cannot store your evaluation results in the measurement database. You will have to use the LOG file to access your results.
*Only start a 3D evaluation if and only if the sample (patient) and measurement index are correct in the ISQ full path! Also, no results will be stored in the database unless the ISQ header info (samp/meas) is correct.
*Many of the UCT_xxx.COM scripts use the whole filename to extract the sample and measurement numbers, so it is possible that some evaluations will not run. UCT_xxx_BATCH_V4.COM is an example of an evaluation that will not run, but UCT_CUTOUT.COM will run (doesn't need any sample/meas info).

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==Draw Contours==
*Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
*Contouring is the first step in the analysis process, which allows you to segment the desired bone from surrounding tissues.

===Contouring Tools Reference Sheet===
*[[Media:Contouring-tools.pdf |'''Contouring Tools Reference Sheet''']]
*Contours must always be drawn COUNTER-CLOCKWISE!!!

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===Contour and Run the Standard Patient Evaluation===
The following instructions are for contouring standard patient radius and tibias.

#Open the Evaluation Program and select your sample.
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.
#Zoom into the desired bone (Radius or Tibia)
#*Using the zoom menu from the top panel, zoom into the Radius or Tibia.
#*Usually 3x zoom is appropriate.
#Draw contours roughly around the bone.
#*Select the first contouring tool (top left button) and draw COUNTER-CLOCKWISE.
#Automatically generate contours for all slices in the scan.
#*Double click the image to bring up the contouring window.
#*Double click again and the program will attempt to snap the contour to the bone. Double click again if needed.
#*Select Forwards, and then Iterate Forwards to have the evaluation program automatically segment the bone.
#Modify any contours as needed.
#*Select the second contouring tool (2nd button from top) to fix any "wrong" contours.
#*Draw COUNTER-CLOCKWISE!!
#*If many contours cannot be automatically generated correctly i.e. cortical bone is porous and evaluation program misses a lot of bone, it may be better to use the Range/Morph function rather than fixing each individual slice.
##This is done by first clearing all the breakpoints (Clear all BP in contouring window). The boxes will now become red.
##Manually fix the slice that does not have the correct contour automatically drawn, skip a few slices and manually fix that slice as well. The slices that you have fixed will turn green, indicating that it is a breakpoint (BP).
##Now you can morph between the two breakpoints (BP, green boxes) you have just created. Select the BP with the higher slice number, select range (first column on left) from the contouring window, followed by morph (second column from left).
#Save Contour (.GOBJ): Make sure you save your work!
#Run the 3D Standard Evaluation for your specific project (and timepoint).
#*Select 3D evaluation under Tasks to bring up the window. You'll then need to Select... the evaluation specific for your project.
#*There are a variety of evaluations to choose from, you can search for your project's evaluation script by typing in the name of your project in the filter window.
#Check the queue to ensure that the evaluation is running properly.
#*Type <code>$ show que</code> in a terminal window will allow you to see all running processes.

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===Correct Trabecular Contours and Run the Cortical Evaluation===
Once the standard evaluation has been completed, an auto-segmentation process is completed to segment the cortical from the trabecular bone. However, the auto-segmentation is not always accurate, and hence the contour (TRAB.GOBJ) will need to be checked.

#Load TRAB.GOBJ by selecting File, then load GOBJ from the top panel.
#*You will now see a list of all GOBJ files pertaining to your sample. You'll need to load the TRAB.GOBJ.
#*When the TRAB.GOBJ has loaded, you will see that the loaded contour is between the cortical and trabecular bone.
#Correct contours as needed
#*Can manually adjust the slices or use the Range/Morph function.
#*Remember to draw COUNTER-CLOCKWISE!
#Run the 3D cortical evaluation for your specific project (and timepoint, if relevant).
#*Select 3D evaluation under Tasks to select the appropriate evaluation script.

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==Evaluation Scripts==
===Scanco Standard Evaluation Scripts===
The following are descriptions of some of the standard evaluation scripts provided by Scanco Medical.

*'''3D Segmentation of VOI, 1 solid object'''
:Produces a 3D segmented (binary) object with values 0 (background, hidden) and 127 (solid). Input Gaussian filtering and threshold parameters. Draw contour to isolate the object of interest (optional).

*'''3D Seg. of 2 VOIs: solid dense in transparent low dens obj'''
:Produces a 3D segmented object with values -1 (transparent), 0 (background, hidden), and 127 (solid). Input two sets of Gaussian filtering and threshold parameters (input the second set by pressing the red 2 button). The preview shows the solid object in white and the transparent object in red. Draw one contour to isolate the object of interest (optional). This script is useful for showing soft tissue and bone.

*'''Bone Trab. Morphometry (3D Seg, 3D Calc, Print Sheet)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour to isolate the trabecular bone. Performs model-independent (direct) measurements on the trabecular region. Outputs: BV, TV, BV/TV, TbBMD, TbTMD, BS, SMI, DA, ConnD, TbTh, TbThSD, TbSp, TbSpSD, TbN, and Tb1/NSD.

*'''BV/Density only Bone Eval. (3D Seg, BV and Dens Calc, Print)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour to isolate the region of interest. Outputs: BV, TV, BV/TV, BMD, and TMD.

*'''Bone Midshaft Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour on the outer surface of the bone. Outputs: BV, TV, BV/TV, BMD, TMD, and moment of inertia parameters.

*'''Bone Midshaft more than e.g. 50 slices Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour on the outer surface of the bone. If you wish to exclude the medullary area from the analysis, then draw a counterclockwise contour on the outer surface of the bone and a clockwise contour on the inner surface of the bone. Performs direct measurements in addition to the standard midshaft analysis. Outputs: BV, TV, BV/TV, BMD, TMD, moment of inertia parameters, Th, and Sp.

*'''Convert to TIFF'''
:Converts the grayscale data to TIFF slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Convert to DICOM'''
:Converts the grayscale data to DICOM slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Reformat to Axial Cuts'''
:Flips the dataset from the XY plane to the XZ or YZ planes (specify in the advanced options for the script). This is useful if you want to contour your sample in a different plane. The flipped sample is imported as a new measurement under the same sample number as the original data.

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===Understanding Evaluation Scripts===
Following are some example evaluation scripts full of comments to promote understanding:
*[[Media:IPLV6_VOI.pdf|IPLV6_VOI script]]
*[[Media:IPLV6_MIDSHAFT.pdf|IPLV6_MIDSHAFT script]]
*[[Media:IPLV6_TRABECULAR_BONE.pdf|IPLV6_TRABECULAR_BONE script]]

===Setup Customized Evaluation Scripts===
To setup an evaluation script customized to your project, in the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']]:
*Choose "Scripts" then "Import from" then "TEMPLATES", pick a Scanco Standard Evaluation Scripts and Save.
*Choose "Scripts" then "Modify". Choose the script that was just imported and click "OK", Change the name of the script.
*Modify the default segmentation and other parameters for the script. When finished making changes press "Save" then "OK".

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==Image Processing Language (IPL) Scripting==
The following documentations related to IPL scripting, as it applies to image analysis was compiled by Jan Owoc in July 2013 based on numerous sources including own experience.

===Your First IPL Script===
*'''Prerequisite''': you are familiar with navigating the VMS system.
*'''"$" or "ipl>"''': the DCL and IPL prompts respectively, and you should only type the text after the prompt.
*If you FTP the file to the OpenVMS system, ensure you use "binary" to transfer the file.
You can run these commands on almost any greyscale AIM file. Example file here: MJ7101.AIM

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====Interactive IPL====
*Command <code>$ ipl</code> starts IPL interactively, that is you see the result of each command as you run it.
*While it is useful for testing, running large scripts interactively may interfere with others using the computer.
 
*'''Reading an AIM file'''
:Before you can run any analysis on the AIM file, you need to read it into IPL and assign it a file handle. This is done using the command <pre>ipl> read in MJ7101.AIM</pre>
:A fraction of a second later, the file should have been read into memory and assigned the internal name "in". If we want to do some basic density calculations on it, we can use the command<pre>ipl> vox_ in 0</pre>
:*IPL, much like DCL, will automatically complete the command if it is given enough characters.
:The "vox_" was expanded to the command "vox_scanco_param" (calculates voxel-counting parameters) and told you that the mean density of the cube is 114 mg HA/cm3 and a standard deviation of 283 mg HA/cm3.
:The argument "in" is the internal name of the image.
:The argument "0" is the region. The command vox_scanco_param supports several numbered regions if, for example, you wanted to separately compute the density for the trabecular region and the cortical region.
 
*'''Segmenting an AIM file'''
:Some parameters, like average density, are computed from the [[Scanco_User_Instructions#Grayscale_Images|'''Greyscale Image''']]. Other parameters, like the trabecular number, require an image that has been segmented to [[Scanco_User_Instructions#Binary_Images|'''Binary Images''']], that is converted into "bone" and "not bone".
:There are many ways to separate bone from non-bone, and parameters that work well for one dataset will not generally work for images of different samples, or acquired at different resolutions.
:One of the simplest segmentation methods "seg_gauss" is to apply Gaussian smoothing to the sample, to eliminate the noise present in the image, followed by a semi-arbitrary threshold that preserves the trabecular structure.
<pre>
ipl> seg_gauss in seg

-sigma [1.000000] >
-support [2] >
-lower_in_perm_aut_al [300.000000] >
-upper_in_perm_aut_al [100000.000000] >
-value_in_range [127] >
-unit [0] > 2
</pre>
:seg_gauss expects 8 parameters, and we have provided only 2. It will now prompt us for the remaining 6 one-by-one.
:Leave everything at the defaults (simply hit "Enter") except the unit, which we will change to "2".
:For young human trabecular bone from the distal tibia scanned at 20 um in the uCT 35, but then downscaled to 80 um, the above parameters give a reasonable representation of the trabecular structure. With other bones at other resolution, you may need to change the sigma, the support, and the lower threshold.
:The unit of "2" simply means that we are working in units of mg HA/cm3.
:Now that the cube is segmented, we can run the same voxel-counting command as above and obtain more information. <pre>ipl> vox_ seg 0</pre>
:We now know that our combination of smoothing and threshold resulted in an object volume of 103 mm3 (i.e. volume of bone) and a bone volume ratio of 22.88%.
 
*'''Writing out a file'''
:we can write the segmented file out for future use. Accept the defaults for the remaining arguments. <pre>ipl> write seg MJ7101_SEG.AIM</pre>
:Now you can quit IPL and verify that the segmented file has been written out. <pre>ipl> quit</pre>

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====Batch IPL====
*Command <code>$ ipl_batch</code> starts IPL inside a script that would be submitted to a queue.
While the following code is likely to work, it is not very readable:
<pre>
$ IPL_BATCH
read in MJ7101.AIM
vox_ in
seg_gauss in seg 1 2 300 100000 127 2
vox_ seg
write seg MJ7101_SEG.AIM
..
$ EXIT
</pre>
*Instead, it is recommended that you copy and paste the "pretty" output of the command after you have run it once interactively.
*Values that are likely to change should be variables, defined at the top of the script.
*To substitute a variable from DCL into IPL, use a double-quote character before the variable name, as shown in the example below.
Copy and paste the below into a text editor.
<pre>
$ modelname :== MJ7101.AIM
$ threshold == 300
$ outputfile :== MJ7101_SEG.AIM
$
$ IPL_BATCH

/read
-name in
-filename "modelname

/vox_scanco_param
-input in

/seg_gauss
-input in
-output seg
-sigma 1.000000
-support 2
-lower_in_perm_aut_al "threshold
-value_in_range 127
-unit 2

/vox_scanco_param
-input seg

/write
-name seg
-filename "outputfile

..
$ EXIT
</pre>
Now, it is clear what the full names of the commands are, and what the parameters mean.
*If a parameter isn't important and can be left at the default (for example the region number during vox_scanco_param), you can leave it out of the file.
Save the file as MYSCRIPT.COM and run it using <code>@MYSCRIPT.COM</code>.

 
*'''Submitting to the queue'''
:As mentioned in the introduction, running IPL interactively on larger models negatively impacts other users of the system. Copying the commands to a file and running it from the command line has the same effect.
:*The correct way to run larger scripts is to submit the job to the queue. <pre>SUBMIT/QUE=SYS$FAST MYSCRIPT.COM</pre>

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===IPL Reference===
*[[Media:SCANCO_-_Software_-_IPL_instruction_manual_0.pdf|'''Official Scanco IPL Documentation''']]
*[[Media:scanco-software-ipl-instruction-manual.pdf|'''Scanco IPL Manual]]

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====Standard Read Write etc. Functions====
*'''/read''': Reads a file into ipl and gives the file an internal name
*'''/aim_read''':
*'''/read_versatile''':
*'''/write_v020''': Writes an aim file to the directory in which ipl is open (or specified directory if in a script)
*'''/write_new''':
*'''/write_part''':
*'''/copy''': Copies an internal file (a file that is already in the ipl system) and allows the copy to be given a new name.
*'''/delete''': Deletes an internal file (a file that is already in the ipl system)
*'''/rename''': Changes the name of the file (input is the old name and output the new name)
*'''/list''':
*'''/options''':
*'''/release_history''':
*'''/commands_write_log''':

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====Segmentation Functions====
*'''/gauss_lp''': Applies a low pass gaussian filter with specified sigma and support values
*'''/fft_laplace_hamming''':
*'''/median_filter''': Applies a low pass median filter to reduce unwanted noise in an image
*'''/seg_gauss''': Segments aim files using the input sigma of gauss and the filter support for gauss. A threshold can also be applied using this function.
*'''/threshold''': Removes data outside of the specified range
*'''/absolute_threshold''':
*'''/adaptive_threshold''':
*'''/adaptive_iter_threshold''':
*'''/matching_threshold''':

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====Gobj and Masking Functions====
*'''/gobj_maskaimpeel_ow''': Cuts an aim file with a gobj so that only the portion of the aim within the gobj remains. Peel_iter value used to specify the number of pixels within the gobj the function will need to cut.
*'''/gobj_to_aim''': Reads a gobj file from the directory and makes an aim file (the aim file is in ipl, to output it to the directory use write).
*'''/togobj_from_aim''': Takes an aim file and writes a gobj file (the gobj is output to directory).
*'''/gobj_circumf_area''':
*'''/gobj_join''':
*'''/gobj_join_consec''':
*'''/gobj_scale''':
*'''/gobj_isotrop''':
*'''/cortex_maskoff''':
*'''/peel3d''':

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====Voxel-Counting, Density and Triangulation Functions====
*'''/db_scanco_activate''':
*'''/db_clear_eval''':
*'''/db_calib_unit_fill''':
*'''/db_set_mean_accur''':
*'''/voxgobj_scanco_param''': Inputs an aim file and a gobj and provides information (including total volume, object volume and the mean value of the points) on the region within the gobj.
*'''/vox_scanco_param''': Inputs an aim and provides information including total volume, object volume and the mean value of the points.
*'''/tri_da_metric_db''':
*'''/tri_direc_distr''':
*'''/connectivity''': Receives a component labelled aim object and calculates the connectivity of the labelled components.
*'''/conn_nocl''':
*'''/conn_bgcl''':
*'''/fractal_dimension''':

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====Distance Transformation (Sphere Filling) Functions====
*'''/dt_object_param''':
*'''/dt_ow_object_param''':
*'''/dt_background_param''':
*'''/dt_mat_param''':
*'''/dt_cortex_obj_param''':
*'''/dt_value_output''':
*'''/dt_mat_output''':

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====Statistical Functions====
*'''/examine''': Receives an AIM object and outputs specified information based on the item input.
*'''/histo''':
*'''/moment2d_of_inertia''':
*'''/moment3d_of_inertia''':
*'''/zmeanmax''':

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====Voxelsize-Scaling Functions====
*'''/isotrop''':
*'''/scale_elsize''':
*'''/ipscale_elsize''':
*'''/noipscale_elsize''':
*'''/scale_ow_elsize_noip''':

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====Component Labeling Functions====
*'''/cl_ow_rank_extract''': Receives AIM file and over writes it with an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl_rank_extract''': Receives AIM file and outputs an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl26_rank_extract''':
*'''/cl_image''':
*'''/cl_extract''':
*'''/cl_slicewise_extractow''':
*'''/cl_nr_extract''':

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====Add, Concat, Cut etc. Functions====
*'''/add_aims''': Adds the values of two AIM images in a 3D space.
*'''/add_constant_ow''':
*'''/border_change''':
*'''/bounding_box_cut''': Cuts extra space out of an aim file so that only the region with the data remains. A border can be added to the image using the border input.
*'''/concat''': Takes two aim files and combines them. The data from both aims or just the common region can be kept. To add the images add_not_overlay is set to true (for example if image 1 has a value of 41 and image 2 has a value of 82, the combined value will be 123).
*'''/concat_adapt''':
*'''/divide_volumes''':
*'''/fill_min_max_ow''':
*'''/header_geo_set''':
*'''/header_log_set''':
*'''/header_calib_ov''':
*'''/invert_ow''':
*'''/mult_constant_ow''':
*'''/multiply_volumes''':
*'''/sqr_to_float''':
*'''/sqrt_to_float''':
*'''/offset_add''':
*'''/offset_set''':
*'''/clear_offset''':
*'''/fill_offset_mirror''':
*'''/fill_offset_duplicate''':
*'''/set_value''': Sets the values of the object and background of an aim file to chosen values
*'''/sub_get''': Extract a portion of an image 
**-pos corresponds to x,y,z origin -1 -1 -1 maintains the original coordinates 
**-dim corresponds to x,y,z dimensions -1 -1 -1 maintains the original dimensions (within maximum range) 
**indexing starts at 0 instead of 1
*'''/sub_pick''':
*'''/subtract_aims''': Subtracts one aim from another and outputs the remaining region.
*'''/sup_divide''':
*'''/transparent_concat''':

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====Erosion Dilation Open Close Functions====
*'''/erosion''':
*'''/dilation''':
*'''/open''':
*'''/close''':
*'''/erosion_dilat_variable''':

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====Import Export Conversion Norming Functions====
*'''/import_freeformat''':
*'''/dicom_to_aim''':
*'''/todicom_from_aim''':
*'''/dicom_list_series''':
*'''/isq_to_aim''':
*'''/isq_gobjfit_to_aim''':
*'''/toisq_from_aim''': Writes an isq file to the directory ipl is open in (or specified directory) from an aim file. The isq name should be 8 characters long.
*'''/mesh''':
*'''/msq_from_aim''':
*'''/rsq_to_aim''':
*'''/stl_tri''':
*'''/convert_to_type''':
*'''/convert_unsigned''':
*'''/norm_max''':

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====Functions for Root Canal Evaluations====
*'''/separ_roots''':
*'''/calc_ctr_mass_list''':
*'''/calc_ctr_mass_diff''':
*'''/treated_surf''':
*'''/match_cut''':
*'''/match_cut_adapt''':

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====Miscellaneous Functions====
*'''/align_z''':
*'''/dcl''':
*'''/flip_aim''':
*'''/growback_to_orig''':
*'''/turn3d''':
*'''/turn2d''':
*'''/upat_filldb''': Fill special Upat DB for patient (radius/tibia) evaluation
*'''/xray''':

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====Obsolete, Experimental and Duplicate Functions====
*'''/curv_tri''':
*'''/cut2D_shape_ow''':
*'''/join_uncompress''':
*'''/mil_param''':
*'''/milv1_param''':
*'''/gauss_seg''': duplicate of /seg_gauss
*'''/from_aim_to_isq''': The function toisq_from_aim will also convert an aim to an isq
*'''/local_threshold''':
*'''/edge_canny''':
*'''/sobel_grad''':
*'''/hysteresis_thresholg''':

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====Functions only available in iplfe====
*'''/register''': Registers two aim files and output a transformation matrix of the transformation to moving input 2 into the space of input 1. Gobjs can be input (registration is more successful with gobjs). Orientation search can be done with masscenter, and/or moment of inertia (MoI), or degree intervals.
*'''/transform''': Transforms an aim file using a transformation matrix (a text file of the matrix can be input). Interpolation options are nearest neighbor, linear, and cubic interpolation. The inverse of the transform provided can be done by setting Tmat_invert to true.
*'''/fe_solveD''': A number of finite element functions are available in iplfe, not all are listed here

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=Results=

==Images and Animations==
Refer to [[Scanco_User_Instructions#.C2.B5CT_Ray|'''µCT Ray''']] for detailed instructions.

===[[#Change_the_View|Change View]]===
===[[#Change_the_Colours|Change Object Colors]]===
===[[#Cutplane_and_Subdim|Show a Section-View of an Object]]===

===Save a Screetshot Image===
#Open XV from a dec terminal on a workstation by typing <code>$ xv</code>.
#Open and frame the image, program etc. that you would like to save an image of.
#In XV, click GRAB. You can either autograb the entire screen after a delay or manually grab a desired area.
#After grabbing the desired section, click Save in XV.

===[[#Save_the_Image|Save Image]]===
===[[#Save_for_Animation|Save Frames for an Animation]]===

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===Convert AIM to TIF series===

Use the utility SEQ_TO_IMAGE located in the UT directory. A symbol has been set up to run this called TIF.

<pre>
$ mcr ut:seq_to_image
Program: seq_to_image V1.1b
Input-File []: WISDOM_L_R05.AIM
File Format [TIF]:
Default TIF Names: WISDOM_L_R05_xxxx.TIF

Output-File [WISDOM_L_R05]:
!> Reading AimVersion020
Start Slice [0]:
End Slice [179]: 5
Number of images thereof (count) [6]:
Scale Factor (Integer) [1]:
global_pos (1=true, 0=false) [0]:
Max value to norm to 255 [32767]:
Slice: 0
Slice: 1
Slice: 2
Slice: 3
Slice: 4
Slice: 5
$ dir wisdom*

Directory DISK1:[MICROCT.SCRATCH]

WISDOM_L_R05.AIM;1 WISDOM_L_R05_0000.TIF;1 WISDOM_L_R05_0001.TIF;1
WISDOM_L_R05_0002.TIF;1 WISDOM_L_R05_0003.TIF;1
WISDOM_L_R05_0004.TIF;1 WISDOM_L_R05_0005.TIF;1

Total of 7 files.
$
</pre>

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===Generate TIF (or others) from 3D rendered volume===

This replaces uct_movie that operated on the alpha systems. UCT_3D can be called in batch mode.

A pdf describing this tool is located here: [[Media:UCT_RAY V4.0-1.pdf]]

To interactively declare the desired settings:
<pre>
$ uct_3d_batch
?CT RAY_BATCH V4.0-1

UCT_R: Application initialized
Filename []:
Print-Filename [SYS$SCRATCH:TEMP_3D.PS]:
Ambient (0.0..1.0) [0.200]:
Shadows (0/1) [1]:
Size (1..1024) [1024]:
Elevation (-90..90) [30]:
Rotation (-180..180) [35]:
Copies (0..9) [1]:

</pre>

To apply a saved set of settings, a setup-file can be created by running uct_3d in interactive mode. Select "Presets" from the toolbar and save the settings you desire (e.g. elevation 90, rotation 0).

<pre>
$ uct_3d_batch setup-file [data-file printfile]

Examples:

$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.ps
$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.tif

</pre>

To automatically generate tifs for many files, a script was created to replace PRINT_3D.COM
The script is currently stored in the xtremect2 com directory.

<pre>
@COM:PRINT_REG_TIF.COM

Generates a 3D image from a segmented file.

The outputs include:
- two 3D renderings (TIF)

Use full pathnames for the segmented AIM.

P1 - Segmented AIM

Usage:
@COM:PRINT_REG_TIF.COM DISK2:[MICROCT.DATA.00000379.00001376]C0001234_SEG.AIM
</pre>

This script can be modified to use a custom preset file.

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===Make an Animation===

To calculate an Animation, two (separate) tools of the 3D program are used: the set-up of start and end point of the Animation, and the 'Auto-Print' tool that automatically creates the TIF files for every rendered image.

This is a 'step by step' guide to create an animation using TIFF files:
:* Open your sample in the 3D program.
:* Now, open 'options','Animation'
:* Render your Image the way you want your animation to start. e.g. observer rotation -179 degrees. You may interrupt if you want. If you are satisfied with all the settings (rotation, elevation, transparency, colors etc.) the Click on 'Get Settings A'
:* Then, adjust all the settings for the endpoint of your animation (with the mouse or the sliders) e.g. observer rotation +179, and start the rendering. If satisfied, click 'Get settings B'

Note: To test, put # of views to 5 or 10... You can also interrupt the build-ups for faster viewing.
:* Click the START button again, wait till the build-up of the 3D image is finished.
:* DO NOT HIT 'START CALCULATION' YET!
:* First, you also need to set-up the 'Auto-Print' mode:
:* Go to the 'Print' menu (file --> print), choose print to TIF and to File and enter THE BEGINNING OF A FILENAME, e.g. sys$scratch:test_ (the program will append 0000.TIF, 0001.TIF etc afterwards) Or enter (possibly with middle-mouse-click): "DK0:[MICROCT.DATA.00001234.00003456]ANIMATION_" to have the result go to the measurement directory.
:* Click on the 'Auto-Print' box. Then 'ok'
:* Adjust the number of views (e.g. 200), then click on 'Start Calculation', and it will render. This may well take a long time.
:* Take those TIFF files to your PC, and combine the sequences in the program that you are using to convert the TIFF files to AVI or MOV files (like Windows Movie Maker 2, or Quick Time Pro, or Adobe Premiere etc.)

Notes/Hints:
:* The order in the above list can also be reversed: You can first set up the 'Auto-Print', and then go into the 'Animation' menu, choose start and end settings, and hit 'Start Calculation'
:* The positions A and B can be any: e.g. with subdim, you can first take everything (A), then slide it back to nothing (B).
:* You can even slowly change the color of an object. Or slowly hiding objects: choose 'transparent' for object, but change from 0.0 (A) to 1.0 (B)
:* If you want to create a movie with different sections, e.g. first rotate around, then slowly make bone transparent, then cut in: Do this in multiple sections with the 3D program, e.g. first create Auto-Print files 'rotation_0000 to rotation_0200', then 'transp_0000 to transp_0050', and then 'cut_0000 to cut_0100'. Make sure ALL the settings from the last view of the previous section match those of the first view of the next section so you get smoot transitions.
:* The 'Auto-Print' box is also usable without the 'Animation' Menu: Activate it, Like above, with sys$scratch:test_ only the beginning of filename. 'ok' Then, whenever a 3D image is completely built-up (so when you are happy with a view and you do not interrupt the build-up), automatically a TIF file is generated, numbered sequentially.

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===Combine two volumes to create transparent image===

First create your two start "seg.aim" images
Start by running either the normal eval, or $ voi to get one _seg.aim file of one region

Rename it to a better name in the session manager, e.g. c0001234_all.aim

Then either by choosing different contours, or a different threshold, start the $ voi or the normal evaluation again, which will create another _seg.aim file.

Load them in the 3D viewer ('all files') to check that they look like expected.

Now we will go into IPL and concatenate those two volumes.

<pre>
$ ipl
/read all xx_all.aim
/read trab xx_seg.aim
/transparent
-input_solid trab
-input_transp all
-output out
</pre>

Note: the solid volume is OVERWRITING the transparent input volume, so usually, it
is the smaller (inner) of the two.

<pre>
/write out xxx_transp.aim
/quit
</pre>

Then load the _transp.aim file in 3D, go to 3D program FAQ to see how to change transparency levels in the Display options there.

See IPL FAQ or 3D program FAQ if you need help with these parts.

Step by Step Example: Showing your chosen trab VOI within whole bone
:* $ voi, enter threshold in ipl_voi.com, start 3d eval WITHOUT contours
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_all.aim
:* Start up normal eval program, draw trabecular contours, check threshold in ipl_fixed_batch_v4.com, start 3D eval.
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished

Step by Step Example: Showing high-dense volume surronded by lower density volume

:* Start normal 3D eval with HIGH threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_high.aim
:* If wished: read out 3d result database with $ uct_list
:* Start normal 3D eval with LOW threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished

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==Image Tours==
===XtremeCT Image Tours===

===MicroCT Image Tours===
*Refer to [[Media:Tours_image_gallery.pdf|'''MicroCT Image Gallery''']] with its [[Media:Tours_image_notes.pdf|'''Image Notes''']].
*Refer to [https://youtu.be/tT3dz4VrwfE '''MicroCT Image Tour YouTube Video''']
*Hover over a thumbnail and click on its overlaid description to see the animated GIF or a larger version of the image.

<gallery mode="packed-hover" heights=220px caption="Micro-CT Scans">
Image:MOUSE_SKELETON_PIC01.jpg|[[Media:MOUSE_SKELETON_360.gif|Mouse (38µm)]]
Image:Segmented_Mouse_Femur.jpg|[[Media:Segmented_Mouse_Femur.jpg|Mouse Femur showing Cortical and Trabecular Bone (10µm)]]
Image:LIZARD_WHOLE_VIEW_P1_0044.jpg|[[Media:LIZARD_SKELETON_360.gif|Lizard (88µm)]]
Image:LIZARD_SKULL.jpg|[[Media:LIZARD_SKULL.jpg|Lizard Skull showing Thickness Distribution (25µm)]]
Image:DUCK_BEAK_PIC01.jpg|[[Media:DUCK_BEAK_360.gif|Duck Beak (60µm) Courtesy of Dr. A. Iwaniuk]]
Image:Human_Tooth.jpg|[[Media:Human_Tooth.jpg|Human Tooth (30µm) Courtesy of Dr. C. Stewart]]
Image:PINECONE_TH_PIC05.jpg|[[Media:PINECONE_360.gif|Pinecone showing Thickness Distribution (69µm)]]
Image:SHELL01_SEG_PIC01.jpg|[[Media:SEASHELL_360.gif|Seashell (50µm)]]
Image:TURTLE_SKULL.jpg|[[Media:TURTLE_SKULL_360.gif|Turtle Skull (60µm)]]
Image:SAND_DOLLAR.jpg|[[Media:SAND_DOLLAR.jpg|Sand Dollar (37µm)]]
Image:MOUSE_L1-L6.jpg|[[Media:MOUSE_SPINE_SEG_360.gif|Mouse Spine showing Cortical and Trabecular Bone (10µm)]]
Image:MOLAR.jpg|[[Media:MOLAR.gif|Human Tooth (60µm) Courtesy of Dr. C. Stewart]]
</gallery>

<gallery mode="packed-hover" heights=220px caption="Contrast-Enhanced Micro-CT Scans">
Image:Contrast_mouse_head_XZ_thumb.jpg|[[Media:Contrast mouse head XZ.jpg|Mouse Head (60µm, XZ plane)]]
Image:Contrast_mouse_head_XY_thumb.jpg|[[Media:Contrast mouse head XY.jpg|Mouse Head (60µm, XY plane)]]
Image:Contrast_mouse_head_YZ_thumb.jpg|[[Media:Contrast mouse head YZ.jpg|Mouse Head (60µm, YZ plane)]]
</gallery>

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==Extract Results==
===Automatic Results===
Results are generally automatically extracted after each analysis to the UCT_RESULTS directory. 
The results files have the form of:
*UCT_LIST_*''PROJECT''*.TXT for XtremeCTs: e.g. result file UCT_LIST_KYLA.TXT for the following project.
*UCT_LIST_3DLOG_*''PROJECT''*.TXT for microCTs: e.g. result file UCT_LIST_3DLOG_KYLA.TXT for the following project.
*where ''PROJECT'' is specified in the evaluation tool script setup.
[[File:Script_modify_basic_project.jpg|500px]]

Open the result file and copy and paste it into Excel, e.g.
<pre>
$ dir uct_results:*kyla*
$ eve uct_results:UCT_LIST_3DLOG_KYLA.TXT
</pre>

Or transfer the file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].
*microct/vivact account UCT_RESULTS location: ADISK1:[MICROCT.RESULTS]
*invivo/invitro account UCT_RESULTS location: ADISK1:[BONELAB.RESULTS]

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===Extract Results from XtremeCT Database using UPAT_LIST===
*Run <code>$ UPAT_LIST</code> to take in a range of samples and extract the standard patient results, which may include scans from other projects.
**Run <code>$ UPAT_LIST -h</code> to print out help for all parameters.
**For standard analysis on XtremeCT2, the default Evaluation Type 4=XT1 is not applicable. To get results for XtremeCT2, you need to run upat_list twice. Once for evaluation 5 and once for 6.
<pre> Evaluation type (1-6) [4]: Type code of evaluation (4=XT1, 5=trabecular, 6=cortical, default=4) </pre>

*Run <code>$ @com:EXTRACT_UPAT_LIST</code> to take in a list of sample numbers and extract the standard patient results with follow-ups and append them to a result file.
<pre>
$ @COM:EXTRACT_UPAT_LIST P1 P2 P3 P4 P5

P1 = Sample List
P2 = Site (RR, RL, TR, TL, R*, T*, *)
P3 = Number of Follow-Ups (max 19)
P4 = Results Output File
P5 = Eval type (4=XT1, 5=Trab, 6=Cort)
</pre>

:An example to extract all sites:
<pre>
$ @com:EXTRACT_UPAT_LIST mysamples.txt * 19 myresults.txt 5
</pre>

*Run <code>$ @com:EXTRACT_UPAT_LIST_NOMATCH</code> to take in a list of sample numbers and extract the standard patient results without matching follow-ups and append them to a result file.
<pre>
$ @com:EXTRACT_UPAT_LIST_NOMATCH P1 P2 P3 P4 P5

P1 = Sample List
P2 = Site (RR, RL, TR, TL, R*, T*, *)
P3 = Number of Follow-Ups (max 19)
P4 = Results Output File
P5 = Eval type (4=XT1, 5=Trab, 6=Cort)
</pre>

:An example to extract all sites:
<pre>
$ @com:EXTRACT_UPAT_LIST_NOMATCH mysamples.txt * 19 myresults.txt 5
</pre>

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===Extracts Results from microCT Database using UCT_LIST===
*Run <code>$ UCT_LIST</code> to take in a range of samples and extract the results, by specifying the first and last measurement numbers for the range they want to extract
*This may include scans results from other projects, but you can delete unrelated results that are extracted afterwards.
*The program will output a tab-delimited text file, which can be read into Excel or other analysis programs.
<pre>
$ uct_list

UCT_LIST.EXE Version V5.22
Template-File [UCT_3D_LIST_SHEET]: !Press Enter to use the default results sheet.
Output-File [SYS$SCRATCH:UCT_EVAL.TXT]: !Enter a filename, e.g., BUIE_RESULTS.TXT.
Density units (0 default) [0]: !Press Enter.
From Meas. # [0]: !Enter the first measurement number, e.g., 100.
To Meas. # [0]: !Enter the last measurement number, e.g., 101.

Processing measurement 100
Processing measurement 101
</pre>
*An example output file: [[Media:Buie_results.xlsx|Buie_results.txt]]
*Or Run <code>$ @com:extract_results.com</code>

*References of results template:
:*Formatted [[Media:Results_template_uct_list.xlsx|Excel template 1]] for results extracted with uct_list.
:*Formatted [[Media:Results_template_extract_results.xlsx|Excel template 2]] for results extracted with extract_results.com.
:*In vivo spreadsheet template for UCT data: [[Media:In vivo results template.xls| In vivo results template.xls]]
:*In vitro spreadsheet template for UCT data: [[Media:In vitro results template.xls| In vitro results template.xls]]

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===Understand Morphological Parameters===
*Refer to [[Media:Reference_Document_-_Parameters_from_upat_list.doc|'''Explanation of UPAT_LIST Output''']] to understand the result file.
*Refer to [[Media:Reference_Document_-_Parameters_from_uct_list.doc|'''Explanation of UCT_LIST Output''']] to understand the result file.

All values are determined on a slice-by-slice basis, then averaged over all the slices to calculate morphological results:

:*BV/TV -> Sum all raw data within the GOBJ and divide by 1200 mg/cc HA
:*Tb.N -> As per standard method
:*Tb.Th and Tb.Sp -> Derived from BV/TV and Tb.N above (semi-derived method)
:*D100 -> Average density of entire cross section
:*DTrab -> Average density of trabecular region
:*Ct.Th -> Cortical area (from seg) divided by circumference (from GOBJ)
:*GOBJ circumference can be determined with /gobj_circum.

<pre>
BV/TV -> VOX-BV/TV
BS/BV -> TRI-BS/BV
Tb.Th -> DT-Tb.Th
Tb.Sp -> DT-Tb.Sp
Tb.N -> DT-Tb.N
ConnD -> Conn-Dens
SMI -> TRI-SMI
DA -> TRI-DA
</pre>

Usually I'd use the names on the left for the plots, but these correspond to the names on the right of the arrow in the Scanco output files.

Note, if you use the TRI-Tb.Th rather than the DT-Tb.Th*, then you are using the derived (plate-model) morphological parameters. These are less accurate than the direct parameters. They are calculated by triangulating the surface (marching cubes) to get BS, and then calculate thickness
Th = 2 * BV / BS, etc...

'''Mean Values'''
<pre>
mean 1: mean of bone AND marrow --> 'apparent density'
mean 2: mean of what was considered bone only (i.e. what was segmented)
'bone tissue density'
</pre>

Note, there are five possible categories for the mean Mu. They are assigned by setting <code>-region_number</code> in the <code>/voxgobj_scanco_param</code> function. The region number is zero-based, so setting it to 0 corresponds to mean1, 1 corresponds to mean2, etc. So, although mean1 and mean2 are typically apparent and tissue density, respectively, this can be adjusted in the IPL script by setting the region_number. Mean3 might be useful for storing cortical bone density, for example.

<pre>
/voxgobj_scanco_param Voxel or Mu Scanco Parameters
-input Gray scale or Segmented AIM object
-gobj_filename GOBJ: input or Automatic
-peel_iter Peel Iterations or Automatic
-region_number Region number for Mu only

! -region_number 0 ! mean1
! -region_number 1 ! mean2
! -region_number 2 ! mean3
! -region_number 3 ! mean4
! -region_number 4 ! mean5
</pre>

What you should also know: because of partial voluming effects, for Mean2, we are DISCARDING the 2 surface voxels of EVERY trabeculae - thus, to get meaningful Mean2, you have to do your scan with the chosen resolution high enough, such that the mean trabeculae is depicted by at the very least 5 pixels, better actually more than 6 pixels thickness. (You can do this check at the end in the XLS sheet: divide DT-Tb.Th* by el-size-mm.x, and you need to get numbers bigger than 6 or 7 or 10 or so.

For parameters such as ConnD where no GOBJ is taken as input, the TV is determined from the processing log stored in an AIM that has previously had a GOBJ applied (stored as the relative region of interest; ROI). So, it is important to apply a GOBJ prior to ConnD measurements to ensure the TV is correctly determined (and not taken as the whole AIM).

'''Trabecular Number (TbN)'''
The epsilon values can be set to account for differences in scanner resolution, and hence 'surface roughness' for individual pixel suppression.

For microct, for good resolution: if there is a pixel 'sticking out' from a flat surface we do not assign that pixel with a thickness value of 1, but we let it 'get eaten' by the bigger sphere that sits in the center of the trabeculae. So this is nice for 'noise' (0.9/1.5).

For XT resolution, where also many 'good' features are just one or two pixels wide, I liked a lower epsilon value better (0.9/0.5).

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==Generate Report==
===Generate Standard Patient Report===
The standard patient reports are extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.
*The number of follow-ups specified will determine if a baseline or follow-up report is generated.

<pre>
$ upat_list

Mode (1 = list, 2 = print, 3 = show) [1]: 2
Patient # (1-3162) [1]: !input the patient's sample number
Site (found RR) [RR]: !RR or RL or TR or TL
Maximum # of follow-ups (0-19) [19]: !0 for baseline report, press return for follow-ups
Template file [default]: !press return to use the default template
Output filename [SYS$SCRATCH:UPAT...]: !default output file (with sample number and the site) goes to sys$scratch
# copies [1]: !the number of printouts, 0 if no printout is desired
</pre>

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===Generate CaMos Patient Report===
The [http://www.camos.org '''CaMos'''] patient report is extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.
*To ensure the report is generated using the appropriate normative results, the patient's sample remarks should be in the form "F-RHRF" where the first character indicates the sex of the individual, otherwise the patient is assumed to be male.
<pre>
$ upat_list

Mode (1 = list, 2 = print, 3 = show) [1]: 2
Patient # (1-3162) [1]: !input the patient's sample number
Site (found RR) [RR]: !RR or RL or TR or TL
Maximum # of follow-ups (0-19) [19]: !0 - 1st scan, 1 - 2nd scan, 2 - 3rd scan...press return for latest scan report
Template file [default]: COM:UPAT_EVAL_CAMOS.PS
Output filename [SYS$SCRATCH:UPAT...]: !default output file (with sample number and the site) goes to sys$scratch
# copies [1]: !the number of printouts, 0 if no printout is desired
</pre>

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===Print out report sheets===

The postscript report sheets can be generated and printed on the command line. For the XtremeCT system, use <code>UPAT_PRINT_LIST.EXE</code> which can be run (using the symbol):
<pre>
$ UPAT_LIST
</pre>

Look in the UU: directory to see options for the template files (UPAT*.TXT) and the postscript output files (*.PS).
:* UU:UPAT_EVAL_FUP05_SCUSA.PS
:* UU:UPAT_EVAL_BASELINE_SCUSA.PS

For other options, see the upat_list help:
<pre>
$ UPAT_LIST -h
</pre>

One particular option that may be useful, is to turn off slice matching:
<pre>
$ UPAT_LIST -nomatch
</pre>

Here is an example of producing a report for the third measurement of TL for a patient, where we want only the most recent results in the report, without slice matching:
<pre>
$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=UU:UPAT_EVAL_BASELINE_SCUSA.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_0fu.ps

$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=DISK1:[MICROCT.COMMANDS]UPAT_EVAL_CAMOS.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_camos.ps
</pre>
The first command line generates a normal Scanco report, and the second command line generates a CAMOS report.

For reports from non-patient measurements (i.e., the vivaCT system or non-patient scans on the XtremeCT), the template files are different (UCT*.TXT) and the postscript outputs are different (UCT*.PS). To print a result sheet use:
<pre>
$ RUN UM:UCT_RAY_BATCH.EXE
</pre>

If you want to create a postscript file, but not send it to the printer, set the number of copies to zero (interactive). Then, find the postscript file from the <code>SYS$SCRATCH</code> directory and transfer it to your PC. You must transfer the postscript file in ASCII mode. The files are typically called TEMP_3D.PS or UPAT_PAT_62_RR.PS. A program such as Adobe Photoshop can convert the postscript file to a different format.

See also our custom scripts:
<pre>
$ @COM:PRINT_2D.COM
$ @COM:PRINT_3D.COM
</pre>

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===Convert PS to PDF report===
The report can be converted to PDF using <code>$ @SCOM:PS_TO_PDF</code> by:

#Follow the instructions above for creating a report, using "2" to print and "0" for the number of copies. (Use the default template file and output filename.)
#Locate the file on the sys$scratch by <code>$ cd sys$scratch</code> and <code>$ dir</code>
#*The file should read "UPAT_PAT_[sample #]_[site].PS;1" (e.g. UPAT_PAT_0010_RL.PS;1)
#*You can view this file on the monitor by typing <code>$ gs UPAT_PAT_0010_RL.PS;1</code>
#Convert the postscript to PDF by typing in the command followed by the .PS file to convert <pre>$ @SCOM:PS_TO_PDF UPAT_PAT_0010_RL.PS;1</pre>
#The PDF file can then be located again in the sys$scratch directory.

You can transfer the result file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].

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=Data Management=
==Trainee’s Data Responsibility==
#Perform '''Contouring and Data Analysis''' on Data Disk ideally 1-2 months after scanning.
#After finished onsite analysis, [[Scanco_User_Instructions#Move_data_from_Data_Disk_to_Project_Disk|'''use Scripts''']] to '''Copy and Rename''' image data (no RSQ, no ISQ, only AIM, SEG.AIM, GOBJ, COM, LOG, PDF, PS ect) to your specific project folder on Project Disk.
#After finished copying all your image data to Project Disk, '''Notify''' lab personal to delete your data on Data Disk by providing a [[Media:Data_Scans_to_delete_template.xlsx|'''Data Scans to Delete Template''']].
#'''Notify''' lab personal to backup your project folder on Project Disk to Winston server on a monthly basis.
#*Only the two most recent backups (A or B version) are kept for each project on Winston:
#:Backup version "_A" for odd months (Jan, Mar, May, Jul, Sep, Nov), e.g. YZHU_A_OTHER_2017-01-12.SAV
#:Backup version "_B" for even months (Feb, Apr, Jun, Aug, Oct, Dec), e.g. YZHU_B_OTHER_2020-04-08.SAV
#When a project is finished, '''Notify''' lab personal to archive your project to HOG server.
#When a trainee is about leaving, '''Notify''' Steve and lab personal to determine either to backup or to archive your project.

[[File:BoneLabDataManagement.JPG|800px]]

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==Move data from Data Disk to Project Disk==
This is generally done after onsite analysis (i.e. autocontour, cortical porosity, FE etc.) is done. Examples of this can be found in DISK3:[MICROCT.PROJECTS.GRACE.COM] 
1. Go to the specific project's .COM directory, for example:
<pre>
$ cd DISK3:[MICROCT.PROJECTS.GRACE.COM]
</pre>
2. Create a script that will move all IMA (i.e. .AIM, .GOBJ, _SEG.AIM, _CORTEX.AIM, _LHTH_DTN.AIM) to the .MODELS directory for the project. You will use the rename_to_models.com script to generate this script. To move Grace data for example, with a measurement range of 2684 to 2685, you would use:
$ @com:rename_to_models.com meas#1:meas#2 DESTINATION DIR
$ @com:rename_to_models.com 2684:2685 DISK3:[MICROCT.PROJECTS.GRACE.MODELS]

3.This will create a file named RENAME_ALL.COM to the project's COM directory. You will now have to open the RENAME_ALL.COM file and add site + other details into the script. Following the same example as above, it should look like this:
$ eve RENAME_ALL.COM ! to open the file using a text editor
$ COPY DISK2:[MICROCT.DATA.00000700.00002684]C0002040.AIM -
DISK3:[MICROCT.PROJECTS.GRACE.MODELS]GRACE_020_00MTH_RR.AIM
$! DELETE/CONFIRM DISK2:[MICROCT.DATA.00000700.00002684]C0002040.AIM;1
$ COPY DISK2:[MICROCT.DATA.00000700.00002685]C0002041.AIM -
DISK3:[MICROCT.PROJECTS.GRACE.MODELS]GRACE_020_00MTH_RL.AIM
$! DELETE/CONFIRM DISK2:[MICROCT.DATA.00000700.00002685]C0002041.AIM;1
4. You also need to copy the rest of the standard patient image files (i.e. .AIM, .GOBJ, _SEG.AIM, _CORTEX.AIM, _LHTH_DTN.AIM) which is easily done by copying the above lines and replacing .AIM with the respective files.

[[Image:Bones2.jpg|20px]] Warning: Always use the same account consistently to create all files and subfolders within their Project folder, otherwise you way miss data when doing Project Backup or Archive!

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=Import and Export=
==Import Foreign Data to Scanco System==
Only RSQ and ISQ files can be imported into the database, however it is possible to convert other types of data into ISQ files (i.e., stacks of BMPs into ISQ).

PART 1:

After transfering your data to the VMS system (use the data disk <code>disk2</code>, NOT the user disk <code>disk1</code>), use the IPL commands <code>/import_freeformat</code> or <code>/read_aim function</code> to import your data for conversion to an ISQ.

For AIM files, navigate to the location of the AIM file. Then open IPL by:

<pre>$ IPL</pre>

In IPL, read in the .AIM file:

<pre>ipl> read in [.AIM file]</pre>

IPL will do the following:

<pre>ipl> read in STUDYID_001_RL.AIM

/read
-name in
-filename STUDYID_001_RL.AIM
!> Reading AimVersion020

!% /read completed: CPU: 00:01.03 ELAP: 00:01.55 </pre>

For DICOM files, start IPL and run the <code>/dicom</code> function to import. For DICOM, if your object is a single 3D file (-multifile false) or many many individual slice files (-multifile true, and give beginning of filenames, and –extension).

There may be requests by IPL to convert your data to <code>signed short</code> or <code>signed char</code> from other data types. Obey these requests and do it by running the <code>/convert_unsigned</code> function.

Then, write the ISQ file using either the "toisq" or "from_aim" commands:
<pre>ipl> toisq
-aim_name [in] >[leave blank as you defined “in” as .AIM file.]
-isq_filename [default_file_name] > C0001234.ISQ [Create a 1 letter and 7 digit file name]
-square_flag [true] > false
-original_position [true] > false

ipl>toisq_from_aim
-aim_name in
-isq_filename C0001234.ISQ
-square_flag false
-original_position false

!% Dimensions of ISQ file: dim.x dim.y dim.z 558 638 168
Write_ctdata_headerext_new: no mhext found. Init mhext.
Extended header successfully added of type 8

!% Writing ISQ slice 167 (Done: 168/168)

!% /toisq_from_aim completed: CPU: 00:05.12 ELAP: 00:10.47 </pre>

Type ipl>help toisq [or ipl>help from_aim] to see details of the command.

This writes the ISQ file. Make note of the ISQ file name.

Remember, the ISQ name must be 8 characters long (1 character followed by seven digits)!!! The letters and numbers can be chosen freely.

Exit IPL:

<pre>ipl>quit</pre>

PART 2:

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

The measurement can be verified by looking at the Header Information. (File, Header)

If you only needed to view the ISQ, delete the file when finished by:

<pre>$ dir/sincet
$del [.ISQ file]</pre>

PART 3:

To use the ISQ further (e.g. for evaluations, contouring, etc.) create a sample in the database and write down the sample and measurement number. Then, run:

<pre>$ run um:uct_import ! will import both RSQ and ISQ (modify patient index, etc)</pre>

and give the new ISQ file, the new sample-number and check that the feedback is correct (i.e., that the name from the database is matching the name from the ISQ file header). If the Patient Name in the ISQ header doesn't match the measurement database Patient Name (very likely), then upon importing the RSQ/ISQ the headers will be updated to the new Patient Name.

Operator and controlfile can be left 0 if you want. However, controlfile should be set appropriately if the data being imported is for the XtremeCT patient database.

If you are also importing the RSQ, put it in the same directory as the ISQ.

Then it changes the sample and measurement number in the ISQ file, makes the correct directory on <code>DK0</code>, and gives you the line on the screen of how to rename the file to the correct, new directory. Take this line and use it on the command line. Done!

You can now use the normal <code>uct_evaluation</code> program with this file. If the control file was set properly, then the evaluation will be done correctly (i.e., for XtremeCT patient measurements).

Note: Any AIMs created from the original ISQ should be recreated. So, it is important that you re-evaluate your newly imported ISQ. It is OK to move the GOBJ from the old directory to the same directly as the newly imported ISQ (it does not have a 'registry' in the database).

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==Import DICOM to Scanco System==
#Load MRI's or CT's DICOM data in Osirix
#Export from Osirix
#*Click export button in top left in osirix.
#*Select "flat" and "decompress all DICOM files"
#Copy files to correct folder in scanco system
#*Use Fillezilla or FTP (make sure it's set to binary mode)
#Use IPL to convert dicom to aim or isq

<pre>
/dicom_to_aim
-aim_name in
-dicom_filename IM-0001-0001.DCM ! Note - choose the first filename of the series
-multifiles true

/convert_unsigned
-input in
-shift_flag false
-divide_by_2 true

/write_v020
-name in
-filename PREOA_023_L_MR.aim
-compress_type bin
-version_020 true

/toisq_from_aim
-aim_name in
-isq_filename MROA023L.isq
-square_flag true
-original_position true''

</pre>

5. Delete dicoms

<pre>
/del *.dcm;1
</pre>

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==Import Xradia *.bin to Scanco System==
Xradia scanner exports a *.bin image that is:

- 16-bit unsigned ! This is "short" (8-bit is char - we don't want this for a grey-scale image)
- 2 bytes per voxel
- little endian notation

To upload this binary image to Scanco database, the steps are as follows:

#Ftp the *.bin to Scanco system using binary transfer (not ascii)
#Convert it to an AIM or ISQ in IPL

$ipl

/import_freeformat
-internal_name in
-file_name BMLPL_006.BIN
-sample_name BMLPL_006
-data_offset 0
-data_dim 1000 1024 1016 !dimensions from header file
-data_el_size 0.013 0.013 0.013 !voxel size from header file
-bytes_per_voxel 2
-data_endian little_endian
-data_type integer
-signed_type unsigned !correct
-multifiles false

/convert_unsigned
-input in
-shift_flag true !shift_flag = TRUE will produce an ISQ/AIM with negative values which may not be visualized properly using uct_evaluation, but keeps the original image resolution.
-divide_by_2 false !divide_by_2 = TRUE will down grade image resolution, but all positive values in an ISQ/AIM will be visualized properly using uct_evaluation.

/write_v020
-name in
-filename test.aim
-compress_type bin
-version_020 true

/from_aim_to_isq
-aim_name in
-isq_filename bmlpl006.isq !ISQ name requires 8 characters
-square_flag true
-original_position true

quit

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

Alternatively the image can be converted to a 16-bit signed in ImageJ (and cropped) before importing to ipl. It then becomes:

- 16-bit signed
- 2 bytes per voxel
- big endian notation

It can then be imported into ipl without the need to run <code>/convert_unsigned</code>.

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==Get Your Files==
===MAC/Linux Options===
====Fetch====
#Download and install [http://fetchsoftworks.com/fetch/|'''Fetch''']
#*This program is free for university staff and students.
#Fill out [http://fetchsoftworks.com/fetch/free|'''a form'''].

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====FTP from Terminal====
#Open a terminal
#*MAC: open the "Applications" folder, choose "Utilities", then "Terminal".
#Navigate to where you want to transfer the files to.
#Connect to the micro-CT ftp server using the ftp command in the terminal:
#*Login with the micro-CT user account and password.
#Navigate to the directory of interest on the micro-CT system.
#*Logicals such as "ur" can be used as short cuts. Whole directory names must be used.
#Set a filename mapping convention to remove OpenVMS version numbers.
#*The command <code>ftp> nmap $1;$2 $1</code> sets anything before the version number to parameter $1 and anything after the version number to $2. The file output will be set to $1, therefore the version number will not be kept.
#Set the file transfer mode.
#*[[File:Important.JPG|20px]] If you transfer an .AIM file in ascii mode, you will receive a "mesh generation" errors and "material ID out of range" message.
#Transfer your files.
#*Option: Turn off prompt so does not ask you whether or not to transfer each file.
#*If you do not turn off the prompt prior to transferring the files, press "a" (for all) to transfer all files at once.
#Exit FTP.

<pre>
$ FTP 136.159.74.231 !Connect to an FTP Server. Need to input user name and password.
$ FTP emily.ucalgary.ca !Connect to an FTP Server. Need to input user name and password.
$ FTP microct@emily.ucalgary.ca !Connect to an FTP Server. Need to input password.

FTP> cd ur !Navigate to the directory containing the target files.
FTP> cd sys$scratch !Navigate to the directory containing the target files.

FTP> nmap $1;$2 $1 !Set a filename mapping convention to remove OpenVMS version numbers.

FTP> bin !Set transfer mode to binary (.aim, .gobj, .isq, and most image file types).
FTP> ascii !Set transfer mode to ascii (.txt, .log, .com, .ps, .pdf and all other files in general).

FTP> put test.aim !Put the file
FTP> get test.aim !Get the file

FTP> prompt !Interactive mode off before transferring multiple files without having to be prompted.
FTP> mput *.aim !Put all files with the .aim extension on the FTP server (mput = multiple put).
FTP> mget *.aim !Get all files with the .aim extension from the FTP server (mget = multiple get).
FTP> mget *.aim; !Transfer the latest version of all aim files in a directory.

FTP> quit !Disconnect from the FTP Server.
</pre>

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===Windows Options===
====Scanco Medical µCT FTP====
#Downlod '''Scanco Medical MicroCT FTP 3.4''' from BoydDrive:\\04 - Resources\04 - Software\Scanco Medical MicroCT FTP 3.4\
#Install the software using the default parameters.
#Click on FTP Connection and input the host to connect to, the username, password.
#Give this profile a name.
#:[[File:Microct_FTP_pic01.jpg|600px]]
#Click on the options tab to set the locations to connect to (e.g., project disk, scratch) and the location on your computer to transfer files to.
#:[[File:Microct_FTP_pic02.jpg|600px]]
#Go back to FTP Connection and press the Connect button.
#*If you are connecting from off campus to the XtremeCT you will need to use the VPN to gain access through the firewall.
#Use the left tree to navigate folders.
#*Use the file filter to search for specific file types or file names (bottom left).
#Select files to download and press the Download Selected Files button (bottom right).
#:[[File:Microct_FTP_pic03.jpg|600px]]
#Press the Exit button to disconnect.

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====Filezilla====
#Download '''Filezilla 2.2.32''' from BoydDrive:\\04 - Resources\04 - Software\Filezilla 2.2.32\
#*This version of Filezilla will remove the OpenVMS version number from files, the new version will not!
#*The left side of the program shows your computer, the right side will show the micro-CT system once you have connected.
#:[[File:Filezilla_pic01.jpg|500px]]
#On the top menu, choose "File", then "Site Manager".
#Create a "New Site" for all the directories that you frequently access.
#*Give the site a meaningful name.
#*For the host, you may connect to "emily.ucalgary.ca" or "sceval.ucalgary.ca".
#*For the logon type choose "Normal" and input the micro-CT user name and password.
#:[[File:Filezilla_pic02.jpg|400px]]
#Click on the "Advanced..." button to set the default remote directory (i.e., on the micro-CT system).
#Set the default local directory if there is a specific location you plan to always transfer files to.
#Setup any additional sites you want then press "Save and Exit".
#:[[File:Filezilla_pic03.jpg|300px]]
#To connect to a session, hold the left mouse button down over the arrow next to the site manager button (computer icon under "File") to bring up your list of sites. Highlight the site of interest then release the mouse button to connect.
#Once connected, you can drag and drop files from the remote site to your local computer.

;*Common FTP locations
{| class="wikitable"
|-
! scope="col"| Account
! scope="col"| Location
! scope="col"| Path
|-
| microct / vivact || Data Disk ||DISK2:[MICROCT.DATA]
|-
| microct / vivact || Projects Disk ||DISK3:[MICROCT.PROJECTS]
|-
| microct / vivact || Scratch Disk ||ADISK1:[MICROCT.SCRATCH]
|-
| invivo / invitro || Data Disk ||DISK4:[BONELAB.DATA]
|-
| invivo / invitro || Projects Disk ||DISK5:[BONELAB.PROJECTS]
|-
| invivo / invitro || Scratch Disk ||ADISK1:[BONELAB.SCRATCH]
|}

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=Remote Access=

== VPN Setup ==

Access to the OpenVMS workstations from campus does not require VPN setup; however, to access from off the campus requires establishing a VPN connection prior to connecting.

*The VPN server is: gpvpn2.ucalgary.ca

*The client needed for VPN connection is '''FortiClient SSL''' which is available through [https://ucalgary.service-now.com/it| UofC IT Service Request] "Order Something".

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== Setup for MAC/Linux ==

=== Terminal and XQuartz ===
You need following to access the MicroCT system remotely.
#'''Terminal''': an SSH client
#*Preinstalled in MAC/Linux.
#'''XQuartz''': an X server for X11 forwarding
#*X11 was previously distributed with Mac OSX but has since stopped.
#*Check if preinstalled in MAC: open the "Applications" folder, choose "Utilities", there should be a file called "XQuartz". No need to open.
#*If not preinstalled, download the most recent [https://www.xquartz.org/ '''XQuartz.dmg'''].
#*Once downloaded, double click the .dmg file to follow the instructions and install.
 
;SSH from terminal
#Open a terminal.
#*MAC: Open the "Applications" folder, choose "Utilities", then "Terminal".
#Type <pre>$ ssh xtremect2@emily.ucalgary.ca -Y</pre>
#*The -Y flag activates X11 forwarding.
#Or type <pre>$ ssh -Y -p22 -c 3des-cbc -o KexAlgorithms=+diffie-hellman-group1-sha1 -o HostKeyAlgorithms=+ssh-dss xt2recalib@emily.ucalgary.ca </pre>
#*Type <pre>$ alias xt2recalib='<ssh command above>'</pre> allows you to only type <pre>"$ xt2recalib"</pre> in the terminal from here on out to access the MicroCT system.
#You're good to go!

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== Setup for Windows ==
=== MobaXterm ===

There is only one program required to access MicroCT remotely: MobaXterm. It will act as both an SSH client and as an X server.

*Download [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Home Edition (Portable Edition)]
 
;Configure MobaXterm
*Run the .exe file after downloading MobaXterm.
:[[File:MobaXterm_init.PNG|500px]]

*Click on "Sessions" -> "User Sessions" and choose "SSH" in the top left of the "Session settings" window.
*Input your host info into the "Remote host" dialogue box such as "emily.ucalgary.ca", check on "Specify username" and input your username such as "xt2recalib" and ensure "X-11 Forwarding" is checked in "Advanced SSH Settings" tab, and click OK.
:[[File:MobaXterm_SSH.PNG|500px]]
 
;Start the session
*Launch the MobaXterm client and under "Sessions" -> "User session" you should have something titled "xt2recalib@emily.ucalgary.ca".
*Double click that session and you're good to go!
:[[File:MobaXterm_Session.PNG|500px]]

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=== PuTTY and Xming ===
There are two programs required:
#'''PuTTY''': an SSH client
#*Download [http://www.chiark.greenend.org.uk/~sgtatham/putty/ '''PuTTY'''] or from BoydDrive:\\04 - Resources\04 - Software\PuTTY.
#'''Xming''': an X server
#*Download [https://sourceforge.net/projects/xming/files/latest/download?source=files '''Xming 6.9.0.31''']
#*Download [https://sourceforge.net/projects/xming/files/Xming-fonts/7.5.0.93/Xming-fonts-7-5-0-93-setup.exe/download '''Xming Fonts''']
 
;Configure PuTTY
*Under categories, expand the "Connection" and "SSH" trees. Click on "X11" and check the "Enable X11forwarding" box.
:[[File:Putty1.png|400px]]
*Under categories, now choose "Sessions".
*Under host name, put in "emily.ucalgary.ca". Choose "SSH" for the connection type.
*Under Saved Sessions, give the session a name (e.g., Emily). Click the "Save" button.
:[[File:Putty2.png|400px]]
 
;Start the Session
*Launch the Xming program, nothing should open except the Xming icon on the task bar.
*Open PuTTY. Double-click on the saved session, which will open a DEC terminal.
*Any program that you run remotely will be displayed by Xming.

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==Remote Access FAQ==
=== MAC Open SSH Authentication Issue ===
You might get an error similar to the following especially after a recent OS update:
Unsupported KEX algorithm "+diffie-hellman-group1-sha1"
command-line line 0: Bad SSH2 KexAlgorithms '+diffie-hellman-group1-sha1
This is not Apple’s fault, it’s OpenSSH version 7. SHA1 is weak, so support for it has been removed. Which is fine, but VMS clients are probably using RSA/SHA1. So until they’re all updated (i.e. never!) we need to re-enable SHA1.

Open a terminal windows and execute the following:
sudo nano /etc/ssh/ssh_config
ENTER YOUR PASSWORD

Locate the line ‘# MACs hmac-md5,hmac-sha1,umac-64@openssh.com,hmac-ripemd160′ and remove the Hash/Pound sight from the beginning.

Locate the line ‘# Ciphers aes128-ctr,aes192-ctr,aes256-ctr,aes128-cbc,3des-cbc’ and remove the Hash/Pound sight from the beginning.

Then paste the following on the end;

HostkeyAlgorithms ssh-dss,ssh-rsa
KexAlgorithms +diffie-hellman-group1-sha1
There’s no reason to reboot, it should work straight away.
 

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=== SSH Speed Issues ===
 
If you notice that the remote display is quite slow, you may prefer to enter the 'manual' X display redirection after connecting with ssh. 
 
The steps to enter the 'manual' X display redirection are outlined in one of Scanco's FAQs found [http://www.scanco.ch/en/support/customer-login/faq-customers/faq-customers-general.html here]. 
Click the "Remote Graphical Access from your PC to the MicroCT" tab (5th tab) and scroll down to "SSH Speed Issue" for more information.

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=== MobaXterm Backspace Issue ===
If the Backspace/Delete key doesn't work on your MobaXterm

#Right-click on a session name on the left column and click "Edit session"
#:[[File:MobaXterm1.png|500px]]
#: 
#Under "SSH" page "Terminal settings" tab, toggle off "Backspace sends ^H" and "Save"
#:[[File:MobaXterm2.JPG|500px]]

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Scanco User Instructions

2021-06-10T20:29:43Z

Yingzhu: /* Extract Results from XtremeCT Database using UPAT_LIST */

=OpenVMS Basics=
The micro-CT scanners in the lab are manufactured by [http://www.scanco.ch Scanco Medical] and most analyses are performed using their custom software. The micro-CT workstations run OpenVMS as its operating system and it is useful to learn some basic commands.

==OpenVMS Beginner's Reference==
OpenVMS (informally known as VMS) is a high-end computer server operating system with reliable, multitasking, real-time and batch processing. OpenVMS supports computer clustering via a LAN, enabling computers to share resources such as processors and disks to balance workload efficiently.

*[http://saf.bio.caltech.edu/vms_beginners_faq.html '''OpenVMS Beginner's FAQ''']

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==Session Manager==

The session manager automatically starts after a user logs in locally. For remote sessions, the session manager can be started with the command <code>$ vue </code>.

[[Image:SessionManager.jpg|600px]]

===Session===
Here you will find an option to "End Session", which you should do when you are finished using a workstation. You can click "Work in Progress..." when you have to leave in the middle of a session without logging out but showing a work in progress screen to other users to prevent interference.

===Views (directory shortcuts)===
The session manager is a graphical user interface that can be used to navigate directories (left side of session manager) and open files (right side of session manager). There are shortcuts to key directories under "Views". Single-click on a directory to list its subdirectories and files. Double-click on a file to open it.

===Commands and Utilities===
Under commands you will find tools such as copy, delete, and rename; however, it is much more practical to do these sorts of operations from a DEC terminal.

===Applications===
Under applications you can launch various applications including:
*DECterm: opens a DEC terminal
*MICROCT: opens the micro-ct control panel (buttons for Scanco Medical programs)
*Mozilla/Netscape: opens a web browser
*XV: opens a screen capture program

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==DEC Terminal and Digital Command Language (DCL)==
This is a DEC terminal: Commands issued in a DEC terminal are DCL commands.

[[Image:decterm.jpg|600px]]

===Copy and paste using the mouse in DEC terminal===
In the DEC terminal, you can highlight text by holding down and moving the mouse. Highlighted text can be pasted into applications or in the terminal using the middle mouse button. You can also highlight files in the Session Manager and paste the filename (with its full path) using the middle mouse button.

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===What is a symbol===
DCL can store information such as strings or integers in "symbols". DCL can also manipulate these symbols to create other symbols.
Symbols are primarily used to define short strings that replace long commands, perform certain calculations and replacements within DCL
procedures, hold status information.
<pre>
$ UR == "SET DEFAULT DISK4:[BONELAB.PROJECTS]" !A short hand to change locations to the project disk.
$ UR :== SET DEFAULT DISK4:[BONELAB.PROJECTS] !Another way to define the symbol without quotations.
$ x == 3 !Store the value 3 in the symbol x.
$ SHOW SYMBOL x !Displays the value of the specified symbol, x.
$ DELETE/SYMBOL/GLOBAL x !Deletes the specified symbol, x.
</pre>
Selected symbols on the Scanco system:
<pre>
$ UD !Changes to the data directory.
$ UR !Changes to the projects directory.
$ DISKS !Shows the current disk usage.
$ DEC !Opens a new DEC terminal.
$ EVE file.txt !Opens the file in the text editor.
$ AIX file.aim !Shows the processing log for an aim file.
$ AIX -L file.aim !The "-L" is used to show the full processing log.
$ QUE !Shows all entries in the queue.
$ GS file.ps or file.pdf !Opens *.ps and *.pdf files in GhostScript.
$ CTHEADER file.isq or file.rsq !Shows scan information for an *.isq or *.rsq file.
</pre>

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===What is a logical===
Logical names are strings, like symbols, but can be passed into programs whereas symbols can usually only be interpreted by the command line interpreter. For example, if the logical name UD was defined to be DISK2:[XTREMECT2.DATA] then UD: could be used as a substitute when entering the path to search for files from within a program.
<pre>
$ DEFINE UD DISK2:[XTREMECT2.DATA] !Defines a logical ud to point to the data directory.
$ DEFINE uct_default_isq myfile.isq !Defines the default isq file for Scanco Medical programs. The isq filename must contain the full path to the file to be evaluated, whereas the path can be left out if you just want to contour the scan.
</pre>
Selected logicals on the micro-CT system:
<pre>
COM !Logical pointing to the commands directory IDISK1:[XTREMECT2.COMMANDS]
UD !Logical pointing to the data directory DISK2:[XTREMECT2.DATA]
UD6 !Logical pointing to the data directory DISK6:[XTREMECT2.DATA]
UR !Logical pointing to the projects directory DISK4:[BONELAB.PROJECTS]
UE !Logical pointing to the evaluation script directory MICROCT_ROOT:[EVAL]
UU !Logical pointing to the templates directory MICROCT_ROOT:[UIL]
UCT_RESULTS !Logical pointing to the results directory MICROCT_USER:[RESULTS]
</pre>

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===Arithmetic operations===
{| class="wikitable"
|style="width: 10%"|Addition ||style="width: 5%;text-align:center;"| + ||The plus sign (+) adds two numbers.
|-
|style="width: 10%"|Subtraction ||style="width: 5%;text-align:center;"| - ||The minus sign (-) subtracts the second specified number from the first specified number.
|-
|style="width: 10%"|Multiplication ||style="width: 5%;text-align:center;"| * ||The asterisk (*) multiplies two numbers.
|-
|style="width: 10%"|Division ||style="width: 5%;text-align:center;"| / ||The slash (/) divides the first specified number by the second specified number. If a number does not divide evenly, the remainder is lost. No rounding takes place.
|}

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===Logical expressions===
{| class="wikitable" style="width: 100%;"
|style="width: 10%"|And||.AND.||The operator .AND. combines two logical values as follows
true .AND. true = true true .AND. false = false false .AND. true = false false .AND. false = false
|-
|style="width: 10%"|Or||.OR.||The operator .OR. combines two logical values as follows
true .OR. true = true true .OR. false = true false .OR. true = true false .OR. false = false
|-
|style="width: 10%"|Not||.NOT.||The operator .NOT. reverses the bit configuration of a logical value. A true value becomes false and a false value becomes true.
|}

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===Numeric comparisons===
{| class="wikitable"
|style="width: 15%"|Equal to||style="width: 5%;text-align:center;"|.EQ.||Compares one number to another for equality.
|-
|style="width: 15%"|Not equal||style="width: 5%;text-align:center;"|.NE.||Compares one number to another for inequality.
|-
|style="width: 15%"|Greater than||style="width: 5%;text-align:center;"|.GT.||Compares one number to another for a greater value in the first number.
|-
|style="width: 15%"|Greater than or equal to||style="width: 5%;text-align:center;"|.GE.||Compares one number to another for greater or equal value in the first number.
|-
|style="width: 15%"|Less than or equal to||style="width: 5%;text-align:center;"|.LE.||Compares one number to another for a lesser or equal value in the first number.
|-
|style="width: 15%"|Less than||style="width: 5%;text-align:center;"|.LT.||Compares one number to another for a lesser value in the first number.
|}

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===String comparisons===
The operators for string comparisons are the same as for numeric comparisons with an added "S" for string.
{| class="wikitable"
|style="width: 15%"|Equal to||style="width: 5%;text-align:center;"|.EQS.||Compares one character string to another for equality.
|-
|style="width: 15%"|Not equal||style="width: 5%;text-align:center;"|.NES.||Compares one character string to another for inequality.
|-
|style="width: 15%"|Greater than||style="width: 5%;text-align:center;"|.GTS.||Compares one character string to another for a greater value in the first specified string.
|-
|style="width: 15%"|Greater than or equal to||style="width: 5%;text-align:center;"|.GES.||Compares one character string to another for greater or equal value in the first specified string.
|-
|style="width: 15%"|Less than or equal to||style="width: 5%;text-align:center;"|.LES.||Compares one character string to another for a lesser or equal value in the first specified string.
|-
|style="width: 15%"|Less than||style="width: 5%;text-align:center;"|.LTS.||Compares one character string to another for a lesser value in the first specified string.
|}

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==DCL Programming Guide==
The OpenVMS systems allow for scripts to be written in a language called '''DCL (DIGITAL Command Language)'''. It was not designed to be more difficult than other scripting languages, but learning any new programming language comes with its learning curve.

*DCL has 243 commands, but most programs can be written with a base set of about 20 commands. The goal of this section is to provide a convenient reference for these commonly-used commands.

It is recommended to open a text editor, enter the whole series of commands, and then run them as a whole program. The terminal on OpenVMS is technically a DCL interpreter, so these commands could be typed in sequence into a terminal with the same result. Typing code interactively is helpful when testing a small code snippet in more detail.

===Your First DCL Script===
Ever since Kernighan and Ritchie wrote the book "The C Programming Language", it has been custom to start with a program that prints the text "Hello, world" to the screen. Open a text editor (for example "EVE") and enter the text below.
<pre>
$! My First DCL Script
$ mymessage = "Hello, world"
$ WRITE SYS$OUTPUT mymessage
$ EXIT
</pre>
Now save the file as HELLO1.COM, and run it using <pre>$ @HELLO1.COM</pre>

Several things are happening in the above program:
*'''Comment !''': The exclamation mark can appear anywhere on the line, and everything following the mark will be treated as a comment.
*'''Variable''': "mymessage" variable is populated with the string "Hello, world", which can be used in the rest of the script.
*'''Command''' "WRITE" send text to various places, in this case to "SYS$OUTPUT", that is to the standard output (i.e. screen).
*'''EXIT''' command tells the DCL interpreter that the script is done and we should exit.
*Commands in DCL are '''NOT case sensitive''', so the command "write sys$output mymessage" would produce the exact same result, but by convention we write commands in all uppercase.

*'''Special Comment !!''' automatically prints the contents of the comment to the screen/logfile. It is useful when you want to know what part of the script you are in.

===Basic Arithmetic===
The DCL language supports several types of data in variables. In the "Hello, world" example above, we saw how to store a string in a variable. We could have stored an integer, that is a positive or negative whole number, in the variable, and done some basic math.
*Refer to [[Scanco_User_Instructions#Arithmetic_operations|'''Arithmetic Operations''']], For example:
<pre>
$ i = 1
$ WRITE SYS$OUTPUT i+1
$ j = 3
$ k = j * (i + 1)
$ WRITE SYS$OUTPUT k
$ WRITE SYS$OUTPUT (k / 4)
$ WRITE SYS$OUTPUT 2 + 2 * 2
$ EXIT
will return:

2
6
1
6
</pre>
Two things are worth noting.
*Because we are limited to integers, division of 6 / 4 needs to return an integer (1.5 is not an integer); the value is truncated, which means rounding is always done toward zero.
*Order of operations is done in the "correct" order, and not left-to-right, so "2 + 2 * 2" is interpreted as "2 + (2 * 2)".

===Conditional Statements===
Sooner or later, you will want to run a program with some logic. The general syntax is:
<pre>
IF [condition]
THEN
[do something]
ELSE
[do something else]
ENDIF
</pre>
*The "ELSE" component is optional.
*If you need a very simple if..then with only one command, it can be written on one line without the "ENDIF":
<pre>
IF [condition] THEN [do something]
</pre>
*Refer to [[Scanco_User_Instructions#Numeric_comparisons|'''Numeric Comparisons''']], [[Scanco_User_Instructions#String_comparisons|'''String Comparisons''']] and [[Scanco_User_Instructions#Logical_expressions|''' Logical Expressions''']] for all possible logical operators (very similar to Fortran).

===Loops===
Most programming languages have 3 kinds of loops:
*Precondition Loops: Condition is tested at the beginning of the loop
*Postcondition Loops: Condition is tested after the loop has executed at least once
*Iterative Loops: A variable changes in a predetermined fashion each time the loop is called.

DCL has none of these. Instead, it has the concept of a "label" and the "GOTO" command. A loop in DCL would look like this:
<pre>
$ i = 1
$loop1:
$ IF i .GE. 10 THEN GOTO exitloop1
$ WRITE SYS$OUTPUT i
$ i = i + 1
$ GOTO loop1
$exitloop1:
$ EXIT
</pre>
This program will print the numbers from 1 to 10 in sequence.

===Subroutines===
Most programming languages allow to define a set of commands that can be called from various parts of the program.
*In DCL, the subroutine can be defined anywhere in the file (unlike C or Python, where the definition must precede the call).
<pre>
$ CALL mycustomsub Joe
$ CALL mycustomsub Mary
$ EXIT
$mycustomsub: SUBROUTINE
$ WRITE SYS$OUTPUT "Hello, ", P1, "!"
$ EXIT
$ ENDSUBROUTINE
</pre>

The first line calls a subroutine named "mycustomsub", which jumps execution to the 4th line. The parameters after the name of the function get copied over to local variables named "P1", "P2", "P3" etc. (in this example, only one parameter, but the maximum is 8) that are available to the subroutine. Note that the command "WRITE" accepts several arguments separated by commas, which get printed on one line.
*The subroutine should be terminated with the command "EXIT" followed by "ENDSUBROUTINE".
*Note that the parameters get passed literally to the subroutine, that is the subroutine gets the text "Joe", and not the contents of a variable named "Joe".
*To force symbol substitution, the parameter would need to be enclosed in single quotes.
<pre>
$ Joe = "Joe Smith"
$ Mary = "Mary Jane"
$ CALL mycustomsub 'Joe'
$ CALL mycustomsub 'Mary'
$ EXIT
$mycustomsub: SUBROUTINE
$ WRITE SYS$OUTPUT "Hello, ", P1, "!"
$ EXIT
$ ENDSUBROUTINE
</pre>

===Reading from files===
Sometimes you have a list of files (for example Micro-CT scans) that are to be processed in a certain way. The obvious way is to copy-paste the code several times, changing only the name of the file, but this is error-prone and inefficient.
*A better way is to put the list of models into a text file, and then call a subroutine on each model file. For example:
<pre>
$ CLOSE/NOLOG foo
$ OPEN/READ foo DISK3:[MICROCT.PROJECTS.OWOC.COM]MYLIST.TXT
$read_loop:
$ READ/END=done foo myline
$ CALL process_me 'myline'
$ GOTO read_loop
$done:
$ CLOSE/NOLOG foo
$ EXIT
$process_me: SUBROUTINE
$ scriptname = DISK3:[MICROCT.PROJECTS.OWOC.COM]MYSCRIPT.COM
$ SUBMIT/NOPRINT/QUE=SYS$FAST/PARAM='P1' 'scriptname'
$ EXIT
$ ENDSUBROUTINE
</pre>
*The first line closes the file handle, in case it was left open in a previous script.
*The second opens the file "MYLIST.TXT" for reading, and assigns the open file a handle named "foo".
*A loop reads the file line-by-line, calling a subroutine with the contents of each line.
*When the end of the file is reached, the file is closed and the script exits.

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==List of basic commands==
<pre>
$ VUE !Start the session manager. Press enter after to regain prompt.
$ DEC !Open a new DEC terminal
$ UCT !Open the micro-CT control panel.
$ UCT_SAMPLE !Start µCT Samples.
$ UCT_MEASUREMENT !Start µCT Tomography.
$ UCT_EVALUATION !Start µCT Evaluation Program.
$ UCT_3D !Start µCT Ray.
$ UCT_BACKUP !Start µCT Disk-Utility.
$ CD UD !Change location to the data directory.
$ CD UR !Change location to the projects directory.
$ CD SYS$SCRATCH !Change location to the scratch directory.
$ CD UCT_RESULTS !Change location to the results directory.
$ DIR UE !List files in the evaluation directory.
$ DIR UU !List files in the templates directory.
$ DIR COM !List files in the commands directory.
$ UCT_LIST !Extract results from the database.
$ AIX -L !View the header of an AIM file.
$ CTHEADER !View the header of an RSQ or ISQ file.
$ EVE !Start the text editor.
$ DISKS !Show the current disk usage (all hard drives).
$ LOGOUT !End a session. For remote sessions, logout from the main (initial) login terminal.
</pre>

===How to move to a different directory===
Use the SET DEFAULT command. You can use an absolute directory path or a relative directory path.
<pre>
$ SET DEFAULT disk:[dir.subdir] !Moves to specified path.
$ SET DEFAULT [.subdir] !Moves one level into subdirectory subdir.
</pre>

Use the CD (i.e., change directory) command (this calls the script $ @SCOM:CD.COM).
<pre>
$ CD subdir !Moves into subdirectory subdir.
$ CD subdir1 subdir2 !Moves into subdirectory subdir1, then into subdir2.
$ CD .. !Moves up one level (i.e., out of one directory).
</pre>

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===How to list the files in a directory===
Use the DIRECTORY command, which may be abbreviated to DIR.
<pre>
$ DIR !List everything in the current directory.
$ DIR disk:[dir.subdir] !Lists everything in the specified directory.
$ DIR disk:[dir.subdir...] !Lists everything in the specified directory and subdirectories.
$ DIR/COL=1 *.aim !Lists all files with the extension .aim in a single column.
$ DIR /VERSIONS=1 !Show only the newest version of each file in the directory.
$ DIR/SINCE=TODAY !Lists all files created today.
$ DIR [...*.aim] !The "..." indicates to do so recursively (i.e., counting all files in all subdirectories).
$ DIR/SIZE !Lists each file and its size.
$ dir/size/grand_total [.subdir...] !List the total size of all files in the SUBDIR directory.
$ HELP DIR !More information on the DIRECTORY command.
</pre>

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===How to copy files===
Use the COPY or BACKUP command.
<pre>
$ COPY file1.ext disk:[dir.subdir1]file2.ext !Make a copy of file1.ext to another location and call it file2.ext
$ COPY *.aim;* disk:[dir.subdir1] !Copy all .aim files (including all versions) to another location keeping the same name.
$ HELP COPY !More information on the COPY command.
</pre>
<pre>
$ BACKUP/VERIFY [.subdir1...]*.*;* [.subdir2...] !Copy entire directory SUBDIR1, including all subdirectories and files, into SUBDIR2.
$ BACKUP/VERIFY [.subdir1...]*.*;* []subdir1.sav/SAVE !Copy entire directory SUBDIR1, including all subdirectories and files, into a save set. The save set could be transferred and unpacked on another OpenVMS machine.
$ HELP BACKUP !More information on the BACKUP command.
</pre>

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===How to delete files===
Use the DELETE command, which may be abbreviated to DEL.
<pre>
$ DEL myfile.txt; !Delete the most recent version of myfile.txt.
$ DEL myfile.txt;* !Delete all versions of myfile.txt.
$ HELP DELETE !More information on the DELETE command.
</pre>
[[Image:Bones2.jpg|20px]] Warning: Extreme caution!
<pre>
$ DEL *.*;* !Delete everything in the current directory!
</pre>

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===How to create a directory===
Use the CREATE/DIR command.
<pre>
$ CREATE/DIR [.subdir] !Creates a subdirectory named subdir.dir in the current directory.
$ CREATE/DIR disk:[dir.subdir] !Creates the subdirectory subdir at the specified path.
</pre>

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===How to rename files and directories===
Use the RENAME command.
<pre>
$ SET FILE/PROTECTION=O:RWED olddir.dir !Sets protections so you can rename the directory.
$ RENAME oldfile.ext newfile.ext !Renames oldfile.ext to newfile.ext.
</pre>

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===How to check the queue===
Use the SHOW QUEUE command, which may be abbreviated to SH QUE.
<pre>
$ SHOW QUEUE !Shows all the queues, there are many!
$ SH QUE *FAST !Shows all queues whose names end with "fast", these are used for evaluations.
$ SH QUE *SLOW !Shows all queues whose names end with "slow", these are used for reconstructions.
$ SH QUE *FAST/ALL !By default you are only shown queue entries for the user you are logged in as. To show jobs for all users, use the /ALL qualifier.
$ SH QUE *FAST/BY=EXE/ALL !Show only jobs that are currently executing for all users.
</pre>

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===How to get queue information===
Use the SHOW ENTRY command to obtain information about batch jobs in the queues.
<pre>
$ SHOW ENTRY !Shows all the batch jobs for your user, there may be lots!
$ SHOW ENTRY 251 !Shows information for batch job number 251.
$ SHOW ENTRY 251/FULL !Shows detailed information for batch job number 251.
$ SHOW ENTRY/ALL !Shows all the batch jobs for all users.
</pre>

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=Micro-Computed Tomography (µCT) Basics=

==User Tutorials==
For Scanco MicroCT Systems and Software:
:*[[Media:Microct-v14.pdf | '''Scanco MicroCT Systems and Software''']]

For XtremeCT II and I:
:*[[Media:SOP Berlin V1.0.pdf | '''Scanco XtremeCT I SOP (Berlin)''']]
:*[[Media:XtremectIIB-v4-us.pdf | '''Scanco XtremeCT II Specs''']]

For MicroCT35, VivaCT40 and VivaCT80:
:*[[Media:ScancoMicro-CT_User_Policy_Guidelines_19052005.pdf| '''MicroCT User Policy & Guidelines''']]
:*[[Media:MicroCT_Starter_Package.pdf | '''MicroCT Starter Package''']] and its [[Media:Microctstarterpackagejun2012.docx| '''Word format''']].
:*[[Media:Scanco-training-uct35-and-vivact40.pdf | '''MicroCT Customer Training Guide''']]
:*[[Media:Vivact_80_v3-nomarks.pdf | '''VivaCT 80 Specifications''']]

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==Micro-CT Image Basics==
Computed tomography is a non-destructive x-ray imaging modality that enables three-dimensional (3D) virtual models of an object to be created, which can be subsequently visualized and analyzed. Micro-CT refers to CT in which the [http://www.scanco.ch/index.php?id=faq_general#c779 resolution] lies in the micro-scale, which is achieved with a high-resolution x-ray detector and a field of view that is much smaller than conventional CT. Structural detail provided by CT depends on differences in x-ray attenuation properties. Components with very different x-ray attenuation properties, for example air, soft tissue, and bone, can be differentiated in a CT scans whereas different types of soft tissues, for example muscle and cartilage, do not have sufficient differences in attenuation to be distinguish.

===Dark Field===
Detector response with x-rays off. Enables corrections of non-uniformities of the detector. Acquired automatically by the scanning software before each scan.

[[File:Dark_field_single.img_assist_custom-400x97.jpg|400px]]

===Bright Field===
Detector response with x-rays on but no sample. Enables corrections of non-uniformities of the x-ray beam. Acquired automatically by the scanning software before each scan.

[[File:Bright_field_single.jpg|400px]]

===Raw Projection===
A raw x-ray projection of a mouse leg. The darker regions correspond with higher x-ray attenuation. The discontinuities result from overlaps where the detector was shifted to acquire the large region of interest (3x2 detector frames in this example). Projections are acquired at many incremental rotations around the sample.

[[File:Raw_projection_notes.jpg|400px]]

===Sinogram===
The sinogram is a different representation of the projection data. The sinogram represents the attenuation values of one row of the detector at each rotational increment around the sample.

[[File:Sinogram.jpg|400px]]

===Attenuation Projection===
Accounting for the inhomogeneities of the detector and beam, we can calculate the x-ray attenuation caused by the sample. Bright regions correspond with higher attenuation.

[[File:Attenuation_projection.jpg|400px]]

===Reconstructed Image===
From the attenuation projections, the original structure can be calculate using filtered back projection.

*[https://youtu.be/DBLYSETYbe8 CT Back-projection Reconstruction]
*[https://youtu.be/NWeM35_KR2w CT Reconstruction of a Head]

[[File:Reconstruction_xy_yz_planes.jpg|400px]]

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==Image Data==
===Image Data Type===
====Binary Images====
Binary images are images whose pixels contain only two possible intensity values (off-on, or black-white B&W). The off or black value is usually 0 and the on or white value is usually 1 (1-bit pixel) or 255 (8-bit pixel). This type of image is commonly used as a multiplier to mask regions within another image.

====Grayscale Images====
Grayscale images represent intensities. Pixels range from least intense (black) to most intense (white). Pixel values usually range from 0 to 255 or are scaled to this range when displayed.

====Indexed Images====
An indexed image uses direct mapping of pixel values to colormap values. Instead of intensities, a pixel value within an indexed image relates to a color value within a color lookup table. An indexed image consists of a data matrix and a colormap matrix. The data matrix can be of class uint8, uint16, or double. The colormap matrix is an m-by-3 array of class double containing floating-point values in the range [0,1]. Each row of map specifies the red, green, and blue components of a single color. Since indexed images reference color tables composed of up to 256 colors, the data values of these images are usually scaled to range from 0 to 255.

====RGB Images====
Within the three-dimensional array of an RGB image, two of the dimensions specify the location of a pixel within an image. The other dimension specifies the color of each pixel. The color dimension always has a size of 3 and is composed of the red, green, and blue color bands (channels) of the image.

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===Image Data Pixel Values===
The image data type is determined by the pixel depth in bits per channel, or bit depth. Bit depth for each channel can be 8, 16, 32 or 64. The data may be signed, unsigned (u), floating-point (f), real or complex (c) for some arithmetic functions, where each channel value is represented by two numbers: real and imaginary part. All channels in an image must have the same data type.

{| class="wikitable"
|-
! scope="col"| Image Data Type
! scope="col"| Name
! scope="col"| Byte
! scope="col"| Value Range
! scope='col'| Comments
|-
! scope="row"| char
| 8-bit signed integer
| 1
| -128 ~ 127
| Scanco SEG.AIM, GOBJ
|-
! scope="row"| uchar
| 8-bit unsigned integer
| 1
| 0 ~ 255
|
|-
! scope="row"| int
| 16-bit signed integer
| 2
| −32768 ~ 32767
| Scanco grey-scaled images, ISQ, AIM
|-
! scope="row"| uint
| 16-bit unsigned integer
| 2
| 0 ~ 65535
| Converted format of Scanco grey-scaled images
|-
! scope="row"| long
| 32-bit signed integer
| 4
| −2^31 ~ 2^31 - 1
|
|-
! scope="row"| ulong
| 32-bit unsigned integer
| 4
| 0 ~ 2^32 - 1
|
|-
! scope="row"| float
| floating point
| 4
| ±3.40282347 E+38
| 32-bit single-precision with 6~7 significant digits
|-
! scope="row"| long64
| 64-bit signed integer
| 8
| −2^63 ~ 2^63 - 1
|
|-
! scope="row"| ulong64
| 64-bit unsigned integer
| 8
| 0 ~ 2^64 - 1
|
|-
! scope="row"| double
| double precision floating point
| 8
| ±1.79769313486231570 E+308
| 64-bit double-precision with 15~16 significant digits
|-
! scope="row"| complex
| floating point complex
| 8
| same as floating-point
| same as floating-point
|-
! scope="row"| dcomplex
| double precision complex
| 16
| same as double-precision
| same as double-precision
|}

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===Scanco Image File Types===

{| class="wikitable"
! scope="col"| Extension
! scope="col", style="width: 65%"| Description
! scope="col"| Creation
! scope="col"| Opens with
|-
! scope="row"| RSQ
| '''R'''aw '''S'''e'''Q'''uence data. This is the raw data collected after the scan. This file contains the bright and dark field corrections and the raw projections. || created with scan || $ x
|-
! scope="row"| ISQ
| '''I'''mage '''S'''e'''Q'''uence data. This is the reconstructed 3D image, which you see in the µCT Evaluation Program. || created from RSQ
| $ uct_evaluation
$ x
|-
! scope="row"| AIM
| '''A'''ny '''IM'''age data. This is a binary raw data format (16-bit signed data, little endian) 3D discretized data you see using the µCT Ray Program and used for the analysis. The AIM file is a volume of interest isolated from the ISQ file. || extracted from ISQ
|$ uct_3d
$ uct_evaluation
|-
! scope="row"| GOBJ
| '''G'''raphical '''OBJ'''ect data. These are the green contours in the µCT Evaluation Program, which are used to isolate regions of interest from an AIM file for analysis. || extracted from ISQ/AIM || $ uct_evaluation
|-
! scope="row"| SCV
| '''SC'''out '''V'''iew || created with scan || $ x
|-
! scope="row"| RAD
| Scout View || created with scan || $ x
|-
! scope="row"| RSW
| raw data (RSQ) || created with scan || $ x
|-
! scope="row"| IMA
| image data (AIM, ISQ, GOBJ)|| created from RSQ || $ uct_evaluation
|}
*Refer to [[Media:Aimpack_documentation.pdf|'''Scanco Aim Format''' ]] or its [[Media:Scanco_Aim_File_Format.doc|'''Doc Format''']] for its header info.

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==Scanco Medical Micro-CT Software==
In the bottom left hand corner of the micro-CT workstation desktop is the micro-CT control panel, from which the micro-CT programs can be launched. The standard operating procedure for scanning a samples involves proceeding through the programs in the control panel from left to right:
<pre>
$ UCT_SAMPLE !Samples: Registering a sample
$ UCT_MEASUREMENT !Tomography: Scanning
$ UCT_EVALUATION !Evaluation: Evaluating the scan
$ UCT_3D !Ray: Viewing the 3D scan
$ UCT_BACKUP !Disk-Utility: Archiving the data
</pre>
You must specify an operator in the control panel to use the scanning and evaluation programs.
* XtremeCT
[[File:XCTcontrol_panel.img_assist_custom-302x100.jpg|300px]]
* MicroCT35, VivaCT40 and VivaCT80
[[File:Uct35_control_panel.jpg|300px]]
[[File:VivaCT40_control_panel.jpg|300px]]
[[File:VivaCT80_control_panel.jpg|300px]]

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===µCT Samples===
The µCT-Samples program is used to register new samples to be scanned and update sample names (e.g., to correct a sample name). To start the program type <code>$ uct_sample</code> in a DEC terminal, or use the sample button.

[[File:Xtremect_button_samples.jpg|40px]]
[[File:Uct_sample_uct35.jpg|40px]]
[[File:Uct_sample_vivact40.jpg|40px]]

#'''Prepare Sample Names''' according to [[Scanco_User_Instructions#Sample_Name_Convention|'''Sample Name Convention''']]
#'''Register Sample Names'''
#*Create a new sample by clicking “New” and typing in your sample name where it says “Name.” “Save” the sample.
#*You are now given a sample number. Record the sample number on the log sheet.
#:[[File:Uct_sample_pic01.jpg|500px]]
#'''Create Additional Sample Names Using Copy and Paste'''
#*If you have many samples to register, you can copy and paste part of the sample name you just created. Highlight the part of the sample name you want to copy by holding down the left mouse button while dragging the mouse, then release the mouse button.
#:[[File:Uct_sample_pic02.jpg|500px]]
#*Paste the highlighted text into a DEC terminal by pressing the middle mouse button. Now highlight the text in the DEC term.
#:[[File:Uct_sample_pic03.jpg|300px]]
#*Go back to the µCT-sample window, click "New", and paste the information next to "Name" using the middle mouse button. Update the name as required and "Save."
#'''Add Additional Sample Details'''
#*When a patient comes in for their first scan, you need to update their sample with their date of birth, sex, and hand/foot dominance.
#*Use the "Find..." button to search for a sample that has already been registered. You can search by sample number or by project name (e.g., CAMOS).
#*Date of birth: DD/MMM/YYYY. Example: 14/JAN/1951
#*Remarks: include the sex and hand/foot dominance. Example: F-RHRF for female that is right hand dominant and right foot dominant

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===µCT Tomography===
The µCT-Tomography program is used to perform a scan.

NOTE: Only Authorized Operators are permitted to use uCT or XtremeCT scanners. For the XtremeCT scanners, this is a formal process. To inquire about authorization, speak to your supervisor. The below description is intended to provide general understanding of how scans are acquired. It is not a substitute for complete training.

To start the program type <code>$ uct_measurement</code> in a DEC terminal on the scanner computer (remote access does not allow this functionality), or use the scanner button. If you use the button, you must specify an operator prior to using the program.

[[File:Xtremect_button_scan.jpg|40px]]
[[File:Uct_measurement_uct35.jpg|40px]]
[[File:Uct_measurement_vivact40.jpg|40px]]
[[File:VivaCT80_scan.jpg|40px]]

[[File:Uct_tomography_pic00.jpg|600px]]

#'''Select Sample'''
#*When the µCT-Tomography program is first started, you will be prompted to enter the sample name or number of the specimen you are about to scan.
#*If you have not registered your sample, press "Cancel" to close the select sample box, then press "New..." in the measurement sample box to register a new sample (see [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT-Samples''']]).
#*Once you have entered your sample information, the measurement sample box will show details for that sample, including the sample name and scan (measurement) history.
#:[[File:Uct_tomography_pic01.jpg|400px]]
#*After your first scan you will need to press the "Other..." button to open the sample selection box and find your next sample.
#'''Select a Controlfile'''
#*The controlfile contains scan parameters such as the x-ray energy, current, and more (see [[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29 controlfiles |'''Controlfiles''']]).
#*Once the controlfile is setup, you need only to select it. If there are many controlfiles, you may want to search for yours using the file filter by entering part of the name or number in the white box and pressing enter; if you do this, you still must click on the controlfile so that it is highlighted in black as shown below.
#:[[File:Uct_tomography_pic02.jpg|400px]]
#'''Precalibrate'''
#*Calibrations are done before loading your patient/animal and scanning for quality control and to reduce the time the patient/animal is under preparation/anaesthesia. Start the calibration by pressing the "Precalibrate" button.
#:[[File:Uct_tomography_pic03.jpg|400px]]
#*Press "Start Calibration". The calibration will start with an "X-Ray Warmup", followed by "Measuring Dark" and "Measuring I0" and usually takes about 2-3 minutes to complete.
#:[[File:Precalibrate.jpg|300px]]
#*The precalibration is good for 15~20 min. The time remaining is shown on the "Precalibrate" button.
#:[[File:Uct_tomography_pic5.jpg|400px]]
#*The precalibrate option cannot be used with batch measurements, and it's not available for MicroCT35 which is not intended for invivo/live scan.
#'''Load and Position the Patient/Sample'''
#*Instruct the patient to remove any jewelry in the scan areas (wrist/ankle/knee/elbow ect). With the patient seated, put the wrist/ankle/knee/elbow into the appropriate cast. Different pads with different sizes can be used to fit the patient.
#*For invivo/invitro samples, prepare your sample in terms of orientation, immobilization, hydration ect.
#*After the precalibration is complete, you can now open the bore cover and insert the patient's wrist/ankle/knee/elbow or sample into the scanner. Gently move the wrist/ankle/knee/elbow or sample into the scanner until you can snap in the cast at the gantry. Check that the cast is positioned correctly and the patient/sample is comfortable.
#*Close the bore cover.
#'''Scout-View'''
#*A scout-view is similar to a 2D x-ray image and allows the user to set where to start and stop the scan.
#*After loading your sample, press the "Scout-View..." button to bring up the scout-view window.
#*The start position (top of the scanner) and end position (bottom of the scanner) can be modified to zoom in on the region of interest.
#*The angle of the scout view can also be changed to see the object in a different orientation.
#*Once pressed the "Scout-View" button but the scout view is found not in an appropriate position, press "Cancel", modify the start position, end position, or angle and press "Scout-View" again.
#:[[File:Scout_view_window.jpg|400px]]
#*Scout view image is displayed in the top right hand corner of the program and will start by showing the right half of the image, followed by the left half of the image.
#'''Set Reference Line and Launch a Scan'''
#*A reference line (solid green line) is placed to set the scan region (green block).
#*Press the "Reference-Line" button to show the reference line and default scan region over the scout view.
#*To change the number of slices to scan, move the reference line to the top of the scan region, then hold down the shift button while dragging the mouse to extend the scan region and press the left mouse button to set the reference line.
#*To centre the scan region between two reference lines, move the reference line to the top of the scan region, then hold down the alt key while dragging the mouse until the second green reference line is in place, then press the left mouse button to set while still holding down the alt key!
#:[[File:Uct_tomography_pic06.jpg|700px]]
#*For a single scan, select "OK", "Scan" and "Start Measurement". Record measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']].
#*For a batch scan which is only available on microCTs, select "Batch Measurement" and record the measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']]. You may now setup a new scan (select new sample and controlfile, perform scout, etc). When you have finished setting up all scans, press "Start Batch Scans." (See [[Scanco_User_Instructions&action=edit&section=48#Perform_Batch_Scans|'''Perform Batch Scans''']] for detailed instructions)
#'''Cancel or Reposition a Scan'''
#*If you need to interrupt a scan, press the cancel button and restart the scan or if you do not want to rescan then "unload" the scanner.
#*If you have not started a scan and need to reposition the patient, you also must "unload" the scanner.
#'''Remove Patient/Sample from Scanner'''
#*After the scanning is complete, open the bore cover and slide the patient's wrist/ankle/knee/elbow or sample out of the scanner. Release the cast by pushing down the cast release handle.

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===µCT Evaluation Program===
The µCT Evaluation Program is used to evaluate a scan. To start the program type <code>$ uct_evaluation</code> in a DEC terminal, or use the graph button. If you use the button, you must specify an operator prior to using the program.

[[File:Uct_evaluation.jpg|40px]]

'''SCREEN SHOT TO BE ADDED SHORTLY'''

#'''Find Your Sample'''
#:Enter the first part of your sample name in the file filter box and press enter. The samples are shown in the left hand box. The measurement box on the right shows scans for the selected sample (highlighted in black). Select a measurement and press "OK."
'''SCREEN SHOT TO BE ADDED SHORTLY'''
#'''Draw Contours (If Applicable)'''
#*Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
#*Contours must always be drawn COUNTER-CLOCKWISE!!!
#*[[Media:Contouring-tools.pdf |'''Contouring tools reference sheet''']]
#*For this sample, we are only interested in viewing the object in 3D and drew contours to isolate the bone and soft tissue from the sample tube.
#:[[File:Uct evaluation pic03.jpg|600px]]
#'''Evaluate'''
#*Scanco Medical provides several standard evaluation scripts. Open the 3D-Evaluation menu either using the "T..." button or from the top menu by going to "Tasks" and "Evaluation 3D...". If you set a default evaluation script in your scanning controlfile, it will be listed under "Task/Evaluation."
#:[[File:Uct_evaluation_pic04.jpg|400px]]
#*If you want to run a different evaluation press "Select...", highlight the evaluation script of interest, and press "OK".
#:[[File:Uct_evaluation_pic05.jpg|400px]]
#*When the 3D-Evaluation window is activated, a white box will appear on your reconstructed image. The white box is the region of interest that will be "cut out" of the full scan. If you have drawn contours, the white box will automatically be adjusted to fit the contours. Adjust the box if necessary by grabbing one of the white handles; use the left mouse button to move the box and the right mouse button to resize. The box can also be resized using the "VOI Start" and "Dimensions" in the 3D-Evaluation window.
#*For most evaluation scripts, you will be required to specify parameters for a Gaussian filter, to reduce noise, and a threshold, to isolate your object (e.g., bone) from the background. Check that the parameters used provide a good representation of your scanned sample by flipping back and forth between the segmented and grayscale image using the "Preview" and "Grayscale" buttons.
#:[[File:Uct_evaluation_pic06.jpg|400px]]
#*When you are satisfied with the segmentation parameters, press "Start Evaluation", which will submit the job to the queue.

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===µCT Ray===
The µCT Ray program is used to view scanned objects in 3D, create images, and create image sequences for animations. To start the program type <code>$ uct_3d</code> in a DEC terminal, or use the 3D object button.

[[File:Uct_3d.jpg|40px]]

'''SCREEN SHOT TO BE ADDED SHORTLY'''

#'''Select and Render Your Sample'''
#*'''Select:''' If you have used the default Scanco Medical scripts, then
#:*If your data is on the "data disk" and you can search for your files using the file filter to select a sample and measurement then press "OK". To open a new file, File --> Open.
#:*If your data is not in the standard location (e.g., it was copied to the projects disk), then use File --> Read and navigate to find the file to open.
#:*Alternatively you can start the program with a file to open <code>$ uct_3d myfile_seg.aim</code>
#: 
#*'''Rendering:'''
#:*Use a single click of the left mouse button to start or to stop rendering the sample.
#:*You can also use the "Start" and "Stop" buttons at the bottom of the options on the left.
#:*You must stop rendering to change viewing options on the left.
#: 
#*'''Change View:'''
#:*To adjust the view, move the "Rotation" and "Elevation" slider bars in the options on the left.
#:*The slider bar is located above its label.
#:[[File:Uct_3d_pic02.jpg|600px]]
#: 
#*'''Change Colours''' (Object and Background):
#:*From the top menu choose "Options" then "Object/Display Properties...".
#:*A segmented image typically only has two values, 0 (black, background) and 127 (white, object). To change the colour of the object only, we need to set the value 127 to a specific colour.
#:*In this example, the slider bar value "1" corresponds with the value 127 and we will set both slider bars to "1" so that we are adjusting values "127 ... 127", in other words, only value "127".
#:*Under "Surface" click on the "white box" to open the "Color Mixing" window.
#:*Choose the new colour for the object (e.g., orange) and press "OK."
#:*Close the "Object Properties" window or move it to the side.
#:*Now re-render the object with a single click of the left mouse button.
#:[[File:Uct_3d_pic03.jpg|300px]] [[File:Uct_3d_pic04.jpg|300px]]
#: 
#*'''Cutplane (left options) and Subdim (top menu):''' 
#:*The cutplane and subdim functions allow you to show a cross-section of your object.
#:*The subdim function tends to work better than the cutplane but is limited to axes of the scan.
#:[[File:Uct_3d_pic05.jpg|600px]]
#: 
#'''Print an Image to File'''
#*An image must be fully rendered in order to be saved.
#*From the top menu choose "File" then "Print". Set the print format to "TIFF" and the directory to "Scratch/Temp" (or another location using the "Specify in Filename" option).
#*Change the filename to something meaningful then press "OK."
#:[[File:Uct_3d_pic06.jpg|300px]]
#: 
#'''Auto-Print Images for an Animation'''
#*Creating an animation involves saving a sequence of rendered images, which can then be compiled into an animated GIF or other video format using various software packages (e.g., Photoshop, Quicktime Pro).
#*From the top menu choose "Options" and "Animation..." to open the Animation Settings window. Set the viewing parameters for the start of the animation, fully render the image, then press the "Get Settings A" button.
#*Set the parameters for the end of the animation, fully render the image, then press the "Get Settings B" button.
#*Set the number of frames you want, the higher the number frames, the smoother the animation will be, but also the larger the file size.
#*Now setup the auto-print feature. From the top menu choose "File", then "Print". Choose "TIFF" for the print format, and the "Scratch/Temp" for the directory (or use the "Specify in Filename"). Specify a filename prefix, to which numbers will be appended for the image sequence.
#*Activate the "Auto-Print" feature. Press "OK" then press the "Start Calculation" button on the Animation Settings window.
#*Do not interrupt the program while the frames are being rendered and saved. When the program is done rendering all the frames, transfer them to your computer to compile into an animation.
#:[[File:Uct_3d_pic07.jpg|200px]] [[File:Uct_3d_pic08.jpg|300px]]

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===XImage===
The XImage program is used to view the raw data (RSQ file) and scout view. To start the program type <code>$ run um:ximage</code> or <code>$ x </code>in a DEC terminal.

When loading an RSQ, the default view (XY plane) is of the sinogram.

[[File:Ximage_1.jpg|600px]]

To view the attenuations, choose the XZ plane. The first slice in this orientation is the dark field, the second slice is the bright field , and slices three and onward are the raw projections (attenuations).

[[File:Ximage_2.jpg|600px]]

To view the corrected projections, from the Evaluations menu, choose Projection Mode.

[[File:Ximage_3.jpg|400px]]

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=Scanning=
==Sample Name Convention==
*At the Bone Imaging Laboratory, all sample naming must conform to the following format
:'''PROJECT IDENTIFIER _ SAMPLE DETAILS'''
*In CAPITAL LETTERS (filenames are case sensitive, so this makes it easy to remember how you input your sample name)
*No special characters (spaces, /, %, etc.) as further evaluations will not work if spaces are present.
:Examples: CAMOS_771, TESTS_0001, TESTS_0002, TESTS_0003

==Register Samples for Scanning==
*Although samples can be registered immediately prior to a scan, it is much more efficient to register all your samples beforehand.
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT Samples''']] for instructional details.

==Log Sheets==
*Log sheets are used to record important information about scans that are performed, such as sample and measurement numbers ect.
*Log sheets are to remain in the lab. If you would like a copy of your log sheets, please make a photocopy or print two copies to record the scan information.
*Use the PDF file to print blank log sheets. Use the Excel file to make your own custom log sheet.

#Bone Lab for General Patients
#*[[Media:XCT_II_Log_(Studies).pdf|'''XCT II Log Sheet for Studies''']]
#*[[Media:XCT_II_Log_(Miscellaneous).pdf|'''XCT II Log Sheet for Miscellaneous''']]
#MicroCT Lab for General Non-Patients
#*[[Media:UCT_log_sheet_general.pdf|'''MicroCT Log Sheet for Studies (PDF)''']]
#*[[Media:UCT_log_sheet_general.xlsx|'''MicroCT Log Sheet for Studies (Excel)''']]

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==Patient Casts and Sample Holders==
===Patient Casts for XtremeCTs===
Regardless of what cast is used, the X-, Y-, and Z- dimensions remain the same:
*X=14cm
*Y=14cm
*Z=designated 20cm distance in the scanner

Standard Scanco Distal Radius Cast
*Used for distal radius scans of 1-3 stacks. Designed with the hand to be in a curved position. The field-of-view allows for scanning of approximately the most distal 1/4 of the forearm.
Standard Scanco Distal Tibia Cast
*Used for distal tibia scans of 1+ stacks. Designed with the foot to be in a flexed (upright) position. The field-of-view allows for scanning of approximately the most distal 1/4 of the tibia.
Standard Scanco Sample Holder
*This is a cylindrical tube with a cut-out window on the top.
*Allows for scanning small ex-vivo and other samples. The tube provides support for the sample during scanning.
*Also used for in-vivo scans of the hand along with a platform that conforms to the hand and slides into the tube.
Elbow Holder
*Used for scans of the elbow. Designed to support the forearm during scanning.
Knee Holder
*A long cylinder cast cut in half lengthwise and with a foot holder at the end. This cast is designed to slide over the gantry tongue, placing the leg further into the gantry, in order to scan at distances closer to the core of the body.
*Used for distal femur and proximal tibia (i.e. knee) scans.
*Used for mid-shaft tibia scans.
*Used for larger ex-vivo and other samples.

===Sample Holders and Scan SOP for microCTs===
====Ex Vivo Sample Holders====
*Ex vivo and inanimate samples are scanned in sample holder tubes. These tubes come in a variety of diameters. It is extremely important that the tube diameter corresponds to, or is smaller than, the field of view (FOV) set in your scanning control file.

*Biological tissues should be hydrated and wrapped in plastic wrap to prevent drying of the sample. Your sample should then be secured in the sample holder using foam to prevent it from shifting around during scanning, which would lead to poor image quality.

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=====Chemical Resistivity of Sample Holders=====
*White tube sample holders are made of PMMA (poly-methyl-methacrylate).
*Yellow tube samples holders are made of PEI (poly-ether-imide).
*Use the yellow tubes if you will need to disinfect the sample holder after scanning.

{| class="wikitable"
!colspan="3"|Thermal and chemical compatibility of sample holders
|-
! scope="col"| Properties
! scope="col"| White Tubes (PMMA)
! scope="col"| Yellow Tubes (PEI)
|-
! scope="row"| Max. Temperature
| +85°C
| +170°C
|-
! scope="row"| Sterilization Steam Autoclave
|non resistant
|resistant (138°C for 20 Min. at 1 bar)
|-
! scope="row"| Water
|resistant
|resistant
|-
! scope="row"| Inorganic Acids
|limited resistance
|resistant
|-
! scope="row"| Inorganic Bases
|non resistant
|limited resistance
|-
! scope="row"| Aldehydes (Formaldehyde)
|limited resistance only in diluted form
|resistant
|-
! scope="row"| Alcohols
|limited resistance
|resistant
|-
! scope="row"| Bleach
|non resistant
|resistant
|}

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=====Mounting of Sample Holders=====
[[File:Uct35_holder.jpg|thumb|right|100px|µCT35 setup]]
*The spindle (metal bit) of the sample holder has a slot, which must be aligned in the scanner or adapter plate.
*The sample holder sits vertically in the µCT35 while horizontally in the VivaCT80 and VivaCT40.
*For the vivaCT40, attach the adapter plate for the tube sample holders to one of the animal bed. The tube sample holders are held horizontally in the vivaCT 40.
:[[File:Vivact40_holder.jpg|thumb|none|700px|VivaCT40 setup]]

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=====Ex vivo rodent scanning SOP=====
*Refer to [[Media:Ex_vivo_scan_sop.pdf|'''Ex Vivo Rodent Scanning''']] for its scan SOP.
*Refer to [[Media:Ex_vivo_scan_sop.docx|'''Ex Vivo Rodent Scanning in docx''']] for its Word version.

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====In Vivo Sample Fixtures and Anesthetic System====
*[[Media:VivaCT40_Anaesthetic_System.pdf |'''Anaesthetic System''']] : You must receive training to use the anaesthetic system.
*[[Media:VivaCT40_Mouse_and_Rat_Tibia_Fixture.pdf |'''Mouse/Rat Tibia Fixture''']]
*[[Media:VivaCT40_Mouse_Lower_Body_Fixture.pdf|'''Mouse Lower Body Fixture''']]
*[[Media:VivaCT40_Mouse_Whole_Body_Tube.pdf|'''Mouse Whole Body Tube''']]

=====In vivo rodent scanning SOP=====
*Refer to [[Media:In_vivo_scan_sop.pdf|'''In vivo rodent scanning''']] for its scan SOP.
*Refer to [[Media:In_vivo_scan_sop.docx|'''In vivo rodent scanning in docx''']] for its Word version.

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====Align whole body device in FOV====

It's important to have your whole sample in the field of view for accurate density measurements.
* Refer to [[Media:wholebody.pdf |'''Align the device''']] for detailed instructions.

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==Scan Parameters (Controlfiles)==

:{| class="wikitable" style="text-align:center;"
|-
! scope="row"| Manufacturer
| colspan="5"|[http://www.scanco.ch '''Scanco Medical AG''']
| [https://www.zeiss.com/microscopy/int/products/x-ray-microscopy.html '''Carl Zeiss X-ray Microscopy''']
|-
! scope="col" rowspan="2"| Model
! scope="col"| XtremeCT II || XtremeCT I || VivaCT80 || VivaCT40 || µCT35 || Xradia 520 Versa
|-
|[[File:XtremeCT.jpg|150px]]
|[[File:XtremeCT.jpg|150px]]
|[[File:VivaCT80.jpg|120px]]
|[[File:VivaCT40.jpg|135px]]
|[[File:UCT35.JPG|150px]]
|[[File:Xradia-520-versa-small.jpg|160px]]
|-
! scope="row"| Application
|colspan="2"| Clinical studies for human extremities in vivo
Horizontal static patient setup
|colspan="2"| Preclinical in vivo animal studies
Horizontal static animal setup
|colspan="2"| High resolution ex vivo specimen scans
Vertical rotational sample setup
|-
! scope="row"| E (KVp)
| 68 || 60
|colspan="3"| 45, 55, 70
| 30 ~ 160
|-
! scope="row"| Power (W)
| 100 || 54
|colspan="3"| 4, 8
|4 ~ 10
|-
! scope="row"| Filter
| Fixed 0.2mm Cu + 1mm Al
(Equivalent 6.7mm Al)
| Fixed 0.1mm Cu + 0.6mm Al
| Default 0.5mm Al,
Air, 0.1mm Al, 0. mm Cu
| Fixed 0.5mm Al
| Fixed 0.5mm Al
| Air, LE1~LE6, HE1~HE6,
customizable filter
|-
! scope="row"| FOV (⌀ * L) (mm^2)
| 140 ⌀ * 200 L
| 126 ⌀ * 150 L
| 31.9 ~ 80 ⌀ * 145 L
| 21.5 ~ 38.9 ⌀ * 148 L
| 7.2 ~ 38 ⌀ * 140 L
(75 L standard)
| 90 ⌀ * 100 L
|-
! scope="row"| Image Matrix
| 4608*4608 ~ 512*512
| 3072*3072 ~ 512*512
| 4096*4096 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
|-
! scope="row"| Voxel Size (µm)
| Standard 60.7
(30.3 ~ 273.4)
| Standard 82.0
(41.0 ~ 246.0)
| 5 ~ 156
| 10.5 ~ 76
| 3.5 ~ 74
| 0.7 ~ 50
|-
! scope="row"| Sample Image
|[[File:XCT2_human_distal_femur.png|160px]]
human distal femur
|[[File:XCT1_human_distal_tibia.JPG|160px]]
human distal tibia
|[[File:VivaCT80_Rat_distal_femur.JPG|160px]]
rat distal femur
|[[File:Vivact40_in-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Uct35_ex-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Xradia_mouse_distal_femur.png|160px]]
mouse distal femur
|}

Controlfiles are used to specify the parameters for the scans. Once your controlfile is setup, you should not modify it over the course of your project.

[[File:XCT2 ControlFile.JPG|right|600px]]

*'''Control File Name''': Specify a meaningful name so that others can reuse yours.

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===General Settings===
*'''Holder Type''': Choose the used holder type for XtremeCT II from Standard Casts, Knee Cast and Elbow Cast. No option for XtremeCT I scanner. For microCTs, Choose the used sample holder type with the correct diameter.

*'''Mode of operation''': Default is continuous operation for all scanners. Gated operation mode is available for VivaCT80 and VivaCT40 scanners.

*'''Evaluation Script''': This sets the default evaluation script used for the analysis. You can manually select a different script from the evaluation program.

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===X-ray Settings===
*'''Tube Energy (KVp)''': Fixed energy for XtremeCTs while having 3 options for each of microCTs: Use the 70 KVp for most samples, use the 55 or 45 KVp for low density objects (e.g., soft tissue) or specimens with a diameter less than 20 mm. Lower energies provide better contrast while higher energies provide better signal to noise (SNR).

*'''Tube Current (µA)''': Fixed current for XtremeCTs while having 2 options for each of energy settings of each microCTs: Use the higher current except when the voxel size is set for the best resolution of the scanner. The higher current will yield better SNR but a larger spot size.

:{| class="wikitable" style="text-align:center;"
|-
! scope="col"|
! scope="col"| XtremeCT II
! scope="col"| XtremeCT I
! colspan="3"| vivaCT80，vivaCT40， µCT35
|-
! scope="row"| E (KVp)
| 68
| 60
| 70
| 55
| 45
|-
! scope="row"| I (µA)
| 1470
| 900
| 114, 57
| 145, 72
| 177, 88
|-
! scope="row"| Power (W)
| 100
| 54
|colspan="3"| 8, 4
|}

*'''Filter''': Fixed filter settings for all scanners except VivaCT 80 has 4 filter options.

*'''Calibration''': This sets the mu scaling factor, density and beam hardening correction used for the reconstruction. For standard patient scans use 200 mg HA/cm3. For ex vivo bone scans, use 1200 mg HA/cm3, for soft tissue use the plexi scaling, and for non-biological tissues use the aluminum scaling.

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===Scout-View Settings===
Normally you will want to enable this and here you can specify the default start and end position, and scout-view angle, which you may override for each scan.

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===CT Scan Settings===

*'''Resolution''': This setting includes the reconstruction matrix size (2048x2048, 1536x1536, 1024x1024, or 512x512) and the number of projections per 180°. The lower the resolution setting, the better the SNR and larger the voxel size.

*'''FOV / Diameter''': This field of view must fully contain the sample holder for accurate density measurements. Fixed FOV for XtremeCTs while having 5 options for each of microCTs: If you choose a smaller FOV than the sample holder, the scan may be aborted to prevent damage to the scanner. For the best resolution, you should choose the smallest holder that contains your sample.

*'''Voxel Size''': The nominal isotropic voxel size is determined by the FOV and the reconstruction matrix.

*'''Number of Slices''': You can specify a specific number of slices or image stacks to acquire (1x110 = 1 image stacks of 110 slices). The scan time increases with each image stack, therefore pay attention to the stack boundaries (e.g., 111 slices will take 2x longer to scan than 110 slices).

*'''Rel Position of First Slice''': This option enables you to offset the scan region from the reference line. This is useful for scanning a region a specific distance from the growth plate or centering the scan region around the reference line. If you disable the scout view, then the position is relative to the absolute 0 position of the scanner (top of the sample holder for the µCT35 and towards the back of the scanner for the vivaCT40).

*'''Integration Time''': The higher the integration time, the better the SNR and longer the scan time. Use 100 ms for patient scans and higher values for ex vivo scans of better image quality. To get the highest integration time, uncheck the "Continuous ROT" button. For standard microCT measurements, use ~400 ms for the µCT35 and ~200 ms for the vivaCT40. The maximum integration time is scanner-specific and limited to prevent saturation of its detector.

*'''Average Data''': This is often referred to as frame averaging and is used to improve a scan's SNR. Multiply the average data value by the integration time to calculate the effective integration time. Only use this if the integration time is maxed out.

*'''Measurement Time''': This is the estimated scan time without the time performing the scout view or warm-up of the scanner.

*'''CTDIvol''': Computed Tomography Dose Index (CTDI) is a standardized measure of radiation dose output of a CT scanner for scanner settings' comparison purposes only, and it represents the average absorbed dose along the longitudinal axis from a series of contiguous CT exposures. Volumetric CTDI is the ratio of the weighted-CTDI to the level of overlap between slices (pitch). CTDIvol has no consideration of real scan length and does not represent actual dose administered to the patient.
:[[File:CTDI.JPG|600px]]

*'''DLP''': Dose Length Product DLP = CTDIvol * Scan Length in unit of mGy-cm.

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====XtremeCT II Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 4608
| 2304
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 3000
| 900
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 140 mm
| 30.3
| 60.7
| 91.1
| 136.7
| 273.4
|-
! colspan="2"| Slices/Stack
| 338
| 168
| 112
| 74
| 37
|-
! colspan="2"| Stack Thickness (mm)
| 10.24
| 10.20
| 10.20
| 10.12
| 10.12
|-
! colspan="2"| Time/Stack (min, at 43 ms Integration Time)
| 8.1
| 2.0
| 2.0
| 1.4
| 0.7
|-
! colspan="2"| Time Current Product (mAs)
| 238
| 71
| 59
| 40
| 20
|-
! colspan="2"| CTDIvol (mGy)
| 37.4
| 11.2
| 9.3
| 6.4
| 3.2
|-
! colspan="2"| DLP (mGycm)
| 38.3
| 11.4
| 9.5
| 6.4
| 3.2
|}

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====XtremeCT I Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 3072
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 126 mm
| 41
| 82
| 123
| 246
|-
! colspan="2"| Slices/Stack
| 221
| 110
| 73
| 36
|-
! colspan="2"| Stack Thickness (mm)
| 9.06
| 9.02
| 8.98
| 8.86
|-
! colspan="2"| Time/Stack (min, at 100 ms Integration Time)
| 3.7
| 2.8
| 1.9
| 1.0
|-
! colspan="2"| Time Current Product (mAs)
| 114
| 86
| 57
| 29
|-
! colspan="2"| CTDIvol (mGy)
| 7.3
| 5.5
| 3.6
| 1.9
|}

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====VivaCT80 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 3072
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1500
| 1000
| 500
| 250
| 125
|-
! rowspan="6"| Voxel Size (µm)
! scope="row"| FOV/Diameter 31.9 mm
| 10.4
| 15.6
| 31.9
| 31.2
| 62.4
|-
! scope="row"| FOV/Diameter 35.9 mm
| 11.6
| 17.5
| 35
| 35
| 70.1
|-
! scope="row"| FOV/Diameter 39.9 mm
| 13
| 19.5
| 39
| 39
| 78
|-
! scope="row"| FOV/Diameter 49.8 mm
| 16.1
| 24.2
| 48.5
| 48.5
| 97.1
|-
! scope="row"| FOV/Diameter 63.9 mm
| 20.8
| 31.2
| 62.4
| 62.4
| 124.8
|-
! scope="row"| FOV/Diameter 79.9 mm
| 26
| 39
| 78
| 78
| 156
|-
! colspan="2"| Slices/Stack
| 333 ~ 328
| 222 ~ 219
| 111 ~ 109
| 111 ~ 109
| 55 ~ 54
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 14.9
| 10.0
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 73
| 48
| 24
| 12
| 6
|}

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====VivaCT40 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 21.5 mm
| 10.5
| 21
| 21
| 42
|-
! scope="row"| FOV/Diameter 25.6 mm
| 12.5
| 25
| 25
| 50
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 35.8 mm
| 17.5
| 35
| 35
| 70
|-
! scope="row"| FOV/Diameter 38.9 mm
| 19
| 38
| 38
| 76
|-
! colspan="2"| Slices/Stack
| 213
| 106
| 106
| 53
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 9.9
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 61
| 31
| 15
| 8
|}

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====µCT35 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 7.2 mm
| 3.5
| 7
| 7
| 14
|-
! scope="row"| FOV/Diameter 12.3 mm
| 6
| 12
| 12
| 24
|-
! scope="row"| FOV/Diameter 20.5 mm
| 10
| 20
| 20
| 40
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 37.9 mm
| 18.5
| 37
| 37
| 74
|-
! colspan="2"| Slices/Stack
| 232 ~ 235
| 116 ~ 117
| 116 ~ 117
| 58
|-
! colspan="2"| Time/Stack (min, at 400 ms Integration Time)
| 23.9
| 12.3
| 6.5
| 3.5
|-
! colspan="2"| Time Current Product (mAs)
| 119
| 60
| 30
| 15
|}

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===Advanced Settings===
*'''Number of Det-lines (for Scout-View)''': Defines how many lines on the detector shall be used during the Scout-View. Using all available lines provides faster Scout-Views but some faint horizontal lines might be seen between the stacks. Limit the number of lines to a small number to obtain Scout-Views without these artifacts but the time of the Scout-View will increase.

*'''Number of Det-lines (for CT-scan)''': Defines how many lines on the detector should be used. This number influences the number of slices within a stack. Limit the number of detection lines if you see residual cone beam artifacts.

*'''FOV/Scan Diameter''': Chose the diameter of the FOV. This action is cropping the area of the detector.

*'''Software binning''': factor of the pixels on the detector.

*'''Hardware binning''':

*'''Samples''': number of (possibly binned) pixels on the detector that are used for each slice (note: this number is given for the whole FOV).
*'''Proj/180°''': number of projections taken per 180° turn of the sample.

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===Reconstruction===

*After each image stack is acquired, it is automatically submitted to the queue (sys$slow) for reconstruction. The reconstruction for each image stack is split into four jobs to make efficient use of processors.
*The reconstruction time depends on the resolution setting, with low resolution scans reconstructing faster than high resolution scans. Normally scans are reconstructed within a day or two.
*It is possible to resubmit a scan for reconstruction (refer to [[Scanco_Administration#Reconstruction | '''Scanco Administration's Reconstruction''']]) for details. This may be necessary or desirable for several reasons:
#The sample did not reconstruct properly (e.g., due to a power failure)
#To reconstruct the object at an angle (e.g., so that the anterior surface of a bone is always in the same direction).
#A new beam hardening correction was applied to the sample
#The scaling was changed for the sample to change the brightness

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==Perform a Scan==
===Perform a Single Scan===
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] for instructional details.

===Perform Batch Scans===
*Batch scan mode is only available on microCT scanners.
*Batch scans can be setup for different regions of interest (ROI) within a sample or for different samples contained within a sample holder.

#'''Setup the First Scan'''
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] to use the "Other..." button to find your sample number, choose a controlfile, perform a scout view (a mouse's whole body in this example), use the reference line to setup the first scan region (mouse skull in this example).
#*To add a batch scan press the "Batch Measurement" button.
#:[[File:Batch_scan_01.preview.jpg|600px]]
#*An information window is displayed with the scan measurement number. Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']] then press "OK" to close the window. An entry is also added to the measurement history for the sample.
#:[[File:Batch_scan_02.preview.jpg|600px]]
#'''Setup the Next Scan'''
#*Using the "Other..." button, find your next sample number, choose a new control file (if desired).
#*If the next region of interest or sample is not in view of the current scout view, adjust the parameters of the scout view and obtain a new one.
#*Use the reference line to set a new scan region (upper limbs in this example).
#*To add a batch scan press the "Batch Measurement" button.
#*As the first scan, a measurement number is assigned for this new scan. Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']].
#:[[File:Batch_scan_03.preview.jpg|600px]]
#*Repeat this process until you have added all your scans.
#'''Start the Batch Scans'''
#:There are two ways to start a batch scan:
##Click the "Start Batch Scans" button: the program will automatically close so that control of the scanner can be allotted to the queue.
##Exit the scanning program.
#:[[File:Batch_scan_04.preview.jpg|600px]]
#'''Check the Queue'''
#*Batch jobs will be submitted to the SCEVA2_BATCH queue for µCT35 or SC5019_BATCH queue for vivaCT40.
#*Initially the jobs will show up as temporary (TMP) jobs:
#:[[File:Batch_scan_05.preview.jpg]]
#*After about 30 seconds, the sample number will show up in entrie names:
#:[[File:Batch_scan_06.preview.jpg]]
#'''Request an Email Notification'''
#*There is a script in the commands (com) directory that will put an entry into the batch queue to send an email. Run the script and input parameters (queue and email) as prompted.
#:[[File:Batch_scan_07.preview.jpg]]
#'''Cancel a Batch Scan'''
#*For errors made during batch scan setup, to cancel a scan in progress, or to cancel a pending scan.
#:[[File:Batch_scan_08.preview.jpg]]
#*If you cancel all the scans and the scanner door does not unlock automatically (µCT 35 only), then start the measurement program and the scanner will unload, unlocking the door.

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==Action on Image Artifacts==
===Rescan for===
*'''Motion Artifacts'''
*'''Sample Out of the Field of View'''

===Contact Scanco Medical for===
*'''Ring Artifacts''' (Bad Detector)
:*Ring artifacts are caused by a faulty detector pixel and show up in the reconstructed image as a full or partial white circle.
:*For uCT scanners: When noticed, please notify lab technicians who will contact Scanco Medical to perform a "Pixel Correction", which will correct this artifact for future scans and can be used to update previous scans. You should not rescan the sample if there is a ring artifact.
:*For XtremeCT scanners: A small number of rings artifacts are expected and acceptable. For a 168-slice scan, ring artifacts present in <5 slices total is acceptable. If you observe ring artifacts in a larger number of slices, notify a staff member. Do not repeat scans for ring artifacts. In most cases, it is also unnecessary to perform a correction to already acquired data.
<div><ul>
<li style="display: inline-block;"> [[File:Ring_artifact.jpg|thumb|none|350px|Image with Ring Artifact]] </li>
<li style="display: inline-block;"> [[File:Ring_artifact_corrected.jpg|thumb|none|350px|Same Image after with Detector Correction]]</li>
</ul></div>

*'''Bad Centre Calibration Values'''
*'''Defective Shutter Artifact'''

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=Evaluation=
==Evaluate a Scan==
*To evaluate a scan, refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.

===Open default ISQ===
You can load a defualt ISQ usig uct_evaluation program:

<pre>
$ def uct_default_isq DISK3:[MICROCT.PROJECTS.VALIDATION.MODELS]C0000123.ISQ ! or
$ def uct_default_isq DISK2:[MICROCT.DATA.00001234.00005678]C0003456.ISQ
$ uct_evaluation
</pre>

Hit <code>cancel</code> when asked files to load, and the file you just set as default will be loaded.

*Use the whole pathname for ISQ.
*If you don't import your data into the system, you cannot store your evaluation results in the measurement database. You will have to use the LOG file to access your results.
*Only start a 3D evaluation if and only if the sample (patient) and measurement index are correct in the ISQ full path! Also, no results will be stored in the database unless the ISQ header info (samp/meas) is correct.
*Many of the UCT_xxx.COM scripts use the whole filename to extract the sample and measurement numbers, so it is possible that some evaluations will not run. UCT_xxx_BATCH_V4.COM is an example of an evaluation that will not run, but UCT_CUTOUT.COM will run (doesn't need any sample/meas info).

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==Draw Contours==
*Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
*Contouring is the first step in the analysis process, which allows you to segment the desired bone from surrounding tissues.

===Contouring Tools Reference Sheet===
*[[Media:Contouring-tools.pdf |'''Contouring Tools Reference Sheet''']]
*Contours must always be drawn COUNTER-CLOCKWISE!!!

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===Contour and Run the Standard Patient Evaluation===
The following instructions are for contouring standard patient radius and tibias.

#Open the Evaluation Program and select your sample.
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.
#Zoom into the desired bone (Radius or Tibia)
#*Using the zoom menu from the top panel, zoom into the Radius or Tibia.
#*Usually 3x zoom is appropriate.
#Draw contours roughly around the bone.
#*Select the first contouring tool (top left button) and draw COUNTER-CLOCKWISE.
#Automatically generate contours for all slices in the scan.
#*Double click the image to bring up the contouring window.
#*Double click again and the program will attempt to snap the contour to the bone. Double click again if needed.
#*Select Forwards, and then Iterate Forwards to have the evaluation program automatically segment the bone.
#Modify any contours as needed.
#*Select the second contouring tool (2nd button from top) to fix any "wrong" contours.
#*Draw COUNTER-CLOCKWISE!!
#*If many contours cannot be automatically generated correctly i.e. cortical bone is porous and evaluation program misses a lot of bone, it may be better to use the Range/Morph function rather than fixing each individual slice.
##This is done by first clearing all the breakpoints (Clear all BP in contouring window). The boxes will now become red.
##Manually fix the slice that does not have the correct contour automatically drawn, skip a few slices and manually fix that slice as well. The slices that you have fixed will turn green, indicating that it is a breakpoint (BP).
##Now you can morph between the two breakpoints (BP, green boxes) you have just created. Select the BP with the higher slice number, select range (first column on left) from the contouring window, followed by morph (second column from left).
#Save Contour (.GOBJ): Make sure you save your work!
#Run the 3D Standard Evaluation for your specific project (and timepoint).
#*Select 3D evaluation under Tasks to bring up the window. You'll then need to Select... the evaluation specific for your project.
#*There are a variety of evaluations to choose from, you can search for your project's evaluation script by typing in the name of your project in the filter window.
#Check the queue to ensure that the evaluation is running properly.
#*Type <code>$ show que</code> in a terminal window will allow you to see all running processes.

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===Correct Trabecular Contours and Run the Cortical Evaluation===
Once the standard evaluation has been completed, an auto-segmentation process is completed to segment the cortical from the trabecular bone. However, the auto-segmentation is not always accurate, and hence the contour (TRAB.GOBJ) will need to be checked.

#Load TRAB.GOBJ by selecting File, then load GOBJ from the top panel.
#*You will now see a list of all GOBJ files pertaining to your sample. You'll need to load the TRAB.GOBJ.
#*When the TRAB.GOBJ has loaded, you will see that the loaded contour is between the cortical and trabecular bone.
#Correct contours as needed
#*Can manually adjust the slices or use the Range/Morph function.
#*Remember to draw COUNTER-CLOCKWISE!
#Run the 3D cortical evaluation for your specific project (and timepoint, if relevant).
#*Select 3D evaluation under Tasks to select the appropriate evaluation script.

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==Evaluation Scripts==
===Scanco Standard Evaluation Scripts===
The following are descriptions of some of the standard evaluation scripts provided by Scanco Medical.

*'''3D Segmentation of VOI, 1 solid object'''
:Produces a 3D segmented (binary) object with values 0 (background, hidden) and 127 (solid). Input Gaussian filtering and threshold parameters. Draw contour to isolate the object of interest (optional).

*'''3D Seg. of 2 VOIs: solid dense in transparent low dens obj'''
:Produces a 3D segmented object with values -1 (transparent), 0 (background, hidden), and 127 (solid). Input two sets of Gaussian filtering and threshold parameters (input the second set by pressing the red 2 button). The preview shows the solid object in white and the transparent object in red. Draw one contour to isolate the object of interest (optional). This script is useful for showing soft tissue and bone.

*'''Bone Trab. Morphometry (3D Seg, 3D Calc, Print Sheet)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour to isolate the trabecular bone. Performs model-independent (direct) measurements on the trabecular region. Outputs: BV, TV, BV/TV, TbBMD, TbTMD, BS, SMI, DA, ConnD, TbTh, TbThSD, TbSp, TbSpSD, TbN, and Tb1/NSD.

*'''BV/Density only Bone Eval. (3D Seg, BV and Dens Calc, Print)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour to isolate the region of interest. Outputs: BV, TV, BV/TV, BMD, and TMD.

*'''Bone Midshaft Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour on the outer surface of the bone. Outputs: BV, TV, BV/TV, BMD, TMD, and moment of inertia parameters.

*'''Bone Midshaft more than e.g. 50 slices Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour on the outer surface of the bone. If you wish to exclude the medullary area from the analysis, then draw a counterclockwise contour on the outer surface of the bone and a clockwise contour on the inner surface of the bone. Performs direct measurements in addition to the standard midshaft analysis. Outputs: BV, TV, BV/TV, BMD, TMD, moment of inertia parameters, Th, and Sp.

*'''Convert to TIFF'''
:Converts the grayscale data to TIFF slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Convert to DICOM'''
:Converts the grayscale data to DICOM slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Reformat to Axial Cuts'''
:Flips the dataset from the XY plane to the XZ or YZ planes (specify in the advanced options for the script). This is useful if you want to contour your sample in a different plane. The flipped sample is imported as a new measurement under the same sample number as the original data.

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===Understanding Evaluation Scripts===
Following are some example evaluation scripts full of comments to promote understanding:
*[[Media:IPLV6_VOI.pdf|IPLV6_VOI script]]
*[[Media:IPLV6_MIDSHAFT.pdf|IPLV6_MIDSHAFT script]]
*[[Media:IPLV6_TRABECULAR_BONE.pdf|IPLV6_TRABECULAR_BONE script]]

===Setup Customized Evaluation Scripts===
To setup an evaluation script customized to your project, in the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']]:
*Choose "Scripts" then "Import from" then "TEMPLATES", pick a Scanco Standard Evaluation Scripts and Save.
*Choose "Scripts" then "Modify". Choose the script that was just imported and click "OK", Change the name of the script.
*Modify the default segmentation and other parameters for the script. When finished making changes press "Save" then "OK".

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==Image Processing Language (IPL) Scripting==
The following documentations related to IPL scripting, as it applies to image analysis was compiled by Jan Owoc in July 2013 based on numerous sources including own experience.

===Your First IPL Script===
*'''Prerequisite''': you are familiar with navigating the VMS system.
*'''"$" or "ipl>"''': the DCL and IPL prompts respectively, and you should only type the text after the prompt.
*If you FTP the file to the OpenVMS system, ensure you use "binary" to transfer the file.
You can run these commands on almost any greyscale AIM file. Example file here: MJ7101.AIM

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====Interactive IPL====
*Command <code>$ ipl</code> starts IPL interactively, that is you see the result of each command as you run it.
*While it is useful for testing, running large scripts interactively may interfere with others using the computer.
 
*'''Reading an AIM file'''
:Before you can run any analysis on the AIM file, you need to read it into IPL and assign it a file handle. This is done using the command <pre>ipl> read in MJ7101.AIM</pre>
:A fraction of a second later, the file should have been read into memory and assigned the internal name "in". If we want to do some basic density calculations on it, we can use the command<pre>ipl> vox_ in 0</pre>
:*IPL, much like DCL, will automatically complete the command if it is given enough characters.
:The "vox_" was expanded to the command "vox_scanco_param" (calculates voxel-counting parameters) and told you that the mean density of the cube is 114 mg HA/cm3 and a standard deviation of 283 mg HA/cm3.
:The argument "in" is the internal name of the image.
:The argument "0" is the region. The command vox_scanco_param supports several numbered regions if, for example, you wanted to separately compute the density for the trabecular region and the cortical region.
 
*'''Segmenting an AIM file'''
:Some parameters, like average density, are computed from the [[Scanco_User_Instructions#Grayscale_Images|'''Greyscale Image''']]. Other parameters, like the trabecular number, require an image that has been segmented to [[Scanco_User_Instructions#Binary_Images|'''Binary Images''']], that is converted into "bone" and "not bone".
:There are many ways to separate bone from non-bone, and parameters that work well for one dataset will not generally work for images of different samples, or acquired at different resolutions.
:One of the simplest segmentation methods "seg_gauss" is to apply Gaussian smoothing to the sample, to eliminate the noise present in the image, followed by a semi-arbitrary threshold that preserves the trabecular structure.
<pre>
ipl> seg_gauss in seg

-sigma [1.000000] >
-support [2] >
-lower_in_perm_aut_al [300.000000] >
-upper_in_perm_aut_al [100000.000000] >
-value_in_range [127] >
-unit [0] > 2
</pre>
:seg_gauss expects 8 parameters, and we have provided only 2. It will now prompt us for the remaining 6 one-by-one.
:Leave everything at the defaults (simply hit "Enter") except the unit, which we will change to "2".
:For young human trabecular bone from the distal tibia scanned at 20 um in the uCT 35, but then downscaled to 80 um, the above parameters give a reasonable representation of the trabecular structure. With other bones at other resolution, you may need to change the sigma, the support, and the lower threshold.
:The unit of "2" simply means that we are working in units of mg HA/cm3.
:Now that the cube is segmented, we can run the same voxel-counting command as above and obtain more information. <pre>ipl> vox_ seg 0</pre>
:We now know that our combination of smoothing and threshold resulted in an object volume of 103 mm3 (i.e. volume of bone) and a bone volume ratio of 22.88%.
 
*'''Writing out a file'''
:we can write the segmented file out for future use. Accept the defaults for the remaining arguments. <pre>ipl> write seg MJ7101_SEG.AIM</pre>
:Now you can quit IPL and verify that the segmented file has been written out. <pre>ipl> quit</pre>

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====Batch IPL====
*Command <code>$ ipl_batch</code> starts IPL inside a script that would be submitted to a queue.
While the following code is likely to work, it is not very readable:
<pre>
$ IPL_BATCH
read in MJ7101.AIM
vox_ in
seg_gauss in seg 1 2 300 100000 127 2
vox_ seg
write seg MJ7101_SEG.AIM
..
$ EXIT
</pre>
*Instead, it is recommended that you copy and paste the "pretty" output of the command after you have run it once interactively.
*Values that are likely to change should be variables, defined at the top of the script.
*To substitute a variable from DCL into IPL, use a double-quote character before the variable name, as shown in the example below.
Copy and paste the below into a text editor.
<pre>
$ modelname :== MJ7101.AIM
$ threshold == 300
$ outputfile :== MJ7101_SEG.AIM
$
$ IPL_BATCH

/read
-name in
-filename "modelname

/vox_scanco_param
-input in

/seg_gauss
-input in
-output seg
-sigma 1.000000
-support 2
-lower_in_perm_aut_al "threshold
-value_in_range 127
-unit 2

/vox_scanco_param
-input seg

/write
-name seg
-filename "outputfile

..
$ EXIT
</pre>
Now, it is clear what the full names of the commands are, and what the parameters mean.
*If a parameter isn't important and can be left at the default (for example the region number during vox_scanco_param), you can leave it out of the file.
Save the file as MYSCRIPT.COM and run it using <code>@MYSCRIPT.COM</code>.

 
*'''Submitting to the queue'''
:As mentioned in the introduction, running IPL interactively on larger models negatively impacts other users of the system. Copying the commands to a file and running it from the command line has the same effect.
:*The correct way to run larger scripts is to submit the job to the queue. <pre>SUBMIT/QUE=SYS$FAST MYSCRIPT.COM</pre>

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===IPL Reference===
*[[Media:SCANCO_-_Software_-_IPL_instruction_manual_0.pdf|'''Official Scanco IPL Documentation''']]
*[[Media:scanco-software-ipl-instruction-manual.pdf|'''Scanco IPL Manual]]

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====Standard Read Write etc. Functions====
*'''/read''': Reads a file into ipl and gives the file an internal name
*'''/aim_read''':
*'''/read_versatile''':
*'''/write_v020''': Writes an aim file to the directory in which ipl is open (or specified directory if in a script)
*'''/write_new''':
*'''/write_part''':
*'''/copy''': Copies an internal file (a file that is already in the ipl system) and allows the copy to be given a new name.
*'''/delete''': Deletes an internal file (a file that is already in the ipl system)
*'''/rename''': Changes the name of the file (input is the old name and output the new name)
*'''/list''':
*'''/options''':
*'''/release_history''':
*'''/commands_write_log''':

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====Segmentation Functions====
*'''/gauss_lp''': Applies a low pass gaussian filter with specified sigma and support values
*'''/fft_laplace_hamming''':
*'''/median_filter''': Applies a low pass median filter to reduce unwanted noise in an image
*'''/seg_gauss''': Segments aim files using the input sigma of gauss and the filter support for gauss. A threshold can also be applied using this function.
*'''/threshold''': Removes data outside of the specified range
*'''/absolute_threshold''':
*'''/adaptive_threshold''':
*'''/adaptive_iter_threshold''':
*'''/matching_threshold''':

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====Gobj and Masking Functions====
*'''/gobj_maskaimpeel_ow''': Cuts an aim file with a gobj so that only the portion of the aim within the gobj remains. Peel_iter value used to specify the number of pixels within the gobj the function will need to cut.
*'''/gobj_to_aim''': Reads a gobj file from the directory and makes an aim file (the aim file is in ipl, to output it to the directory use write).
*'''/togobj_from_aim''': Takes an aim file and writes a gobj file (the gobj is output to directory).
*'''/gobj_circumf_area''':
*'''/gobj_join''':
*'''/gobj_join_consec''':
*'''/gobj_scale''':
*'''/gobj_isotrop''':
*'''/cortex_maskoff''':
*'''/peel3d''':

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====Voxel-Counting, Density and Triangulation Functions====
*'''/db_scanco_activate''':
*'''/db_clear_eval''':
*'''/db_calib_unit_fill''':
*'''/db_set_mean_accur''':
*'''/voxgobj_scanco_param''': Inputs an aim file and a gobj and provides information (including total volume, object volume and the mean value of the points) on the region within the gobj.
*'''/vox_scanco_param''': Inputs an aim and provides information including total volume, object volume and the mean value of the points.
*'''/tri_da_metric_db''':
*'''/tri_direc_distr''':
*'''/connectivity''': Receives a component labelled aim object and calculates the connectivity of the labelled components.
*'''/conn_nocl''':
*'''/conn_bgcl''':
*'''/fractal_dimension''':

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====Distance Transformation (Sphere Filling) Functions====
*'''/dt_object_param''':
*'''/dt_ow_object_param''':
*'''/dt_background_param''':
*'''/dt_mat_param''':
*'''/dt_cortex_obj_param''':
*'''/dt_value_output''':
*'''/dt_mat_output''':

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====Statistical Functions====
*'''/examine''': Receives an AIM object and outputs specified information based on the item input.
*'''/histo''':
*'''/moment2d_of_inertia''':
*'''/moment3d_of_inertia''':
*'''/zmeanmax''':

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====Voxelsize-Scaling Functions====
*'''/isotrop''':
*'''/scale_elsize''':
*'''/ipscale_elsize''':
*'''/noipscale_elsize''':
*'''/scale_ow_elsize_noip''':

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====Component Labeling Functions====
*'''/cl_ow_rank_extract''': Receives AIM file and over writes it with an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl_rank_extract''': Receives AIM file and outputs an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl26_rank_extract''':
*'''/cl_image''':
*'''/cl_extract''':
*'''/cl_slicewise_extractow''':
*'''/cl_nr_extract''':

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====Add, Concat, Cut etc. Functions====
*'''/add_aims''': Adds the values of two AIM images in a 3D space.
*'''/add_constant_ow''':
*'''/border_change''':
*'''/bounding_box_cut''': Cuts extra space out of an aim file so that only the region with the data remains. A border can be added to the image using the border input.
*'''/concat''': Takes two aim files and combines them. The data from both aims or just the common region can be kept. To add the images add_not_overlay is set to true (for example if image 1 has a value of 41 and image 2 has a value of 82, the combined value will be 123).
*'''/concat_adapt''':
*'''/divide_volumes''':
*'''/fill_min_max_ow''':
*'''/header_geo_set''':
*'''/header_log_set''':
*'''/header_calib_ov''':
*'''/invert_ow''':
*'''/mult_constant_ow''':
*'''/multiply_volumes''':
*'''/sqr_to_float''':
*'''/sqrt_to_float''':
*'''/offset_add''':
*'''/offset_set''':
*'''/clear_offset''':
*'''/fill_offset_mirror''':
*'''/fill_offset_duplicate''':
*'''/set_value''': Sets the values of the object and background of an aim file to chosen values
*'''/sub_get''': Extract a portion of an image 
**-pos corresponds to x,y,z origin -1 -1 -1 maintains the original coordinates 
**-dim corresponds to x,y,z dimensions -1 -1 -1 maintains the original dimensions (within maximum range) 
**indexing starts at 0 instead of 1
*'''/sub_pick''':
*'''/subtract_aims''': Subtracts one aim from another and outputs the remaining region.
*'''/sup_divide''':
*'''/transparent_concat''':

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====Erosion Dilation Open Close Functions====
*'''/erosion''':
*'''/dilation''':
*'''/open''':
*'''/close''':
*'''/erosion_dilat_variable''':

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====Import Export Conversion Norming Functions====
*'''/import_freeformat''':
*'''/dicom_to_aim''':
*'''/todicom_from_aim''':
*'''/dicom_list_series''':
*'''/isq_to_aim''':
*'''/isq_gobjfit_to_aim''':
*'''/toisq_from_aim''': Writes an isq file to the directory ipl is open in (or specified directory) from an aim file. The isq name should be 8 characters long.
*'''/mesh''':
*'''/msq_from_aim''':
*'''/rsq_to_aim''':
*'''/stl_tri''':
*'''/convert_to_type''':
*'''/convert_unsigned''':
*'''/norm_max''':

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====Functions for Root Canal Evaluations====
*'''/separ_roots''':
*'''/calc_ctr_mass_list''':
*'''/calc_ctr_mass_diff''':
*'''/treated_surf''':
*'''/match_cut''':
*'''/match_cut_adapt''':

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====Miscellaneous Functions====
*'''/align_z''':
*'''/dcl''':
*'''/flip_aim''':
*'''/growback_to_orig''':
*'''/turn3d''':
*'''/turn2d''':
*'''/upat_filldb''': Fill special Upat DB for patient (radius/tibia) evaluation
*'''/xray''':

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====Obsolete, Experimental and Duplicate Functions====
*'''/curv_tri''':
*'''/cut2D_shape_ow''':
*'''/join_uncompress''':
*'''/mil_param''':
*'''/milv1_param''':
*'''/gauss_seg''': duplicate of /seg_gauss
*'''/from_aim_to_isq''': The function toisq_from_aim will also convert an aim to an isq
*'''/local_threshold''':
*'''/edge_canny''':
*'''/sobel_grad''':
*'''/hysteresis_thresholg''':

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====Functions only available in iplfe====
*'''/register''': Registers two aim files and output a transformation matrix of the transformation to moving input 2 into the space of input 1. Gobjs can be input (registration is more successful with gobjs). Orientation search can be done with masscenter, and/or moment of inertia (MoI), or degree intervals.
*'''/transform''': Transforms an aim file using a transformation matrix (a text file of the matrix can be input). Interpolation options are nearest neighbor, linear, and cubic interpolation. The inverse of the transform provided can be done by setting Tmat_invert to true.
*'''/fe_solveD''': A number of finite element functions are available in iplfe, not all are listed here

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=Results=

==Images and Animations==
Refer to [[Scanco_User_Instructions#.C2.B5CT_Ray|'''µCT Ray''']] for detailed instructions.

===[[#Change_the_View|Change View]]===
===[[#Change_the_Colours|Change Object Colors]]===
===[[#Cutplane_and_Subdim|Show a Section-View of an Object]]===

===Save a Screetshot Image===
#Open XV from a dec terminal on a workstation by typing <code>$ xv</code>.
#Open and frame the image, program etc. that you would like to save an image of.
#In XV, click GRAB. You can either autograb the entire screen after a delay or manually grab a desired area.
#After grabbing the desired section, click Save in XV.

===[[#Save_the_Image|Save Image]]===
===[[#Save_for_Animation|Save Frames for an Animation]]===

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===Convert AIM to TIF series===

Use the utility SEQ_TO_IMAGE located in the UT directory. A symbol has been set up to run this called TIF.

<pre>
$ mcr ut:seq_to_image
Program: seq_to_image V1.1b
Input-File []: WISDOM_L_R05.AIM
File Format [TIF]:
Default TIF Names: WISDOM_L_R05_xxxx.TIF

Output-File [WISDOM_L_R05]:
!> Reading AimVersion020
Start Slice [0]:
End Slice [179]: 5
Number of images thereof (count) [6]:
Scale Factor (Integer) [1]:
global_pos (1=true, 0=false) [0]:
Max value to norm to 255 [32767]:
Slice: 0
Slice: 1
Slice: 2
Slice: 3
Slice: 4
Slice: 5
$ dir wisdom*

Directory DISK1:[MICROCT.SCRATCH]

WISDOM_L_R05.AIM;1 WISDOM_L_R05_0000.TIF;1 WISDOM_L_R05_0001.TIF;1
WISDOM_L_R05_0002.TIF;1 WISDOM_L_R05_0003.TIF;1
WISDOM_L_R05_0004.TIF;1 WISDOM_L_R05_0005.TIF;1

Total of 7 files.
$
</pre>

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===Generate TIF (or others) from 3D rendered volume===

This replaces uct_movie that operated on the alpha systems. UCT_3D can be called in batch mode.

A pdf describing this tool is located here: [[Media:UCT_RAY V4.0-1.pdf]]

To interactively declare the desired settings:
<pre>
$ uct_3d_batch
?CT RAY_BATCH V4.0-1

UCT_R: Application initialized
Filename []:
Print-Filename [SYS$SCRATCH:TEMP_3D.PS]:
Ambient (0.0..1.0) [0.200]:
Shadows (0/1) [1]:
Size (1..1024) [1024]:
Elevation (-90..90) [30]:
Rotation (-180..180) [35]:
Copies (0..9) [1]:

</pre>

To apply a saved set of settings, a setup-file can be created by running uct_3d in interactive mode. Select "Presets" from the toolbar and save the settings you desire (e.g. elevation 90, rotation 0).

<pre>
$ uct_3d_batch setup-file [data-file printfile]

Examples:

$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.ps
$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.tif

</pre>

To automatically generate tifs for many files, a script was created to replace PRINT_3D.COM
The script is currently stored in the xtremect2 com directory.

<pre>
@COM:PRINT_REG_TIF.COM

Generates a 3D image from a segmented file.

The outputs include:
- two 3D renderings (TIF)

Use full pathnames for the segmented AIM.

P1 - Segmented AIM

Usage:
@COM:PRINT_REG_TIF.COM DISK2:[MICROCT.DATA.00000379.00001376]C0001234_SEG.AIM
</pre>

This script can be modified to use a custom preset file.

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===Make an Animation===

To calculate an Animation, two (separate) tools of the 3D program are used: the set-up of start and end point of the Animation, and the 'Auto-Print' tool that automatically creates the TIF files for every rendered image.

This is a 'step by step' guide to create an animation using TIFF files:
:* Open your sample in the 3D program.
:* Now, open 'options','Animation'
:* Render your Image the way you want your animation to start. e.g. observer rotation -179 degrees. You may interrupt if you want. If you are satisfied with all the settings (rotation, elevation, transparency, colors etc.) the Click on 'Get Settings A'
:* Then, adjust all the settings for the endpoint of your animation (with the mouse or the sliders) e.g. observer rotation +179, and start the rendering. If satisfied, click 'Get settings B'

Note: To test, put # of views to 5 or 10... You can also interrupt the build-ups for faster viewing.
:* Click the START button again, wait till the build-up of the 3D image is finished.
:* DO NOT HIT 'START CALCULATION' YET!
:* First, you also need to set-up the 'Auto-Print' mode:
:* Go to the 'Print' menu (file --> print), choose print to TIF and to File and enter THE BEGINNING OF A FILENAME, e.g. sys$scratch:test_ (the program will append 0000.TIF, 0001.TIF etc afterwards) Or enter (possibly with middle-mouse-click): "DK0:[MICROCT.DATA.00001234.00003456]ANIMATION_" to have the result go to the measurement directory.
:* Click on the 'Auto-Print' box. Then 'ok'
:* Adjust the number of views (e.g. 200), then click on 'Start Calculation', and it will render. This may well take a long time.
:* Take those TIFF files to your PC, and combine the sequences in the program that you are using to convert the TIFF files to AVI or MOV files (like Windows Movie Maker 2, or Quick Time Pro, or Adobe Premiere etc.)

Notes/Hints:
:* The order in the above list can also be reversed: You can first set up the 'Auto-Print', and then go into the 'Animation' menu, choose start and end settings, and hit 'Start Calculation'
:* The positions A and B can be any: e.g. with subdim, you can first take everything (A), then slide it back to nothing (B).
:* You can even slowly change the color of an object. Or slowly hiding objects: choose 'transparent' for object, but change from 0.0 (A) to 1.0 (B)
:* If you want to create a movie with different sections, e.g. first rotate around, then slowly make bone transparent, then cut in: Do this in multiple sections with the 3D program, e.g. first create Auto-Print files 'rotation_0000 to rotation_0200', then 'transp_0000 to transp_0050', and then 'cut_0000 to cut_0100'. Make sure ALL the settings from the last view of the previous section match those of the first view of the next section so you get smoot transitions.
:* The 'Auto-Print' box is also usable without the 'Animation' Menu: Activate it, Like above, with sys$scratch:test_ only the beginning of filename. 'ok' Then, whenever a 3D image is completely built-up (so when you are happy with a view and you do not interrupt the build-up), automatically a TIF file is generated, numbered sequentially.

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===Combine two volumes to create transparent image===

First create your two start "seg.aim" images
Start by running either the normal eval, or $ voi to get one _seg.aim file of one region

Rename it to a better name in the session manager, e.g. c0001234_all.aim

Then either by choosing different contours, or a different threshold, start the $ voi or the normal evaluation again, which will create another _seg.aim file.

Load them in the 3D viewer ('all files') to check that they look like expected.

Now we will go into IPL and concatenate those two volumes.

<pre>
$ ipl
/read all xx_all.aim
/read trab xx_seg.aim
/transparent
-input_solid trab
-input_transp all
-output out
</pre>

Note: the solid volume is OVERWRITING the transparent input volume, so usually, it
is the smaller (inner) of the two.

<pre>
/write out xxx_transp.aim
/quit
</pre>

Then load the _transp.aim file in 3D, go to 3D program FAQ to see how to change transparency levels in the Display options there.

See IPL FAQ or 3D program FAQ if you need help with these parts.

Step by Step Example: Showing your chosen trab VOI within whole bone
:* $ voi, enter threshold in ipl_voi.com, start 3d eval WITHOUT contours
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_all.aim
:* Start up normal eval program, draw trabecular contours, check threshold in ipl_fixed_batch_v4.com, start 3D eval.
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished

Step by Step Example: Showing high-dense volume surronded by lower density volume

:* Start normal 3D eval with HIGH threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_high.aim
:* If wished: read out 3d result database with $ uct_list
:* Start normal 3D eval with LOW threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished

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==Image Tours==
===XtremeCT Image Tours===

===MicroCT Image Tours===
*Refer to [[Media:Tours_image_gallery.pdf|'''MicroCT Image Gallery''']] with its [[Media:Tours_image_notes.pdf|'''Image Notes''']].
*Refer to [https://youtu.be/tT3dz4VrwfE '''MicroCT Image Tour YouTube Video''']
*Hover over a thumbnail and click on its overlaid description to see the animated GIF or a larger version of the image.

<gallery mode="packed-hover" heights=220px caption="Micro-CT Scans">
Image:MOUSE_SKELETON_PIC01.jpg|[[Media:MOUSE_SKELETON_360.gif|Mouse (38µm)]]
Image:Segmented_Mouse_Femur.jpg|[[Media:Segmented_Mouse_Femur.jpg|Mouse Femur showing Cortical and Trabecular Bone (10µm)]]
Image:LIZARD_WHOLE_VIEW_P1_0044.jpg|[[Media:LIZARD_SKELETON_360.gif|Lizard (88µm)]]
Image:LIZARD_SKULL.jpg|[[Media:LIZARD_SKULL.jpg|Lizard Skull showing Thickness Distribution (25µm)]]
Image:DUCK_BEAK_PIC01.jpg|[[Media:DUCK_BEAK_360.gif|Duck Beak (60µm) Courtesy of Dr. A. Iwaniuk]]
Image:Human_Tooth.jpg|[[Media:Human_Tooth.jpg|Human Tooth (30µm) Courtesy of Dr. C. Stewart]]
Image:PINECONE_TH_PIC05.jpg|[[Media:PINECONE_360.gif|Pinecone showing Thickness Distribution (69µm)]]
Image:SHELL01_SEG_PIC01.jpg|[[Media:SEASHELL_360.gif|Seashell (50µm)]]
Image:TURTLE_SKULL.jpg|[[Media:TURTLE_SKULL_360.gif|Turtle Skull (60µm)]]
Image:SAND_DOLLAR.jpg|[[Media:SAND_DOLLAR.jpg|Sand Dollar (37µm)]]
Image:MOUSE_L1-L6.jpg|[[Media:MOUSE_SPINE_SEG_360.gif|Mouse Spine showing Cortical and Trabecular Bone (10µm)]]
Image:MOLAR.jpg|[[Media:MOLAR.gif|Human Tooth (60µm) Courtesy of Dr. C. Stewart]]
</gallery>

<gallery mode="packed-hover" heights=220px caption="Contrast-Enhanced Micro-CT Scans">
Image:Contrast_mouse_head_XZ_thumb.jpg|[[Media:Contrast mouse head XZ.jpg|Mouse Head (60µm, XZ plane)]]
Image:Contrast_mouse_head_XY_thumb.jpg|[[Media:Contrast mouse head XY.jpg|Mouse Head (60µm, XY plane)]]
Image:Contrast_mouse_head_YZ_thumb.jpg|[[Media:Contrast mouse head YZ.jpg|Mouse Head (60µm, YZ plane)]]
</gallery>

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==Extract Results==
===Automatic Results===
Results are generally automatically extracted after each analysis to the UCT_RESULTS directory. 
The results files have the form of:
*UCT_LIST_*''PROJECT''*.TXT for XtremeCTs: e.g. result file UCT_LIST_KYLA.TXT for the following project.
*UCT_LIST_3DLOG_*''PROJECT''*.TXT for microCTs: e.g. result file UCT_LIST_3DLOG_KYLA.TXT for the following project.
*where ''PROJECT'' is specified in the evaluation tool script setup.
[[File:Script_modify_basic_project.jpg|500px]]

Open the result file and copy and paste it into Excel, e.g.
<pre>
$ dir uct_results:*kyla*
$ eve uct_results:UCT_LIST_3DLOG_KYLA.TXT
</pre>

Or transfer the file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].
*microct/vivact account UCT_RESULTS location: ADISK1:[MICROCT.RESULTS]
*invivo/invitro account UCT_RESULTS location: ADISK1:[BONELAB.RESULTS]

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===Extract Results from XtremeCT Database using UPAT_LIST===
*Run <code>$ UPAT_LIST</code> to take in a range of samples and extract the standard patient results, which may include scans from other projects.
**Run <code>$ UPAT_LIST -h</code> to print out help for all parameters.
**For standard analysis on XtremeCT2, the default Evaluation Type 4=XT1 is not applicable. To get results for XtremeCT2, you need to run upat_list twice. Once for evaluation 5 and once for 6.
<pre> Evaluation type (1-6) [4]: Type code of evaluation (4=XT1, 5=trabecular, 6=cortical, default=4) </pre>

*Run <code>$ @com:EXTRACT_UPAT_LIST</code> to take in a list of sample numbers and extract the standard patient results with follow-ups and append them to a result file.
<pre>
$@COM:EXTRACT_UPAT_LIST P1 P2 P3 P4 P5

P1 = Sample List
P2 = Site (RR, RL, TR, TL, R*, T*, *)
P3 = Number of Follow-Ups (max 19)
P4 = Results Output File
P5 = Eval type (4=XT1, 5=Trab, 6=Cort)
</pre>

:An example to extract all sites:
<pre>
$ @com:EXTRACT_UPAT_LIST mysamples.txt * 19 myresults.txt 5
</pre>

*Run <code>$ @com:EXTRACT_UPAT_LIST_NOMATCH</code> to take in a list of sample numbers and extract the standard patient results without matching follow-ups and append them to a result file.
<pre>
$@COM:EXTRACT_UPAT_LIST P1 P2 P3 P4 P5

P1 = Sample List
P2 = Site (RR, RL, TR, TL, R*, T*, *)
P3 = Number of Follow-Ups (max 19)
P4 = Results Output File
P5 = Eval type (4=XT1, 5=Trab, 6=Cort)
</pre>

:An example to extract all sites:
<pre>
$ @com:EXTRACT_UPAT_LIST_NOMATCH mysamples.txt * 19 myresults.txt 5
</pre>

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===Extracts Results from microCT Database using UCT_LIST===
*Run <code>$ UCT_LIST</code> to take in a range of samples and extract the results, by specifying the first and last measurement numbers for the range they want to extract
*This may include scans results from other projects, but you can delete unrelated results that are extracted afterwards.
*The program will output a tab-delimited text file, which can be read into Excel or other analysis programs.
<pre>
$ uct_list

UCT_LIST.EXE Version V5.22
Template-File [UCT_3D_LIST_SHEET]: !Press Enter to use the default results sheet.
Output-File [SYS$SCRATCH:UCT_EVAL.TXT]: !Enter a filename, e.g., BUIE_RESULTS.TXT.
Density units (0 default) [0]: !Press Enter.
From Meas. # [0]: !Enter the first measurement number, e.g., 100.
To Meas. # [0]: !Enter the last measurement number, e.g., 101.

Processing measurement 100
Processing measurement 101
</pre>
*An example output file: [[Media:Buie_results.xlsx|Buie_results.txt]]
*Or Run <code>$ @com:extract_results.com</code>

*References of results template:
:*Formatted [[Media:Results_template_uct_list.xlsx|Excel template 1]] for results extracted with uct_list.
:*Formatted [[Media:Results_template_extract_results.xlsx|Excel template 2]] for results extracted with extract_results.com.
:*In vivo spreadsheet template for UCT data: [[Media:In vivo results template.xls| In vivo results template.xls]]
:*In vitro spreadsheet template for UCT data: [[Media:In vitro results template.xls| In vitro results template.xls]]

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===Understand Morphological Parameters===
*Refer to [[Media:Reference_Document_-_Parameters_from_upat_list.doc|'''Explanation of UPAT_LIST Output''']] to understand the result file.
*Refer to [[Media:Reference_Document_-_Parameters_from_uct_list.doc|'''Explanation of UCT_LIST Output''']] to understand the result file.

All values are determined on a slice-by-slice basis, then averaged over all the slices to calculate morphological results:

:*BV/TV -> Sum all raw data within the GOBJ and divide by 1200 mg/cc HA
:*Tb.N -> As per standard method
:*Tb.Th and Tb.Sp -> Derived from BV/TV and Tb.N above (semi-derived method)
:*D100 -> Average density of entire cross section
:*DTrab -> Average density of trabecular region
:*Ct.Th -> Cortical area (from seg) divided by circumference (from GOBJ)
:*GOBJ circumference can be determined with /gobj_circum.

<pre>
BV/TV -> VOX-BV/TV
BS/BV -> TRI-BS/BV
Tb.Th -> DT-Tb.Th
Tb.Sp -> DT-Tb.Sp
Tb.N -> DT-Tb.N
ConnD -> Conn-Dens
SMI -> TRI-SMI
DA -> TRI-DA
</pre>

Usually I'd use the names on the left for the plots, but these correspond to the names on the right of the arrow in the Scanco output files.

Note, if you use the TRI-Tb.Th rather than the DT-Tb.Th*, then you are using the derived (plate-model) morphological parameters. These are less accurate than the direct parameters. They are calculated by triangulating the surface (marching cubes) to get BS, and then calculate thickness
Th = 2 * BV / BS, etc...

'''Mean Values'''
<pre>
mean 1: mean of bone AND marrow --> 'apparent density'
mean 2: mean of what was considered bone only (i.e. what was segmented)
'bone tissue density'
</pre>

Note, there are five possible categories for the mean Mu. They are assigned by setting <code>-region_number</code> in the <code>/voxgobj_scanco_param</code> function. The region number is zero-based, so setting it to 0 corresponds to mean1, 1 corresponds to mean2, etc. So, although mean1 and mean2 are typically apparent and tissue density, respectively, this can be adjusted in the IPL script by setting the region_number. Mean3 might be useful for storing cortical bone density, for example.

<pre>
/voxgobj_scanco_param Voxel or Mu Scanco Parameters
-input Gray scale or Segmented AIM object
-gobj_filename GOBJ: input or Automatic
-peel_iter Peel Iterations or Automatic
-region_number Region number for Mu only

! -region_number 0 ! mean1
! -region_number 1 ! mean2
! -region_number 2 ! mean3
! -region_number 3 ! mean4
! -region_number 4 ! mean5
</pre>

What you should also know: because of partial voluming effects, for Mean2, we are DISCARDING the 2 surface voxels of EVERY trabeculae - thus, to get meaningful Mean2, you have to do your scan with the chosen resolution high enough, such that the mean trabeculae is depicted by at the very least 5 pixels, better actually more than 6 pixels thickness. (You can do this check at the end in the XLS sheet: divide DT-Tb.Th* by el-size-mm.x, and you need to get numbers bigger than 6 or 7 or 10 or so.

For parameters such as ConnD where no GOBJ is taken as input, the TV is determined from the processing log stored in an AIM that has previously had a GOBJ applied (stored as the relative region of interest; ROI). So, it is important to apply a GOBJ prior to ConnD measurements to ensure the TV is correctly determined (and not taken as the whole AIM).

'''Trabecular Number (TbN)'''
The epsilon values can be set to account for differences in scanner resolution, and hence 'surface roughness' for individual pixel suppression.

For microct, for good resolution: if there is a pixel 'sticking out' from a flat surface we do not assign that pixel with a thickness value of 1, but we let it 'get eaten' by the bigger sphere that sits in the center of the trabeculae. So this is nice for 'noise' (0.9/1.5).

For XT resolution, where also many 'good' features are just one or two pixels wide, I liked a lower epsilon value better (0.9/0.5).

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==Generate Report==
===Generate Standard Patient Report===
The standard patient reports are extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.
*The number of follow-ups specified will determine if a baseline or follow-up report is generated.

<pre>
$ upat_list

Mode (1 = list, 2 = print, 3 = show) [1]: 2
Patient # (1-3162) [1]: !input the patient's sample number
Site (found RR) [RR]: !RR or RL or TR or TL
Maximum # of follow-ups (0-19) [19]: !0 for baseline report, press return for follow-ups
Template file [default]: !press return to use the default template
Output filename [SYS$SCRATCH:UPAT...]: !default output file (with sample number and the site) goes to sys$scratch
# copies [1]: !the number of printouts, 0 if no printout is desired
</pre>

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===Generate CaMos Patient Report===
The [http://www.camos.org '''CaMos'''] patient report is extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.
*To ensure the report is generated using the appropriate normative results, the patient's sample remarks should be in the form "F-RHRF" where the first character indicates the sex of the individual, otherwise the patient is assumed to be male.
<pre>
$ upat_list

Mode (1 = list, 2 = print, 3 = show) [1]: 2
Patient # (1-3162) [1]: !input the patient's sample number
Site (found RR) [RR]: !RR or RL or TR or TL
Maximum # of follow-ups (0-19) [19]: !0 - 1st scan, 1 - 2nd scan, 2 - 3rd scan...press return for latest scan report
Template file [default]: COM:UPAT_EVAL_CAMOS.PS
Output filename [SYS$SCRATCH:UPAT...]: !default output file (with sample number and the site) goes to sys$scratch
# copies [1]: !the number of printouts, 0 if no printout is desired
</pre>

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===Print out report sheets===

The postscript report sheets can be generated and printed on the command line. For the XtremeCT system, use <code>UPAT_PRINT_LIST.EXE</code> which can be run (using the symbol):
<pre>
$ UPAT_LIST
</pre>

Look in the UU: directory to see options for the template files (UPAT*.TXT) and the postscript output files (*.PS).
:* UU:UPAT_EVAL_FUP05_SCUSA.PS
:* UU:UPAT_EVAL_BASELINE_SCUSA.PS

For other options, see the upat_list help:
<pre>
$ UPAT_LIST -h
</pre>

One particular option that may be useful, is to turn off slice matching:
<pre>
$ UPAT_LIST -nomatch
</pre>

Here is an example of producing a report for the third measurement of TL for a patient, where we want only the most recent results in the report, without slice matching:
<pre>
$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=UU:UPAT_EVAL_BASELINE_SCUSA.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_0fu.ps

$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=DISK1:[MICROCT.COMMANDS]UPAT_EVAL_CAMOS.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_camos.ps
</pre>
The first command line generates a normal Scanco report, and the second command line generates a CAMOS report.

For reports from non-patient measurements (i.e., the vivaCT system or non-patient scans on the XtremeCT), the template files are different (UCT*.TXT) and the postscript outputs are different (UCT*.PS). To print a result sheet use:
<pre>
$ RUN UM:UCT_RAY_BATCH.EXE
</pre>

If you want to create a postscript file, but not send it to the printer, set the number of copies to zero (interactive). Then, find the postscript file from the <code>SYS$SCRATCH</code> directory and transfer it to your PC. You must transfer the postscript file in ASCII mode. The files are typically called TEMP_3D.PS or UPAT_PAT_62_RR.PS. A program such as Adobe Photoshop can convert the postscript file to a different format.

See also our custom scripts:
<pre>
$ @COM:PRINT_2D.COM
$ @COM:PRINT_3D.COM
</pre>

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===Convert PS to PDF report===
The report can be converted to PDF using <code>$ @SCOM:PS_TO_PDF</code> by:

#Follow the instructions above for creating a report, using "2" to print and "0" for the number of copies. (Use the default template file and output filename.)
#Locate the file on the sys$scratch by <code>$ cd sys$scratch</code> and <code>$ dir</code>
#*The file should read "UPAT_PAT_[sample #]_[site].PS;1" (e.g. UPAT_PAT_0010_RL.PS;1)
#*You can view this file on the monitor by typing <code>$ gs UPAT_PAT_0010_RL.PS;1</code>
#Convert the postscript to PDF by typing in the command followed by the .PS file to convert <pre>$ @SCOM:PS_TO_PDF UPAT_PAT_0010_RL.PS;1</pre>
#The PDF file can then be located again in the sys$scratch directory.

You can transfer the result file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].

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=Data Management=
==Trainee’s Data Responsibility==
#Perform '''Contouring and Data Analysis''' on Data Disk ideally 1-2 months after scanning.
#After finished onsite analysis, [[Scanco_User_Instructions#Move_data_from_Data_Disk_to_Project_Disk|'''use Scripts''']] to '''Copy and Rename''' image data (no RSQ, no ISQ, only AIM, SEG.AIM, GOBJ, COM, LOG, PDF, PS ect) to your specific project folder on Project Disk.
#After finished copying all your image data to Project Disk, '''Notify''' lab personal to delete your data on Data Disk by providing a [[Media:Data_Scans_to_delete_template.xlsx|'''Data Scans to Delete Template''']].
#'''Notify''' lab personal to backup your project folder on Project Disk to Winston server on a monthly basis.
#*Only the two most recent backups (A or B version) are kept for each project on Winston:
#:Backup version "_A" for odd months (Jan, Mar, May, Jul, Sep, Nov), e.g. YZHU_A_OTHER_2017-01-12.SAV
#:Backup version "_B" for even months (Feb, Apr, Jun, Aug, Oct, Dec), e.g. YZHU_B_OTHER_2020-04-08.SAV
#When a project is finished, '''Notify''' lab personal to archive your project to HOG server.
#When a trainee is about leaving, '''Notify''' Steve and lab personal to determine either to backup or to archive your project.

[[File:BoneLabDataManagement.JPG|800px]]

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==Move data from Data Disk to Project Disk==
This is generally done after onsite analysis (i.e. autocontour, cortical porosity, FE etc.) is done. Examples of this can be found in DISK3:[MICROCT.PROJECTS.GRACE.COM] 
1. Go to the specific project's .COM directory, for example:
<pre>
$ cd DISK3:[MICROCT.PROJECTS.GRACE.COM]
</pre>
2. Create a script that will move all IMA (i.e. .AIM, .GOBJ, _SEG.AIM, _CORTEX.AIM, _LHTH_DTN.AIM) to the .MODELS directory for the project. You will use the rename_to_models.com script to generate this script. To move Grace data for example, with a measurement range of 2684 to 2685, you would use:
$ @com:rename_to_models.com meas#1:meas#2 DESTINATION DIR
$ @com:rename_to_models.com 2684:2685 DISK3:[MICROCT.PROJECTS.GRACE.MODELS]

3.This will create a file named RENAME_ALL.COM to the project's COM directory. You will now have to open the RENAME_ALL.COM file and add site + other details into the script. Following the same example as above, it should look like this:
$ eve RENAME_ALL.COM ! to open the file using a text editor
$ COPY DISK2:[MICROCT.DATA.00000700.00002684]C0002040.AIM -
DISK3:[MICROCT.PROJECTS.GRACE.MODELS]GRACE_020_00MTH_RR.AIM
$! DELETE/CONFIRM DISK2:[MICROCT.DATA.00000700.00002684]C0002040.AIM;1
$ COPY DISK2:[MICROCT.DATA.00000700.00002685]C0002041.AIM -
DISK3:[MICROCT.PROJECTS.GRACE.MODELS]GRACE_020_00MTH_RL.AIM
$! DELETE/CONFIRM DISK2:[MICROCT.DATA.00000700.00002685]C0002041.AIM;1
4. You also need to copy the rest of the standard patient image files (i.e. .AIM, .GOBJ, _SEG.AIM, _CORTEX.AIM, _LHTH_DTN.AIM) which is easily done by copying the above lines and replacing .AIM with the respective files.

[[Image:Bones2.jpg|20px]] Warning: Always use the same account consistently to create all files and subfolders within their Project folder, otherwise you way miss data when doing Project Backup or Archive!

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=Import and Export=
==Import Foreign Data to Scanco System==
Only RSQ and ISQ files can be imported into the database, however it is possible to convert other types of data into ISQ files (i.e., stacks of BMPs into ISQ).

PART 1:

After transfering your data to the VMS system (use the data disk <code>disk2</code>, NOT the user disk <code>disk1</code>), use the IPL commands <code>/import_freeformat</code> or <code>/read_aim function</code> to import your data for conversion to an ISQ.

For AIM files, navigate to the location of the AIM file. Then open IPL by:

<pre>$ IPL</pre>

In IPL, read in the .AIM file:

<pre>ipl> read in [.AIM file]</pre>

IPL will do the following:

<pre>ipl> read in STUDYID_001_RL.AIM

/read
-name in
-filename STUDYID_001_RL.AIM
!> Reading AimVersion020

!% /read completed: CPU: 00:01.03 ELAP: 00:01.55 </pre>

For DICOM files, start IPL and run the <code>/dicom</code> function to import. For DICOM, if your object is a single 3D file (-multifile false) or many many individual slice files (-multifile true, and give beginning of filenames, and –extension).

There may be requests by IPL to convert your data to <code>signed short</code> or <code>signed char</code> from other data types. Obey these requests and do it by running the <code>/convert_unsigned</code> function.

Then, write the ISQ file using either the "toisq" or "from_aim" commands:
<pre>ipl> toisq
-aim_name [in] >[leave blank as you defined “in” as .AIM file.]
-isq_filename [default_file_name] > C0001234.ISQ [Create a 1 letter and 7 digit file name]
-square_flag [true] > false
-original_position [true] > false

ipl>toisq_from_aim
-aim_name in
-isq_filename C0001234.ISQ
-square_flag false
-original_position false

!% Dimensions of ISQ file: dim.x dim.y dim.z 558 638 168
Write_ctdata_headerext_new: no mhext found. Init mhext.
Extended header successfully added of type 8

!% Writing ISQ slice 167 (Done: 168/168)

!% /toisq_from_aim completed: CPU: 00:05.12 ELAP: 00:10.47 </pre>

Type ipl>help toisq [or ipl>help from_aim] to see details of the command.

This writes the ISQ file. Make note of the ISQ file name.

Remember, the ISQ name must be 8 characters long (1 character followed by seven digits)!!! The letters and numbers can be chosen freely.

Exit IPL:

<pre>ipl>quit</pre>

PART 2:

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

The measurement can be verified by looking at the Header Information. (File, Header)

If you only needed to view the ISQ, delete the file when finished by:

<pre>$ dir/sincet
$del [.ISQ file]</pre>

PART 3:

To use the ISQ further (e.g. for evaluations, contouring, etc.) create a sample in the database and write down the sample and measurement number. Then, run:

<pre>$ run um:uct_import ! will import both RSQ and ISQ (modify patient index, etc)</pre>

and give the new ISQ file, the new sample-number and check that the feedback is correct (i.e., that the name from the database is matching the name from the ISQ file header). If the Patient Name in the ISQ header doesn't match the measurement database Patient Name (very likely), then upon importing the RSQ/ISQ the headers will be updated to the new Patient Name.

Operator and controlfile can be left 0 if you want. However, controlfile should be set appropriately if the data being imported is for the XtremeCT patient database.

If you are also importing the RSQ, put it in the same directory as the ISQ.

Then it changes the sample and measurement number in the ISQ file, makes the correct directory on <code>DK0</code>, and gives you the line on the screen of how to rename the file to the correct, new directory. Take this line and use it on the command line. Done!

You can now use the normal <code>uct_evaluation</code> program with this file. If the control file was set properly, then the evaluation will be done correctly (i.e., for XtremeCT patient measurements).

Note: Any AIMs created from the original ISQ should be recreated. So, it is important that you re-evaluate your newly imported ISQ. It is OK to move the GOBJ from the old directory to the same directly as the newly imported ISQ (it does not have a 'registry' in the database).

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==Import DICOM to Scanco System==
#Load MRI's or CT's DICOM data in Osirix
#Export from Osirix
#*Click export button in top left in osirix.
#*Select "flat" and "decompress all DICOM files"
#Copy files to correct folder in scanco system
#*Use Fillezilla or FTP (make sure it's set to binary mode)
#Use IPL to convert dicom to aim or isq

<pre>
/dicom_to_aim
-aim_name in
-dicom_filename IM-0001-0001.DCM ! Note - choose the first filename of the series
-multifiles true

/convert_unsigned
-input in
-shift_flag false
-divide_by_2 true

/write_v020
-name in
-filename PREOA_023_L_MR.aim
-compress_type bin
-version_020 true

/toisq_from_aim
-aim_name in
-isq_filename MROA023L.isq
-square_flag true
-original_position true''

</pre>

5. Delete dicoms

<pre>
/del *.dcm;1
</pre>

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==Import Xradia *.bin to Scanco System==
Xradia scanner exports a *.bin image that is:

- 16-bit unsigned ! This is "short" (8-bit is char - we don't want this for a grey-scale image)
- 2 bytes per voxel
- little endian notation

To upload this binary image to Scanco database, the steps are as follows:

#Ftp the *.bin to Scanco system using binary transfer (not ascii)
#Convert it to an AIM or ISQ in IPL

$ipl

/import_freeformat
-internal_name in
-file_name BMLPL_006.BIN
-sample_name BMLPL_006
-data_offset 0
-data_dim 1000 1024 1016 !dimensions from header file
-data_el_size 0.013 0.013 0.013 !voxel size from header file
-bytes_per_voxel 2
-data_endian little_endian
-data_type integer
-signed_type unsigned !correct
-multifiles false

/convert_unsigned
-input in
-shift_flag true !shift_flag = TRUE will produce an ISQ/AIM with negative values which may not be visualized properly using uct_evaluation, but keeps the original image resolution.
-divide_by_2 false !divide_by_2 = TRUE will down grade image resolution, but all positive values in an ISQ/AIM will be visualized properly using uct_evaluation.

/write_v020
-name in
-filename test.aim
-compress_type bin
-version_020 true

/from_aim_to_isq
-aim_name in
-isq_filename bmlpl006.isq !ISQ name requires 8 characters
-square_flag true
-original_position true

quit

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

Alternatively the image can be converted to a 16-bit signed in ImageJ (and cropped) before importing to ipl. It then becomes:

- 16-bit signed
- 2 bytes per voxel
- big endian notation

It can then be imported into ipl without the need to run <code>/convert_unsigned</code>.

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==Get Your Files==
===MAC/Linux Options===
====Fetch====
#Download and install [http://fetchsoftworks.com/fetch/|'''Fetch''']
#*This program is free for university staff and students.
#Fill out [http://fetchsoftworks.com/fetch/free|'''a form'''].

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====FTP from Terminal====
#Open a terminal
#*MAC: open the "Applications" folder, choose "Utilities", then "Terminal".
#Navigate to where you want to transfer the files to.
#Connect to the micro-CT ftp server using the ftp command in the terminal:
#*Login with the micro-CT user account and password.
#Navigate to the directory of interest on the micro-CT system.
#*Logicals such as "ur" can be used as short cuts. Whole directory names must be used.
#Set a filename mapping convention to remove OpenVMS version numbers.
#*The command <code>ftp> nmap $1;$2 $1</code> sets anything before the version number to parameter $1 and anything after the version number to $2. The file output will be set to $1, therefore the version number will not be kept.
#Set the file transfer mode.
#*[[File:Important.JPG|20px]] If you transfer an .AIM file in ascii mode, you will receive a "mesh generation" errors and "material ID out of range" message.
#Transfer your files.
#*Option: Turn off prompt so does not ask you whether or not to transfer each file.
#*If you do not turn off the prompt prior to transferring the files, press "a" (for all) to transfer all files at once.
#Exit FTP.

<pre>
$ FTP 136.159.74.231 !Connect to an FTP Server. Need to input user name and password.
$ FTP emily.ucalgary.ca !Connect to an FTP Server. Need to input user name and password.
$ FTP microct@emily.ucalgary.ca !Connect to an FTP Server. Need to input password.

FTP> cd ur !Navigate to the directory containing the target files.
FTP> cd sys$scratch !Navigate to the directory containing the target files.

FTP> nmap $1;$2 $1 !Set a filename mapping convention to remove OpenVMS version numbers.

FTP> bin !Set transfer mode to binary (.aim, .gobj, .isq, and most image file types).
FTP> ascii !Set transfer mode to ascii (.txt, .log, .com, .ps, .pdf and all other files in general).

FTP> put test.aim !Put the file
FTP> get test.aim !Get the file

FTP> prompt !Interactive mode off before transferring multiple files without having to be prompted.
FTP> mput *.aim !Put all files with the .aim extension on the FTP server (mput = multiple put).
FTP> mget *.aim !Get all files with the .aim extension from the FTP server (mget = multiple get).
FTP> mget *.aim; !Transfer the latest version of all aim files in a directory.

FTP> quit !Disconnect from the FTP Server.
</pre>

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===Windows Options===
====Scanco Medical µCT FTP====
#Downlod '''Scanco Medical MicroCT FTP 3.4''' from BoydDrive:\\04 - Resources\04 - Software\Scanco Medical MicroCT FTP 3.4\
#Install the software using the default parameters.
#Click on FTP Connection and input the host to connect to, the username, password.
#Give this profile a name.
#:[[File:Microct_FTP_pic01.jpg|600px]]
#Click on the options tab to set the locations to connect to (e.g., project disk, scratch) and the location on your computer to transfer files to.
#:[[File:Microct_FTP_pic02.jpg|600px]]
#Go back to FTP Connection and press the Connect button.
#*If you are connecting from off campus to the XtremeCT you will need to use the VPN to gain access through the firewall.
#Use the left tree to navigate folders.
#*Use the file filter to search for specific file types or file names (bottom left).
#Select files to download and press the Download Selected Files button (bottom right).
#:[[File:Microct_FTP_pic03.jpg|600px]]
#Press the Exit button to disconnect.

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====Filezilla====
#Download '''Filezilla 2.2.32''' from BoydDrive:\\04 - Resources\04 - Software\Filezilla 2.2.32\
#*This version of Filezilla will remove the OpenVMS version number from files, the new version will not!
#*The left side of the program shows your computer, the right side will show the micro-CT system once you have connected.
#:[[File:Filezilla_pic01.jpg|500px]]
#On the top menu, choose "File", then "Site Manager".
#Create a "New Site" for all the directories that you frequently access.
#*Give the site a meaningful name.
#*For the host, you may connect to "emily.ucalgary.ca" or "sceval.ucalgary.ca".
#*For the logon type choose "Normal" and input the micro-CT user name and password.
#:[[File:Filezilla_pic02.jpg|400px]]
#Click on the "Advanced..." button to set the default remote directory (i.e., on the micro-CT system).
#Set the default local directory if there is a specific location you plan to always transfer files to.
#Setup any additional sites you want then press "Save and Exit".
#:[[File:Filezilla_pic03.jpg|300px]]
#To connect to a session, hold the left mouse button down over the arrow next to the site manager button (computer icon under "File") to bring up your list of sites. Highlight the site of interest then release the mouse button to connect.
#Once connected, you can drag and drop files from the remote site to your local computer.

;*Common FTP locations
{| class="wikitable"
|-
! scope="col"| Account
! scope="col"| Location
! scope="col"| Path
|-
| microct / vivact || Data Disk ||DISK2:[MICROCT.DATA]
|-
| microct / vivact || Projects Disk ||DISK3:[MICROCT.PROJECTS]
|-
| microct / vivact || Scratch Disk ||ADISK1:[MICROCT.SCRATCH]
|-
| invivo / invitro || Data Disk ||DISK4:[BONELAB.DATA]
|-
| invivo / invitro || Projects Disk ||DISK5:[BONELAB.PROJECTS]
|-
| invivo / invitro || Scratch Disk ||ADISK1:[BONELAB.SCRATCH]
|}

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=Remote Access=

== VPN Setup ==

Access to the OpenVMS workstations from campus does not require VPN setup; however, to access from off the campus requires establishing a VPN connection prior to connecting.

*The VPN server is: gpvpn2.ucalgary.ca

*The client needed for VPN connection is '''FortiClient SSL''' which is available through [https://ucalgary.service-now.com/it| UofC IT Service Request] "Order Something".

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== Setup for MAC/Linux ==

=== Terminal and XQuartz ===
You need following to access the MicroCT system remotely.
#'''Terminal''': an SSH client
#*Preinstalled in MAC/Linux.
#'''XQuartz''': an X server for X11 forwarding
#*X11 was previously distributed with Mac OSX but has since stopped.
#*Check if preinstalled in MAC: open the "Applications" folder, choose "Utilities", there should be a file called "XQuartz". No need to open.
#*If not preinstalled, download the most recent [https://www.xquartz.org/ '''XQuartz.dmg'''].
#*Once downloaded, double click the .dmg file to follow the instructions and install.
 
;SSH from terminal
#Open a terminal.
#*MAC: Open the "Applications" folder, choose "Utilities", then "Terminal".
#Type <pre>$ ssh xtremect2@emily.ucalgary.ca -Y</pre>
#*The -Y flag activates X11 forwarding.
#Or type <pre>$ ssh -Y -p22 -c 3des-cbc -o KexAlgorithms=+diffie-hellman-group1-sha1 -o HostKeyAlgorithms=+ssh-dss xt2recalib@emily.ucalgary.ca </pre>
#*Type <pre>$ alias xt2recalib='<ssh command above>'</pre> allows you to only type <pre>"$ xt2recalib"</pre> in the terminal from here on out to access the MicroCT system.
#You're good to go!

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== Setup for Windows ==
=== MobaXterm ===

There is only one program required to access MicroCT remotely: MobaXterm. It will act as both an SSH client and as an X server.

*Download [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Home Edition (Portable Edition)]
 
;Configure MobaXterm
*Run the .exe file after downloading MobaXterm.
:[[File:MobaXterm_init.PNG|500px]]

*Click on "Sessions" -> "User Sessions" and choose "SSH" in the top left of the "Session settings" window.
*Input your host info into the "Remote host" dialogue box such as "emily.ucalgary.ca", check on "Specify username" and input your username such as "xt2recalib" and ensure "X-11 Forwarding" is checked in "Advanced SSH Settings" tab, and click OK.
:[[File:MobaXterm_SSH.PNG|500px]]
 
;Start the session
*Launch the MobaXterm client and under "Sessions" -> "User session" you should have something titled "xt2recalib@emily.ucalgary.ca".
*Double click that session and you're good to go!
:[[File:MobaXterm_Session.PNG|500px]]

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=== PuTTY and Xming ===
There are two programs required:
#'''PuTTY''': an SSH client
#*Download [http://www.chiark.greenend.org.uk/~sgtatham/putty/ '''PuTTY'''] or from BoydDrive:\\04 - Resources\04 - Software\PuTTY.
#'''Xming''': an X server
#*Download [https://sourceforge.net/projects/xming/files/latest/download?source=files '''Xming 6.9.0.31''']
#*Download [https://sourceforge.net/projects/xming/files/Xming-fonts/7.5.0.93/Xming-fonts-7-5-0-93-setup.exe/download '''Xming Fonts''']
 
;Configure PuTTY
*Under categories, expand the "Connection" and "SSH" trees. Click on "X11" and check the "Enable X11forwarding" box.
:[[File:Putty1.png|400px]]
*Under categories, now choose "Sessions".
*Under host name, put in "emily.ucalgary.ca". Choose "SSH" for the connection type.
*Under Saved Sessions, give the session a name (e.g., Emily). Click the "Save" button.
:[[File:Putty2.png|400px]]
 
;Start the Session
*Launch the Xming program, nothing should open except the Xming icon on the task bar.
*Open PuTTY. Double-click on the saved session, which will open a DEC terminal.
*Any program that you run remotely will be displayed by Xming.

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==Remote Access FAQ==
=== MAC Open SSH Authentication Issue ===
You might get an error similar to the following especially after a recent OS update:
Unsupported KEX algorithm "+diffie-hellman-group1-sha1"
command-line line 0: Bad SSH2 KexAlgorithms '+diffie-hellman-group1-sha1
This is not Apple’s fault, it’s OpenSSH version 7. SHA1 is weak, so support for it has been removed. Which is fine, but VMS clients are probably using RSA/SHA1. So until they’re all updated (i.e. never!) we need to re-enable SHA1.

Open a terminal windows and execute the following:
sudo nano /etc/ssh/ssh_config
ENTER YOUR PASSWORD

Locate the line ‘# MACs hmac-md5,hmac-sha1,umac-64@openssh.com,hmac-ripemd160′ and remove the Hash/Pound sight from the beginning.

Locate the line ‘# Ciphers aes128-ctr,aes192-ctr,aes256-ctr,aes128-cbc,3des-cbc’ and remove the Hash/Pound sight from the beginning.

Then paste the following on the end;

HostkeyAlgorithms ssh-dss,ssh-rsa
KexAlgorithms +diffie-hellman-group1-sha1
There’s no reason to reboot, it should work straight away.
 

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=== SSH Speed Issues ===
 
If you notice that the remote display is quite slow, you may prefer to enter the 'manual' X display redirection after connecting with ssh. 
 
The steps to enter the 'manual' X display redirection are outlined in one of Scanco's FAQs found [http://www.scanco.ch/en/support/customer-login/faq-customers/faq-customers-general.html here]. 
Click the "Remote Graphical Access from your PC to the MicroCT" tab (5th tab) and scroll down to "SSH Speed Issue" for more information.

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=== MobaXterm Backspace Issue ===
If the Backspace/Delete key doesn't work on your MobaXterm

#Right-click on a session name on the left column and click "Edit session"
#:[[File:MobaXterm1.png|500px]]
#: 
#Under "SSH" page "Terminal settings" tab, toggle off "Backspace sends ^H" and "Save"
#:[[File:MobaXterm2.JPG|500px]]

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Scanco User Instructions

2021-06-09T21:56:57Z

Yingzhu: /* Extract Results from XtremeCT Database using UPAT_LIST */

=OpenVMS Basics=
The micro-CT scanners in the lab are manufactured by [http://www.scanco.ch Scanco Medical] and most analyses are performed using their custom software. The micro-CT workstations run OpenVMS as its operating system and it is useful to learn some basic commands.

==OpenVMS Beginner's Reference==
OpenVMS (informally known as VMS) is a high-end computer server operating system with reliable, multitasking, real-time and batch processing. OpenVMS supports computer clustering via a LAN, enabling computers to share resources such as processors and disks to balance workload efficiently.

*[http://saf.bio.caltech.edu/vms_beginners_faq.html '''OpenVMS Beginner's FAQ''']

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==Session Manager==

The session manager automatically starts after a user logs in locally. For remote sessions, the session manager can be started with the command <code>$ vue </code>.

[[Image:SessionManager.jpg|600px]]

===Session===
Here you will find an option to "End Session", which you should do when you are finished using a workstation. You can click "Work in Progress..." when you have to leave in the middle of a session without logging out but showing a work in progress screen to other users to prevent interference.

===Views (directory shortcuts)===
The session manager is a graphical user interface that can be used to navigate directories (left side of session manager) and open files (right side of session manager). There are shortcuts to key directories under "Views". Single-click on a directory to list its subdirectories and files. Double-click on a file to open it.

===Commands and Utilities===
Under commands you will find tools such as copy, delete, and rename; however, it is much more practical to do these sorts of operations from a DEC terminal.

===Applications===
Under applications you can launch various applications including:
*DECterm: opens a DEC terminal
*MICROCT: opens the micro-ct control panel (buttons for Scanco Medical programs)
*Mozilla/Netscape: opens a web browser
*XV: opens a screen capture program

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==DEC Terminal and Digital Command Language (DCL)==
This is a DEC terminal: Commands issued in a DEC terminal are DCL commands.

[[Image:decterm.jpg|600px]]

===Copy and paste using the mouse in DEC terminal===
In the DEC terminal, you can highlight text by holding down and moving the mouse. Highlighted text can be pasted into applications or in the terminal using the middle mouse button. You can also highlight files in the Session Manager and paste the filename (with its full path) using the middle mouse button.

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===What is a symbol===
DCL can store information such as strings or integers in "symbols". DCL can also manipulate these symbols to create other symbols.
Symbols are primarily used to define short strings that replace long commands, perform certain calculations and replacements within DCL
procedures, hold status information.
<pre>
$ UR == "SET DEFAULT DISK4:[BONELAB.PROJECTS]" !A short hand to change locations to the project disk.
$ UR :== SET DEFAULT DISK4:[BONELAB.PROJECTS] !Another way to define the symbol without quotations.
$ x == 3 !Store the value 3 in the symbol x.
$ SHOW SYMBOL x !Displays the value of the specified symbol, x.
$ DELETE/SYMBOL/GLOBAL x !Deletes the specified symbol, x.
</pre>
Selected symbols on the Scanco system:
<pre>
$ UD !Changes to the data directory.
$ UR !Changes to the projects directory.
$ DISKS !Shows the current disk usage.
$ DEC !Opens a new DEC terminal.
$ EVE file.txt !Opens the file in the text editor.
$ AIX file.aim !Shows the processing log for an aim file.
$ AIX -L file.aim !The "-L" is used to show the full processing log.
$ QUE !Shows all entries in the queue.
$ GS file.ps or file.pdf !Opens *.ps and *.pdf files in GhostScript.
$ CTHEADER file.isq or file.rsq !Shows scan information for an *.isq or *.rsq file.
</pre>

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===What is a logical===
Logical names are strings, like symbols, but can be passed into programs whereas symbols can usually only be interpreted by the command line interpreter. For example, if the logical name UD was defined to be DISK2:[XTREMECT2.DATA] then UD: could be used as a substitute when entering the path to search for files from within a program.
<pre>
$ DEFINE UD DISK2:[XTREMECT2.DATA] !Defines a logical ud to point to the data directory.
$ DEFINE uct_default_isq myfile.isq !Defines the default isq file for Scanco Medical programs. The isq filename must contain the full path to the file to be evaluated, whereas the path can be left out if you just want to contour the scan.
</pre>
Selected logicals on the micro-CT system:
<pre>
COM !Logical pointing to the commands directory IDISK1:[XTREMECT2.COMMANDS]
UD !Logical pointing to the data directory DISK2:[XTREMECT2.DATA]
UD6 !Logical pointing to the data directory DISK6:[XTREMECT2.DATA]
UR !Logical pointing to the projects directory DISK4:[BONELAB.PROJECTS]
UE !Logical pointing to the evaluation script directory MICROCT_ROOT:[EVAL]
UU !Logical pointing to the templates directory MICROCT_ROOT:[UIL]
UCT_RESULTS !Logical pointing to the results directory MICROCT_USER:[RESULTS]
</pre>

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===Arithmetic operations===
{| class="wikitable"
|style="width: 10%"|Addition ||style="width: 5%;text-align:center;"| + ||The plus sign (+) adds two numbers.
|-
|style="width: 10%"|Subtraction ||style="width: 5%;text-align:center;"| - ||The minus sign (-) subtracts the second specified number from the first specified number.
|-
|style="width: 10%"|Multiplication ||style="width: 5%;text-align:center;"| * ||The asterisk (*) multiplies two numbers.
|-
|style="width: 10%"|Division ||style="width: 5%;text-align:center;"| / ||The slash (/) divides the first specified number by the second specified number. If a number does not divide evenly, the remainder is lost. No rounding takes place.
|}

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===Logical expressions===
{| class="wikitable" style="width: 100%;"
|style="width: 10%"|And||.AND.||The operator .AND. combines two logical values as follows
true .AND. true = true true .AND. false = false false .AND. true = false false .AND. false = false
|-
|style="width: 10%"|Or||.OR.||The operator .OR. combines two logical values as follows
true .OR. true = true true .OR. false = true false .OR. true = true false .OR. false = false
|-
|style="width: 10%"|Not||.NOT.||The operator .NOT. reverses the bit configuration of a logical value. A true value becomes false and a false value becomes true.
|}

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===Numeric comparisons===
{| class="wikitable"
|style="width: 15%"|Equal to||style="width: 5%;text-align:center;"|.EQ.||Compares one number to another for equality.
|-
|style="width: 15%"|Not equal||style="width: 5%;text-align:center;"|.NE.||Compares one number to another for inequality.
|-
|style="width: 15%"|Greater than||style="width: 5%;text-align:center;"|.GT.||Compares one number to another for a greater value in the first number.
|-
|style="width: 15%"|Greater than or equal to||style="width: 5%;text-align:center;"|.GE.||Compares one number to another for greater or equal value in the first number.
|-
|style="width: 15%"|Less than or equal to||style="width: 5%;text-align:center;"|.LE.||Compares one number to another for a lesser or equal value in the first number.
|-
|style="width: 15%"|Less than||style="width: 5%;text-align:center;"|.LT.||Compares one number to another for a lesser value in the first number.
|}

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===String comparisons===
The operators for string comparisons are the same as for numeric comparisons with an added "S" for string.
{| class="wikitable"
|style="width: 15%"|Equal to||style="width: 5%;text-align:center;"|.EQS.||Compares one character string to another for equality.
|-
|style="width: 15%"|Not equal||style="width: 5%;text-align:center;"|.NES.||Compares one character string to another for inequality.
|-
|style="width: 15%"|Greater than||style="width: 5%;text-align:center;"|.GTS.||Compares one character string to another for a greater value in the first specified string.
|-
|style="width: 15%"|Greater than or equal to||style="width: 5%;text-align:center;"|.GES.||Compares one character string to another for greater or equal value in the first specified string.
|-
|style="width: 15%"|Less than or equal to||style="width: 5%;text-align:center;"|.LES.||Compares one character string to another for a lesser or equal value in the first specified string.
|-
|style="width: 15%"|Less than||style="width: 5%;text-align:center;"|.LTS.||Compares one character string to another for a lesser value in the first specified string.
|}

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==DCL Programming Guide==
The OpenVMS systems allow for scripts to be written in a language called '''DCL (DIGITAL Command Language)'''. It was not designed to be more difficult than other scripting languages, but learning any new programming language comes with its learning curve.

*DCL has 243 commands, but most programs can be written with a base set of about 20 commands. The goal of this section is to provide a convenient reference for these commonly-used commands.

It is recommended to open a text editor, enter the whole series of commands, and then run them as a whole program. The terminal on OpenVMS is technically a DCL interpreter, so these commands could be typed in sequence into a terminal with the same result. Typing code interactively is helpful when testing a small code snippet in more detail.

===Your First DCL Script===
Ever since Kernighan and Ritchie wrote the book "The C Programming Language", it has been custom to start with a program that prints the text "Hello, world" to the screen. Open a text editor (for example "EVE") and enter the text below.
<pre>
$! My First DCL Script
$ mymessage = "Hello, world"
$ WRITE SYS$OUTPUT mymessage
$ EXIT
</pre>
Now save the file as HELLO1.COM, and run it using <pre>$ @HELLO1.COM</pre>

Several things are happening in the above program:
*'''Comment !''': The exclamation mark can appear anywhere on the line, and everything following the mark will be treated as a comment.
*'''Variable''': "mymessage" variable is populated with the string "Hello, world", which can be used in the rest of the script.
*'''Command''' "WRITE" send text to various places, in this case to "SYS$OUTPUT", that is to the standard output (i.e. screen).
*'''EXIT''' command tells the DCL interpreter that the script is done and we should exit.
*Commands in DCL are '''NOT case sensitive''', so the command "write sys$output mymessage" would produce the exact same result, but by convention we write commands in all uppercase.

*'''Special Comment !!''' automatically prints the contents of the comment to the screen/logfile. It is useful when you want to know what part of the script you are in.

===Basic Arithmetic===
The DCL language supports several types of data in variables. In the "Hello, world" example above, we saw how to store a string in a variable. We could have stored an integer, that is a positive or negative whole number, in the variable, and done some basic math.
*Refer to [[Scanco_User_Instructions#Arithmetic_operations|'''Arithmetic Operations''']], For example:
<pre>
$ i = 1
$ WRITE SYS$OUTPUT i+1
$ j = 3
$ k = j * (i + 1)
$ WRITE SYS$OUTPUT k
$ WRITE SYS$OUTPUT (k / 4)
$ WRITE SYS$OUTPUT 2 + 2 * 2
$ EXIT
will return:

2
6
1
6
</pre>
Two things are worth noting.
*Because we are limited to integers, division of 6 / 4 needs to return an integer (1.5 is not an integer); the value is truncated, which means rounding is always done toward zero.
*Order of operations is done in the "correct" order, and not left-to-right, so "2 + 2 * 2" is interpreted as "2 + (2 * 2)".

===Conditional Statements===
Sooner or later, you will want to run a program with some logic. The general syntax is:
<pre>
IF [condition]
THEN
[do something]
ELSE
[do something else]
ENDIF
</pre>
*The "ELSE" component is optional.
*If you need a very simple if..then with only one command, it can be written on one line without the "ENDIF":
<pre>
IF [condition] THEN [do something]
</pre>
*Refer to [[Scanco_User_Instructions#Numeric_comparisons|'''Numeric Comparisons''']], [[Scanco_User_Instructions#String_comparisons|'''String Comparisons''']] and [[Scanco_User_Instructions#Logical_expressions|''' Logical Expressions''']] for all possible logical operators (very similar to Fortran).

===Loops===
Most programming languages have 3 kinds of loops:
*Precondition Loops: Condition is tested at the beginning of the loop
*Postcondition Loops: Condition is tested after the loop has executed at least once
*Iterative Loops: A variable changes in a predetermined fashion each time the loop is called.

DCL has none of these. Instead, it has the concept of a "label" and the "GOTO" command. A loop in DCL would look like this:
<pre>
$ i = 1
$loop1:
$ IF i .GE. 10 THEN GOTO exitloop1
$ WRITE SYS$OUTPUT i
$ i = i + 1
$ GOTO loop1
$exitloop1:
$ EXIT
</pre>
This program will print the numbers from 1 to 10 in sequence.

===Subroutines===
Most programming languages allow to define a set of commands that can be called from various parts of the program.
*In DCL, the subroutine can be defined anywhere in the file (unlike C or Python, where the definition must precede the call).
<pre>
$ CALL mycustomsub Joe
$ CALL mycustomsub Mary
$ EXIT
$mycustomsub: SUBROUTINE
$ WRITE SYS$OUTPUT "Hello, ", P1, "!"
$ EXIT
$ ENDSUBROUTINE
</pre>

The first line calls a subroutine named "mycustomsub", which jumps execution to the 4th line. The parameters after the name of the function get copied over to local variables named "P1", "P2", "P3" etc. (in this example, only one parameter, but the maximum is 8) that are available to the subroutine. Note that the command "WRITE" accepts several arguments separated by commas, which get printed on one line.
*The subroutine should be terminated with the command "EXIT" followed by "ENDSUBROUTINE".
*Note that the parameters get passed literally to the subroutine, that is the subroutine gets the text "Joe", and not the contents of a variable named "Joe".
*To force symbol substitution, the parameter would need to be enclosed in single quotes.
<pre>
$ Joe = "Joe Smith"
$ Mary = "Mary Jane"
$ CALL mycustomsub 'Joe'
$ CALL mycustomsub 'Mary'
$ EXIT
$mycustomsub: SUBROUTINE
$ WRITE SYS$OUTPUT "Hello, ", P1, "!"
$ EXIT
$ ENDSUBROUTINE
</pre>

===Reading from files===
Sometimes you have a list of files (for example Micro-CT scans) that are to be processed in a certain way. The obvious way is to copy-paste the code several times, changing only the name of the file, but this is error-prone and inefficient.
*A better way is to put the list of models into a text file, and then call a subroutine on each model file. For example:
<pre>
$ CLOSE/NOLOG foo
$ OPEN/READ foo DISK3:[MICROCT.PROJECTS.OWOC.COM]MYLIST.TXT
$read_loop:
$ READ/END=done foo myline
$ CALL process_me 'myline'
$ GOTO read_loop
$done:
$ CLOSE/NOLOG foo
$ EXIT
$process_me: SUBROUTINE
$ scriptname = DISK3:[MICROCT.PROJECTS.OWOC.COM]MYSCRIPT.COM
$ SUBMIT/NOPRINT/QUE=SYS$FAST/PARAM='P1' 'scriptname'
$ EXIT
$ ENDSUBROUTINE
</pre>
*The first line closes the file handle, in case it was left open in a previous script.
*The second opens the file "MYLIST.TXT" for reading, and assigns the open file a handle named "foo".
*A loop reads the file line-by-line, calling a subroutine with the contents of each line.
*When the end of the file is reached, the file is closed and the script exits.

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==List of basic commands==
<pre>
$ VUE !Start the session manager. Press enter after to regain prompt.
$ DEC !Open a new DEC terminal
$ UCT !Open the micro-CT control panel.
$ UCT_SAMPLE !Start µCT Samples.
$ UCT_MEASUREMENT !Start µCT Tomography.
$ UCT_EVALUATION !Start µCT Evaluation Program.
$ UCT_3D !Start µCT Ray.
$ UCT_BACKUP !Start µCT Disk-Utility.
$ CD UD !Change location to the data directory.
$ CD UR !Change location to the projects directory.
$ CD SYS$SCRATCH !Change location to the scratch directory.
$ CD UCT_RESULTS !Change location to the results directory.
$ DIR UE !List files in the evaluation directory.
$ DIR UU !List files in the templates directory.
$ DIR COM !List files in the commands directory.
$ UCT_LIST !Extract results from the database.
$ AIX -L !View the header of an AIM file.
$ CTHEADER !View the header of an RSQ or ISQ file.
$ EVE !Start the text editor.
$ DISKS !Show the current disk usage (all hard drives).
$ LOGOUT !End a session. For remote sessions, logout from the main (initial) login terminal.
</pre>

===How to move to a different directory===
Use the SET DEFAULT command. You can use an absolute directory path or a relative directory path.
<pre>
$ SET DEFAULT disk:[dir.subdir] !Moves to specified path.
$ SET DEFAULT [.subdir] !Moves one level into subdirectory subdir.
</pre>

Use the CD (i.e., change directory) command (this calls the script $ @SCOM:CD.COM).
<pre>
$ CD subdir !Moves into subdirectory subdir.
$ CD subdir1 subdir2 !Moves into subdirectory subdir1, then into subdir2.
$ CD .. !Moves up one level (i.e., out of one directory).
</pre>

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===How to list the files in a directory===
Use the DIRECTORY command, which may be abbreviated to DIR.
<pre>
$ DIR !List everything in the current directory.
$ DIR disk:[dir.subdir] !Lists everything in the specified directory.
$ DIR disk:[dir.subdir...] !Lists everything in the specified directory and subdirectories.
$ DIR/COL=1 *.aim !Lists all files with the extension .aim in a single column.
$ DIR /VERSIONS=1 !Show only the newest version of each file in the directory.
$ DIR/SINCE=TODAY !Lists all files created today.
$ DIR [...*.aim] !The "..." indicates to do so recursively (i.e., counting all files in all subdirectories).
$ DIR/SIZE !Lists each file and its size.
$ dir/size/grand_total [.subdir...] !List the total size of all files in the SUBDIR directory.
$ HELP DIR !More information on the DIRECTORY command.
</pre>

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===How to copy files===
Use the COPY or BACKUP command.
<pre>
$ COPY file1.ext disk:[dir.subdir1]file2.ext !Make a copy of file1.ext to another location and call it file2.ext
$ COPY *.aim;* disk:[dir.subdir1] !Copy all .aim files (including all versions) to another location keeping the same name.
$ HELP COPY !More information on the COPY command.
</pre>
<pre>
$ BACKUP/VERIFY [.subdir1...]*.*;* [.subdir2...] !Copy entire directory SUBDIR1, including all subdirectories and files, into SUBDIR2.
$ BACKUP/VERIFY [.subdir1...]*.*;* []subdir1.sav/SAVE !Copy entire directory SUBDIR1, including all subdirectories and files, into a save set. The save set could be transferred and unpacked on another OpenVMS machine.
$ HELP BACKUP !More information on the BACKUP command.
</pre>

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===How to delete files===
Use the DELETE command, which may be abbreviated to DEL.
<pre>
$ DEL myfile.txt; !Delete the most recent version of myfile.txt.
$ DEL myfile.txt;* !Delete all versions of myfile.txt.
$ HELP DELETE !More information on the DELETE command.
</pre>
[[Image:Bones2.jpg|20px]] Warning: Extreme caution!
<pre>
$ DEL *.*;* !Delete everything in the current directory!
</pre>

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===How to create a directory===
Use the CREATE/DIR command.
<pre>
$ CREATE/DIR [.subdir] !Creates a subdirectory named subdir.dir in the current directory.
$ CREATE/DIR disk:[dir.subdir] !Creates the subdirectory subdir at the specified path.
</pre>

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===How to rename files and directories===
Use the RENAME command.
<pre>
$ SET FILE/PROTECTION=O:RWED olddir.dir !Sets protections so you can rename the directory.
$ RENAME oldfile.ext newfile.ext !Renames oldfile.ext to newfile.ext.
</pre>

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===How to check the queue===
Use the SHOW QUEUE command, which may be abbreviated to SH QUE.
<pre>
$ SHOW QUEUE !Shows all the queues, there are many!
$ SH QUE *FAST !Shows all queues whose names end with "fast", these are used for evaluations.
$ SH QUE *SLOW !Shows all queues whose names end with "slow", these are used for reconstructions.
$ SH QUE *FAST/ALL !By default you are only shown queue entries for the user you are logged in as. To show jobs for all users, use the /ALL qualifier.
$ SH QUE *FAST/BY=EXE/ALL !Show only jobs that are currently executing for all users.
</pre>

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===How to get queue information===
Use the SHOW ENTRY command to obtain information about batch jobs in the queues.
<pre>
$ SHOW ENTRY !Shows all the batch jobs for your user, there may be lots!
$ SHOW ENTRY 251 !Shows information for batch job number 251.
$ SHOW ENTRY 251/FULL !Shows detailed information for batch job number 251.
$ SHOW ENTRY/ALL !Shows all the batch jobs for all users.
</pre>

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=Micro-Computed Tomography (µCT) Basics=

==User Tutorials==
For Scanco MicroCT Systems and Software:
:*[[Media:Microct-v14.pdf | '''Scanco MicroCT Systems and Software''']]

For XtremeCT II and I:
:*[[Media:SOP Berlin V1.0.pdf | '''Scanco XtremeCT I SOP (Berlin)''']]
:*[[Media:XtremectIIB-v4-us.pdf | '''Scanco XtremeCT II Specs''']]

For MicroCT35, VivaCT40 and VivaCT80:
:*[[Media:ScancoMicro-CT_User_Policy_Guidelines_19052005.pdf| '''MicroCT User Policy & Guidelines''']]
:*[[Media:MicroCT_Starter_Package.pdf | '''MicroCT Starter Package''']] and its [[Media:Microctstarterpackagejun2012.docx| '''Word format''']].
:*[[Media:Scanco-training-uct35-and-vivact40.pdf | '''MicroCT Customer Training Guide''']]
:*[[Media:Vivact_80_v3-nomarks.pdf | '''VivaCT 80 Specifications''']]

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==Micro-CT Image Basics==
Computed tomography is a non-destructive x-ray imaging modality that enables three-dimensional (3D) virtual models of an object to be created, which can be subsequently visualized and analyzed. Micro-CT refers to CT in which the [http://www.scanco.ch/index.php?id=faq_general#c779 resolution] lies in the micro-scale, which is achieved with a high-resolution x-ray detector and a field of view that is much smaller than conventional CT. Structural detail provided by CT depends on differences in x-ray attenuation properties. Components with very different x-ray attenuation properties, for example air, soft tissue, and bone, can be differentiated in a CT scans whereas different types of soft tissues, for example muscle and cartilage, do not have sufficient differences in attenuation to be distinguish.

===Dark Field===
Detector response with x-rays off. Enables corrections of non-uniformities of the detector. Acquired automatically by the scanning software before each scan.

[[File:Dark_field_single.img_assist_custom-400x97.jpg|400px]]

===Bright Field===
Detector response with x-rays on but no sample. Enables corrections of non-uniformities of the x-ray beam. Acquired automatically by the scanning software before each scan.

[[File:Bright_field_single.jpg|400px]]

===Raw Projection===
A raw x-ray projection of a mouse leg. The darker regions correspond with higher x-ray attenuation. The discontinuities result from overlaps where the detector was shifted to acquire the large region of interest (3x2 detector frames in this example). Projections are acquired at many incremental rotations around the sample.

[[File:Raw_projection_notes.jpg|400px]]

===Sinogram===
The sinogram is a different representation of the projection data. The sinogram represents the attenuation values of one row of the detector at each rotational increment around the sample.

[[File:Sinogram.jpg|400px]]

===Attenuation Projection===
Accounting for the inhomogeneities of the detector and beam, we can calculate the x-ray attenuation caused by the sample. Bright regions correspond with higher attenuation.

[[File:Attenuation_projection.jpg|400px]]

===Reconstructed Image===
From the attenuation projections, the original structure can be calculate using filtered back projection.

*[https://youtu.be/DBLYSETYbe8 CT Back-projection Reconstruction]
*[https://youtu.be/NWeM35_KR2w CT Reconstruction of a Head]

[[File:Reconstruction_xy_yz_planes.jpg|400px]]

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==Image Data==
===Image Data Type===
====Binary Images====
Binary images are images whose pixels contain only two possible intensity values (off-on, or black-white B&W). The off or black value is usually 0 and the on or white value is usually 1 (1-bit pixel) or 255 (8-bit pixel). This type of image is commonly used as a multiplier to mask regions within another image.

====Grayscale Images====
Grayscale images represent intensities. Pixels range from least intense (black) to most intense (white). Pixel values usually range from 0 to 255 or are scaled to this range when displayed.

====Indexed Images====
An indexed image uses direct mapping of pixel values to colormap values. Instead of intensities, a pixel value within an indexed image relates to a color value within a color lookup table. An indexed image consists of a data matrix and a colormap matrix. The data matrix can be of class uint8, uint16, or double. The colormap matrix is an m-by-3 array of class double containing floating-point values in the range [0,1]. Each row of map specifies the red, green, and blue components of a single color. Since indexed images reference color tables composed of up to 256 colors, the data values of these images are usually scaled to range from 0 to 255.

====RGB Images====
Within the three-dimensional array of an RGB image, two of the dimensions specify the location of a pixel within an image. The other dimension specifies the color of each pixel. The color dimension always has a size of 3 and is composed of the red, green, and blue color bands (channels) of the image.

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===Image Data Pixel Values===
The image data type is determined by the pixel depth in bits per channel, or bit depth. Bit depth for each channel can be 8, 16, 32 or 64. The data may be signed, unsigned (u), floating-point (f), real or complex (c) for some arithmetic functions, where each channel value is represented by two numbers: real and imaginary part. All channels in an image must have the same data type.

{| class="wikitable"
|-
! scope="col"| Image Data Type
! scope="col"| Name
! scope="col"| Byte
! scope="col"| Value Range
! scope='col'| Comments
|-
! scope="row"| char
| 8-bit signed integer
| 1
| -128 ~ 127
| Scanco SEG.AIM, GOBJ
|-
! scope="row"| uchar
| 8-bit unsigned integer
| 1
| 0 ~ 255
|
|-
! scope="row"| int
| 16-bit signed integer
| 2
| −32768 ~ 32767
| Scanco grey-scaled images, ISQ, AIM
|-
! scope="row"| uint
| 16-bit unsigned integer
| 2
| 0 ~ 65535
| Converted format of Scanco grey-scaled images
|-
! scope="row"| long
| 32-bit signed integer
| 4
| −2^31 ~ 2^31 - 1
|
|-
! scope="row"| ulong
| 32-bit unsigned integer
| 4
| 0 ~ 2^32 - 1
|
|-
! scope="row"| float
| floating point
| 4
| ±3.40282347 E+38
| 32-bit single-precision with 6~7 significant digits
|-
! scope="row"| long64
| 64-bit signed integer
| 8
| −2^63 ~ 2^63 - 1
|
|-
! scope="row"| ulong64
| 64-bit unsigned integer
| 8
| 0 ~ 2^64 - 1
|
|-
! scope="row"| double
| double precision floating point
| 8
| ±1.79769313486231570 E+308
| 64-bit double-precision with 15~16 significant digits
|-
! scope="row"| complex
| floating point complex
| 8
| same as floating-point
| same as floating-point
|-
! scope="row"| dcomplex
| double precision complex
| 16
| same as double-precision
| same as double-precision
|}

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===Scanco Image File Types===

{| class="wikitable"
! scope="col"| Extension
! scope="col", style="width: 65%"| Description
! scope="col"| Creation
! scope="col"| Opens with
|-
! scope="row"| RSQ
| '''R'''aw '''S'''e'''Q'''uence data. This is the raw data collected after the scan. This file contains the bright and dark field corrections and the raw projections. || created with scan || $ x
|-
! scope="row"| ISQ
| '''I'''mage '''S'''e'''Q'''uence data. This is the reconstructed 3D image, which you see in the µCT Evaluation Program. || created from RSQ
| $ uct_evaluation
$ x
|-
! scope="row"| AIM
| '''A'''ny '''IM'''age data. This is a binary raw data format (16-bit signed data, little endian) 3D discretized data you see using the µCT Ray Program and used for the analysis. The AIM file is a volume of interest isolated from the ISQ file. || extracted from ISQ
|$ uct_3d
$ uct_evaluation
|-
! scope="row"| GOBJ
| '''G'''raphical '''OBJ'''ect data. These are the green contours in the µCT Evaluation Program, which are used to isolate regions of interest from an AIM file for analysis. || extracted from ISQ/AIM || $ uct_evaluation
|-
! scope="row"| SCV
| '''SC'''out '''V'''iew || created with scan || $ x
|-
! scope="row"| RAD
| Scout View || created with scan || $ x
|-
! scope="row"| RSW
| raw data (RSQ) || created with scan || $ x
|-
! scope="row"| IMA
| image data (AIM, ISQ, GOBJ)|| created from RSQ || $ uct_evaluation
|}
*Refer to [[Media:Aimpack_documentation.pdf|'''Scanco Aim Format''' ]] or its [[Media:Scanco_Aim_File_Format.doc|'''Doc Format''']] for its header info.

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==Scanco Medical Micro-CT Software==
In the bottom left hand corner of the micro-CT workstation desktop is the micro-CT control panel, from which the micro-CT programs can be launched. The standard operating procedure for scanning a samples involves proceeding through the programs in the control panel from left to right:
<pre>
$ UCT_SAMPLE !Samples: Registering a sample
$ UCT_MEASUREMENT !Tomography: Scanning
$ UCT_EVALUATION !Evaluation: Evaluating the scan
$ UCT_3D !Ray: Viewing the 3D scan
$ UCT_BACKUP !Disk-Utility: Archiving the data
</pre>
You must specify an operator in the control panel to use the scanning and evaluation programs.
* XtremeCT
[[File:XCTcontrol_panel.img_assist_custom-302x100.jpg|300px]]
* MicroCT35, VivaCT40 and VivaCT80
[[File:Uct35_control_panel.jpg|300px]]
[[File:VivaCT40_control_panel.jpg|300px]]
[[File:VivaCT80_control_panel.jpg|300px]]

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===µCT Samples===
The µCT-Samples program is used to register new samples to be scanned and update sample names (e.g., to correct a sample name). To start the program type <code>$ uct_sample</code> in a DEC terminal, or use the sample button.

[[File:Xtremect_button_samples.jpg|40px]]
[[File:Uct_sample_uct35.jpg|40px]]
[[File:Uct_sample_vivact40.jpg|40px]]

#'''Prepare Sample Names''' according to [[Scanco_User_Instructions#Sample_Name_Convention|'''Sample Name Convention''']]
#'''Register Sample Names'''
#*Create a new sample by clicking “New” and typing in your sample name where it says “Name.” “Save” the sample.
#*You are now given a sample number. Record the sample number on the log sheet.
#:[[File:Uct_sample_pic01.jpg|500px]]
#'''Create Additional Sample Names Using Copy and Paste'''
#*If you have many samples to register, you can copy and paste part of the sample name you just created. Highlight the part of the sample name you want to copy by holding down the left mouse button while dragging the mouse, then release the mouse button.
#:[[File:Uct_sample_pic02.jpg|500px]]
#*Paste the highlighted text into a DEC terminal by pressing the middle mouse button. Now highlight the text in the DEC term.
#:[[File:Uct_sample_pic03.jpg|300px]]
#*Go back to the µCT-sample window, click "New", and paste the information next to "Name" using the middle mouse button. Update the name as required and "Save."
#'''Add Additional Sample Details'''
#*When a patient comes in for their first scan, you need to update their sample with their date of birth, sex, and hand/foot dominance.
#*Use the "Find..." button to search for a sample that has already been registered. You can search by sample number or by project name (e.g., CAMOS).
#*Date of birth: DD/MMM/YYYY. Example: 14/JAN/1951
#*Remarks: include the sex and hand/foot dominance. Example: F-RHRF for female that is right hand dominant and right foot dominant

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===µCT Tomography===
The µCT-Tomography program is used to perform a scan.

NOTE: Only Authorized Operators are permitted to use uCT or XtremeCT scanners. For the XtremeCT scanners, this is a formal process. To inquire about authorization, speak to your supervisor. The below description is intended to provide general understanding of how scans are acquired. It is not a substitute for complete training.

To start the program type <code>$ uct_measurement</code> in a DEC terminal on the scanner computer (remote access does not allow this functionality), or use the scanner button. If you use the button, you must specify an operator prior to using the program.

[[File:Xtremect_button_scan.jpg|40px]]
[[File:Uct_measurement_uct35.jpg|40px]]
[[File:Uct_measurement_vivact40.jpg|40px]]
[[File:VivaCT80_scan.jpg|40px]]

[[File:Uct_tomography_pic00.jpg|600px]]

#'''Select Sample'''
#*When the µCT-Tomography program is first started, you will be prompted to enter the sample name or number of the specimen you are about to scan.
#*If you have not registered your sample, press "Cancel" to close the select sample box, then press "New..." in the measurement sample box to register a new sample (see [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT-Samples''']]).
#*Once you have entered your sample information, the measurement sample box will show details for that sample, including the sample name and scan (measurement) history.
#:[[File:Uct_tomography_pic01.jpg|400px]]
#*After your first scan you will need to press the "Other..." button to open the sample selection box and find your next sample.
#'''Select a Controlfile'''
#*The controlfile contains scan parameters such as the x-ray energy, current, and more (see [[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29 controlfiles |'''Controlfiles''']]).
#*Once the controlfile is setup, you need only to select it. If there are many controlfiles, you may want to search for yours using the file filter by entering part of the name or number in the white box and pressing enter; if you do this, you still must click on the controlfile so that it is highlighted in black as shown below.
#:[[File:Uct_tomography_pic02.jpg|400px]]
#'''Precalibrate'''
#*Calibrations are done before loading your patient/animal and scanning for quality control and to reduce the time the patient/animal is under preparation/anaesthesia. Start the calibration by pressing the "Precalibrate" button.
#:[[File:Uct_tomography_pic03.jpg|400px]]
#*Press "Start Calibration". The calibration will start with an "X-Ray Warmup", followed by "Measuring Dark" and "Measuring I0" and usually takes about 2-3 minutes to complete.
#:[[File:Precalibrate.jpg|300px]]
#*The precalibration is good for 15~20 min. The time remaining is shown on the "Precalibrate" button.
#:[[File:Uct_tomography_pic5.jpg|400px]]
#*The precalibrate option cannot be used with batch measurements, and it's not available for MicroCT35 which is not intended for invivo/live scan.
#'''Load and Position the Patient/Sample'''
#*Instruct the patient to remove any jewelry in the scan areas (wrist/ankle/knee/elbow ect). With the patient seated, put the wrist/ankle/knee/elbow into the appropriate cast. Different pads with different sizes can be used to fit the patient.
#*For invivo/invitro samples, prepare your sample in terms of orientation, immobilization, hydration ect.
#*After the precalibration is complete, you can now open the bore cover and insert the patient's wrist/ankle/knee/elbow or sample into the scanner. Gently move the wrist/ankle/knee/elbow or sample into the scanner until you can snap in the cast at the gantry. Check that the cast is positioned correctly and the patient/sample is comfortable.
#*Close the bore cover.
#'''Scout-View'''
#*A scout-view is similar to a 2D x-ray image and allows the user to set where to start and stop the scan.
#*After loading your sample, press the "Scout-View..." button to bring up the scout-view window.
#*The start position (top of the scanner) and end position (bottom of the scanner) can be modified to zoom in on the region of interest.
#*The angle of the scout view can also be changed to see the object in a different orientation.
#*Once pressed the "Scout-View" button but the scout view is found not in an appropriate position, press "Cancel", modify the start position, end position, or angle and press "Scout-View" again.
#:[[File:Scout_view_window.jpg|400px]]
#*Scout view image is displayed in the top right hand corner of the program and will start by showing the right half of the image, followed by the left half of the image.
#'''Set Reference Line and Launch a Scan'''
#*A reference line (solid green line) is placed to set the scan region (green block).
#*Press the "Reference-Line" button to show the reference line and default scan region over the scout view.
#*To change the number of slices to scan, move the reference line to the top of the scan region, then hold down the shift button while dragging the mouse to extend the scan region and press the left mouse button to set the reference line.
#*To centre the scan region between two reference lines, move the reference line to the top of the scan region, then hold down the alt key while dragging the mouse until the second green reference line is in place, then press the left mouse button to set while still holding down the alt key!
#:[[File:Uct_tomography_pic06.jpg|700px]]
#*For a single scan, select "OK", "Scan" and "Start Measurement". Record measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']].
#*For a batch scan which is only available on microCTs, select "Batch Measurement" and record the measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']]. You may now setup a new scan (select new sample and controlfile, perform scout, etc). When you have finished setting up all scans, press "Start Batch Scans." (See [[Scanco_User_Instructions&action=edit&section=48#Perform_Batch_Scans|'''Perform Batch Scans''']] for detailed instructions)
#'''Cancel or Reposition a Scan'''
#*If you need to interrupt a scan, press the cancel button and restart the scan or if you do not want to rescan then "unload" the scanner.
#*If you have not started a scan and need to reposition the patient, you also must "unload" the scanner.
#'''Remove Patient/Sample from Scanner'''
#*After the scanning is complete, open the bore cover and slide the patient's wrist/ankle/knee/elbow or sample out of the scanner. Release the cast by pushing down the cast release handle.

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===µCT Evaluation Program===
The µCT Evaluation Program is used to evaluate a scan. To start the program type <code>$ uct_evaluation</code> in a DEC terminal, or use the graph button. If you use the button, you must specify an operator prior to using the program.

[[File:Uct_evaluation.jpg|40px]]

'''SCREEN SHOT TO BE ADDED SHORTLY'''

#'''Find Your Sample'''
#:Enter the first part of your sample name in the file filter box and press enter. The samples are shown in the left hand box. The measurement box on the right shows scans for the selected sample (highlighted in black). Select a measurement and press "OK."
'''SCREEN SHOT TO BE ADDED SHORTLY'''
#'''Draw Contours (If Applicable)'''
#*Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
#*Contours must always be drawn COUNTER-CLOCKWISE!!!
#*[[Media:Contouring-tools.pdf |'''Contouring tools reference sheet''']]
#*For this sample, we are only interested in viewing the object in 3D and drew contours to isolate the bone and soft tissue from the sample tube.
#:[[File:Uct evaluation pic03.jpg|600px]]
#'''Evaluate'''
#*Scanco Medical provides several standard evaluation scripts. Open the 3D-Evaluation menu either using the "T..." button or from the top menu by going to "Tasks" and "Evaluation 3D...". If you set a default evaluation script in your scanning controlfile, it will be listed under "Task/Evaluation."
#:[[File:Uct_evaluation_pic04.jpg|400px]]
#*If you want to run a different evaluation press "Select...", highlight the evaluation script of interest, and press "OK".
#:[[File:Uct_evaluation_pic05.jpg|400px]]
#*When the 3D-Evaluation window is activated, a white box will appear on your reconstructed image. The white box is the region of interest that will be "cut out" of the full scan. If you have drawn contours, the white box will automatically be adjusted to fit the contours. Adjust the box if necessary by grabbing one of the white handles; use the left mouse button to move the box and the right mouse button to resize. The box can also be resized using the "VOI Start" and "Dimensions" in the 3D-Evaluation window.
#*For most evaluation scripts, you will be required to specify parameters for a Gaussian filter, to reduce noise, and a threshold, to isolate your object (e.g., bone) from the background. Check that the parameters used provide a good representation of your scanned sample by flipping back and forth between the segmented and grayscale image using the "Preview" and "Grayscale" buttons.
#:[[File:Uct_evaluation_pic06.jpg|400px]]
#*When you are satisfied with the segmentation parameters, press "Start Evaluation", which will submit the job to the queue.

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===µCT Ray===
The µCT Ray program is used to view scanned objects in 3D, create images, and create image sequences for animations. To start the program type <code>$ uct_3d</code> in a DEC terminal, or use the 3D object button.

[[File:Uct_3d.jpg|40px]]

'''SCREEN SHOT TO BE ADDED SHORTLY'''

#'''Select and Render Your Sample'''
#*'''Select:''' If you have used the default Scanco Medical scripts, then
#:*If your data is on the "data disk" and you can search for your files using the file filter to select a sample and measurement then press "OK". To open a new file, File --> Open.
#:*If your data is not in the standard location (e.g., it was copied to the projects disk), then use File --> Read and navigate to find the file to open.
#:*Alternatively you can start the program with a file to open <code>$ uct_3d myfile_seg.aim</code>
#: 
#*'''Rendering:'''
#:*Use a single click of the left mouse button to start or to stop rendering the sample.
#:*You can also use the "Start" and "Stop" buttons at the bottom of the options on the left.
#:*You must stop rendering to change viewing options on the left.
#: 
#*'''Change View:'''
#:*To adjust the view, move the "Rotation" and "Elevation" slider bars in the options on the left.
#:*The slider bar is located above its label.
#:[[File:Uct_3d_pic02.jpg|600px]]
#: 
#*'''Change Colours''' (Object and Background):
#:*From the top menu choose "Options" then "Object/Display Properties...".
#:*A segmented image typically only has two values, 0 (black, background) and 127 (white, object). To change the colour of the object only, we need to set the value 127 to a specific colour.
#:*In this example, the slider bar value "1" corresponds with the value 127 and we will set both slider bars to "1" so that we are adjusting values "127 ... 127", in other words, only value "127".
#:*Under "Surface" click on the "white box" to open the "Color Mixing" window.
#:*Choose the new colour for the object (e.g., orange) and press "OK."
#:*Close the "Object Properties" window or move it to the side.
#:*Now re-render the object with a single click of the left mouse button.
#:[[File:Uct_3d_pic03.jpg|300px]] [[File:Uct_3d_pic04.jpg|300px]]
#: 
#*'''Cutplane (left options) and Subdim (top menu):''' 
#:*The cutplane and subdim functions allow you to show a cross-section of your object.
#:*The subdim function tends to work better than the cutplane but is limited to axes of the scan.
#:[[File:Uct_3d_pic05.jpg|600px]]
#: 
#'''Print an Image to File'''
#*An image must be fully rendered in order to be saved.
#*From the top menu choose "File" then "Print". Set the print format to "TIFF" and the directory to "Scratch/Temp" (or another location using the "Specify in Filename" option).
#*Change the filename to something meaningful then press "OK."
#:[[File:Uct_3d_pic06.jpg|300px]]
#: 
#'''Auto-Print Images for an Animation'''
#*Creating an animation involves saving a sequence of rendered images, which can then be compiled into an animated GIF or other video format using various software packages (e.g., Photoshop, Quicktime Pro).
#*From the top menu choose "Options" and "Animation..." to open the Animation Settings window. Set the viewing parameters for the start of the animation, fully render the image, then press the "Get Settings A" button.
#*Set the parameters for the end of the animation, fully render the image, then press the "Get Settings B" button.
#*Set the number of frames you want, the higher the number frames, the smoother the animation will be, but also the larger the file size.
#*Now setup the auto-print feature. From the top menu choose "File", then "Print". Choose "TIFF" for the print format, and the "Scratch/Temp" for the directory (or use the "Specify in Filename"). Specify a filename prefix, to which numbers will be appended for the image sequence.
#*Activate the "Auto-Print" feature. Press "OK" then press the "Start Calculation" button on the Animation Settings window.
#*Do not interrupt the program while the frames are being rendered and saved. When the program is done rendering all the frames, transfer them to your computer to compile into an animation.
#:[[File:Uct_3d_pic07.jpg|200px]] [[File:Uct_3d_pic08.jpg|300px]]

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===XImage===
The XImage program is used to view the raw data (RSQ file) and scout view. To start the program type <code>$ run um:ximage</code> or <code>$ x </code>in a DEC terminal.

When loading an RSQ, the default view (XY plane) is of the sinogram.

[[File:Ximage_1.jpg|600px]]

To view the attenuations, choose the XZ plane. The first slice in this orientation is the dark field, the second slice is the bright field , and slices three and onward are the raw projections (attenuations).

[[File:Ximage_2.jpg|600px]]

To view the corrected projections, from the Evaluations menu, choose Projection Mode.

[[File:Ximage_3.jpg|400px]]

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=Scanning=
==Sample Name Convention==
*At the Bone Imaging Laboratory, all sample naming must conform to the following format
:'''PROJECT IDENTIFIER _ SAMPLE DETAILS'''
*In CAPITAL LETTERS (filenames are case sensitive, so this makes it easy to remember how you input your sample name)
*No special characters (spaces, /, %, etc.) as further evaluations will not work if spaces are present.
:Examples: CAMOS_771, TESTS_0001, TESTS_0002, TESTS_0003

==Register Samples for Scanning==
*Although samples can be registered immediately prior to a scan, it is much more efficient to register all your samples beforehand.
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT Samples''']] for instructional details.

==Log Sheets==
*Log sheets are used to record important information about scans that are performed, such as sample and measurement numbers ect.
*Log sheets are to remain in the lab. If you would like a copy of your log sheets, please make a photocopy or print two copies to record the scan information.
*Use the PDF file to print blank log sheets. Use the Excel file to make your own custom log sheet.

#Bone Lab for General Patients
#*[[Media:XCT_II_Log_(Studies).pdf|'''XCT II Log Sheet for Studies''']]
#*[[Media:XCT_II_Log_(Miscellaneous).pdf|'''XCT II Log Sheet for Miscellaneous''']]
#MicroCT Lab for General Non-Patients
#*[[Media:UCT_log_sheet_general.pdf|'''MicroCT Log Sheet for Studies (PDF)''']]
#*[[Media:UCT_log_sheet_general.xlsx|'''MicroCT Log Sheet for Studies (Excel)''']]

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==Patient Casts and Sample Holders==
===Patient Casts for XtremeCTs===
Regardless of what cast is used, the X-, Y-, and Z- dimensions remain the same:
*X=14cm
*Y=14cm
*Z=designated 20cm distance in the scanner

Standard Scanco Distal Radius Cast
*Used for distal radius scans of 1-3 stacks. Designed with the hand to be in a curved position. The field-of-view allows for scanning of approximately the most distal 1/4 of the forearm.
Standard Scanco Distal Tibia Cast
*Used for distal tibia scans of 1+ stacks. Designed with the foot to be in a flexed (upright) position. The field-of-view allows for scanning of approximately the most distal 1/4 of the tibia.
Standard Scanco Sample Holder
*This is a cylindrical tube with a cut-out window on the top.
*Allows for scanning small ex-vivo and other samples. The tube provides support for the sample during scanning.
*Also used for in-vivo scans of the hand along with a platform that conforms to the hand and slides into the tube.
Elbow Holder
*Used for scans of the elbow. Designed to support the forearm during scanning.
Knee Holder
*A long cylinder cast cut in half lengthwise and with a foot holder at the end. This cast is designed to slide over the gantry tongue, placing the leg further into the gantry, in order to scan at distances closer to the core of the body.
*Used for distal femur and proximal tibia (i.e. knee) scans.
*Used for mid-shaft tibia scans.
*Used for larger ex-vivo and other samples.

===Sample Holders and Scan SOP for microCTs===
====Ex Vivo Sample Holders====
*Ex vivo and inanimate samples are scanned in sample holder tubes. These tubes come in a variety of diameters. It is extremely important that the tube diameter corresponds to, or is smaller than, the field of view (FOV) set in your scanning control file.

*Biological tissues should be hydrated and wrapped in plastic wrap to prevent drying of the sample. Your sample should then be secured in the sample holder using foam to prevent it from shifting around during scanning, which would lead to poor image quality.

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=====Chemical Resistivity of Sample Holders=====
*White tube sample holders are made of PMMA (poly-methyl-methacrylate).
*Yellow tube samples holders are made of PEI (poly-ether-imide).
*Use the yellow tubes if you will need to disinfect the sample holder after scanning.

{| class="wikitable"
!colspan="3"|Thermal and chemical compatibility of sample holders
|-
! scope="col"| Properties
! scope="col"| White Tubes (PMMA)
! scope="col"| Yellow Tubes (PEI)
|-
! scope="row"| Max. Temperature
| +85°C
| +170°C
|-
! scope="row"| Sterilization Steam Autoclave
|non resistant
|resistant (138°C for 20 Min. at 1 bar)
|-
! scope="row"| Water
|resistant
|resistant
|-
! scope="row"| Inorganic Acids
|limited resistance
|resistant
|-
! scope="row"| Inorganic Bases
|non resistant
|limited resistance
|-
! scope="row"| Aldehydes (Formaldehyde)
|limited resistance only in diluted form
|resistant
|-
! scope="row"| Alcohols
|limited resistance
|resistant
|-
! scope="row"| Bleach
|non resistant
|resistant
|}

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=====Mounting of Sample Holders=====
[[File:Uct35_holder.jpg|thumb|right|100px|µCT35 setup]]
*The spindle (metal bit) of the sample holder has a slot, which must be aligned in the scanner or adapter plate.
*The sample holder sits vertically in the µCT35 while horizontally in the VivaCT80 and VivaCT40.
*For the vivaCT40, attach the adapter plate for the tube sample holders to one of the animal bed. The tube sample holders are held horizontally in the vivaCT 40.
:[[File:Vivact40_holder.jpg|thumb|none|700px|VivaCT40 setup]]

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=====Ex vivo rodent scanning SOP=====
*Refer to [[Media:Ex_vivo_scan_sop.pdf|'''Ex Vivo Rodent Scanning''']] for its scan SOP.
*Refer to [[Media:Ex_vivo_scan_sop.docx|'''Ex Vivo Rodent Scanning in docx''']] for its Word version.

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====In Vivo Sample Fixtures and Anesthetic System====
*[[Media:VivaCT40_Anaesthetic_System.pdf |'''Anaesthetic System''']] : You must receive training to use the anaesthetic system.
*[[Media:VivaCT40_Mouse_and_Rat_Tibia_Fixture.pdf |'''Mouse/Rat Tibia Fixture''']]
*[[Media:VivaCT40_Mouse_Lower_Body_Fixture.pdf|'''Mouse Lower Body Fixture''']]
*[[Media:VivaCT40_Mouse_Whole_Body_Tube.pdf|'''Mouse Whole Body Tube''']]

=====In vivo rodent scanning SOP=====
*Refer to [[Media:In_vivo_scan_sop.pdf|'''In vivo rodent scanning''']] for its scan SOP.
*Refer to [[Media:In_vivo_scan_sop.docx|'''In vivo rodent scanning in docx''']] for its Word version.

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====Align whole body device in FOV====

It's important to have your whole sample in the field of view for accurate density measurements.
* Refer to [[Media:wholebody.pdf |'''Align the device''']] for detailed instructions.

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==Scan Parameters (Controlfiles)==

:{| class="wikitable" style="text-align:center;"
|-
! scope="row"| Manufacturer
| colspan="5"|[http://www.scanco.ch '''Scanco Medical AG''']
| [https://www.zeiss.com/microscopy/int/products/x-ray-microscopy.html '''Carl Zeiss X-ray Microscopy''']
|-
! scope="col" rowspan="2"| Model
! scope="col"| XtremeCT II || XtremeCT I || VivaCT80 || VivaCT40 || µCT35 || Xradia 520 Versa
|-
|[[File:XtremeCT.jpg|150px]]
|[[File:XtremeCT.jpg|150px]]
|[[File:VivaCT80.jpg|120px]]
|[[File:VivaCT40.jpg|135px]]
|[[File:UCT35.JPG|150px]]
|[[File:Xradia-520-versa-small.jpg|160px]]
|-
! scope="row"| Application
|colspan="2"| Clinical studies for human extremities in vivo
Horizontal static patient setup
|colspan="2"| Preclinical in vivo animal studies
Horizontal static animal setup
|colspan="2"| High resolution ex vivo specimen scans
Vertical rotational sample setup
|-
! scope="row"| E (KVp)
| 68 || 60
|colspan="3"| 45, 55, 70
| 30 ~ 160
|-
! scope="row"| Power (W)
| 100 || 54
|colspan="3"| 4, 8
|4 ~ 10
|-
! scope="row"| Filter
| Fixed 0.2mm Cu + 1mm Al
(Equivalent 6.7mm Al)
| Fixed 0.1mm Cu + 0.6mm Al
| Default 0.5mm Al,
Air, 0.1mm Al, 0. mm Cu
| Fixed 0.5mm Al
| Fixed 0.5mm Al
| Air, LE1~LE6, HE1~HE6,
customizable filter
|-
! scope="row"| FOV (⌀ * L) (mm^2)
| 140 ⌀ * 200 L
| 126 ⌀ * 150 L
| 31.9 ~ 80 ⌀ * 145 L
| 21.5 ~ 38.9 ⌀ * 148 L
| 7.2 ~ 38 ⌀ * 140 L
(75 L standard)
| 90 ⌀ * 100 L
|-
! scope="row"| Image Matrix
| 4608*4608 ~ 512*512
| 3072*3072 ~ 512*512
| 4096*4096 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
|-
! scope="row"| Voxel Size (µm)
| Standard 60.7
(30.3 ~ 273.4)
| Standard 82.0
(41.0 ~ 246.0)
| 5 ~ 156
| 10.5 ~ 76
| 3.5 ~ 74
| 0.7 ~ 50
|-
! scope="row"| Sample Image
|[[File:XCT2_human_distal_femur.png|160px]]
human distal femur
|[[File:XCT1_human_distal_tibia.JPG|160px]]
human distal tibia
|[[File:VivaCT80_Rat_distal_femur.JPG|160px]]
rat distal femur
|[[File:Vivact40_in-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Uct35_ex-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Xradia_mouse_distal_femur.png|160px]]
mouse distal femur
|}

Controlfiles are used to specify the parameters for the scans. Once your controlfile is setup, you should not modify it over the course of your project.

[[File:XCT2 ControlFile.JPG|right|600px]]

*'''Control File Name''': Specify a meaningful name so that others can reuse yours.

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===General Settings===
*'''Holder Type''': Choose the used holder type for XtremeCT II from Standard Casts, Knee Cast and Elbow Cast. No option for XtremeCT I scanner. For microCTs, Choose the used sample holder type with the correct diameter.

*'''Mode of operation''': Default is continuous operation for all scanners. Gated operation mode is available for VivaCT80 and VivaCT40 scanners.

*'''Evaluation Script''': This sets the default evaluation script used for the analysis. You can manually select a different script from the evaluation program.

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===X-ray Settings===
*'''Tube Energy (KVp)''': Fixed energy for XtremeCTs while having 3 options for each of microCTs: Use the 70 KVp for most samples, use the 55 or 45 KVp for low density objects (e.g., soft tissue) or specimens with a diameter less than 20 mm. Lower energies provide better contrast while higher energies provide better signal to noise (SNR).

*'''Tube Current (µA)''': Fixed current for XtremeCTs while having 2 options for each of energy settings of each microCTs: Use the higher current except when the voxel size is set for the best resolution of the scanner. The higher current will yield better SNR but a larger spot size.

:{| class="wikitable" style="text-align:center;"
|-
! scope="col"|
! scope="col"| XtremeCT II
! scope="col"| XtremeCT I
! colspan="3"| vivaCT80，vivaCT40， µCT35
|-
! scope="row"| E (KVp)
| 68
| 60
| 70
| 55
| 45
|-
! scope="row"| I (µA)
| 1470
| 900
| 114, 57
| 145, 72
| 177, 88
|-
! scope="row"| Power (W)
| 100
| 54
|colspan="3"| 8, 4
|}

*'''Filter''': Fixed filter settings for all scanners except VivaCT 80 has 4 filter options.

*'''Calibration''': This sets the mu scaling factor, density and beam hardening correction used for the reconstruction. For standard patient scans use 200 mg HA/cm3. For ex vivo bone scans, use 1200 mg HA/cm3, for soft tissue use the plexi scaling, and for non-biological tissues use the aluminum scaling.

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===Scout-View Settings===
Normally you will want to enable this and here you can specify the default start and end position, and scout-view angle, which you may override for each scan.

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===CT Scan Settings===

*'''Resolution''': This setting includes the reconstruction matrix size (2048x2048, 1536x1536, 1024x1024, or 512x512) and the number of projections per 180°. The lower the resolution setting, the better the SNR and larger the voxel size.

*'''FOV / Diameter''': This field of view must fully contain the sample holder for accurate density measurements. Fixed FOV for XtremeCTs while having 5 options for each of microCTs: If you choose a smaller FOV than the sample holder, the scan may be aborted to prevent damage to the scanner. For the best resolution, you should choose the smallest holder that contains your sample.

*'''Voxel Size''': The nominal isotropic voxel size is determined by the FOV and the reconstruction matrix.

*'''Number of Slices''': You can specify a specific number of slices or image stacks to acquire (1x110 = 1 image stacks of 110 slices). The scan time increases with each image stack, therefore pay attention to the stack boundaries (e.g., 111 slices will take 2x longer to scan than 110 slices).

*'''Rel Position of First Slice''': This option enables you to offset the scan region from the reference line. This is useful for scanning a region a specific distance from the growth plate or centering the scan region around the reference line. If you disable the scout view, then the position is relative to the absolute 0 position of the scanner (top of the sample holder for the µCT35 and towards the back of the scanner for the vivaCT40).

*'''Integration Time''': The higher the integration time, the better the SNR and longer the scan time. Use 100 ms for patient scans and higher values for ex vivo scans of better image quality. To get the highest integration time, uncheck the "Continuous ROT" button. For standard microCT measurements, use ~400 ms for the µCT35 and ~200 ms for the vivaCT40. The maximum integration time is scanner-specific and limited to prevent saturation of its detector.

*'''Average Data''': This is often referred to as frame averaging and is used to improve a scan's SNR. Multiply the average data value by the integration time to calculate the effective integration time. Only use this if the integration time is maxed out.

*'''Measurement Time''': This is the estimated scan time without the time performing the scout view or warm-up of the scanner.

*'''CTDIvol''': Computed Tomography Dose Index (CTDI) is a standardized measure of radiation dose output of a CT scanner for scanner settings' comparison purposes only, and it represents the average absorbed dose along the longitudinal axis from a series of contiguous CT exposures. Volumetric CTDI is the ratio of the weighted-CTDI to the level of overlap between slices (pitch). CTDIvol has no consideration of real scan length and does not represent actual dose administered to the patient.
:[[File:CTDI.JPG|600px]]

*'''DLP''': Dose Length Product DLP = CTDIvol * Scan Length in unit of mGy-cm.

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====XtremeCT II Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 4608
| 2304
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 3000
| 900
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 140 mm
| 30.3
| 60.7
| 91.1
| 136.7
| 273.4
|-
! colspan="2"| Slices/Stack
| 338
| 168
| 112
| 74
| 37
|-
! colspan="2"| Stack Thickness (mm)
| 10.24
| 10.20
| 10.20
| 10.12
| 10.12
|-
! colspan="2"| Time/Stack (min, at 43 ms Integration Time)
| 8.1
| 2.0
| 2.0
| 1.4
| 0.7
|-
! colspan="2"| Time Current Product (mAs)
| 238
| 71
| 59
| 40
| 20
|-
! colspan="2"| CTDIvol (mGy)
| 37.4
| 11.2
| 9.3
| 6.4
| 3.2
|-
! colspan="2"| DLP (mGycm)
| 38.3
| 11.4
| 9.5
| 6.4
| 3.2
|}

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====XtremeCT I Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 3072
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 126 mm
| 41
| 82
| 123
| 246
|-
! colspan="2"| Slices/Stack
| 221
| 110
| 73
| 36
|-
! colspan="2"| Stack Thickness (mm)
| 9.06
| 9.02
| 8.98
| 8.86
|-
! colspan="2"| Time/Stack (min, at 100 ms Integration Time)
| 3.7
| 2.8
| 1.9
| 1.0
|-
! colspan="2"| Time Current Product (mAs)
| 114
| 86
| 57
| 29
|-
! colspan="2"| CTDIvol (mGy)
| 7.3
| 5.5
| 3.6
| 1.9
|}

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====VivaCT80 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 3072
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1500
| 1000
| 500
| 250
| 125
|-
! rowspan="6"| Voxel Size (µm)
! scope="row"| FOV/Diameter 31.9 mm
| 10.4
| 15.6
| 31.9
| 31.2
| 62.4
|-
! scope="row"| FOV/Diameter 35.9 mm
| 11.6
| 17.5
| 35
| 35
| 70.1
|-
! scope="row"| FOV/Diameter 39.9 mm
| 13
| 19.5
| 39
| 39
| 78
|-
! scope="row"| FOV/Diameter 49.8 mm
| 16.1
| 24.2
| 48.5
| 48.5
| 97.1
|-
! scope="row"| FOV/Diameter 63.9 mm
| 20.8
| 31.2
| 62.4
| 62.4
| 124.8
|-
! scope="row"| FOV/Diameter 79.9 mm
| 26
| 39
| 78
| 78
| 156
|-
! colspan="2"| Slices/Stack
| 333 ~ 328
| 222 ~ 219
| 111 ~ 109
| 111 ~ 109
| 55 ~ 54
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 14.9
| 10.0
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 73
| 48
| 24
| 12
| 6
|}

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====VivaCT40 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 21.5 mm
| 10.5
| 21
| 21
| 42
|-
! scope="row"| FOV/Diameter 25.6 mm
| 12.5
| 25
| 25
| 50
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 35.8 mm
| 17.5
| 35
| 35
| 70
|-
! scope="row"| FOV/Diameter 38.9 mm
| 19
| 38
| 38
| 76
|-
! colspan="2"| Slices/Stack
| 213
| 106
| 106
| 53
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 9.9
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 61
| 31
| 15
| 8
|}

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====µCT35 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 7.2 mm
| 3.5
| 7
| 7
| 14
|-
! scope="row"| FOV/Diameter 12.3 mm
| 6
| 12
| 12
| 24
|-
! scope="row"| FOV/Diameter 20.5 mm
| 10
| 20
| 20
| 40
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 37.9 mm
| 18.5
| 37
| 37
| 74
|-
! colspan="2"| Slices/Stack
| 232 ~ 235
| 116 ~ 117
| 116 ~ 117
| 58
|-
! colspan="2"| Time/Stack (min, at 400 ms Integration Time)
| 23.9
| 12.3
| 6.5
| 3.5
|-
! colspan="2"| Time Current Product (mAs)
| 119
| 60
| 30
| 15
|}

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===Advanced Settings===
*'''Number of Det-lines (for Scout-View)''': Defines how many lines on the detector shall be used during the Scout-View. Using all available lines provides faster Scout-Views but some faint horizontal lines might be seen between the stacks. Limit the number of lines to a small number to obtain Scout-Views without these artifacts but the time of the Scout-View will increase.

*'''Number of Det-lines (for CT-scan)''': Defines how many lines on the detector should be used. This number influences the number of slices within a stack. Limit the number of detection lines if you see residual cone beam artifacts.

*'''FOV/Scan Diameter''': Chose the diameter of the FOV. This action is cropping the area of the detector.

*'''Software binning''': factor of the pixels on the detector.

*'''Hardware binning''':

*'''Samples''': number of (possibly binned) pixels on the detector that are used for each slice (note: this number is given for the whole FOV).
*'''Proj/180°''': number of projections taken per 180° turn of the sample.

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===Reconstruction===

*After each image stack is acquired, it is automatically submitted to the queue (sys$slow) for reconstruction. The reconstruction for each image stack is split into four jobs to make efficient use of processors.
*The reconstruction time depends on the resolution setting, with low resolution scans reconstructing faster than high resolution scans. Normally scans are reconstructed within a day or two.
*It is possible to resubmit a scan for reconstruction (refer to [[Scanco_Administration#Reconstruction | '''Scanco Administration's Reconstruction''']]) for details. This may be necessary or desirable for several reasons:
#The sample did not reconstruct properly (e.g., due to a power failure)
#To reconstruct the object at an angle (e.g., so that the anterior surface of a bone is always in the same direction).
#A new beam hardening correction was applied to the sample
#The scaling was changed for the sample to change the brightness

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==Perform a Scan==
===Perform a Single Scan===
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] for instructional details.

===Perform Batch Scans===
*Batch scan mode is only available on microCT scanners.
*Batch scans can be setup for different regions of interest (ROI) within a sample or for different samples contained within a sample holder.

#'''Setup the First Scan'''
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] to use the "Other..." button to find your sample number, choose a controlfile, perform a scout view (a mouse's whole body in this example), use the reference line to setup the first scan region (mouse skull in this example).
#*To add a batch scan press the "Batch Measurement" button.
#:[[File:Batch_scan_01.preview.jpg|600px]]
#*An information window is displayed with the scan measurement number. Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']] then press "OK" to close the window. An entry is also added to the measurement history for the sample.
#:[[File:Batch_scan_02.preview.jpg|600px]]
#'''Setup the Next Scan'''
#*Using the "Other..." button, find your next sample number, choose a new control file (if desired).
#*If the next region of interest or sample is not in view of the current scout view, adjust the parameters of the scout view and obtain a new one.
#*Use the reference line to set a new scan region (upper limbs in this example).
#*To add a batch scan press the "Batch Measurement" button.
#*As the first scan, a measurement number is assigned for this new scan. Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']].
#:[[File:Batch_scan_03.preview.jpg|600px]]
#*Repeat this process until you have added all your scans.
#'''Start the Batch Scans'''
#:There are two ways to start a batch scan:
##Click the "Start Batch Scans" button: the program will automatically close so that control of the scanner can be allotted to the queue.
##Exit the scanning program.
#:[[File:Batch_scan_04.preview.jpg|600px]]
#'''Check the Queue'''
#*Batch jobs will be submitted to the SCEVA2_BATCH queue for µCT35 or SC5019_BATCH queue for vivaCT40.
#*Initially the jobs will show up as temporary (TMP) jobs:
#:[[File:Batch_scan_05.preview.jpg]]
#*After about 30 seconds, the sample number will show up in entrie names:
#:[[File:Batch_scan_06.preview.jpg]]
#'''Request an Email Notification'''
#*There is a script in the commands (com) directory that will put an entry into the batch queue to send an email. Run the script and input parameters (queue and email) as prompted.
#:[[File:Batch_scan_07.preview.jpg]]
#'''Cancel a Batch Scan'''
#*For errors made during batch scan setup, to cancel a scan in progress, or to cancel a pending scan.
#:[[File:Batch_scan_08.preview.jpg]]
#*If you cancel all the scans and the scanner door does not unlock automatically (µCT 35 only), then start the measurement program and the scanner will unload, unlocking the door.

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==Action on Image Artifacts==
===Rescan for===
*'''Motion Artifacts'''
*'''Sample Out of the Field of View'''

===Contact Scanco Medical for===
*'''Ring Artifacts''' (Bad Detector)
:*Ring artifacts are caused by a faulty detector pixel and show up in the reconstructed image as a full or partial white circle.
:*For uCT scanners: When noticed, please notify lab technicians who will contact Scanco Medical to perform a "Pixel Correction", which will correct this artifact for future scans and can be used to update previous scans. You should not rescan the sample if there is a ring artifact.
:*For XtremeCT scanners: A small number of rings artifacts are expected and acceptable. For a 168-slice scan, ring artifacts present in <5 slices total is acceptable. If you observe ring artifacts in a larger number of slices, notify a staff member. Do not repeat scans for ring artifacts. In most cases, it is also unnecessary to perform a correction to already acquired data.
<div><ul>
<li style="display: inline-block;"> [[File:Ring_artifact.jpg|thumb|none|350px|Image with Ring Artifact]] </li>
<li style="display: inline-block;"> [[File:Ring_artifact_corrected.jpg|thumb|none|350px|Same Image after with Detector Correction]]</li>
</ul></div>

*'''Bad Centre Calibration Values'''
*'''Defective Shutter Artifact'''

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=Evaluation=
==Evaluate a Scan==
*To evaluate a scan, refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.

===Open default ISQ===
You can load a defualt ISQ usig uct_evaluation program:

<pre>
$ def uct_default_isq DISK3:[MICROCT.PROJECTS.VALIDATION.MODELS]C0000123.ISQ ! or
$ def uct_default_isq DISK2:[MICROCT.DATA.00001234.00005678]C0003456.ISQ
$ uct_evaluation
</pre>

Hit <code>cancel</code> when asked files to load, and the file you just set as default will be loaded.

*Use the whole pathname for ISQ.
*If you don't import your data into the system, you cannot store your evaluation results in the measurement database. You will have to use the LOG file to access your results.
*Only start a 3D evaluation if and only if the sample (patient) and measurement index are correct in the ISQ full path! Also, no results will be stored in the database unless the ISQ header info (samp/meas) is correct.
*Many of the UCT_xxx.COM scripts use the whole filename to extract the sample and measurement numbers, so it is possible that some evaluations will not run. UCT_xxx_BATCH_V4.COM is an example of an evaluation that will not run, but UCT_CUTOUT.COM will run (doesn't need any sample/meas info).

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==Draw Contours==
*Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
*Contouring is the first step in the analysis process, which allows you to segment the desired bone from surrounding tissues.

===Contouring Tools Reference Sheet===
*[[Media:Contouring-tools.pdf |'''Contouring Tools Reference Sheet''']]
*Contours must always be drawn COUNTER-CLOCKWISE!!!

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===Contour and Run the Standard Patient Evaluation===
The following instructions are for contouring standard patient radius and tibias.

#Open the Evaluation Program and select your sample.
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.
#Zoom into the desired bone (Radius or Tibia)
#*Using the zoom menu from the top panel, zoom into the Radius or Tibia.
#*Usually 3x zoom is appropriate.
#Draw contours roughly around the bone.
#*Select the first contouring tool (top left button) and draw COUNTER-CLOCKWISE.
#Automatically generate contours for all slices in the scan.
#*Double click the image to bring up the contouring window.
#*Double click again and the program will attempt to snap the contour to the bone. Double click again if needed.
#*Select Forwards, and then Iterate Forwards to have the evaluation program automatically segment the bone.
#Modify any contours as needed.
#*Select the second contouring tool (2nd button from top) to fix any "wrong" contours.
#*Draw COUNTER-CLOCKWISE!!
#*If many contours cannot be automatically generated correctly i.e. cortical bone is porous and evaluation program misses a lot of bone, it may be better to use the Range/Morph function rather than fixing each individual slice.
##This is done by first clearing all the breakpoints (Clear all BP in contouring window). The boxes will now become red.
##Manually fix the slice that does not have the correct contour automatically drawn, skip a few slices and manually fix that slice as well. The slices that you have fixed will turn green, indicating that it is a breakpoint (BP).
##Now you can morph between the two breakpoints (BP, green boxes) you have just created. Select the BP with the higher slice number, select range (first column on left) from the contouring window, followed by morph (second column from left).
#Save Contour (.GOBJ): Make sure you save your work!
#Run the 3D Standard Evaluation for your specific project (and timepoint).
#*Select 3D evaluation under Tasks to bring up the window. You'll then need to Select... the evaluation specific for your project.
#*There are a variety of evaluations to choose from, you can search for your project's evaluation script by typing in the name of your project in the filter window.
#Check the queue to ensure that the evaluation is running properly.
#*Type <code>$ show que</code> in a terminal window will allow you to see all running processes.

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===Correct Trabecular Contours and Run the Cortical Evaluation===
Once the standard evaluation has been completed, an auto-segmentation process is completed to segment the cortical from the trabecular bone. However, the auto-segmentation is not always accurate, and hence the contour (TRAB.GOBJ) will need to be checked.

#Load TRAB.GOBJ by selecting File, then load GOBJ from the top panel.
#*You will now see a list of all GOBJ files pertaining to your sample. You'll need to load the TRAB.GOBJ.
#*When the TRAB.GOBJ has loaded, you will see that the loaded contour is between the cortical and trabecular bone.
#Correct contours as needed
#*Can manually adjust the slices or use the Range/Morph function.
#*Remember to draw COUNTER-CLOCKWISE!
#Run the 3D cortical evaluation for your specific project (and timepoint, if relevant).
#*Select 3D evaluation under Tasks to select the appropriate evaluation script.

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==Evaluation Scripts==
===Scanco Standard Evaluation Scripts===
The following are descriptions of some of the standard evaluation scripts provided by Scanco Medical.

*'''3D Segmentation of VOI, 1 solid object'''
:Produces a 3D segmented (binary) object with values 0 (background, hidden) and 127 (solid). Input Gaussian filtering and threshold parameters. Draw contour to isolate the object of interest (optional).

*'''3D Seg. of 2 VOIs: solid dense in transparent low dens obj'''
:Produces a 3D segmented object with values -1 (transparent), 0 (background, hidden), and 127 (solid). Input two sets of Gaussian filtering and threshold parameters (input the second set by pressing the red 2 button). The preview shows the solid object in white and the transparent object in red. Draw one contour to isolate the object of interest (optional). This script is useful for showing soft tissue and bone.

*'''Bone Trab. Morphometry (3D Seg, 3D Calc, Print Sheet)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour to isolate the trabecular bone. Performs model-independent (direct) measurements on the trabecular region. Outputs: BV, TV, BV/TV, TbBMD, TbTMD, BS, SMI, DA, ConnD, TbTh, TbThSD, TbSp, TbSpSD, TbN, and Tb1/NSD.

*'''BV/Density only Bone Eval. (3D Seg, BV and Dens Calc, Print)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour to isolate the region of interest. Outputs: BV, TV, BV/TV, BMD, and TMD.

*'''Bone Midshaft Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour on the outer surface of the bone. Outputs: BV, TV, BV/TV, BMD, TMD, and moment of inertia parameters.

*'''Bone Midshaft more than e.g. 50 slices Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour on the outer surface of the bone. If you wish to exclude the medullary area from the analysis, then draw a counterclockwise contour on the outer surface of the bone and a clockwise contour on the inner surface of the bone. Performs direct measurements in addition to the standard midshaft analysis. Outputs: BV, TV, BV/TV, BMD, TMD, moment of inertia parameters, Th, and Sp.

*'''Convert to TIFF'''
:Converts the grayscale data to TIFF slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Convert to DICOM'''
:Converts the grayscale data to DICOM slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Reformat to Axial Cuts'''
:Flips the dataset from the XY plane to the XZ or YZ planes (specify in the advanced options for the script). This is useful if you want to contour your sample in a different plane. The flipped sample is imported as a new measurement under the same sample number as the original data.

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===Understanding Evaluation Scripts===
Following are some example evaluation scripts full of comments to promote understanding:
*[[Media:IPLV6_VOI.pdf|IPLV6_VOI script]]
*[[Media:IPLV6_MIDSHAFT.pdf|IPLV6_MIDSHAFT script]]
*[[Media:IPLV6_TRABECULAR_BONE.pdf|IPLV6_TRABECULAR_BONE script]]

===Setup Customized Evaluation Scripts===
To setup an evaluation script customized to your project, in the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']]:
*Choose "Scripts" then "Import from" then "TEMPLATES", pick a Scanco Standard Evaluation Scripts and Save.
*Choose "Scripts" then "Modify". Choose the script that was just imported and click "OK", Change the name of the script.
*Modify the default segmentation and other parameters for the script. When finished making changes press "Save" then "OK".

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==Image Processing Language (IPL) Scripting==
The following documentations related to IPL scripting, as it applies to image analysis was compiled by Jan Owoc in July 2013 based on numerous sources including own experience.

===Your First IPL Script===
*'''Prerequisite''': you are familiar with navigating the VMS system.
*'''"$" or "ipl>"''': the DCL and IPL prompts respectively, and you should only type the text after the prompt.
*If you FTP the file to the OpenVMS system, ensure you use "binary" to transfer the file.
You can run these commands on almost any greyscale AIM file. Example file here: MJ7101.AIM

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====Interactive IPL====
*Command <code>$ ipl</code> starts IPL interactively, that is you see the result of each command as you run it.
*While it is useful for testing, running large scripts interactively may interfere with others using the computer.
 
*'''Reading an AIM file'''
:Before you can run any analysis on the AIM file, you need to read it into IPL and assign it a file handle. This is done using the command <pre>ipl> read in MJ7101.AIM</pre>
:A fraction of a second later, the file should have been read into memory and assigned the internal name "in". If we want to do some basic density calculations on it, we can use the command<pre>ipl> vox_ in 0</pre>
:*IPL, much like DCL, will automatically complete the command if it is given enough characters.
:The "vox_" was expanded to the command "vox_scanco_param" (calculates voxel-counting parameters) and told you that the mean density of the cube is 114 mg HA/cm3 and a standard deviation of 283 mg HA/cm3.
:The argument "in" is the internal name of the image.
:The argument "0" is the region. The command vox_scanco_param supports several numbered regions if, for example, you wanted to separately compute the density for the trabecular region and the cortical region.
 
*'''Segmenting an AIM file'''
:Some parameters, like average density, are computed from the [[Scanco_User_Instructions#Grayscale_Images|'''Greyscale Image''']]. Other parameters, like the trabecular number, require an image that has been segmented to [[Scanco_User_Instructions#Binary_Images|'''Binary Images''']], that is converted into "bone" and "not bone".
:There are many ways to separate bone from non-bone, and parameters that work well for one dataset will not generally work for images of different samples, or acquired at different resolutions.
:One of the simplest segmentation methods "seg_gauss" is to apply Gaussian smoothing to the sample, to eliminate the noise present in the image, followed by a semi-arbitrary threshold that preserves the trabecular structure.
<pre>
ipl> seg_gauss in seg

-sigma [1.000000] >
-support [2] >
-lower_in_perm_aut_al [300.000000] >
-upper_in_perm_aut_al [100000.000000] >
-value_in_range [127] >
-unit [0] > 2
</pre>
:seg_gauss expects 8 parameters, and we have provided only 2. It will now prompt us for the remaining 6 one-by-one.
:Leave everything at the defaults (simply hit "Enter") except the unit, which we will change to "2".
:For young human trabecular bone from the distal tibia scanned at 20 um in the uCT 35, but then downscaled to 80 um, the above parameters give a reasonable representation of the trabecular structure. With other bones at other resolution, you may need to change the sigma, the support, and the lower threshold.
:The unit of "2" simply means that we are working in units of mg HA/cm3.
:Now that the cube is segmented, we can run the same voxel-counting command as above and obtain more information. <pre>ipl> vox_ seg 0</pre>
:We now know that our combination of smoothing and threshold resulted in an object volume of 103 mm3 (i.e. volume of bone) and a bone volume ratio of 22.88%.
 
*'''Writing out a file'''
:we can write the segmented file out for future use. Accept the defaults for the remaining arguments. <pre>ipl> write seg MJ7101_SEG.AIM</pre>
:Now you can quit IPL and verify that the segmented file has been written out. <pre>ipl> quit</pre>

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====Batch IPL====
*Command <code>$ ipl_batch</code> starts IPL inside a script that would be submitted to a queue.
While the following code is likely to work, it is not very readable:
<pre>
$ IPL_BATCH
read in MJ7101.AIM
vox_ in
seg_gauss in seg 1 2 300 100000 127 2
vox_ seg
write seg MJ7101_SEG.AIM
..
$ EXIT
</pre>
*Instead, it is recommended that you copy and paste the "pretty" output of the command after you have run it once interactively.
*Values that are likely to change should be variables, defined at the top of the script.
*To substitute a variable from DCL into IPL, use a double-quote character before the variable name, as shown in the example below.
Copy and paste the below into a text editor.
<pre>
$ modelname :== MJ7101.AIM
$ threshold == 300
$ outputfile :== MJ7101_SEG.AIM
$
$ IPL_BATCH

/read
-name in
-filename "modelname

/vox_scanco_param
-input in

/seg_gauss
-input in
-output seg
-sigma 1.000000
-support 2
-lower_in_perm_aut_al "threshold
-value_in_range 127
-unit 2

/vox_scanco_param
-input seg

/write
-name seg
-filename "outputfile

..
$ EXIT
</pre>
Now, it is clear what the full names of the commands are, and what the parameters mean.
*If a parameter isn't important and can be left at the default (for example the region number during vox_scanco_param), you can leave it out of the file.
Save the file as MYSCRIPT.COM and run it using <code>@MYSCRIPT.COM</code>.

 
*'''Submitting to the queue'''
:As mentioned in the introduction, running IPL interactively on larger models negatively impacts other users of the system. Copying the commands to a file and running it from the command line has the same effect.
:*The correct way to run larger scripts is to submit the job to the queue. <pre>SUBMIT/QUE=SYS$FAST MYSCRIPT.COM</pre>

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===IPL Reference===
*[[Media:SCANCO_-_Software_-_IPL_instruction_manual_0.pdf|'''Official Scanco IPL Documentation''']]
*[[Media:scanco-software-ipl-instruction-manual.pdf|'''Scanco IPL Manual]]

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====Standard Read Write etc. Functions====
*'''/read''': Reads a file into ipl and gives the file an internal name
*'''/aim_read''':
*'''/read_versatile''':
*'''/write_v020''': Writes an aim file to the directory in which ipl is open (or specified directory if in a script)
*'''/write_new''':
*'''/write_part''':
*'''/copy''': Copies an internal file (a file that is already in the ipl system) and allows the copy to be given a new name.
*'''/delete''': Deletes an internal file (a file that is already in the ipl system)
*'''/rename''': Changes the name of the file (input is the old name and output the new name)
*'''/list''':
*'''/options''':
*'''/release_history''':
*'''/commands_write_log''':

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====Segmentation Functions====
*'''/gauss_lp''': Applies a low pass gaussian filter with specified sigma and support values
*'''/fft_laplace_hamming''':
*'''/median_filter''': Applies a low pass median filter to reduce unwanted noise in an image
*'''/seg_gauss''': Segments aim files using the input sigma of gauss and the filter support for gauss. A threshold can also be applied using this function.
*'''/threshold''': Removes data outside of the specified range
*'''/absolute_threshold''':
*'''/adaptive_threshold''':
*'''/adaptive_iter_threshold''':
*'''/matching_threshold''':

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====Gobj and Masking Functions====
*'''/gobj_maskaimpeel_ow''': Cuts an aim file with a gobj so that only the portion of the aim within the gobj remains. Peel_iter value used to specify the number of pixels within the gobj the function will need to cut.
*'''/gobj_to_aim''': Reads a gobj file from the directory and makes an aim file (the aim file is in ipl, to output it to the directory use write).
*'''/togobj_from_aim''': Takes an aim file and writes a gobj file (the gobj is output to directory).
*'''/gobj_circumf_area''':
*'''/gobj_join''':
*'''/gobj_join_consec''':
*'''/gobj_scale''':
*'''/gobj_isotrop''':
*'''/cortex_maskoff''':
*'''/peel3d''':

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====Voxel-Counting, Density and Triangulation Functions====
*'''/db_scanco_activate''':
*'''/db_clear_eval''':
*'''/db_calib_unit_fill''':
*'''/db_set_mean_accur''':
*'''/voxgobj_scanco_param''': Inputs an aim file and a gobj and provides information (including total volume, object volume and the mean value of the points) on the region within the gobj.
*'''/vox_scanco_param''': Inputs an aim and provides information including total volume, object volume and the mean value of the points.
*'''/tri_da_metric_db''':
*'''/tri_direc_distr''':
*'''/connectivity''': Receives a component labelled aim object and calculates the connectivity of the labelled components.
*'''/conn_nocl''':
*'''/conn_bgcl''':
*'''/fractal_dimension''':

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====Distance Transformation (Sphere Filling) Functions====
*'''/dt_object_param''':
*'''/dt_ow_object_param''':
*'''/dt_background_param''':
*'''/dt_mat_param''':
*'''/dt_cortex_obj_param''':
*'''/dt_value_output''':
*'''/dt_mat_output''':

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====Statistical Functions====
*'''/examine''': Receives an AIM object and outputs specified information based on the item input.
*'''/histo''':
*'''/moment2d_of_inertia''':
*'''/moment3d_of_inertia''':
*'''/zmeanmax''':

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====Voxelsize-Scaling Functions====
*'''/isotrop''':
*'''/scale_elsize''':
*'''/ipscale_elsize''':
*'''/noipscale_elsize''':
*'''/scale_ow_elsize_noip''':

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====Component Labeling Functions====
*'''/cl_ow_rank_extract''': Receives AIM file and over writes it with an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl_rank_extract''': Receives AIM file and outputs an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl26_rank_extract''':
*'''/cl_image''':
*'''/cl_extract''':
*'''/cl_slicewise_extractow''':
*'''/cl_nr_extract''':

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====Add, Concat, Cut etc. Functions====
*'''/add_aims''': Adds the values of two AIM images in a 3D space.
*'''/add_constant_ow''':
*'''/border_change''':
*'''/bounding_box_cut''': Cuts extra space out of an aim file so that only the region with the data remains. A border can be added to the image using the border input.
*'''/concat''': Takes two aim files and combines them. The data from both aims or just the common region can be kept. To add the images add_not_overlay is set to true (for example if image 1 has a value of 41 and image 2 has a value of 82, the combined value will be 123).
*'''/concat_adapt''':
*'''/divide_volumes''':
*'''/fill_min_max_ow''':
*'''/header_geo_set''':
*'''/header_log_set''':
*'''/header_calib_ov''':
*'''/invert_ow''':
*'''/mult_constant_ow''':
*'''/multiply_volumes''':
*'''/sqr_to_float''':
*'''/sqrt_to_float''':
*'''/offset_add''':
*'''/offset_set''':
*'''/clear_offset''':
*'''/fill_offset_mirror''':
*'''/fill_offset_duplicate''':
*'''/set_value''': Sets the values of the object and background of an aim file to chosen values
*'''/sub_get''': Extract a portion of an image 
**-pos corresponds to x,y,z origin -1 -1 -1 maintains the original coordinates 
**-dim corresponds to x,y,z dimensions -1 -1 -1 maintains the original dimensions (within maximum range) 
**indexing starts at 0 instead of 1
*'''/sub_pick''':
*'''/subtract_aims''': Subtracts one aim from another and outputs the remaining region.
*'''/sup_divide''':
*'''/transparent_concat''':

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====Erosion Dilation Open Close Functions====
*'''/erosion''':
*'''/dilation''':
*'''/open''':
*'''/close''':
*'''/erosion_dilat_variable''':

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====Import Export Conversion Norming Functions====
*'''/import_freeformat''':
*'''/dicom_to_aim''':
*'''/todicom_from_aim''':
*'''/dicom_list_series''':
*'''/isq_to_aim''':
*'''/isq_gobjfit_to_aim''':
*'''/toisq_from_aim''': Writes an isq file to the directory ipl is open in (or specified directory) from an aim file. The isq name should be 8 characters long.
*'''/mesh''':
*'''/msq_from_aim''':
*'''/rsq_to_aim''':
*'''/stl_tri''':
*'''/convert_to_type''':
*'''/convert_unsigned''':
*'''/norm_max''':

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====Functions for Root Canal Evaluations====
*'''/separ_roots''':
*'''/calc_ctr_mass_list''':
*'''/calc_ctr_mass_diff''':
*'''/treated_surf''':
*'''/match_cut''':
*'''/match_cut_adapt''':

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====Miscellaneous Functions====
*'''/align_z''':
*'''/dcl''':
*'''/flip_aim''':
*'''/growback_to_orig''':
*'''/turn3d''':
*'''/turn2d''':
*'''/upat_filldb''': Fill special Upat DB for patient (radius/tibia) evaluation
*'''/xray''':

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====Obsolete, Experimental and Duplicate Functions====
*'''/curv_tri''':
*'''/cut2D_shape_ow''':
*'''/join_uncompress''':
*'''/mil_param''':
*'''/milv1_param''':
*'''/gauss_seg''': duplicate of /seg_gauss
*'''/from_aim_to_isq''': The function toisq_from_aim will also convert an aim to an isq
*'''/local_threshold''':
*'''/edge_canny''':
*'''/sobel_grad''':
*'''/hysteresis_thresholg''':

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====Functions only available in iplfe====
*'''/register''': Registers two aim files and output a transformation matrix of the transformation to moving input 2 into the space of input 1. Gobjs can be input (registration is more successful with gobjs). Orientation search can be done with masscenter, and/or moment of inertia (MoI), or degree intervals.
*'''/transform''': Transforms an aim file using a transformation matrix (a text file of the matrix can be input). Interpolation options are nearest neighbor, linear, and cubic interpolation. The inverse of the transform provided can be done by setting Tmat_invert to true.
*'''/fe_solveD''': A number of finite element functions are available in iplfe, not all are listed here

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=Results=

==Images and Animations==
Refer to [[Scanco_User_Instructions#.C2.B5CT_Ray|'''µCT Ray''']] for detailed instructions.

===[[#Change_the_View|Change View]]===
===[[#Change_the_Colours|Change Object Colors]]===
===[[#Cutplane_and_Subdim|Show a Section-View of an Object]]===

===Save a Screetshot Image===
#Open XV from a dec terminal on a workstation by typing <code>$ xv</code>.
#Open and frame the image, program etc. that you would like to save an image of.
#In XV, click GRAB. You can either autograb the entire screen after a delay or manually grab a desired area.
#After grabbing the desired section, click Save in XV.

===[[#Save_the_Image|Save Image]]===
===[[#Save_for_Animation|Save Frames for an Animation]]===

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===Convert AIM to TIF series===

Use the utility SEQ_TO_IMAGE located in the UT directory. A symbol has been set up to run this called TIF.

<pre>
$ mcr ut:seq_to_image
Program: seq_to_image V1.1b
Input-File []: WISDOM_L_R05.AIM
File Format [TIF]:
Default TIF Names: WISDOM_L_R05_xxxx.TIF

Output-File [WISDOM_L_R05]:
!> Reading AimVersion020
Start Slice [0]:
End Slice [179]: 5
Number of images thereof (count) [6]:
Scale Factor (Integer) [1]:
global_pos (1=true, 0=false) [0]:
Max value to norm to 255 [32767]:
Slice: 0
Slice: 1
Slice: 2
Slice: 3
Slice: 4
Slice: 5
$ dir wisdom*

Directory DISK1:[MICROCT.SCRATCH]

WISDOM_L_R05.AIM;1 WISDOM_L_R05_0000.TIF;1 WISDOM_L_R05_0001.TIF;1
WISDOM_L_R05_0002.TIF;1 WISDOM_L_R05_0003.TIF;1
WISDOM_L_R05_0004.TIF;1 WISDOM_L_R05_0005.TIF;1

Total of 7 files.
$
</pre>

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===Generate TIF (or others) from 3D rendered volume===

This replaces uct_movie that operated on the alpha systems. UCT_3D can be called in batch mode.

A pdf describing this tool is located here: [[Media:UCT_RAY V4.0-1.pdf]]

To interactively declare the desired settings:
<pre>
$ uct_3d_batch
?CT RAY_BATCH V4.0-1

UCT_R: Application initialized
Filename []:
Print-Filename [SYS$SCRATCH:TEMP_3D.PS]:
Ambient (0.0..1.0) [0.200]:
Shadows (0/1) [1]:
Size (1..1024) [1024]:
Elevation (-90..90) [30]:
Rotation (-180..180) [35]:
Copies (0..9) [1]:

</pre>

To apply a saved set of settings, a setup-file can be created by running uct_3d in interactive mode. Select "Presets" from the toolbar and save the settings you desire (e.g. elevation 90, rotation 0).

<pre>
$ uct_3d_batch setup-file [data-file printfile]

Examples:

$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.ps
$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.tif

</pre>

To automatically generate tifs for many files, a script was created to replace PRINT_3D.COM
The script is currently stored in the xtremect2 com directory.

<pre>
@COM:PRINT_REG_TIF.COM

Generates a 3D image from a segmented file.

The outputs include:
- two 3D renderings (TIF)

Use full pathnames for the segmented AIM.

P1 - Segmented AIM

Usage:
@COM:PRINT_REG_TIF.COM DISK2:[MICROCT.DATA.00000379.00001376]C0001234_SEG.AIM
</pre>

This script can be modified to use a custom preset file.

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===Make an Animation===

To calculate an Animation, two (separate) tools of the 3D program are used: the set-up of start and end point of the Animation, and the 'Auto-Print' tool that automatically creates the TIF files for every rendered image.

This is a 'step by step' guide to create an animation using TIFF files:
:* Open your sample in the 3D program.
:* Now, open 'options','Animation'
:* Render your Image the way you want your animation to start. e.g. observer rotation -179 degrees. You may interrupt if you want. If you are satisfied with all the settings (rotation, elevation, transparency, colors etc.) the Click on 'Get Settings A'
:* Then, adjust all the settings for the endpoint of your animation (with the mouse or the sliders) e.g. observer rotation +179, and start the rendering. If satisfied, click 'Get settings B'

Note: To test, put # of views to 5 or 10... You can also interrupt the build-ups for faster viewing.
:* Click the START button again, wait till the build-up of the 3D image is finished.
:* DO NOT HIT 'START CALCULATION' YET!
:* First, you also need to set-up the 'Auto-Print' mode:
:* Go to the 'Print' menu (file --> print), choose print to TIF and to File and enter THE BEGINNING OF A FILENAME, e.g. sys$scratch:test_ (the program will append 0000.TIF, 0001.TIF etc afterwards) Or enter (possibly with middle-mouse-click): "DK0:[MICROCT.DATA.00001234.00003456]ANIMATION_" to have the result go to the measurement directory.
:* Click on the 'Auto-Print' box. Then 'ok'
:* Adjust the number of views (e.g. 200), then click on 'Start Calculation', and it will render. This may well take a long time.
:* Take those TIFF files to your PC, and combine the sequences in the program that you are using to convert the TIFF files to AVI or MOV files (like Windows Movie Maker 2, or Quick Time Pro, or Adobe Premiere etc.)

Notes/Hints:
:* The order in the above list can also be reversed: You can first set up the 'Auto-Print', and then go into the 'Animation' menu, choose start and end settings, and hit 'Start Calculation'
:* The positions A and B can be any: e.g. with subdim, you can first take everything (A), then slide it back to nothing (B).
:* You can even slowly change the color of an object. Or slowly hiding objects: choose 'transparent' for object, but change from 0.0 (A) to 1.0 (B)
:* If you want to create a movie with different sections, e.g. first rotate around, then slowly make bone transparent, then cut in: Do this in multiple sections with the 3D program, e.g. first create Auto-Print files 'rotation_0000 to rotation_0200', then 'transp_0000 to transp_0050', and then 'cut_0000 to cut_0100'. Make sure ALL the settings from the last view of the previous section match those of the first view of the next section so you get smoot transitions.
:* The 'Auto-Print' box is also usable without the 'Animation' Menu: Activate it, Like above, with sys$scratch:test_ only the beginning of filename. 'ok' Then, whenever a 3D image is completely built-up (so when you are happy with a view and you do not interrupt the build-up), automatically a TIF file is generated, numbered sequentially.

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===Combine two volumes to create transparent image===

First create your two start "seg.aim" images
Start by running either the normal eval, or $ voi to get one _seg.aim file of one region

Rename it to a better name in the session manager, e.g. c0001234_all.aim

Then either by choosing different contours, or a different threshold, start the $ voi or the normal evaluation again, which will create another _seg.aim file.

Load them in the 3D viewer ('all files') to check that they look like expected.

Now we will go into IPL and concatenate those two volumes.

<pre>
$ ipl
/read all xx_all.aim
/read trab xx_seg.aim
/transparent
-input_solid trab
-input_transp all
-output out
</pre>

Note: the solid volume is OVERWRITING the transparent input volume, so usually, it
is the smaller (inner) of the two.

<pre>
/write out xxx_transp.aim
/quit
</pre>

Then load the _transp.aim file in 3D, go to 3D program FAQ to see how to change transparency levels in the Display options there.

See IPL FAQ or 3D program FAQ if you need help with these parts.

Step by Step Example: Showing your chosen trab VOI within whole bone
:* $ voi, enter threshold in ipl_voi.com, start 3d eval WITHOUT contours
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_all.aim
:* Start up normal eval program, draw trabecular contours, check threshold in ipl_fixed_batch_v4.com, start 3D eval.
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished

Step by Step Example: Showing high-dense volume surronded by lower density volume

:* Start normal 3D eval with HIGH threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_high.aim
:* If wished: read out 3d result database with $ uct_list
:* Start normal 3D eval with LOW threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished

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==Image Tours==
===XtremeCT Image Tours===

===MicroCT Image Tours===
*Refer to [[Media:Tours_image_gallery.pdf|'''MicroCT Image Gallery''']] with its [[Media:Tours_image_notes.pdf|'''Image Notes''']].
*Refer to [https://youtu.be/tT3dz4VrwfE '''MicroCT Image Tour YouTube Video''']
*Hover over a thumbnail and click on its overlaid description to see the animated GIF or a larger version of the image.

<gallery mode="packed-hover" heights=220px caption="Micro-CT Scans">
Image:MOUSE_SKELETON_PIC01.jpg|[[Media:MOUSE_SKELETON_360.gif|Mouse (38µm)]]
Image:Segmented_Mouse_Femur.jpg|[[Media:Segmented_Mouse_Femur.jpg|Mouse Femur showing Cortical and Trabecular Bone (10µm)]]
Image:LIZARD_WHOLE_VIEW_P1_0044.jpg|[[Media:LIZARD_SKELETON_360.gif|Lizard (88µm)]]
Image:LIZARD_SKULL.jpg|[[Media:LIZARD_SKULL.jpg|Lizard Skull showing Thickness Distribution (25µm)]]
Image:DUCK_BEAK_PIC01.jpg|[[Media:DUCK_BEAK_360.gif|Duck Beak (60µm) Courtesy of Dr. A. Iwaniuk]]
Image:Human_Tooth.jpg|[[Media:Human_Tooth.jpg|Human Tooth (30µm) Courtesy of Dr. C. Stewart]]
Image:PINECONE_TH_PIC05.jpg|[[Media:PINECONE_360.gif|Pinecone showing Thickness Distribution (69µm)]]
Image:SHELL01_SEG_PIC01.jpg|[[Media:SEASHELL_360.gif|Seashell (50µm)]]
Image:TURTLE_SKULL.jpg|[[Media:TURTLE_SKULL_360.gif|Turtle Skull (60µm)]]
Image:SAND_DOLLAR.jpg|[[Media:SAND_DOLLAR.jpg|Sand Dollar (37µm)]]
Image:MOUSE_L1-L6.jpg|[[Media:MOUSE_SPINE_SEG_360.gif|Mouse Spine showing Cortical and Trabecular Bone (10µm)]]
Image:MOLAR.jpg|[[Media:MOLAR.gif|Human Tooth (60µm) Courtesy of Dr. C. Stewart]]
</gallery>

<gallery mode="packed-hover" heights=220px caption="Contrast-Enhanced Micro-CT Scans">
Image:Contrast_mouse_head_XZ_thumb.jpg|[[Media:Contrast mouse head XZ.jpg|Mouse Head (60µm, XZ plane)]]
Image:Contrast_mouse_head_XY_thumb.jpg|[[Media:Contrast mouse head XY.jpg|Mouse Head (60µm, XY plane)]]
Image:Contrast_mouse_head_YZ_thumb.jpg|[[Media:Contrast mouse head YZ.jpg|Mouse Head (60µm, YZ plane)]]
</gallery>

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==Extract Results==
===Automatic Results===
Results are generally automatically extracted after each analysis to the UCT_RESULTS directory. 
The results files have the form of:
*UCT_LIST_*''PROJECT''*.TXT for XtremeCTs: e.g. result file UCT_LIST_KYLA.TXT for the following project.
*UCT_LIST_3DLOG_*''PROJECT''*.TXT for microCTs: e.g. result file UCT_LIST_3DLOG_KYLA.TXT for the following project.
*where ''PROJECT'' is specified in the evaluation tool script setup.
[[File:Script_modify_basic_project.jpg|500px]]

Open the result file and copy and paste it into Excel, e.g.
<pre>
$ dir uct_results:*kyla*
$ eve uct_results:UCT_LIST_3DLOG_KYLA.TXT
</pre>

Or transfer the file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].
*microct/vivact account UCT_RESULTS location: ADISK1:[MICROCT.RESULTS]
*invivo/invitro account UCT_RESULTS location: ADISK1:[BONELAB.RESULTS]

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===Extract Results from XtremeCT Database using UPAT_LIST===
*Run <code>$ UPAT_LIST</code> to take in a range of samples and extract the standard patient results, which may include scans from other projects.
*Run <code>$ UPAT_LIST -h</code> to print out help for all parameters.
*For standard analysis on XtremeCT2, the default Evaluation Type 4=XT1 is not applicable. To get results for XtremeCT2, you need to run upat_list twice. Once for evaluation 5 and once for 6.
<pre> Evaluation type (1-6) [4]: Type code of evaluation (4=XT1, 5=trabecular, 6=cortical, default = 4 </pre>
*Run <code>$ @com:EXTRACT_UPAT_LIST</code> to take in a list of sample numbers and extract the standard patient results with follow-ups and append them to a result file.
<pre>
$@COM:EXTRACT_UPAT_LIST P1 P2 P3 P4 P5

P1 = Sample List
P2 = Site (RR, RL, TR, TL, R*, T*, *)
P3 = Number of Follow-Ups (max 19)
P4 = Results Output File
P5 = Eval type (4=XT1, 5=Trab, 6=Cort)
</pre>

An example to extract all sites:
<pre>
$ @com:EXTRACT_UPAT_LIST mysamples.txt * 19 myresults.txt 5
</pre>

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===Extracts Results from microCT Database using UCT_LIST===
*Run <code>$ UCT_LIST</code> to take in a range of samples and extract the results, by specifying the first and last measurement numbers for the range they want to extract
*This may include scans results from other projects, but you can delete unrelated results that are extracted afterwards.
*The program will output a tab-delimited text file, which can be read into Excel or other analysis programs.
<pre>
$ uct_list

UCT_LIST.EXE Version V5.22
Template-File [UCT_3D_LIST_SHEET]: !Press Enter to use the default results sheet.
Output-File [SYS$SCRATCH:UCT_EVAL.TXT]: !Enter a filename, e.g., BUIE_RESULTS.TXT.
Density units (0 default) [0]: !Press Enter.
From Meas. # [0]: !Enter the first measurement number, e.g., 100.
To Meas. # [0]: !Enter the last measurement number, e.g., 101.

Processing measurement 100
Processing measurement 101
</pre>
*An example output file: [[Media:Buie_results.xlsx|Buie_results.txt]]
*Or Run <code>$ @com:extract_results.com</code>

*References of results template:
:*Formatted [[Media:Results_template_uct_list.xlsx|Excel template 1]] for results extracted with uct_list.
:*Formatted [[Media:Results_template_extract_results.xlsx|Excel template 2]] for results extracted with extract_results.com.
:*In vivo spreadsheet template for UCT data: [[Media:In vivo results template.xls| In vivo results template.xls]]
:*In vitro spreadsheet template for UCT data: [[Media:In vitro results template.xls| In vitro results template.xls]]

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===Understand Morphological Parameters===
*Refer to [[Media:Reference_Document_-_Parameters_from_upat_list.doc|'''Explanation of UPAT_LIST Output''']] to understand the result file.
*Refer to [[Media:Reference_Document_-_Parameters_from_uct_list.doc|'''Explanation of UCT_LIST Output''']] to understand the result file.

All values are determined on a slice-by-slice basis, then averaged over all the slices to calculate morphological results:

:*BV/TV -> Sum all raw data within the GOBJ and divide by 1200 mg/cc HA
:*Tb.N -> As per standard method
:*Tb.Th and Tb.Sp -> Derived from BV/TV and Tb.N above (semi-derived method)
:*D100 -> Average density of entire cross section
:*DTrab -> Average density of trabecular region
:*Ct.Th -> Cortical area (from seg) divided by circumference (from GOBJ)
:*GOBJ circumference can be determined with /gobj_circum.

<pre>
BV/TV -> VOX-BV/TV
BS/BV -> TRI-BS/BV
Tb.Th -> DT-Tb.Th
Tb.Sp -> DT-Tb.Sp
Tb.N -> DT-Tb.N
ConnD -> Conn-Dens
SMI -> TRI-SMI
DA -> TRI-DA
</pre>

Usually I'd use the names on the left for the plots, but these correspond to the names on the right of the arrow in the Scanco output files.

Note, if you use the TRI-Tb.Th rather than the DT-Tb.Th*, then you are using the derived (plate-model) morphological parameters. These are less accurate than the direct parameters. They are calculated by triangulating the surface (marching cubes) to get BS, and then calculate thickness
Th = 2 * BV / BS, etc...

'''Mean Values'''
<pre>
mean 1: mean of bone AND marrow --> 'apparent density'
mean 2: mean of what was considered bone only (i.e. what was segmented)
'bone tissue density'
</pre>

Note, there are five possible categories for the mean Mu. They are assigned by setting <code>-region_number</code> in the <code>/voxgobj_scanco_param</code> function. The region number is zero-based, so setting it to 0 corresponds to mean1, 1 corresponds to mean2, etc. So, although mean1 and mean2 are typically apparent and tissue density, respectively, this can be adjusted in the IPL script by setting the region_number. Mean3 might be useful for storing cortical bone density, for example.

<pre>
/voxgobj_scanco_param Voxel or Mu Scanco Parameters
-input Gray scale or Segmented AIM object
-gobj_filename GOBJ: input or Automatic
-peel_iter Peel Iterations or Automatic
-region_number Region number for Mu only

! -region_number 0 ! mean1
! -region_number 1 ! mean2
! -region_number 2 ! mean3
! -region_number 3 ! mean4
! -region_number 4 ! mean5
</pre>

What you should also know: because of partial voluming effects, for Mean2, we are DISCARDING the 2 surface voxels of EVERY trabeculae - thus, to get meaningful Mean2, you have to do your scan with the chosen resolution high enough, such that the mean trabeculae is depicted by at the very least 5 pixels, better actually more than 6 pixels thickness. (You can do this check at the end in the XLS sheet: divide DT-Tb.Th* by el-size-mm.x, and you need to get numbers bigger than 6 or 7 or 10 or so.

For parameters such as ConnD where no GOBJ is taken as input, the TV is determined from the processing log stored in an AIM that has previously had a GOBJ applied (stored as the relative region of interest; ROI). So, it is important to apply a GOBJ prior to ConnD measurements to ensure the TV is correctly determined (and not taken as the whole AIM).

'''Trabecular Number (TbN)'''
The epsilon values can be set to account for differences in scanner resolution, and hence 'surface roughness' for individual pixel suppression.

For microct, for good resolution: if there is a pixel 'sticking out' from a flat surface we do not assign that pixel with a thickness value of 1, but we let it 'get eaten' by the bigger sphere that sits in the center of the trabeculae. So this is nice for 'noise' (0.9/1.5).

For XT resolution, where also many 'good' features are just one or two pixels wide, I liked a lower epsilon value better (0.9/0.5).

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==Generate Report==
===Generate Standard Patient Report===
The standard patient reports are extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.
*The number of follow-ups specified will determine if a baseline or follow-up report is generated.

<pre>
$ upat_list

Mode (1 = list, 2 = print, 3 = show) [1]: 2
Patient # (1-3162) [1]: !input the patient's sample number
Site (found RR) [RR]: !RR or RL or TR or TL
Maximum # of follow-ups (0-19) [19]: !0 for baseline report, press return for follow-ups
Template file [default]: !press return to use the default template
Output filename [SYS$SCRATCH:UPAT...]: !default output file (with sample number and the site) goes to sys$scratch
# copies [1]: !the number of printouts, 0 if no printout is desired
</pre>

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===Generate CaMos Patient Report===
The [http://www.camos.org '''CaMos'''] patient report is extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.
*To ensure the report is generated using the appropriate normative results, the patient's sample remarks should be in the form "F-RHRF" where the first character indicates the sex of the individual, otherwise the patient is assumed to be male.
<pre>
$ upat_list

Mode (1 = list, 2 = print, 3 = show) [1]: 2
Patient # (1-3162) [1]: !input the patient's sample number
Site (found RR) [RR]: !RR or RL or TR or TL
Maximum # of follow-ups (0-19) [19]: !0 - 1st scan, 1 - 2nd scan, 2 - 3rd scan...press return for latest scan report
Template file [default]: COM:UPAT_EVAL_CAMOS.PS
Output filename [SYS$SCRATCH:UPAT...]: !default output file (with sample number and the site) goes to sys$scratch
# copies [1]: !the number of printouts, 0 if no printout is desired
</pre>

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===Print out report sheets===

The postscript report sheets can be generated and printed on the command line. For the XtremeCT system, use <code>UPAT_PRINT_LIST.EXE</code> which can be run (using the symbol):
<pre>
$ UPAT_LIST
</pre>

Look in the UU: directory to see options for the template files (UPAT*.TXT) and the postscript output files (*.PS).
:* UU:UPAT_EVAL_FUP05_SCUSA.PS
:* UU:UPAT_EVAL_BASELINE_SCUSA.PS

For other options, see the upat_list help:
<pre>
$ UPAT_LIST -h
</pre>

One particular option that may be useful, is to turn off slice matching:
<pre>
$ UPAT_LIST -nomatch
</pre>

Here is an example of producing a report for the third measurement of TL for a patient, where we want only the most recent results in the report, without slice matching:
<pre>
$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=UU:UPAT_EVAL_BASELINE_SCUSA.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_0fu.ps

$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=DISK1:[MICROCT.COMMANDS]UPAT_EVAL_CAMOS.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_camos.ps
</pre>
The first command line generates a normal Scanco report, and the second command line generates a CAMOS report.

For reports from non-patient measurements (i.e., the vivaCT system or non-patient scans on the XtremeCT), the template files are different (UCT*.TXT) and the postscript outputs are different (UCT*.PS). To print a result sheet use:
<pre>
$ RUN UM:UCT_RAY_BATCH.EXE
</pre>

If you want to create a postscript file, but not send it to the printer, set the number of copies to zero (interactive). Then, find the postscript file from the <code>SYS$SCRATCH</code> directory and transfer it to your PC. You must transfer the postscript file in ASCII mode. The files are typically called TEMP_3D.PS or UPAT_PAT_62_RR.PS. A program such as Adobe Photoshop can convert the postscript file to a different format.

See also our custom scripts:
<pre>
$ @COM:PRINT_2D.COM
$ @COM:PRINT_3D.COM
</pre>

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===Convert PS to PDF report===
The report can be converted to PDF using <code>$ @SCOM:PS_TO_PDF</code> by:

#Follow the instructions above for creating a report, using "2" to print and "0" for the number of copies. (Use the default template file and output filename.)
#Locate the file on the sys$scratch by <code>$ cd sys$scratch</code> and <code>$ dir</code>
#*The file should read "UPAT_PAT_[sample #]_[site].PS;1" (e.g. UPAT_PAT_0010_RL.PS;1)
#*You can view this file on the monitor by typing <code>$ gs UPAT_PAT_0010_RL.PS;1</code>
#Convert the postscript to PDF by typing in the command followed by the .PS file to convert <pre>$ @SCOM:PS_TO_PDF UPAT_PAT_0010_RL.PS;1</pre>
#The PDF file can then be located again in the sys$scratch directory.

You can transfer the result file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].

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=Data Management=
==Trainee’s Data Responsibility==
#Perform '''Contouring and Data Analysis''' on Data Disk ideally 1-2 months after scanning.
#After finished onsite analysis, [[Scanco_User_Instructions#Move_data_from_Data_Disk_to_Project_Disk|'''use Scripts''']] to '''Copy and Rename''' image data (no RSQ, no ISQ, only AIM, SEG.AIM, GOBJ, COM, LOG, PDF, PS ect) to your specific project folder on Project Disk.
#After finished copying all your image data to Project Disk, '''Notify''' lab personal to delete your data on Data Disk by providing a [[Media:Data_Scans_to_delete_template.xlsx|'''Data Scans to Delete Template''']].
#'''Notify''' lab personal to backup your project folder on Project Disk to Winston server on a monthly basis.
#*Only the two most recent backups (A or B version) are kept for each project on Winston:
#:Backup version "_A" for odd months (Jan, Mar, May, Jul, Sep, Nov), e.g. YZHU_A_OTHER_2017-01-12.SAV
#:Backup version "_B" for even months (Feb, Apr, Jun, Aug, Oct, Dec), e.g. YZHU_B_OTHER_2020-04-08.SAV
#When a project is finished, '''Notify''' lab personal to archive your project to HOG server.
#When a trainee is about leaving, '''Notify''' Steve and lab personal to determine either to backup or to archive your project.

[[File:BoneLabDataManagement.JPG|800px]]

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==Move data from Data Disk to Project Disk==
This is generally done after onsite analysis (i.e. autocontour, cortical porosity, FE etc.) is done. Examples of this can be found in DISK3:[MICROCT.PROJECTS.GRACE.COM] 
1. Go to the specific project's .COM directory, for example:
<pre>
$ cd DISK3:[MICROCT.PROJECTS.GRACE.COM]
</pre>
2. Create a script that will move all IMA (i.e. .AIM, .GOBJ, _SEG.AIM, _CORTEX.AIM, _LHTH_DTN.AIM) to the .MODELS directory for the project. You will use the rename_to_models.com script to generate this script. To move Grace data for example, with a measurement range of 2684 to 2685, you would use:
$ @com:rename_to_models.com meas#1:meas#2 DESTINATION DIR
$ @com:rename_to_models.com 2684:2685 DISK3:[MICROCT.PROJECTS.GRACE.MODELS]

3.This will create a file named RENAME_ALL.COM to the project's COM directory. You will now have to open the RENAME_ALL.COM file and add site + other details into the script. Following the same example as above, it should look like this:
$ eve RENAME_ALL.COM ! to open the file using a text editor
$ COPY DISK2:[MICROCT.DATA.00000700.00002684]C0002040.AIM -
DISK3:[MICROCT.PROJECTS.GRACE.MODELS]GRACE_020_00MTH_RR.AIM
$! DELETE/CONFIRM DISK2:[MICROCT.DATA.00000700.00002684]C0002040.AIM;1
$ COPY DISK2:[MICROCT.DATA.00000700.00002685]C0002041.AIM -
DISK3:[MICROCT.PROJECTS.GRACE.MODELS]GRACE_020_00MTH_RL.AIM
$! DELETE/CONFIRM DISK2:[MICROCT.DATA.00000700.00002685]C0002041.AIM;1
4. You also need to copy the rest of the standard patient image files (i.e. .AIM, .GOBJ, _SEG.AIM, _CORTEX.AIM, _LHTH_DTN.AIM) which is easily done by copying the above lines and replacing .AIM with the respective files.

[[Image:Bones2.jpg|20px]] Warning: Always use the same account consistently to create all files and subfolders within their Project folder, otherwise you way miss data when doing Project Backup or Archive!

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=Import and Export=
==Import Foreign Data to Scanco System==
Only RSQ and ISQ files can be imported into the database, however it is possible to convert other types of data into ISQ files (i.e., stacks of BMPs into ISQ).

PART 1:

After transfering your data to the VMS system (use the data disk <code>disk2</code>, NOT the user disk <code>disk1</code>), use the IPL commands <code>/import_freeformat</code> or <code>/read_aim function</code> to import your data for conversion to an ISQ.

For AIM files, navigate to the location of the AIM file. Then open IPL by:

<pre>$ IPL</pre>

In IPL, read in the .AIM file:

<pre>ipl> read in [.AIM file]</pre>

IPL will do the following:

<pre>ipl> read in STUDYID_001_RL.AIM

/read
-name in
-filename STUDYID_001_RL.AIM
!> Reading AimVersion020

!% /read completed: CPU: 00:01.03 ELAP: 00:01.55 </pre>

For DICOM files, start IPL and run the <code>/dicom</code> function to import. For DICOM, if your object is a single 3D file (-multifile false) or many many individual slice files (-multifile true, and give beginning of filenames, and –extension).

There may be requests by IPL to convert your data to <code>signed short</code> or <code>signed char</code> from other data types. Obey these requests and do it by running the <code>/convert_unsigned</code> function.

Then, write the ISQ file using either the "toisq" or "from_aim" commands:
<pre>ipl> toisq
-aim_name [in] >[leave blank as you defined “in” as .AIM file.]
-isq_filename [default_file_name] > C0001234.ISQ [Create a 1 letter and 7 digit file name]
-square_flag [true] > false
-original_position [true] > false

ipl>toisq_from_aim
-aim_name in
-isq_filename C0001234.ISQ
-square_flag false
-original_position false

!% Dimensions of ISQ file: dim.x dim.y dim.z 558 638 168
Write_ctdata_headerext_new: no mhext found. Init mhext.
Extended header successfully added of type 8

!% Writing ISQ slice 167 (Done: 168/168)

!% /toisq_from_aim completed: CPU: 00:05.12 ELAP: 00:10.47 </pre>

Type ipl>help toisq [or ipl>help from_aim] to see details of the command.

This writes the ISQ file. Make note of the ISQ file name.

Remember, the ISQ name must be 8 characters long (1 character followed by seven digits)!!! The letters and numbers can be chosen freely.

Exit IPL:

<pre>ipl>quit</pre>

PART 2:

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

The measurement can be verified by looking at the Header Information. (File, Header)

If you only needed to view the ISQ, delete the file when finished by:

<pre>$ dir/sincet
$del [.ISQ file]</pre>

PART 3:

To use the ISQ further (e.g. for evaluations, contouring, etc.) create a sample in the database and write down the sample and measurement number. Then, run:

<pre>$ run um:uct_import ! will import both RSQ and ISQ (modify patient index, etc)</pre>

and give the new ISQ file, the new sample-number and check that the feedback is correct (i.e., that the name from the database is matching the name from the ISQ file header). If the Patient Name in the ISQ header doesn't match the measurement database Patient Name (very likely), then upon importing the RSQ/ISQ the headers will be updated to the new Patient Name.

Operator and controlfile can be left 0 if you want. However, controlfile should be set appropriately if the data being imported is for the XtremeCT patient database.

If you are also importing the RSQ, put it in the same directory as the ISQ.

Then it changes the sample and measurement number in the ISQ file, makes the correct directory on <code>DK0</code>, and gives you the line on the screen of how to rename the file to the correct, new directory. Take this line and use it on the command line. Done!

You can now use the normal <code>uct_evaluation</code> program with this file. If the control file was set properly, then the evaluation will be done correctly (i.e., for XtremeCT patient measurements).

Note: Any AIMs created from the original ISQ should be recreated. So, it is important that you re-evaluate your newly imported ISQ. It is OK to move the GOBJ from the old directory to the same directly as the newly imported ISQ (it does not have a 'registry' in the database).

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==Import DICOM to Scanco System==
#Load MRI's or CT's DICOM data in Osirix
#Export from Osirix
#*Click export button in top left in osirix.
#*Select "flat" and "decompress all DICOM files"
#Copy files to correct folder in scanco system
#*Use Fillezilla or FTP (make sure it's set to binary mode)
#Use IPL to convert dicom to aim or isq

<pre>
/dicom_to_aim
-aim_name in
-dicom_filename IM-0001-0001.DCM ! Note - choose the first filename of the series
-multifiles true

/convert_unsigned
-input in
-shift_flag false
-divide_by_2 true

/write_v020
-name in
-filename PREOA_023_L_MR.aim
-compress_type bin
-version_020 true

/toisq_from_aim
-aim_name in
-isq_filename MROA023L.isq
-square_flag true
-original_position true''

</pre>

5. Delete dicoms

<pre>
/del *.dcm;1
</pre>

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==Import Xradia *.bin to Scanco System==
Xradia scanner exports a *.bin image that is:

- 16-bit unsigned ! This is "short" (8-bit is char - we don't want this for a grey-scale image)
- 2 bytes per voxel
- little endian notation

To upload this binary image to Scanco database, the steps are as follows:

#Ftp the *.bin to Scanco system using binary transfer (not ascii)
#Convert it to an AIM or ISQ in IPL

$ipl

/import_freeformat
-internal_name in
-file_name BMLPL_006.BIN
-sample_name BMLPL_006
-data_offset 0
-data_dim 1000 1024 1016 !dimensions from header file
-data_el_size 0.013 0.013 0.013 !voxel size from header file
-bytes_per_voxel 2
-data_endian little_endian
-data_type integer
-signed_type unsigned !correct
-multifiles false

/convert_unsigned
-input in
-shift_flag true !shift_flag = TRUE will produce an ISQ/AIM with negative values which may not be visualized properly using uct_evaluation, but keeps the original image resolution.
-divide_by_2 false !divide_by_2 = TRUE will down grade image resolution, but all positive values in an ISQ/AIM will be visualized properly using uct_evaluation.

/write_v020
-name in
-filename test.aim
-compress_type bin
-version_020 true

/from_aim_to_isq
-aim_name in
-isq_filename bmlpl006.isq !ISQ name requires 8 characters
-square_flag true
-original_position true

quit

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

Alternatively the image can be converted to a 16-bit signed in ImageJ (and cropped) before importing to ipl. It then becomes:

- 16-bit signed
- 2 bytes per voxel
- big endian notation

It can then be imported into ipl without the need to run <code>/convert_unsigned</code>.

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==Get Your Files==
===MAC/Linux Options===
====Fetch====
#Download and install [http://fetchsoftworks.com/fetch/|'''Fetch''']
#*This program is free for university staff and students.
#Fill out [http://fetchsoftworks.com/fetch/free|'''a form'''].

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====FTP from Terminal====
#Open a terminal
#*MAC: open the "Applications" folder, choose "Utilities", then "Terminal".
#Navigate to where you want to transfer the files to.
#Connect to the micro-CT ftp server using the ftp command in the terminal:
#*Login with the micro-CT user account and password.
#Navigate to the directory of interest on the micro-CT system.
#*Logicals such as "ur" can be used as short cuts. Whole directory names must be used.
#Set a filename mapping convention to remove OpenVMS version numbers.
#*The command <code>ftp> nmap $1;$2 $1</code> sets anything before the version number to parameter $1 and anything after the version number to $2. The file output will be set to $1, therefore the version number will not be kept.
#Set the file transfer mode.
#*[[File:Important.JPG|20px]] If you transfer an .AIM file in ascii mode, you will receive a "mesh generation" errors and "material ID out of range" message.
#Transfer your files.
#*Option: Turn off prompt so does not ask you whether or not to transfer each file.
#*If you do not turn off the prompt prior to transferring the files, press "a" (for all) to transfer all files at once.
#Exit FTP.

<pre>
$ FTP 136.159.74.231 !Connect to an FTP Server. Need to input user name and password.
$ FTP emily.ucalgary.ca !Connect to an FTP Server. Need to input user name and password.
$ FTP microct@emily.ucalgary.ca !Connect to an FTP Server. Need to input password.

FTP> cd ur !Navigate to the directory containing the target files.
FTP> cd sys$scratch !Navigate to the directory containing the target files.

FTP> nmap $1;$2 $1 !Set a filename mapping convention to remove OpenVMS version numbers.

FTP> bin !Set transfer mode to binary (.aim, .gobj, .isq, and most image file types).
FTP> ascii !Set transfer mode to ascii (.txt, .log, .com, .ps, .pdf and all other files in general).

FTP> put test.aim !Put the file
FTP> get test.aim !Get the file

FTP> prompt !Interactive mode off before transferring multiple files without having to be prompted.
FTP> mput *.aim !Put all files with the .aim extension on the FTP server (mput = multiple put).
FTP> mget *.aim !Get all files with the .aim extension from the FTP server (mget = multiple get).
FTP> mget *.aim; !Transfer the latest version of all aim files in a directory.

FTP> quit !Disconnect from the FTP Server.
</pre>

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===Windows Options===
====Scanco Medical µCT FTP====
#Downlod '''Scanco Medical MicroCT FTP 3.4''' from BoydDrive:\\04 - Resources\04 - Software\Scanco Medical MicroCT FTP 3.4\
#Install the software using the default parameters.
#Click on FTP Connection and input the host to connect to, the username, password.
#Give this profile a name.
#:[[File:Microct_FTP_pic01.jpg|600px]]
#Click on the options tab to set the locations to connect to (e.g., project disk, scratch) and the location on your computer to transfer files to.
#:[[File:Microct_FTP_pic02.jpg|600px]]
#Go back to FTP Connection and press the Connect button.
#*If you are connecting from off campus to the XtremeCT you will need to use the VPN to gain access through the firewall.
#Use the left tree to navigate folders.
#*Use the file filter to search for specific file types or file names (bottom left).
#Select files to download and press the Download Selected Files button (bottom right).
#:[[File:Microct_FTP_pic03.jpg|600px]]
#Press the Exit button to disconnect.

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====Filezilla====
#Download '''Filezilla 2.2.32''' from BoydDrive:\\04 - Resources\04 - Software\Filezilla 2.2.32\
#*This version of Filezilla will remove the OpenVMS version number from files, the new version will not!
#*The left side of the program shows your computer, the right side will show the micro-CT system once you have connected.
#:[[File:Filezilla_pic01.jpg|500px]]
#On the top menu, choose "File", then "Site Manager".
#Create a "New Site" for all the directories that you frequently access.
#*Give the site a meaningful name.
#*For the host, you may connect to "emily.ucalgary.ca" or "sceval.ucalgary.ca".
#*For the logon type choose "Normal" and input the micro-CT user name and password.
#:[[File:Filezilla_pic02.jpg|400px]]
#Click on the "Advanced..." button to set the default remote directory (i.e., on the micro-CT system).
#Set the default local directory if there is a specific location you plan to always transfer files to.
#Setup any additional sites you want then press "Save and Exit".
#:[[File:Filezilla_pic03.jpg|300px]]
#To connect to a session, hold the left mouse button down over the arrow next to the site manager button (computer icon under "File") to bring up your list of sites. Highlight the site of interest then release the mouse button to connect.
#Once connected, you can drag and drop files from the remote site to your local computer.

;*Common FTP locations
{| class="wikitable"
|-
! scope="col"| Account
! scope="col"| Location
! scope="col"| Path
|-
| microct / vivact || Data Disk ||DISK2:[MICROCT.DATA]
|-
| microct / vivact || Projects Disk ||DISK3:[MICROCT.PROJECTS]
|-
| microct / vivact || Scratch Disk ||ADISK1:[MICROCT.SCRATCH]
|-
| invivo / invitro || Data Disk ||DISK4:[BONELAB.DATA]
|-
| invivo / invitro || Projects Disk ||DISK5:[BONELAB.PROJECTS]
|-
| invivo / invitro || Scratch Disk ||ADISK1:[BONELAB.SCRATCH]
|}

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=Remote Access=

== VPN Setup ==

Access to the OpenVMS workstations from campus does not require VPN setup; however, to access from off the campus requires establishing a VPN connection prior to connecting.

*The VPN server is: gpvpn2.ucalgary.ca

*The client needed for VPN connection is '''FortiClient SSL''' which is available through [https://ucalgary.service-now.com/it| UofC IT Service Request] "Order Something".

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== Setup for MAC/Linux ==

=== Terminal and XQuartz ===
You need following to access the MicroCT system remotely.
#'''Terminal''': an SSH client
#*Preinstalled in MAC/Linux.
#'''XQuartz''': an X server for X11 forwarding
#*X11 was previously distributed with Mac OSX but has since stopped.
#*Check if preinstalled in MAC: open the "Applications" folder, choose "Utilities", there should be a file called "XQuartz". No need to open.
#*If not preinstalled, download the most recent [https://www.xquartz.org/ '''XQuartz.dmg'''].
#*Once downloaded, double click the .dmg file to follow the instructions and install.
 
;SSH from terminal
#Open a terminal.
#*MAC: Open the "Applications" folder, choose "Utilities", then "Terminal".
#Type <pre>$ ssh xtremect2@emily.ucalgary.ca -Y</pre>
#*The -Y flag activates X11 forwarding.
#Or type <pre>$ ssh -Y -p22 -c 3des-cbc -o KexAlgorithms=+diffie-hellman-group1-sha1 -o HostKeyAlgorithms=+ssh-dss xt2recalib@emily.ucalgary.ca </pre>
#*Type <pre>$ alias xt2recalib='<ssh command above>'</pre> allows you to only type <pre>"$ xt2recalib"</pre> in the terminal from here on out to access the MicroCT system.
#You're good to go!

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== Setup for Windows ==
=== MobaXterm ===

There is only one program required to access MicroCT remotely: MobaXterm. It will act as both an SSH client and as an X server.

*Download [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Home Edition (Portable Edition)]
 
;Configure MobaXterm
*Run the .exe file after downloading MobaXterm.
:[[File:MobaXterm_init.PNG|500px]]

*Click on "Sessions" -> "User Sessions" and choose "SSH" in the top left of the "Session settings" window.
*Input your host info into the "Remote host" dialogue box such as "emily.ucalgary.ca", check on "Specify username" and input your username such as "xt2recalib" and ensure "X-11 Forwarding" is checked in "Advanced SSH Settings" tab, and click OK.
:[[File:MobaXterm_SSH.PNG|500px]]
 
;Start the session
*Launch the MobaXterm client and under "Sessions" -> "User session" you should have something titled "xt2recalib@emily.ucalgary.ca".
*Double click that session and you're good to go!
:[[File:MobaXterm_Session.PNG|500px]]

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=== PuTTY and Xming ===
There are two programs required:
#'''PuTTY''': an SSH client
#*Download [http://www.chiark.greenend.org.uk/~sgtatham/putty/ '''PuTTY'''] or from BoydDrive:\\04 - Resources\04 - Software\PuTTY.
#'''Xming''': an X server
#*Download [https://sourceforge.net/projects/xming/files/latest/download?source=files '''Xming 6.9.0.31''']
#*Download [https://sourceforge.net/projects/xming/files/Xming-fonts/7.5.0.93/Xming-fonts-7-5-0-93-setup.exe/download '''Xming Fonts''']
 
;Configure PuTTY
*Under categories, expand the "Connection" and "SSH" trees. Click on "X11" and check the "Enable X11forwarding" box.
:[[File:Putty1.png|400px]]
*Under categories, now choose "Sessions".
*Under host name, put in "emily.ucalgary.ca". Choose "SSH" for the connection type.
*Under Saved Sessions, give the session a name (e.g., Emily). Click the "Save" button.
:[[File:Putty2.png|400px]]
 
;Start the Session
*Launch the Xming program, nothing should open except the Xming icon on the task bar.
*Open PuTTY. Double-click on the saved session, which will open a DEC terminal.
*Any program that you run remotely will be displayed by Xming.

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==Remote Access FAQ==
=== MAC Open SSH Authentication Issue ===
You might get an error similar to the following especially after a recent OS update:
Unsupported KEX algorithm "+diffie-hellman-group1-sha1"
command-line line 0: Bad SSH2 KexAlgorithms '+diffie-hellman-group1-sha1
This is not Apple’s fault, it’s OpenSSH version 7. SHA1 is weak, so support for it has been removed. Which is fine, but VMS clients are probably using RSA/SHA1. So until they’re all updated (i.e. never!) we need to re-enable SHA1.

Open a terminal windows and execute the following:
sudo nano /etc/ssh/ssh_config
ENTER YOUR PASSWORD

Locate the line ‘# MACs hmac-md5,hmac-sha1,umac-64@openssh.com,hmac-ripemd160′ and remove the Hash/Pound sight from the beginning.

Locate the line ‘# Ciphers aes128-ctr,aes192-ctr,aes256-ctr,aes128-cbc,3des-cbc’ and remove the Hash/Pound sight from the beginning.

Then paste the following on the end;

HostkeyAlgorithms ssh-dss,ssh-rsa
KexAlgorithms +diffie-hellman-group1-sha1
There’s no reason to reboot, it should work straight away.
 

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=== SSH Speed Issues ===
 
If you notice that the remote display is quite slow, you may prefer to enter the 'manual' X display redirection after connecting with ssh. 
 
The steps to enter the 'manual' X display redirection are outlined in one of Scanco's FAQs found [http://www.scanco.ch/en/support/customer-login/faq-customers/faq-customers-general.html here]. 
Click the "Remote Graphical Access from your PC to the MicroCT" tab (5th tab) and scroll down to "SSH Speed Issue" for more information.

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=== MobaXterm Backspace Issue ===
If the Backspace/Delete key doesn't work on your MobaXterm

#Right-click on a session name on the left column and click "Edit session"
#:[[File:MobaXterm1.png|500px]]
#: 
#Under "SSH" page "Terminal settings" tab, toggle off "Backspace sends ^H" and "Save"
#:[[File:MobaXterm2.JPG|500px]]

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Scanco User Instructions

2021-05-07T18:49:09Z

Yingzhu: /* Import MRI DICOM to Scanco System */

=OpenVMS Basics=
The micro-CT scanners in the lab are manufactured by [http://www.scanco.ch Scanco Medical] and most analyses are performed using their custom software. The micro-CT workstations run OpenVMS as its operating system and it is useful to learn some basic commands.

==OpenVMS Beginner's Reference==
OpenVMS (informally known as VMS) is a high-end computer server operating system with reliable, multitasking, real-time and batch processing. OpenVMS supports computer clustering via a LAN, enabling computers to share resources such as processors and disks to balance workload efficiently.

*[http://saf.bio.caltech.edu/vms_beginners_faq.html '''OpenVMS Beginner's FAQ''']

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==Session Manager==

The session manager automatically starts after a user logs in locally. For remote sessions, the session manager can be started with the command <code>$ vue </code>.

[[Image:SessionManager.jpg|600px]]

===Session===
Here you will find an option to "End Session", which you should do when you are finished using a workstation. You can click "Work in Progress..." when you have to leave in the middle of a session without logging out but showing a work in progress screen to other users to prevent interference.

===Views (directory shortcuts)===
The session manager is a graphical user interface that can be used to navigate directories (left side of session manager) and open files (right side of session manager). There are shortcuts to key directories under "Views". Single-click on a directory to list its subdirectories and files. Double-click on a file to open it.

===Commands and Utilities===
Under commands you will find tools such as copy, delete, and rename; however, it is much more practical to do these sorts of operations from a DEC terminal.

===Applications===
Under applications you can launch various applications including:
*DECterm: opens a DEC terminal
*MICROCT: opens the micro-ct control panel (buttons for Scanco Medical programs)
*Mozilla/Netscape: opens a web browser
*XV: opens a screen capture program

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==DEC Terminal and Digital Command Language (DCL)==
This is a DEC terminal: Commands issued in a DEC terminal are DCL commands.

[[Image:decterm.jpg|600px]]

===Copy and paste using the mouse in DEC terminal===
In the DEC terminal, you can highlight text by holding down and moving the mouse. Highlighted text can be pasted into applications or in the terminal using the middle mouse button. You can also highlight files in the Session Manager and paste the filename (with its full path) using the middle mouse button.

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===What is a symbol===
DCL can store information such as strings or integers in "symbols". DCL can also manipulate these symbols to create other symbols.
Symbols are primarily used to define short strings that replace long commands, perform certain calculations and replacements within DCL
procedures, hold status information.
<pre>
$ UR == "SET DEFAULT DISK4:[BONELAB.PROJECTS]" !A short hand to change locations to the project disk.
$ UR :== SET DEFAULT DISK4:[BONELAB.PROJECTS] !Another way to define the symbol without quotations.
$ x == 3 !Store the value 3 in the symbol x.
$ SHOW SYMBOL x !Displays the value of the specified symbol, x.
$ DELETE/SYMBOL/GLOBAL x !Deletes the specified symbol, x.
</pre>
Selected symbols on the Scanco system:
<pre>
$ UD !Changes to the data directory.
$ UR !Changes to the projects directory.
$ DISKS !Shows the current disk usage.
$ DEC !Opens a new DEC terminal.
$ EVE file.txt !Opens the file in the text editor.
$ AIX file.aim !Shows the processing log for an aim file.
$ AIX -L file.aim !The "-L" is used to show the full processing log.
$ QUE !Shows all entries in the queue.
$ GS file.ps or file.pdf !Opens *.ps and *.pdf files in GhostScript.
$ CTHEADER file.isq or file.rsq !Shows scan information for an *.isq or *.rsq file.
</pre>

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===What is a logical===
Logical names are strings, like symbols, but can be passed into programs whereas symbols can usually only be interpreted by the command line interpreter. For example, if the logical name UD was defined to be DISK2:[XTREMECT2.DATA] then UD: could be used as a substitute when entering the path to search for files from within a program.
<pre>
$ DEFINE UD DISK2:[XTREMECT2.DATA] !Defines a logical ud to point to the data directory.
$ DEFINE uct_default_isq myfile.isq !Defines the default isq file for Scanco Medical programs. The isq filename must contain the full path to the file to be evaluated, whereas the path can be left out if you just want to contour the scan.
</pre>
Selected logicals on the micro-CT system:
<pre>
COM !Logical pointing to the commands directory IDISK1:[XTREMECT2.COMMANDS]
UD !Logical pointing to the data directory DISK2:[XTREMECT2.DATA]
UD6 !Logical pointing to the data directory DISK6:[XTREMECT2.DATA]
UR !Logical pointing to the projects directory DISK4:[BONELAB.PROJECTS]
UE !Logical pointing to the evaluation script directory MICROCT_ROOT:[EVAL]
UU !Logical pointing to the templates directory MICROCT_ROOT:[UIL]
UCT_RESULTS !Logical pointing to the results directory MICROCT_USER:[RESULTS]
</pre>

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===Arithmetic operations===
{| class="wikitable"
|style="width: 10%"|Addition ||style="width: 5%;text-align:center;"| + ||The plus sign (+) adds two numbers.
|-
|style="width: 10%"|Subtraction ||style="width: 5%;text-align:center;"| - ||The minus sign (-) subtracts the second specified number from the first specified number.
|-
|style="width: 10%"|Multiplication ||style="width: 5%;text-align:center;"| * ||The asterisk (*) multiplies two numbers.
|-
|style="width: 10%"|Division ||style="width: 5%;text-align:center;"| / ||The slash (/) divides the first specified number by the second specified number. If a number does not divide evenly, the remainder is lost. No rounding takes place.
|}

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===Logical expressions===
{| class="wikitable" style="width: 100%;"
|style="width: 10%"|And||.AND.||The operator .AND. combines two logical values as follows
true .AND. true = true true .AND. false = false false .AND. true = false false .AND. false = false
|-
|style="width: 10%"|Or||.OR.||The operator .OR. combines two logical values as follows
true .OR. true = true true .OR. false = true false .OR. true = true false .OR. false = false
|-
|style="width: 10%"|Not||.NOT.||The operator .NOT. reverses the bit configuration of a logical value. A true value becomes false and a false value becomes true.
|}

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===Numeric comparisons===
{| class="wikitable"
|style="width: 15%"|Equal to||style="width: 5%;text-align:center;"|.EQ.||Compares one number to another for equality.
|-
|style="width: 15%"|Not equal||style="width: 5%;text-align:center;"|.NE.||Compares one number to another for inequality.
|-
|style="width: 15%"|Greater than||style="width: 5%;text-align:center;"|.GT.||Compares one number to another for a greater value in the first number.
|-
|style="width: 15%"|Greater than or equal to||style="width: 5%;text-align:center;"|.GE.||Compares one number to another for greater or equal value in the first number.
|-
|style="width: 15%"|Less than or equal to||style="width: 5%;text-align:center;"|.LE.||Compares one number to another for a lesser or equal value in the first number.
|-
|style="width: 15%"|Less than||style="width: 5%;text-align:center;"|.LT.||Compares one number to another for a lesser value in the first number.
|}

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===String comparisons===
The operators for string comparisons are the same as for numeric comparisons with an added "S" for string.
{| class="wikitable"
|style="width: 15%"|Equal to||style="width: 5%;text-align:center;"|.EQS.||Compares one character string to another for equality.
|-
|style="width: 15%"|Not equal||style="width: 5%;text-align:center;"|.NES.||Compares one character string to another for inequality.
|-
|style="width: 15%"|Greater than||style="width: 5%;text-align:center;"|.GTS.||Compares one character string to another for a greater value in the first specified string.
|-
|style="width: 15%"|Greater than or equal to||style="width: 5%;text-align:center;"|.GES.||Compares one character string to another for greater or equal value in the first specified string.
|-
|style="width: 15%"|Less than or equal to||style="width: 5%;text-align:center;"|.LES.||Compares one character string to another for a lesser or equal value in the first specified string.
|-
|style="width: 15%"|Less than||style="width: 5%;text-align:center;"|.LTS.||Compares one character string to another for a lesser value in the first specified string.
|}

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==DCL Programming Guide==
The OpenVMS systems allow for scripts to be written in a language called '''DCL (DIGITAL Command Language)'''. It was not designed to be more difficult than other scripting languages, but learning any new programming language comes with its learning curve.

*DCL has 243 commands, but most programs can be written with a base set of about 20 commands. The goal of this section is to provide a convenient reference for these commonly-used commands.

It is recommended to open a text editor, enter the whole series of commands, and then run them as a whole program. The terminal on OpenVMS is technically a DCL interpreter, so these commands could be typed in sequence into a terminal with the same result. Typing code interactively is helpful when testing a small code snippet in more detail.

===Your First DCL Script===
Ever since Kernighan and Ritchie wrote the book "The C Programming Language", it has been custom to start with a program that prints the text "Hello, world" to the screen. Open a text editor (for example "EVE") and enter the text below.
<pre>
$! My First DCL Script
$ mymessage = "Hello, world"
$ WRITE SYS$OUTPUT mymessage
$ EXIT
</pre>
Now save the file as HELLO1.COM, and run it using <pre>$ @HELLO1.COM</pre>

Several things are happening in the above program:
*'''Comment !''': The exclamation mark can appear anywhere on the line, and everything following the mark will be treated as a comment.
*'''Variable''': "mymessage" variable is populated with the string "Hello, world", which can be used in the rest of the script.
*'''Command''' "WRITE" send text to various places, in this case to "SYS$OUTPUT", that is to the standard output (i.e. screen).
*'''EXIT''' command tells the DCL interpreter that the script is done and we should exit.
*Commands in DCL are '''NOT case sensitive''', so the command "write sys$output mymessage" would produce the exact same result, but by convention we write commands in all uppercase.

*'''Special Comment !!''' automatically prints the contents of the comment to the screen/logfile. It is useful when you want to know what part of the script you are in.

===Basic Arithmetic===
The DCL language supports several types of data in variables. In the "Hello, world" example above, we saw how to store a string in a variable. We could have stored an integer, that is a positive or negative whole number, in the variable, and done some basic math.
*Refer to [[Scanco_User_Instructions#Arithmetic_operations|'''Arithmetic Operations''']], For example:
<pre>
$ i = 1
$ WRITE SYS$OUTPUT i+1
$ j = 3
$ k = j * (i + 1)
$ WRITE SYS$OUTPUT k
$ WRITE SYS$OUTPUT (k / 4)
$ WRITE SYS$OUTPUT 2 + 2 * 2
$ EXIT
will return:

2
6
1
6
</pre>
Two things are worth noting.
*Because we are limited to integers, division of 6 / 4 needs to return an integer (1.5 is not an integer); the value is truncated, which means rounding is always done toward zero.
*Order of operations is done in the "correct" order, and not left-to-right, so "2 + 2 * 2" is interpreted as "2 + (2 * 2)".

===Conditional Statements===
Sooner or later, you will want to run a program with some logic. The general syntax is:
<pre>
IF [condition]
THEN
[do something]
ELSE
[do something else]
ENDIF
</pre>
*The "ELSE" component is optional.
*If you need a very simple if..then with only one command, it can be written on one line without the "ENDIF":
<pre>
IF [condition] THEN [do something]
</pre>
*Refer to [[Scanco_User_Instructions#Numeric_comparisons|'''Numeric Comparisons''']], [[Scanco_User_Instructions#String_comparisons|'''String Comparisons''']] and [[Scanco_User_Instructions#Logical_expressions|''' Logical Expressions''']] for all possible logical operators (very similar to Fortran).

===Loops===
Most programming languages have 3 kinds of loops:
*Precondition Loops: Condition is tested at the beginning of the loop
*Postcondition Loops: Condition is tested after the loop has executed at least once
*Iterative Loops: A variable changes in a predetermined fashion each time the loop is called.

DCL has none of these. Instead, it has the concept of a "label" and the "GOTO" command. A loop in DCL would look like this:
<pre>
$ i = 1
$loop1:
$ IF i .GE. 10 THEN GOTO exitloop1
$ WRITE SYS$OUTPUT i
$ i = i + 1
$ GOTO loop1
$exitloop1:
$ EXIT
</pre>
This program will print the numbers from 1 to 10 in sequence.

===Subroutines===
Most programming languages allow to define a set of commands that can be called from various parts of the program.
*In DCL, the subroutine can be defined anywhere in the file (unlike C or Python, where the definition must precede the call).
<pre>
$ CALL mycustomsub Joe
$ CALL mycustomsub Mary
$ EXIT
$mycustomsub: SUBROUTINE
$ WRITE SYS$OUTPUT "Hello, ", P1, "!"
$ EXIT
$ ENDSUBROUTINE
</pre>

The first line calls a subroutine named "mycustomsub", which jumps execution to the 4th line. The parameters after the name of the function get copied over to local variables named "P1", "P2", "P3" etc. (in this example, only one parameter, but the maximum is 8) that are available to the subroutine. Note that the command "WRITE" accepts several arguments separated by commas, which get printed on one line.
*The subroutine should be terminated with the command "EXIT" followed by "ENDSUBROUTINE".
*Note that the parameters get passed literally to the subroutine, that is the subroutine gets the text "Joe", and not the contents of a variable named "Joe".
*To force symbol substitution, the parameter would need to be enclosed in single quotes.
<pre>
$ Joe = "Joe Smith"
$ Mary = "Mary Jane"
$ CALL mycustomsub 'Joe'
$ CALL mycustomsub 'Mary'
$ EXIT
$mycustomsub: SUBROUTINE
$ WRITE SYS$OUTPUT "Hello, ", P1, "!"
$ EXIT
$ ENDSUBROUTINE
</pre>

===Reading from files===
Sometimes you have a list of files (for example Micro-CT scans) that are to be processed in a certain way. The obvious way is to copy-paste the code several times, changing only the name of the file, but this is error-prone and inefficient.
*A better way is to put the list of models into a text file, and then call a subroutine on each model file. For example:
<pre>
$ CLOSE/NOLOG foo
$ OPEN/READ foo DISK3:[MICROCT.PROJECTS.OWOC.COM]MYLIST.TXT
$read_loop:
$ READ/END=done foo myline
$ CALL process_me 'myline'
$ GOTO read_loop
$done:
$ CLOSE/NOLOG foo
$ EXIT
$process_me: SUBROUTINE
$ scriptname = DISK3:[MICROCT.PROJECTS.OWOC.COM]MYSCRIPT.COM
$ SUBMIT/NOPRINT/QUE=SYS$FAST/PARAM='P1' 'scriptname'
$ EXIT
$ ENDSUBROUTINE
</pre>
*The first line closes the file handle, in case it was left open in a previous script.
*The second opens the file "MYLIST.TXT" for reading, and assigns the open file a handle named "foo".
*A loop reads the file line-by-line, calling a subroutine with the contents of each line.
*When the end of the file is reached, the file is closed and the script exits.

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==List of basic commands==
<pre>
$ VUE !Start the session manager. Press enter after to regain prompt.
$ DEC !Open a new DEC terminal
$ UCT !Open the micro-CT control panel.
$ UCT_SAMPLE !Start µCT Samples.
$ UCT_MEASUREMENT !Start µCT Tomography.
$ UCT_EVALUATION !Start µCT Evaluation Program.
$ UCT_3D !Start µCT Ray.
$ UCT_BACKUP !Start µCT Disk-Utility.
$ CD UD !Change location to the data directory.
$ CD UR !Change location to the projects directory.
$ CD SYS$SCRATCH !Change location to the scratch directory.
$ CD UCT_RESULTS !Change location to the results directory.
$ DIR UE !List files in the evaluation directory.
$ DIR UU !List files in the templates directory.
$ DIR COM !List files in the commands directory.
$ UCT_LIST !Extract results from the database.
$ AIX -L !View the header of an AIM file.
$ CTHEADER !View the header of an RSQ or ISQ file.
$ EVE !Start the text editor.
$ DISKS !Show the current disk usage (all hard drives).
$ LOGOUT !End a session. For remote sessions, logout from the main (initial) login terminal.
</pre>

===How to move to a different directory===
Use the SET DEFAULT command. You can use an absolute directory path or a relative directory path.
<pre>
$ SET DEFAULT disk:[dir.subdir] !Moves to specified path.
$ SET DEFAULT [.subdir] !Moves one level into subdirectory subdir.
</pre>

Use the CD (i.e., change directory) command (this calls the script $ @SCOM:CD.COM).
<pre>
$ CD subdir !Moves into subdirectory subdir.
$ CD subdir1 subdir2 !Moves into subdirectory subdir1, then into subdir2.
$ CD .. !Moves up one level (i.e., out of one directory).
</pre>

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===How to list the files in a directory===
Use the DIRECTORY command, which may be abbreviated to DIR.
<pre>
$ DIR !List everything in the current directory.
$ DIR disk:[dir.subdir] !Lists everything in the specified directory.
$ DIR disk:[dir.subdir...] !Lists everything in the specified directory and subdirectories.
$ DIR/COL=1 *.aim !Lists all files with the extension .aim in a single column.
$ DIR /VERSIONS=1 !Show only the newest version of each file in the directory.
$ DIR/SINCE=TODAY !Lists all files created today.
$ DIR [...*.aim] !The "..." indicates to do so recursively (i.e., counting all files in all subdirectories).
$ DIR/SIZE !Lists each file and its size.
$ dir/size/grand_total [.subdir...] !List the total size of all files in the SUBDIR directory.
$ HELP DIR !More information on the DIRECTORY command.
</pre>

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===How to copy files===
Use the COPY or BACKUP command.
<pre>
$ COPY file1.ext disk:[dir.subdir1]file2.ext !Make a copy of file1.ext to another location and call it file2.ext
$ COPY *.aim;* disk:[dir.subdir1] !Copy all .aim files (including all versions) to another location keeping the same name.
$ HELP COPY !More information on the COPY command.
</pre>
<pre>
$ BACKUP/VERIFY [.subdir1...]*.*;* [.subdir2...] !Copy entire directory SUBDIR1, including all subdirectories and files, into SUBDIR2.
$ BACKUP/VERIFY [.subdir1...]*.*;* []subdir1.sav/SAVE !Copy entire directory SUBDIR1, including all subdirectories and files, into a save set. The save set could be transferred and unpacked on another OpenVMS machine.
$ HELP BACKUP !More information on the BACKUP command.
</pre>

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===How to delete files===
Use the DELETE command, which may be abbreviated to DEL.
<pre>
$ DEL myfile.txt; !Delete the most recent version of myfile.txt.
$ DEL myfile.txt;* !Delete all versions of myfile.txt.
$ HELP DELETE !More information on the DELETE command.
</pre>
[[Image:Bones2.jpg|20px]] Warning: Extreme caution!
<pre>
$ DEL *.*;* !Delete everything in the current directory!
</pre>

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===How to create a directory===
Use the CREATE/DIR command.
<pre>
$ CREATE/DIR [.subdir] !Creates a subdirectory named subdir.dir in the current directory.
$ CREATE/DIR disk:[dir.subdir] !Creates the subdirectory subdir at the specified path.
</pre>

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===How to rename files and directories===
Use the RENAME command.
<pre>
$ SET FILE/PROTECTION=O:RWED olddir.dir !Sets protections so you can rename the directory.
$ RENAME oldfile.ext newfile.ext !Renames oldfile.ext to newfile.ext.
</pre>

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===How to check the queue===
Use the SHOW QUEUE command, which may be abbreviated to SH QUE.
<pre>
$ SHOW QUEUE !Shows all the queues, there are many!
$ SH QUE *FAST !Shows all queues whose names end with "fast", these are used for evaluations.
$ SH QUE *SLOW !Shows all queues whose names end with "slow", these are used for reconstructions.
$ SH QUE *FAST/ALL !By default you are only shown queue entries for the user you are logged in as. To show jobs for all users, use the /ALL qualifier.
$ SH QUE *FAST/BY=EXE/ALL !Show only jobs that are currently executing for all users.
</pre>

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===How to get queue information===
Use the SHOW ENTRY command to obtain information about batch jobs in the queues.
<pre>
$ SHOW ENTRY !Shows all the batch jobs for your user, there may be lots!
$ SHOW ENTRY 251 !Shows information for batch job number 251.
$ SHOW ENTRY 251/FULL !Shows detailed information for batch job number 251.
$ SHOW ENTRY/ALL !Shows all the batch jobs for all users.
</pre>

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=Micro-Computed Tomography (µCT) Basics=

==User Tutorials==
For Scanco MicroCT Systems and Software:
:*[[Media:Microct-v14.pdf | '''Scanco MicroCT Systems and Software''']]

For XtremeCT II and I:
:*[[Media:SOP Berlin V1.0.pdf | '''Scanco XtremeCT I SOP (Berlin)''']]
:*[[Media:XtremectIIB-v4-us.pdf | '''Scanco XtremeCT II Specs''']]

For MicroCT35, VivaCT40 and VivaCT80:
:*[[Media:ScancoMicro-CT_User_Policy_Guidelines_19052005.pdf| '''MicroCT User Policy & Guidelines''']]
:*[[Media:MicroCT_Starter_Package.pdf | '''MicroCT Starter Package''']] and its [[Media:Microctstarterpackagejun2012.docx| '''Word format''']].
:*[[Media:Scanco-training-uct35-and-vivact40.pdf | '''MicroCT Customer Training Guide''']]
:*[[Media:Vivact_80_v3-nomarks.pdf | '''VivaCT 80 Specifications''']]

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==Micro-CT Image Basics==
Computed tomography is a non-destructive x-ray imaging modality that enables three-dimensional (3D) virtual models of an object to be created, which can be subsequently visualized and analyzed. Micro-CT refers to CT in which the [http://www.scanco.ch/index.php?id=faq_general#c779 resolution] lies in the micro-scale, which is achieved with a high-resolution x-ray detector and a field of view that is much smaller than conventional CT. Structural detail provided by CT depends on differences in x-ray attenuation properties. Components with very different x-ray attenuation properties, for example air, soft tissue, and bone, can be differentiated in a CT scans whereas different types of soft tissues, for example muscle and cartilage, do not have sufficient differences in attenuation to be distinguish.

===Dark Field===
Detector response with x-rays off. Enables corrections of non-uniformities of the detector. Acquired automatically by the scanning software before each scan.

[[File:Dark_field_single.img_assist_custom-400x97.jpg|400px]]

===Bright Field===
Detector response with x-rays on but no sample. Enables corrections of non-uniformities of the x-ray beam. Acquired automatically by the scanning software before each scan.

[[File:Bright_field_single.jpg|400px]]

===Raw Projection===
A raw x-ray projection of a mouse leg. The darker regions correspond with higher x-ray attenuation. The discontinuities result from overlaps where the detector was shifted to acquire the large region of interest (3x2 detector frames in this example). Projections are acquired at many incremental rotations around the sample.

[[File:Raw_projection_notes.jpg|400px]]

===Sinogram===
The sinogram is a different representation of the projection data. The sinogram represents the attenuation values of one row of the detector at each rotational increment around the sample.

[[File:Sinogram.jpg|400px]]

===Attenuation Projection===
Accounting for the inhomogeneities of the detector and beam, we can calculate the x-ray attenuation caused by the sample. Bright regions correspond with higher attenuation.

[[File:Attenuation_projection.jpg|400px]]

===Reconstructed Image===
From the attenuation projections, the original structure can be calculate using filtered back projection.

*[https://youtu.be/DBLYSETYbe8 CT Back-projection Reconstruction]
*[https://youtu.be/NWeM35_KR2w CT Reconstruction of a Head]

[[File:Reconstruction_xy_yz_planes.jpg|400px]]

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==Image Data==
===Image Data Type===
====Binary Images====
Binary images are images whose pixels contain only two possible intensity values (off-on, or black-white B&W). The off or black value is usually 0 and the on or white value is usually 1 (1-bit pixel) or 255 (8-bit pixel). This type of image is commonly used as a multiplier to mask regions within another image.

====Grayscale Images====
Grayscale images represent intensities. Pixels range from least intense (black) to most intense (white). Pixel values usually range from 0 to 255 or are scaled to this range when displayed.

====Indexed Images====
An indexed image uses direct mapping of pixel values to colormap values. Instead of intensities, a pixel value within an indexed image relates to a color value within a color lookup table. An indexed image consists of a data matrix and a colormap matrix. The data matrix can be of class uint8, uint16, or double. The colormap matrix is an m-by-3 array of class double containing floating-point values in the range [0,1]. Each row of map specifies the red, green, and blue components of a single color. Since indexed images reference color tables composed of up to 256 colors, the data values of these images are usually scaled to range from 0 to 255.

====RGB Images====
Within the three-dimensional array of an RGB image, two of the dimensions specify the location of a pixel within an image. The other dimension specifies the color of each pixel. The color dimension always has a size of 3 and is composed of the red, green, and blue color bands (channels) of the image.

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===Image Data Pixel Values===
The image data type is determined by the pixel depth in bits per channel, or bit depth. Bit depth for each channel can be 8, 16, 32 or 64. The data may be signed, unsigned (u), floating-point (f), real or complex (c) for some arithmetic functions, where each channel value is represented by two numbers: real and imaginary part. All channels in an image must have the same data type.

{| class="wikitable"
|-
! scope="col"| Image Data Type
! scope="col"| Name
! scope="col"| Byte
! scope="col"| Value Range
! scope='col'| Comments
|-
! scope="row"| char
| 8-bit signed integer
| 1
| -128 ~ 127
| Scanco SEG.AIM, GOBJ
|-
! scope="row"| uchar
| 8-bit unsigned integer
| 1
| 0 ~ 255
|
|-
! scope="row"| int
| 16-bit signed integer
| 2
| −32768 ~ 32767
| Scanco grey-scaled images, ISQ, AIM
|-
! scope="row"| uint
| 16-bit unsigned integer
| 2
| 0 ~ 65535
| Converted format of Scanco grey-scaled images
|-
! scope="row"| long
| 32-bit signed integer
| 4
| −2^31 ~ 2^31 - 1
|
|-
! scope="row"| ulong
| 32-bit unsigned integer
| 4
| 0 ~ 2^32 - 1
|
|-
! scope="row"| float
| floating point
| 4
| ±3.40282347 E+38
| 32-bit single-precision with 6~7 significant digits
|-
! scope="row"| long64
| 64-bit signed integer
| 8
| −2^63 ~ 2^63 - 1
|
|-
! scope="row"| ulong64
| 64-bit unsigned integer
| 8
| 0 ~ 2^64 - 1
|
|-
! scope="row"| double
| double precision floating point
| 8
| ±1.79769313486231570 E+308
| 64-bit double-precision with 15~16 significant digits
|-
! scope="row"| complex
| floating point complex
| 8
| same as floating-point
| same as floating-point
|-
! scope="row"| dcomplex
| double precision complex
| 16
| same as double-precision
| same as double-precision
|}

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===Scanco Image File Types===

{| class="wikitable"
! scope="col"| Extension
! scope="col", style="width: 65%"| Description
! scope="col"| Creation
! scope="col"| Opens with
|-
! scope="row"| RSQ
| '''R'''aw '''S'''e'''Q'''uence data. This is the raw data collected after the scan. This file contains the bright and dark field corrections and the raw projections. || created with scan || $ x
|-
! scope="row"| ISQ
| '''I'''mage '''S'''e'''Q'''uence data. This is the reconstructed 3D image, which you see in the µCT Evaluation Program. || created from RSQ
| $ uct_evaluation
$ x
|-
! scope="row"| AIM
| '''A'''ny '''IM'''age data. This is a binary raw data format (16-bit signed data, little endian) 3D discretized data you see using the µCT Ray Program and used for the analysis. The AIM file is a volume of interest isolated from the ISQ file. || extracted from ISQ
|$ uct_3d
$ uct_evaluation
|-
! scope="row"| GOBJ
| '''G'''raphical '''OBJ'''ect data. These are the green contours in the µCT Evaluation Program, which are used to isolate regions of interest from an AIM file for analysis. || extracted from ISQ/AIM || $ uct_evaluation
|-
! scope="row"| SCV
| '''SC'''out '''V'''iew || created with scan || $ x
|-
! scope="row"| RAD
| Scout View || created with scan || $ x
|-
! scope="row"| RSW
| raw data (RSQ) || created with scan || $ x
|-
! scope="row"| IMA
| image data (AIM, ISQ, GOBJ)|| created from RSQ || $ uct_evaluation
|}
*Refer to [[Media:Aimpack_documentation.pdf|'''Scanco Aim Format''' ]] or its [[Media:Scanco_Aim_File_Format.doc|'''Doc Format''']] for its header info.

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==Scanco Medical Micro-CT Software==
In the bottom left hand corner of the micro-CT workstation desktop is the micro-CT control panel, from which the micro-CT programs can be launched. The standard operating procedure for scanning a samples involves proceeding through the programs in the control panel from left to right:
<pre>
$ UCT_SAMPLE !Samples: Registering a sample
$ UCT_MEASUREMENT !Tomography: Scanning
$ UCT_EVALUATION !Evaluation: Evaluating the scan
$ UCT_3D !Ray: Viewing the 3D scan
$ UCT_BACKUP !Disk-Utility: Archiving the data
</pre>
You must specify an operator in the control panel to use the scanning and evaluation programs.
* XtremeCT
[[File:XCTcontrol_panel.img_assist_custom-302x100.jpg|300px]]
* MicroCT35, VivaCT40 and VivaCT80
[[File:Uct35_control_panel.jpg|300px]]
[[File:VivaCT40_control_panel.jpg|300px]]
[[File:VivaCT80_control_panel.jpg|300px]]

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===µCT Samples===
The µCT-Samples program is used to register new samples to be scanned and update sample names (e.g., to correct a sample name). To start the program type <code>$ uct_sample</code> in a DEC terminal, or use the sample button.

[[File:Xtremect_button_samples.jpg|40px]]
[[File:Uct_sample_uct35.jpg|40px]]
[[File:Uct_sample_vivact40.jpg|40px]]

#'''Prepare Sample Names''' according to [[Scanco_User_Instructions#Sample_Name_Convention|'''Sample Name Convention''']]
#'''Register Sample Names'''
#*Create a new sample by clicking “New” and typing in your sample name where it says “Name.” “Save” the sample.
#*You are now given a sample number. Record the sample number on the log sheet.
#:[[File:Uct_sample_pic01.jpg|500px]]
#'''Create Additional Sample Names Using Copy and Paste'''
#*If you have many samples to register, you can copy and paste part of the sample name you just created. Highlight the part of the sample name you want to copy by holding down the left mouse button while dragging the mouse, then release the mouse button.
#:[[File:Uct_sample_pic02.jpg|500px]]
#*Paste the highlighted text into a DEC terminal by pressing the middle mouse button. Now highlight the text in the DEC term.
#:[[File:Uct_sample_pic03.jpg|300px]]
#*Go back to the µCT-sample window, click "New", and paste the information next to "Name" using the middle mouse button. Update the name as required and "Save."
#'''Add Additional Sample Details'''
#*When a patient comes in for their first scan, you need to update their sample with their date of birth, sex, and hand/foot dominance.
#*Use the "Find..." button to search for a sample that has already been registered. You can search by sample number or by project name (e.g., CAMOS).
#*Date of birth: DD/MMM/YYYY. Example: 14/JAN/1951
#*Remarks: include the sex and hand/foot dominance. Example: F-RHRF for female that is right hand dominant and right foot dominant

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===µCT Tomography===
The µCT-Tomography program is used to perform a scan. To start the program type <code>$ uct_measurement</code> in a DEC terminal on the scanner computer (remote access does not allow this functionality), or use the scanner button. If you use the button, you must specify an operator prior to using the program.

[[File:Xtremect_button_scan.jpg|40px]]
[[File:Uct_measurement_uct35.jpg|40px]]
[[File:Uct_measurement_vivact40.jpg|40px]]
[[File:VivaCT80_scan.jpg|40px]]

[[File:Uct_tomography_pic00.jpg|600px]]

#'''Select Sample'''
#*When the µCT-Tomography program is first started, you will be prompted to enter the sample name or number of the specimen you are about to scan.
#*If you have not registered your sample, press "Cancel" to close the select sample box, then press "New..." in the measurement sample box to register a new sample (see [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT-Samples''']]).
#*Once you have entered your sample information, the measurement sample box will show details for that sample, including the sample name and scan (measurement) history.
#:[[File:Uct_tomography_pic01.jpg|400px]]
#*After your first scan you will need to press the "Other..." button to open the sample selection box and find your next sample.
#'''Select a Controlfile'''
#*The controlfile contains scan parameters such as the x-ray energy, current, and more (see [[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29 controlfiles |'''Controlfiles''']]).
#*Once the controlfile is setup, you need only to select it. If there are many controlfiles, you may want to search for yours using the file filter by entering part of the name or number in the white box and pressing enter; if you do this, you still must click on the controlfile so that it is highlighted in black as shown below.
#:[[File:Uct_tomography_pic02.jpg|400px]]
#'''Precalibrate'''
#*Calibrations are done before loading your patient/animal and scanning for quality control and to reduce the time the patient/animal is under preparation/anaesthesia. Start the calibration by pressing the "Precalibrate" button.
#:[[File:Uct_tomography_pic03.jpg|400px]]
#*Press "Start Calibration". The calibration will start with an "X-Ray Warmup", followed by "Measuring Dark" and "Measuring I0" and usually takes about 2-3 minutes to complete.
#:[[File:Precalibrate.jpg|300px]]
#*The precalibration is good for 15~20 min. The time remaining is shown on the "Precalibrate" button.
#:[[File:Uct_tomography_pic5.jpg|400px]]
#*The precalibrate option cannot be used with batch measurements, and it's not available for MicroCT35 which is not intended for invivo/live scan.
#'''Load and Position the Patient/Sample'''
#*Instruct the patient to remove any jewelry in the scan areas (wrist/ankle/knee/elbow ect). With the patient seated, put the wrist/ankle/knee/elbow into the appropriate cast. Different pads with different sizes can be used to fit the patient.
#*For invivo/invitro samples, prepare your sample in terms of orientation, immobilization, hydration ect.
#*After the precalibration is complete, you can now open the bore cover and insert the patient's wrist/ankle/knee/elbow or sample into the scanner. Gently move the wrist/ankle/knee/elbow or sample into the scanner until you can snap in the cast at the gantry. Check that the cast is positioned correctly and the patient/sample is comfortable.
#*Close the bore cover.
#'''Scout-View'''
#*A scout-view is similar to a 2D x-ray image and allows the user to set where to start and stop the scan.
#*After loading your sample, press the "Scout-View..." button to bring up the scout-view window.
#*The start position (top of the scanner) and end position (bottom of the scanner) can be modified to zoom in on the region of interest.
#*The angle of the scout view can also be changed to see the object in a different orientation.
#*Once pressed the "Scout-View" button but the scout view is found not in an appropriate position, press "Cancel", modify the start position, end position, or angle and press "Scout-View" again.
#:[[File:Scout_view_window.jpg|400px]]
#*Scout view image is displayed in the top right hand corner of the program and will start by showing the right half of the image, followed by the left half of the image.
#'''Set Reference Line and Launch a Scan'''
#*A reference line (solid green line) is placed to set the scan region (green block).
#*Press the "Reference-Line" button to show the reference line and default scan region over the scout view.
#*To change the number of slices to scan, move the reference line to the top of the scan region, then hold down the shift button while dragging the mouse to extend the scan region and press the left mouse button to set the reference line.
#*To centre the scan region between two reference lines, move the reference line to the top of the scan region, then hold down the alt key while dragging the mouse until the second green reference line is in place, then press the left mouse button to set while still holding down the alt key!
#:[[File:Uct_tomography_pic06.jpg|700px]]
#*For a single scan, select "OK", "Scan" and "Start Measurement". Record measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']].
#*For a batch scan which is only available on microCTs, select "Batch Measurement" and record the measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']]. You may now setup a new scan (select new sample and controlfile, perform scout, etc). When you have finished setting up all scans, press "Start Batch Scans." (See [[Scanco_User_Instructions&action=edit&section=48#Perform_Batch_Scans|'''Perform Batch Scans''']] for detailed instructions)
#'''Cancel or Reposition a Scan'''
#*If you need to interrupt a scan, press the cancel button and restart the scan or if you do not want to rescan then "unload" the scanner.
#*If you have not started a scan and need to reposition the patient, you also must "unload" the scanner.
#'''Remove Patient/Sample from Scanner'''
#*After the scanning is complete, open the bore cover and slide the patient's wrist/ankle/knee/elbow or sample out of the scanner. Release the cast by pushing down the cast release handle.

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===µCT Evaluation Program===
The µCT Evaluation Program is used to evaluate a scan. To start the program type <code>$ uct_evaluation</code> in a DEC terminal, or use the graph button. If you use the button, you must specify an operator prior to using the program.

[[File:Uct_evaluation.jpg|40px]]

[[File:Uct_evaluation_pic01.jpg|600px]]

#'''Find Your Sample'''
#:Enter the first part of your sample name in the file filter box and press enter. The samples are shown in the left hand box. The measurement box on the right shows scans for the selected sample (highlighted in black). Select a measurement and press "OK."
#:[[File:Uct_evaluation_pic02.jpg|500px]]
#'''Draw Contours (If Applicable)'''
#*Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
#*Contours must always be drawn COUNTER-CLOCKWISE!!!
#*[[Media:Contouring-tools.pdf |'''Contouring tools reference sheet''']]
#*For this sample, we are only interested in viewing the object in 3D and drew contours to isolate the bone and soft tissue from the sample tube.
#:[[File:Uct evaluation pic03.jpg|600px]]
#'''Evaluate'''
#*Scanco Medical provides several standard evaluation scripts. Open the 3D-Evaluation menu either using the "T..." button or from the top menu by going to "Tasks" and "Evaluation 3D...". If you set a default evaluation script in your scanning controlfile, it will be listed under "Task/Evaluation."
#:[[File:Uct_evaluation_pic04.jpg|400px]]
#*If you want to run a different evaluation press "Select...", highlight the evaluation script of interest, and press "OK".
#:[[File:Uct_evaluation_pic05.jpg|400px]]
#*When the 3D-Evaluation window is activated, a white box will appear on your reconstructed image. The white box is the region of interest that will be "cut out" of the full scan. If you have drawn contours, the white box will automatically be adjusted to fit the contours. Adjust the box if necessary by grabbing one of the white handles; use the left mouse button to move the box and the right mouse button to resize. The box can also be resized using the "VOI Start" and "Dimensions" in the 3D-Evaluation window.
#*For most evaluation scripts, you will be required to specify parameters for a Gaussian filter, to reduce noise, and a threshold, to isolate your object (e.g., bone) from the background. Check that the parameters used provide a good representation of your scanned sample by flipping back and forth between the segmented and grayscale image using the "Preview" and "Grayscale" buttons.
#:[[File:Uct_evaluation_pic06.jpg|400px]]
#*When you are satisfied with the segmentation parameters, press "Start Evaluation", which will submit the job to the queue.

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===µCT Ray===
The µCT Ray program is used to view scanned objects in 3D, create images, and create image sequences for animations. To start the program type <code>$ uct_3d</code> in a DEC terminal, or use the 3D object button.

[[File:Uct_3d.jpg|40px]]

[[File:Uct_3d_pic01.jpg|600px]]

#'''Select and Render Your Sample'''
#*'''Select:''' If you have used the default Scanco Medical scripts, then
#:*If your data is on the "data disk" and you can search for your files using the file filter to select a sample and measurement then press "OK". To open a new file, File --> Open.
#:*If your data is not in the standard location (e.g., it was copied to the projects disk), then use File --> Read and navigate to find the file to open.
#:*Alternatively you can start the program with a file to open <code>$ uct_3d myfile_seg.aim</code>
#: 
#*'''Rendering:'''
#:*Use a single click of the left mouse button to start or to stop rendering the sample.
#:*You can also use the "Start" and "Stop" buttons at the bottom of the options on the left.
#:*You must stop rendering to change viewing options on the left.
#: 
#*'''Change View:'''
#:*To adjust the view, move the "Rotation" and "Elevation" slider bars in the options on the left.
#:*The slider bar is located above its label.
#:[[File:Uct_3d_pic02.jpg|600px]]
#: 
#*'''Change Colours''' (Object and Background):
#:*From the top menu choose "Options" then "Object/Display Properties...".
#:*A segmented image typically only has two values, 0 (black, background) and 127 (white, object). To change the colour of the object only, we need to set the value 127 to a specific colour.
#:*In this example, the slider bar value "1" corresponds with the value 127 and we will set both slider bars to "1" so that we are adjusting values "127 ... 127", in other words, only value "127".
#:*Under "Surface" click on the "white box" to open the "Color Mixing" window.
#:*Choose the new colour for the object (e.g., orange) and press "OK."
#:*Close the "Object Properties" window or move it to the side.
#:*Now re-render the object with a single click of the left mouse button.
#:[[File:Uct_3d_pic03.jpg|300px]] [[File:Uct_3d_pic04.jpg|300px]]
#: 
#*'''Cutplane (left options) and Subdim (top menu):''' 
#:*The cutplane and subdim functions allow you to show a cross-section of your object.
#:*The subdim function tends to work better than the cutplane but is limited to axes of the scan.
#:[[File:Uct_3d_pic05.jpg|600px]]
#: 
#'''Print an Image to File'''
#*An image must be fully rendered in order to be saved.
#*From the top menu choose "File" then "Print". Set the print format to "TIFF" and the directory to "Scratch/Temp" (or another location using the "Specify in Filename" option).
#*Change the filename to something meaningful then press "OK."
#:[[File:Uct_3d_pic06.jpg|300px]]
#: 
#'''Auto-Print Images for an Animation'''
#*Creating an animation involves saving a sequence of rendered images, which can then be compiled into an animated GIF or other video format using various software packages (e.g., Photoshop, Quicktime Pro).
#*From the top menu choose "Options" and "Animation..." to open the Animation Settings window. Set the viewing parameters for the start of the animation, fully render the image, then press the "Get Settings A" button.
#*Set the parameters for the end of the animation, fully render the image, then press the "Get Settings B" button.
#*Set the number of frames you want, the higher the number frames, the smoother the animation will be, but also the larger the file size.
#*Now setup the auto-print feature. From the top menu choose "File", then "Print". Choose "TIFF" for the print format, and the "Scratch/Temp" for the directory (or use the "Specify in Filename"). Specify a filename prefix, to which numbers will be appended for the image sequence.
#*Activate the "Auto-Print" feature. Press "OK" then press the "Start Calculation" button on the Animation Settings window.
#*Do not interrupt the program while the frames are being rendered and saved. When the program is done rendering all the frames, transfer them to your computer to compile into an animation.
#:[[File:Uct_3d_pic07.jpg|200px]] [[File:Uct_3d_pic08.jpg|300px]]

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===XImage===
The XImage program is used to view the raw data (RSQ file) and scout view. To start the program type <code>$ run um:ximage</code> or <code>$ x </code>in a DEC terminal.

When loading an RSQ, the default view (XY plane) is of the sinogram.

[[File:Ximage_1.jpg|600px]]

To view the attenuations, choose the XZ plane. The first slice in this orientation is the dark field, the second slice is the bright field , and slices three and onward are the raw projections (attenuations).

[[File:Ximage_2.jpg|600px]]

To view the corrected projections, from the Evaluations menu, choose Projection Mode.

[[File:Ximage_3.jpg|400px]]

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=Scanning=
==Sample Name Convention==
*At the Bone Imaging Laboratory, all sample naming must conform to the following format
:'''PROJECT IDENTIFIER _ SAMPLE DETAILS'''
*In CAPITAL LETTERS (filenames are case sensitive, so this makes it easy to remember how you input your sample name)
*No special characters (spaces, /, %, etc.) as further evaluations will not work if spaces are present.
:Examples: CAMOS_771, TESTS_0001, TESTS_0002, TESTS_0003

==Register Samples for Scanning==
*Although samples can be registered immediately prior to a scan, it is much more efficient to register all your samples beforehand.
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT Samples''']] for instructional details.

==Log Sheets==
*Log sheets are used to record important information about scans that are performed, such as sample and measurement numbers ect.
*Log sheets are to remain in the lab. If you would like a copy of your log sheets, please make a photocopy or print two copies to record the scan information.
*Use the PDF file to print blank log sheets. Use the Excel file to make your own custom log sheet.

#Bone Lab for General Patients
#*[[Media:XCT_II_Log_(Studies).pdf|'''XCT II Log Sheet for Studies''']]
#*[[Media:XCT_II_Log_(Miscellaneous).pdf|'''XCT II Log Sheet for Miscellaneous''']]
#MicroCT Lab for General Non-Patients
#*[[Media:UCT_log_sheet_general.pdf|'''MicroCT Log Sheet for Studies (PDF)''']]
#*[[Media:UCT_log_sheet_general.xlsx|'''MicroCT Log Sheet for Studies (Excel)''']]

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==Patient Casts and Sample Holders==
===Patient Casts for XtremeCTs===

===Sample Holders and Scan SOP for microCTs===
====Ex Vivo Sample Holders====
*Ex vivo and inanimate samples are scanned in sample holder tubes. These tubes come in a variety of diameters. It is extremely important that the tube diameter corresponds to, or is smaller than, the field of view (FOV) set in your scanning control file.

*Biological tissues should be hydrated and wrapped in plastic wrap to prevent drying of the sample. Your sample should then be secured in the sample holder using foam to prevent it from shifting around during scanning, which would lead to poor image quality.

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=====Chemical Resistivity of Sample Holders=====
*White tube sample holders are made of PMMA (poly-methyl-methacrylate).
*Yellow tube samples holders are made of PEI (poly-ether-imide).
*Use the yellow tubes if you will need to disinfect the sample holder after scanning.

{| class="wikitable"
!colspan="3"|Thermal and chemical compatibility of sample holders
|-
! scope="col"| Properties
! scope="col"| White Tubes (PMMA)
! scope="col"| Yellow Tubes (PEI)
|-
! scope="row"| Max. Temperature
| +85°C
| +170°C
|-
! scope="row"| Sterilization Steam Autoclave
|non resistant
|resistant (138°C for 20 Min. at 1 bar)
|-
! scope="row"| Water
|resistant
|resistant
|-
! scope="row"| Inorganic Acids
|limited resistance
|resistant
|-
! scope="row"| Inorganic Bases
|non resistant
|limited resistance
|-
! scope="row"| Aldehydes (Formaldehyde)
|limited resistance only in diluted form
|resistant
|-
! scope="row"| Alcohols
|limited resistance
|resistant
|-
! scope="row"| Bleach
|non resistant
|resistant
|}

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=====Mounting of Sample Holders=====
[[File:Uct35_holder.jpg|thumb|right|100px|µCT35 setup]]
*The spindle (metal bit) of the sample holder has a slot, which must be aligned in the scanner or adapter plate.
*The sample holder sits vertically in the µCT35 while horizontally in the VivaCT80 and VivaCT40.
*For the vivaCT40, attach the adapter plate for the tube sample holders to one of the animal bed. The tube sample holders are held horizontally in the vivaCT 40.
:[[File:Vivact40_holder.jpg|thumb|none|700px|VivaCT40 setup]]

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=====Ex vivo rodent scanning SOP=====
*Refer to [[Media:Ex_vivo_scan_sop.pdf|'''Ex Vivo Rodent Scanning''']] for its scan SOP.
*Refer to [[Media:Ex_vivo_scan_sop.docx|'''Ex Vivo Rodent Scanning in docx''']] for its Word version.

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====In Vivo Sample Fixtures and Anesthetic System====
*[[Media:VivaCT40_Anaesthetic_System.pdf |'''Anaesthetic System''']] : You must receive training to use the anaesthetic system.
*[[Media:VivaCT40_Mouse_and_Rat_Tibia_Fixture.pdf |'''Mouse/Rat Tibia Fixture''']]
*[[Media:VivaCT40_Mouse_Lower_Body_Fixture.pdf|'''Mouse Lower Body Fixture''']]
*[[Media:VivaCT40_Mouse_Whole_Body_Tube.pdf|'''Mouse Whole Body Tube''']]

=====In vivo rodent scanning SOP=====
*Refer to [[Media:In_vivo_scan_sop.pdf|'''In vivo rodent scanning''']] for its scan SOP.
*Refer to [[Media:In_vivo_scan_sop.docx|'''In vivo rodent scanning in docx''']] for its Word version.

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====Align whole body device in FOV====

It's important to have your whole sample in the field of view for accurate density measurements.
* Refer to [[Media:wholebody.pdf |'''Align the device''']] for detailed instructions.

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==Scan Parameters (Controlfiles)==

:{| class="wikitable" style="text-align:center;"
|-
! scope="row"| Manufacturer
| colspan="5"|[http://www.scanco.ch '''Scanco Medical AG''']
| [https://www.zeiss.com/microscopy/int/products/x-ray-microscopy.html '''Carl Zeiss X-ray Microscopy''']
|-
! scope="col" rowspan="2"| Model
! scope="col"| XtremeCT II || XtremeCT I || VivaCT80 || VivaCT40 || µCT35 || Xradia 520 Versa
|-
|[[File:XtremeCT.jpg|150px]]
|[[File:XtremeCT.jpg|150px]]
|[[File:VivaCT80.jpg|120px]]
|[[File:VivaCT40.jpg|135px]]
|[[File:UCT35.JPG|150px]]
|[[File:Xradia-520-versa-small.jpg|160px]]
|-
! scope="row"| Application
|colspan="2"| Clinical studies for human extremities in vivo
Horizontal static patient setup
|colspan="2"| Preclinical in vivo animal studies
Horizontal static animal setup
|colspan="2"| High resolution ex vivo specimen scans
Vertical rotational sample setup
|-
! scope="row"| E (KVp)
| 68 || 60
|colspan="3"| 45, 55, 70
| 30 ~ 160
|-
! scope="row"| Power (W)
| 100 || 54
|colspan="3"| 4, 8
|4 ~ 10
|-
! scope="row"| Filter
| Fixed 0.2mm Cu + 1mm Al
(Equivalent 6.7mm Al)
| Fixed 0.1mm Cu + 0.6mm Al
| Default 0.5mm Al,
Air, 0.1mm Al, 0. mm Cu
| Fixed 0.5mm Al
| Fixed 0.5mm Al
| Air, LE1~LE6, HE1~HE6,
customizable filter
|-
! scope="row"| FOV (⌀ * L) (mm^2)
| 140 ⌀ * 200 L
| 126 ⌀ * 150 L
| 31.9 ~ 80 ⌀ * 145 L
| 21.5 ~ 38.9 ⌀ * 148 L
| 7.2 ~ 38 ⌀ * 140 L
(75 L standard)
| 90 ⌀ * 100 L
|-
! scope="row"| Image Matrix
| 4608*4608 ~ 512*512
| 3072*3072 ~ 512*512
| 4096*4096 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
|-
! scope="row"| Voxel Size (µm)
| Standard 60.7
(30.3 ~ 273.4)
| Standard 82.0
(41.0 ~ 246.0)
| 5 ~ 156
| 10.5 ~ 76
| 3.5 ~ 74
| 0.7 ~ 50
|-
! scope="row"| Sample Image
|[[File:XCT2_human_distal_femur.png|160px]]
human distal femur
|[[File:XCT1_human_distal_tibia.JPG|160px]]
human distal tibia
|[[File:VivaCT80_Rat_distal_femur.JPG|160px]]
rat distal femur
|[[File:Vivact40_in-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Uct35_ex-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Xradia_mouse_distal_femur.png|160px]]
mouse distal femur
|}

Controlfiles are used to specify the parameters for the scans. Once your controlfile is setup, you should not modify it over the course of your project.

[[File:XCT2 ControlFile.JPG|right|600px]]

*'''Control File Name''': Specify a meaningful name so that others can reuse yours.

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===General Settings===
*'''Holder Type''': Choose the used holder type for XtremeCT II from Standard Casts, Knee Cast and Elbow Cast. No option for XtremeCT I scanner. For microCTs, Choose the used sample holder type with the correct diameter.

*'''Mode of operation''': Default is continuous operation for all scanners. Gated operation mode is available for VivaCT80 and VivaCT40 scanners.

*'''Evaluation Script''': This sets the default evaluation script used for the analysis. You can manually select a different script from the evaluation program.

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===X-ray Settings===
*'''Tube Energy (KVp)''': Fixed energy for XtremeCTs while having 3 options for each of microCTs: Use the 70 KVp for most samples, use the 55 or 45 KVp for low density objects (e.g., soft tissue) or specimens with a diameter less than 20 mm. Lower energies provide better contrast while higher energies provide better signal to noise (SNR).

*'''Tube Current (µA)''': Fixed current for XtremeCTs while having 2 options for each of energy settings of each microCTs: Use the higher current except when the voxel size is set for the best resolution of the scanner. The higher current will yield better SNR but a larger spot size.

:{| class="wikitable" style="text-align:center;"
|-
! scope="col"|
! scope="col"| XtremeCT II
! scope="col"| XtremeCT I
! colspan="3"| vivaCT80，vivaCT40， µCT35
|-
! scope="row"| E (KVp)
| 68
| 60
| 70
| 55
| 45
|-
! scope="row"| I (µA)
| 1470
| 900
| 114, 57
| 145, 72
| 177, 88
|-
! scope="row"| Power (W)
| 100
| 54
|colspan="3"| 8, 4
|}

*'''Filter''': Fixed filter settings for all scanners except VivaCT 80 has 4 filter options.

*'''Calibration''': This sets the mu scaling factor, density and beam hardening correction used for the reconstruction. For standard patient scans use 200 mg HA/cm3. For ex vivo bone scans, use 1200 mg HA/cm3, for soft tissue use the plexi scaling, and for non-biological tissues use the aluminum scaling.

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===Scout-View Settings===
Normally you will want to enable this and here you can specify the default start and end position, and scout-view angle, which you may override for each scan.

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===CT Scan Settings===

*'''Resolution''': This setting includes the reconstruction matrix size (2048x2048, 1536x1536, 1024x1024, or 512x512) and the number of projections per 180°. The lower the resolution setting, the better the SNR and larger the voxel size.

*'''FOV / Diameter''': This field of view must fully contain the sample holder for accurate density measurements. Fixed FOV for XtremeCTs while having 5 options for each of microCTs: If you choose a smaller FOV than the sample holder, the scan may be aborted to prevent damage to the scanner. For the best resolution, you should choose the smallest holder that contains your sample.

*'''Voxel Size''': The nominal isotropic voxel size is determined by the FOV and the reconstruction matrix.

*'''Number of Slices''': You can specify a specific number of slices or image stacks to acquire (1x110 = 1 image stacks of 110 slices). The scan time increases with each image stack, therefore pay attention to the stack boundaries (e.g., 111 slices will take 2x longer to scan than 110 slices).

*'''Rel Position of First Slice''': This option enables you to offset the scan region from the reference line. This is useful for scanning a region a specific distance from the growth plate or centering the scan region around the reference line. If you disable the scout view, then the position is relative to the absolute 0 position of the scanner (top of the sample holder for the µCT35 and towards the back of the scanner for the vivaCT40).

*'''Integration Time''': The higher the integration time, the better the SNR and longer the scan time. Use 100 ms for patient scans and higher values for ex vivo scans of better image quality. To get the highest integration time, uncheck the "Continuous ROT" button. For standard microCT measurements, use ~400 ms for the µCT35 and ~200 ms for the vivaCT40. The maximum integration time is scanner-specific and limited to prevent saturation of its detector.

*'''Average Data''': This is often referred to as frame averaging and is used to improve a scan's SNR. Multiply the average data value by the integration time to calculate the effective integration time. Only use this if the integration time is maxed out.

*'''Measurement Time''': This is the estimated scan time without the time performing the scout view or warm-up of the scanner.

*'''CTDIvol''': Computed Tomography Dose Index (CTDI) is a standardized measure of radiation dose output of a CT scanner for scanner settings' comparison purposes only, and it represents the average absorbed dose along the longitudinal axis from a series of contiguous CT exposures. Volumetric CTDI is the ratio of the weighted-CTDI to the level of overlap between slices (pitch). CTDIvol has no consideration of real scan length and does not represent actual dose administered to the patient.
:[[File:CTDI.JPG|600px]]

*'''DLP''': Dose Length Product DLP = CTDIvol * Scan Length in unit of mGy-cm.

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====XtremeCT II Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 4608
| 2304
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 3000
| 900
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 140 mm
| 30.3
| 60.7
| 91.1
| 136.7
| 273.4
|-
! colspan="2"| Slices/Stack
| 338
| 168
| 112
| 74
| 37
|-
! colspan="2"| Stack Thickness (mm)
| 10.24
| 10.20
| 10.20
| 10.12
| 10.12
|-
! colspan="2"| Time/Stack (min, at 43 ms Integration Time)
| 8.1
| 2.0
| 2.0
| 1.4
| 0.7
|-
! colspan="2"| Time Current Product (mAs)
| 238
| 71
| 59
| 40
| 20
|-
! colspan="2"| CTDIvol (mGy)
| 37.4
| 11.2
| 9.3
| 6.4
| 3.2
|-
! colspan="2"| DLP (mGycm)
| 38.3
| 11.4
| 9.5
| 6.4
| 3.2
|}

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====XtremeCT I Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 3072
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 126 mm
| 41
| 82
| 123
| 246
|-
! colspan="2"| Slices/Stack
| 221
| 110
| 73
| 36
|-
! colspan="2"| Stack Thickness (mm)
| 9.06
| 9.02
| 8.98
| 8.86
|-
! colspan="2"| Time/Stack (min, at 100 ms Integration Time)
| 3.7
| 2.8
| 1.9
| 1.0
|-
! colspan="2"| Time Current Product (mAs)
| 114
| 86
| 57
| 29
|-
! colspan="2"| CTDIvol (mGy)
| 7.3
| 5.5
| 3.6
| 1.9
|}

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====VivaCT80 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 3072
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1500
| 1000
| 500
| 250
| 125
|-
! rowspan="6"| Voxel Size (µm)
! scope="row"| FOV/Diameter 31.9 mm
| 10.4
| 15.6
| 31.9
| 31.2
| 62.4
|-
! scope="row"| FOV/Diameter 35.9 mm
| 11.6
| 17.5
| 35
| 35
| 70.1
|-
! scope="row"| FOV/Diameter 39.9 mm
| 13
| 19.5
| 39
| 39
| 78
|-
! scope="row"| FOV/Diameter 49.8 mm
| 16.1
| 24.2
| 48.5
| 48.5
| 97.1
|-
! scope="row"| FOV/Diameter 63.9 mm
| 20.8
| 31.2
| 62.4
| 62.4
| 124.8
|-
! scope="row"| FOV/Diameter 79.9 mm
| 26
| 39
| 78
| 78
| 156
|-
! colspan="2"| Slices/Stack
| 333 ~ 328
| 222 ~ 219
| 111 ~ 109
| 111 ~ 109
| 55 ~ 54
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 14.9
| 10.0
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 73
| 48
| 24
| 12
| 6
|}

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====VivaCT40 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 21.5 mm
| 10.5
| 21
| 21
| 42
|-
! scope="row"| FOV/Diameter 25.6 mm
| 12.5
| 25
| 25
| 50
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 35.8 mm
| 17.5
| 35
| 35
| 70
|-
! scope="row"| FOV/Diameter 38.9 mm
| 19
| 38
| 38
| 76
|-
! colspan="2"| Slices/Stack
| 213
| 106
| 106
| 53
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 9.9
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 61
| 31
| 15
| 8
|}

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====µCT35 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 7.2 mm
| 3.5
| 7
| 7
| 14
|-
! scope="row"| FOV/Diameter 12.3 mm
| 6
| 12
| 12
| 24
|-
! scope="row"| FOV/Diameter 20.5 mm
| 10
| 20
| 20
| 40
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 37.9 mm
| 18.5
| 37
| 37
| 74
|-
! colspan="2"| Slices/Stack
| 232 ~ 235
| 116 ~ 117
| 116 ~ 117
| 58
|-
! colspan="2"| Time/Stack (min, at 400 ms Integration Time)
| 23.9
| 12.3
| 6.5
| 3.5
|-
! colspan="2"| Time Current Product (mAs)
| 119
| 60
| 30
| 15
|}

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===Advanced Settings===
*'''Number of Det-lines (for Scout-View)''': Defines how many lines on the detector shall be used during the Scout-View. Using all available lines provides faster Scout-Views but some faint horizontal lines might be seen between the stacks. Limit the number of lines to a small number to obtain Scout-Views without these artifacts but the time of the Scout-View will increase.

*'''Number of Det-lines (for CT-scan)''': Defines how many lines on the detector should be used. This number influences the number of slices within a stack. Limit the number of detection lines if you see residual cone beam artifacts.

*'''FOV/Scan Diameter''': Chose the diameter of the FOV. This action is cropping the area of the detector.

*'''Software binning''': factor of the pixels on the detector.

*'''Hardware binning''':

*'''Samples''': number of (possibly binned) pixels on the detector that are used for each slice (note: this number is given for the whole FOV).
*'''Proj/180°''': number of projections taken per 180° turn of the sample.

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===Reconstruction===

*After each image stack is acquired, it is automatically submitted to the queue (sys$slow) for reconstruction. The reconstruction for each image stack is split into four jobs to make efficient use of processors.
*The reconstruction time depends on the resolution setting, with low resolution scans reconstructing faster than high resolution scans. Normally scans are reconstructed within a day or two.
*It is possible to resubmit a scan for reconstruction (refer to [[Scanco_Administration#Reconstruction | '''Scanco Administration's Reconstruction''']]) for details. This may be necessary or desirable for several reasons:
#The sample did not reconstruct properly (e.g., due to a power failure)
#To reconstruct the object at an angle (e.g., so that the anterior surface of a bone is always in the same direction).
#A new beam hardening correction was applied to the sample
#The scaling was changed for the sample to change the brightness

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==Perform a Scan==
===Perform a Single Scan===
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] for instructional details.

===Perform Batch Scans===
*Batch scan mode is only available on microCT scanners.
*Batch scans can be setup for different regions of interest (ROI) within a sample or for different samples contained within a sample holder.

#'''Setup the First Scan'''
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] to use the "Other..." button to find your sample number, choose a controlfile, perform a scout view (a mouse's whole body in this example), use the reference line to setup the first scan region (mouse skull in this example).
#*To add a batch scan press the "Batch Measurement" button.
#:[[File:Batch_scan_01.preview.jpg|600px]]
#*An information window is displayed with the scan measurement number. Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']] then press "OK" to close the window. An entry is also added to the measurement history for the sample.
#:[[File:Batch_scan_02.preview.jpg|600px]]
#'''Setup the Next Scan'''
#*Using the "Other..." button, find your next sample number, choose a new control file (if desired).
#*If the next region of interest or sample is not in view of the current scout view, adjust the parameters of the scout view and obtain a new one.
#*Use the reference line to set a new scan region (upper limbs in this example).
#*To add a batch scan press the "Batch Measurement" button.
#*As the first scan, a measurement number is assigned for this new scan. Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']].
#:[[File:Batch_scan_03.preview.jpg|600px]]
#*Repeat this process until you have added all your scans.
#'''Start the Batch Scans'''
#:There are two ways to start a batch scan:
##Click the "Start Batch Scans" button: the program will automatically close so that control of the scanner can be allotted to the queue.
##Exit the scanning program.
#:[[File:Batch_scan_04.preview.jpg|600px]]
#'''Check the Queue'''
#*Batch jobs will be submitted to the SCEVA2_BATCH queue for µCT35 or SC5019_BATCH queue for vivaCT40.
#*Initially the jobs will show up as temporary (TMP) jobs:
#:[[File:Batch_scan_05.preview.jpg]]
#*After about 30 seconds, the sample number will show up in entrie names:
#:[[File:Batch_scan_06.preview.jpg]]
#'''Request an Email Notification'''
#*There is a script in the commands (com) directory that will put an entry into the batch queue to send an email. Run the script and input parameters (queue and email) as prompted.
#:[[File:Batch_scan_07.preview.jpg]]
#'''Cancel a Batch Scan'''
#*For errors made during batch scan setup, to cancel a scan in progress, or to cancel a pending scan.
#:[[File:Batch_scan_08.preview.jpg]]
#*If you cancel all the scans and the scanner door does not unlock automatically (µCT 35 only), then start the measurement program and the scanner will unload, unlocking the door.

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==Action on Image Artifacts==
===Rescan for===
*'''Motion Artifacts'''
*'''Sample Out of the Field of View'''

===Contact Scanco Medical for===
*'''Ring Artifacts''' (Bad Detector)
:*Ring artifacts are caused by a faulty detector pixel and show up in the reconstructed image as a full or partial white circle.
:*When noticed, please notify lab technicians who will contact Scanco Medical to perform a "Pixel Correction", which will correct this artifact for future scans and can be used to update previous scans.
:*You should not rescan the sample if there is a ring artifact.
<div><ul>
<li style="display: inline-block;"> [[File:Ring_artifact.jpg|thumb|none|350px|Image with Ring Artifact]] </li>
<li style="display: inline-block;"> [[File:Ring_artifact_corrected.jpg|thumb|none|350px|Same Image after with Detector Correction]]</li>
</ul></div>

*'''Bad Centre Calibration Values'''
*'''Defective Shutter Artifact'''

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=Evaluation=
==Evaluate a Scan==
*To evaluate a scan, refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.

===Open default ISQ===
You can load a defual ISQ usig uct_evaluation program:

<pre>
$ def uct_default_isq DISK3:[MICROCT.PROJECTS.VALIDATION.MODELS]C0000123.ISQ ! or
$ def uct_default_isq DISK2:[MICROCT.DATA.00001234.00005678]C0003456.ISQ
$ uct_evaluation
</pre>

Hit <code>cancel</code> when asked files to load, and the file you just set as default will be loaded.

*Use the whole pathname for ISQ.
*If you don't import your data into the system, you cannot store your evaluation results in the measurement database. You will have to use the LOG file to access your results.
*Only start a 3D evaluation if and only if the sample (patient) and measurement index are correct in the ISQ full path! Also, no results will be stored in the database unless the ISQ header info (samp/meas) is correct.
*Many of the UCT_xxx.COM scripts use the whole filename to extract the sample and measurement numbers, so it is possible that some evaluations will not run. UCT_xxx_BATCH_V4.COM is an example of an evaluation that will not run, but UCT_CUTOUT.COM will run (doesn't need any sample/meas info).

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==Draw Contours==
*Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
*Contouring is the first step in the analysis process, which allows you to segment the desired bone from surrounding tissues.

===Contouring Tools Reference Sheet===
*[[Media:Contouring-tools.pdf |'''Contouring Tools Reference Sheet''']]
*Contours must always be drawn COUNTER-CLOCKWISE!!!

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===Contour and Run the Standard Patient Evaluation===
The following instructions are for contouring standard patient radius and tibias.

#Open the Evaluation Program and select your sample.
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.
#Zoom into the desired bone (Radius or Tibia)
#*Using the zoom menu from the top panel, zoom into the Radius or Tibia.
#*Usually 3x zoom is appropriate.
#Draw contours roughly around the bone.
#*Select the first contouring tool (top left button) and draw COUNTER-CLOCKWISE.
#Automatically generate contours for all slices in the scan.
#*Double click the image to bring up the contouring window.
#*Double click again and the program will attempt to snap the contour to the bone. Double click again if needed.
#*Select Forwards, and then Iterate Forwards to have the evaluation program automatically segment the bone.
#Modify any contours as needed.
#*Select the second contouring tool (2nd button from top) to fix any "wrong" contours.
#*Draw COUNTER-CLOCKWISE!!
#*If many contours cannot be automatically generated correctly i.e. cortical bone is porous and evaluation program misses a lot of bone, it may be better to use the Range/Morph function rather than fixing each individual slice.
##This is done by first clearing all the breakpoints (Clear all BP in contouring window). The boxes will now become red.
##Manually fix the slice that does not have the correct contour automatically drawn, skip a few slices and manually fix that slice as well. The slices that you have fixed will turn green, indicating that it is a breakpoint (BP).
##Now you can morph between the two breakpoints (BP, green boxes) you have just created. Select the BP with the higher slice number, select range (first column on left) from the contouring window, followed by morph (second column from left).
#Save Contour (.GOBJ): Make sure you save your work!
#Run the 3D Standard Evaluation for your specific project (and timepoint).
#*Select 3D evaluation under Tasks to bring up the window. You'll then need to Select... the evaluation specific for your project.
#*There are a variety of evaluations to choose from, you can search for your project's evaluation script by typing in the name of your project in the filter window.
#Check the queue to ensure that the evaluation is running properly.
#*Type <code>$ show que</code> in a terminal window will allow you to see all running processes.

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===Correct Trabecular Contours and Run the Cortical Evaluation===
Once the standard evaluation has been completed, an auto-segmentation process is completed to segment the cortical from the trabecular bone. However, the auto-segmentation is not always accurate, and hence the contour (TRAB.GOBJ) will need to be checked.

#Load TRAB.GOBJ by selecting File, then load GOBJ from the top panel.
#*You will now see a list of all GOBJ files pertaining to your sample. You'll need to load the TRAB.GOBJ.
#*When the TRAB.GOBJ has loaded, you will see that the loaded contour is between the cortical and trabecular bone.
#Correct contours as needed
#*Can manually adjust the slices or use the Range/Morph function.
#*Remember to draw COUNTER-CLOCKWISE!
#Run the 3D cortical evaluation for your specific project (and timepoint, if relevant).
#*Select 3D evaluation under Tasks to select the appropriate evaluation script.

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==Evaluation Scripts==
===Scanco Standard Evaluation Scripts===
The following are descriptions of some of the standard evaluation scripts provided by Scanco Medical.

*'''3D Segmentation of VOI, 1 solid object'''
:Produces a 3D segmented (binary) object with values 0 (background, hidden) and 127 (solid). Input Gaussian filtering and threshold parameters. Draw contour to isolate the object of interest (optional).

*'''3D Seg. of 2 VOIs: solid dense in transparent low dens obj'''
:Produces a 3D segmented object with values -1 (transparent), 0 (background, hidden), and 127 (solid). Input two sets of Gaussian filtering and threshold parameters (input the second set by pressing the red 2 button). The preview shows the solid object in white and the transparent object in red. Draw one contour to isolate the object of interest (optional). This script is useful for showing soft tissue and bone.

*'''Bone Trab. Morphometry (3D Seg, 3D Calc, Print Sheet)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour to isolate the trabecular bone. Performs model-independent (direct) measurements on the trabecular region. Outputs: BV, TV, BV/TV, TbBMD, TbTMD, BS, SMI, DA, ConnD, TbTh, TbThSD, TbSp, TbSpSD, TbN, and Tb1/NSD.

*'''BV/Density only Bone Eval. (3D Seg, BV and Dens Calc, Print)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour to isolate the region of interest. Outputs: BV, TV, BV/TV, BMD, and TMD.

*'''Bone Midshaft Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour on the outer surface of the bone. Outputs: BV, TV, BV/TV, BMD, TMD, and moment of inertia parameters.

*'''Bone Midshaft more than e.g. 50 slices Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour on the outer surface of the bone. If you wish to exclude the medullary area from the analysis, then draw a counterclockwise contour on the outer surface of the bone and a clockwise contour on the inner surface of the bone. Performs direct measurements in addition to the standard midshaft analysis. Outputs: BV, TV, BV/TV, BMD, TMD, moment of inertia parameters, Th, and Sp.

*'''Convert to TIFF'''
:Converts the grayscale data to TIFF slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Convert to DICOM'''
:Converts the grayscale data to DICOM slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Reformat to Axial Cuts'''
:Flips the dataset from the XY plane to the XZ or YZ planes (specify in the advanced options for the script). This is useful if you want to contour your sample in a different plane. The flipped sample is imported as a new measurement under the same sample number as the original data.

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===Understanding Evaluation Scripts===
Following are some example evaluation scripts full of comments to promote understanding:
*[[Media:IPLV6_VOI.pdf|IPLV6_VOI script]]
*[[Media:IPLV6_MIDSHAFT.pdf|IPLV6_MIDSHAFT script]]
*[[Media:IPLV6_TRABECULAR_BONE.pdf|IPLV6_TRABECULAR_BONE script]]

===Setup Customized Evaluation Scripts===
To setup an evaluation script customized to your project, in the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']]:
*Choose "Scripts" then "Import from" then "TEMPLATES", pick a Scanco Standard Evaluation Scripts and Save.
*Choose "Scripts" then "Modify". Choose the script that was just imported and click "OK", Change the name of the script.
*Modify the default segmentation and other parameters for the script. When finished making changes press "Save" then "OK".

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==Image Processing Language (IPL) Scripting==
The following documentations related to IPL scripting, as it applies to image analysis was compiled by Jan Owoc in July 2013 based on numerous sources including own experience.

===Your First IPL Script===
*'''Prerequisite''': you are familiar with navigating the VMS system.
*'''"$" or "ipl>"''': the DCL and IPL prompts respectively, and you should only type the text after the prompt.
*If you FTP the file to the OpenVMS system, ensure you use "binary" to transfer the file.
You can run these commands on almost any greyscale AIM file. Example file here: MJ7101.AIM

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====Interactive IPL====
*Command <code>$ ipl</code> starts IPL interactively, that is you see the result of each command as you run it.
*While it is useful for testing, running large scripts interactively may interfere with others using the computer.
 
*'''Reading an AIM file'''
:Before you can run any analysis on the AIM file, you need to read it into IPL and assign it a file handle. This is done using the command <pre>ipl> read in MJ7101.AIM</pre>
:A fraction of a second later, the file should have been read into memory and assigned the internal name "in". If we want to do some basic density calculations on it, we can use the command<pre>ipl> vox_ in 0</pre>
:*IPL, much like DCL, will automatically complete the command if it is given enough characters.
:The "vox_" was expanded to the command "vox_scanco_param" (calculates voxel-counting parameters) and told you that the mean density of the cube is 114 mg HA/cm3 and a standard deviation of 283 mg HA/cm3.
:The argument "in" is the internal name of the image.
:The argument "0" is the region. The command vox_scanco_param supports several numbered regions if, for example, you wanted to separately compute the density for the trabecular region and the cortical region.
 
*'''Segmenting an AIM file'''
:Some parameters, like average density, are computed from the [[Scanco_User_Instructions#Grayscale_Images|'''Greyscale Image''']]. Other parameters, like the trabecular number, require an image that has been segmented to [[Scanco_User_Instructions#Binary_Images|'''Binary Images''']], that is converted into "bone" and "not bone".
:There are many ways to separate bone from non-bone, and parameters that work well for one dataset will not generally work for images of different samples, or acquired at different resolutions.
:One of the simplest segmentation methods "seg_gauss" is to apply Gaussian smoothing to the sample, to eliminate the noise present in the image, followed by a semi-arbitrary threshold that preserves the trabecular structure.
<pre>
ipl> seg_gauss in seg

-sigma [1.000000] >
-support [2] >
-lower_in_perm_aut_al [300.000000] >
-upper_in_perm_aut_al [100000.000000] >
-value_in_range [127] >
-unit [0] > 2
</pre>
:seg_gauss expects 8 parameters, and we have provided only 2. It will now prompt us for the remaining 6 one-by-one.
:Leave everything at the defaults (simply hit "Enter") except the unit, which we will change to "2".
:For young human trabecular bone from the distal tibia scanned at 20 um in the uCT 35, but then downscaled to 80 um, the above parameters give a reasonable representation of the trabecular structure. With other bones at other resolution, you may need to change the sigma, the support, and the lower threshold.
:The unit of "2" simply means that we are working in units of mg HA/cm3.
:Now that the cube is segmented, we can run the same voxel-counting command as above and obtain more information. <pre>ipl> vox_ seg 0</pre>
:We now know that our combination of smoothing and threshold resulted in an object volume of 103 mm3 (i.e. volume of bone) and a bone volume ratio of 22.88%.
 
*'''Writing out a file'''
:we can write the segmented file out for future use. Accept the defaults for the remaining arguments. <pre>ipl> write seg MJ7101_SEG.AIM</pre>
:Now you can quit IPL and verify that the segmented file has been written out. <pre>ipl> quit</pre>

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====Batch IPL====
*Command <code>$ ipl_batch</code> starts IPL inside a script that would be submitted to a queue.
While the following code is likely to work, it is not very readable:
<pre>
$ IPL_BATCH
read in MJ7101.AIM
vox_ in
seg_gauss in seg 1 2 300 100000 127 2
vox_ seg
write seg MJ7101_SEG.AIM
..
$ EXIT
</pre>
*Instead, it is recommended that you copy and paste the "pretty" output of the command after you have run it once interactively.
*Values that are likely to change should be variables, defined at the top of the script.
*To substitute a variable from DCL into IPL, use a double-quote character before the variable name, as shown in the example below.
Copy and paste the below into a text editor.
<pre>
$ modelname :== MJ7101.AIM
$ threshold == 300
$ outputfile :== MJ7101_SEG.AIM
$
$ IPL_BATCH

/read
-name in
-filename "modelname

/vox_scanco_param
-input in

/seg_gauss
-input in
-output seg
-sigma 1.000000
-support 2
-lower_in_perm_aut_al "threshold
-value_in_range 127
-unit 2

/vox_scanco_param
-input seg

/write
-name seg
-filename "outputfile

..
$ EXIT
</pre>
Now, it is clear what the full names of the commands are, and what the parameters mean.
*If a parameter isn't important and can be left at the default (for example the region number during vox_scanco_param), you can leave it out of the file.
Save the file as MYSCRIPT.COM and run it using <code>@MYSCRIPT.COM</code>.

 
*'''Submitting to the queue'''
:As mentioned in the introduction, running IPL interactively on larger models negatively impacts other users of the system. Copying the commands to a file and running it from the command line has the same effect.
:*The correct way to run larger scripts is to submit the job to the queue. <pre>SUBMIT/QUE=SYS$FAST MYSCRIPT.COM</pre>

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===IPL Reference===
*[[Media:SCANCO_-_Software_-_IPL_instruction_manual_0.pdf|'''Official Scanco IPL Documentation''']]
*[[Media:scanco-software-ipl-instruction-manual.pdf|'''Scanco IPL Manual]]

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====Standard Read Write etc. Functions====
*'''/read''': Reads a file into ipl and gives the file an internal name
*'''/aim_read''':
*'''/read_versatile''':
*'''/write_v020''': Writes an aim file to the directory in which ipl is open (or specified directory if in a script)
*'''/write_new''':
*'''/write_part''':
*'''/copy''': Copies an internal file (a file that is already in the ipl system) and allows the copy to be given a new name.
*'''/delete''': Deletes an internal file (a file that is already in the ipl system)
*'''/rename''': Changes the name of the file (input is the old name and output the new name)
*'''/list''':
*'''/options''':
*'''/release_history''':
*'''/commands_write_log''':

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====Segmentation Functions====
*'''/gauss_lp''': Applies a low pass gaussian filter with specified sigma and support values
*'''/fft_laplace_hamming''':
*'''/median_filter''': Applies a low pass median filter to reduce unwanted noise in an image
*'''/seg_gauss''': Segments aim files using the input sigma of gauss and the filter support for gauss. A threshold can also be applied using this function.
*'''/threshold''': Removes data outside of the specified range
*'''/absolute_threshold''':
*'''/adaptive_threshold''':
*'''/adaptive_iter_threshold''':
*'''/matching_threshold''':

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====Gobj and Masking Functions====
*'''/gobj_maskaimpeel_ow''': Cuts an aim file with a gobj so that only the portion of the aim within the gobj remains. Peel_iter value used to specify the number of pixels within the gobj the function will need to cut.
*'''/gobj_to_aim''': Reads a gobj file from the directory and makes an aim file (the aim file is in ipl, to output it to the directory use write).
*'''/togobj_from_aim''': Takes an aim file and writes a gobj file (the gobj is output to directory).
*'''/gobj_circumf_area''':
*'''/gobj_join''':
*'''/gobj_join_consec''':
*'''/gobj_scale''':
*'''/gobj_isotrop''':
*'''/cortex_maskoff''':
*'''/peel3d''':

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====Voxel-Counting, Density and Triangulation Functions====
*'''/db_scanco_activate''':
*'''/db_clear_eval''':
*'''/db_calib_unit_fill''':
*'''/db_set_mean_accur''':
*'''/voxgobj_scanco_param''': Inputs an aim file and a gobj and provides information (including total volume, object volume and the mean value of the points) on the region within the gobj.
*'''/vox_scanco_param''': Inputs an aim and provides information including total volume, object volume and the mean value of the points.
*'''/tri_da_metric_db''':
*'''/tri_direc_distr''':
*'''/connectivity''': Receives a component labelled aim object and calculates the connectivity of the labelled components.
*'''/conn_nocl''':
*'''/conn_bgcl''':
*'''/fractal_dimension''':

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====Distance Transformation (Sphere Filling) Functions====
*'''/dt_object_param''':
*'''/dt_ow_object_param''':
*'''/dt_background_param''':
*'''/dt_mat_param''':
*'''/dt_cortex_obj_param''':
*'''/dt_value_output''':
*'''/dt_mat_output''':

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====Statistical Functions====
*'''/examine''': Receives an AIM object and outputs specified information based on the item input.
*'''/histo''':
*'''/moment2d_of_inertia''':
*'''/moment3d_of_inertia''':
*'''/zmeanmax''':

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====Voxelsize-Scaling Functions====
*'''/isotrop''':
*'''/scale_elsize''':
*'''/ipscale_elsize''':
*'''/noipscale_elsize''':
*'''/scale_ow_elsize_noip''':

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====Component Labeling Functions====
*'''/cl_ow_rank_extract''': Receives AIM file and over writes it with an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl_rank_extract''': Receives AIM file and outputs an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl26_rank_extract''':
*'''/cl_image''':
*'''/cl_extract''':
*'''/cl_slicewise_extractow''':
*'''/cl_nr_extract''':

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====Add, Concat, Cut etc. Functions====
*'''/add_aims''': Adds the values of two AIM images in a 3D space.
*'''/add_constant_ow''':
*'''/border_change''':
*'''/bounding_box_cut''': Cuts extra space out of an aim file so that only the region with the data remains. A border can be added to the image using the border input.
*'''/concat''': Takes two aim files and combines them. The data from both aims or just the common region can be kept. To add the images add_not_overlay is set to true (for example if image 1 has a value of 41 and image 2 has a value of 82, the combined value will be 123).
*'''/concat_adapt''':
*'''/divide_volumes''':
*'''/fill_min_max_ow''':
*'''/header_geo_set''':
*'''/header_log_set''':
*'''/header_calib_ov''':
*'''/invert_ow''':
*'''/mult_constant_ow''':
*'''/multiply_volumes''':
*'''/sqr_to_float''':
*'''/sqrt_to_float''':
*'''/offset_add''':
*'''/offset_set''':
*'''/clear_offset''':
*'''/fill_offset_mirror''':
*'''/fill_offset_duplicate''':
*'''/set_value''': Sets the values of the object and background of an aim file to chosen values
*'''/sub_get''': Extract a portion of an image 
**-pos corresponds to x,y,z origin -1 -1 -1 maintains the original coordinates 
**-dim corresponds to x,y,z dimensions -1 -1 -1 maintains the original dimensions (within maximum range) 
**indexing starts at 0 instead of 1
*'''/sub_pick''':
*'''/subtract_aims''': Subtracts one aim from another and outputs the remaining region.
*'''/sup_divide''':
*'''/transparent_concat''':

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====Erosion Dilation Open Close Functions====
*'''/erosion''':
*'''/dilation''':
*'''/open''':
*'''/close''':
*'''/erosion_dilat_variable''':

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====Import Export Conversion Norming Functions====
*'''/import_freeformat''':
*'''/dicom_to_aim''':
*'''/todicom_from_aim''':
*'''/dicom_list_series''':
*'''/isq_to_aim''':
*'''/isq_gobjfit_to_aim''':
*'''/toisq_from_aim''': Writes an isq file to the directory ipl is open in (or specified directory) from an aim file. The isq name should be 8 characters long.
*'''/mesh''':
*'''/msq_from_aim''':
*'''/rsq_to_aim''':
*'''/stl_tri''':
*'''/convert_to_type''':
*'''/convert_unsigned''':
*'''/norm_max''':

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====Functions for Root Canal Evaluations====
*'''/separ_roots''':
*'''/calc_ctr_mass_list''':
*'''/calc_ctr_mass_diff''':
*'''/treated_surf''':
*'''/match_cut''':
*'''/match_cut_adapt''':

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====Miscellaneous Functions====
*'''/align_z''':
*'''/dcl''':
*'''/flip_aim''':
*'''/growback_to_orig''':
*'''/turn3d''':
*'''/turn2d''':
*'''/upat_filldb''': Fill special Upat DB for patient (radius/tibia) evaluation
*'''/xray''':

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====Obsolete, Experimental and Duplicate Functions====
*'''/curv_tri''':
*'''/cut2D_shape_ow''':
*'''/join_uncompress''':
*'''/mil_param''':
*'''/milv1_param''':
*'''/gauss_seg''': duplicate of /seg_gauss
*'''/from_aim_to_isq''': The function toisq_from_aim will also convert an aim to an isq
*'''/local_threshold''':
*'''/edge_canny''':
*'''/sobel_grad''':
*'''/hysteresis_thresholg''':

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====Functions only available in iplfe====
*'''/register''': Registers two aim files and output a transformation matrix of the transformation to moving input 2 into the space of input 1. Gobjs can be input (registration is more successful with gobjs). Orientation search can be done with masscenter, and/or moment of inertia (MoI), or degree intervals.
*'''/transform''': Transforms an aim file using a transformation matrix (a text file of the matrix can be input). Interpolation options are nearest neighbor, linear, and cubic interpolation. The inverse of the transform provided can be done by setting Tmat_invert to true.
*'''/fe_solveD''': A number of finite element functions are available in iplfe, not all are listed here

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=Results=

==Images and Animations==
Refer to [[Scanco_User_Instructions#.C2.B5CT_Ray|'''µCT Ray''']] for detailed instructions.

===[[#Change_the_View|Change View]]===
===[[#Change_the_Colours|Change Object Colors]]===
===[[#Cutplane_and_Subdim|Show a Section-View of an Object]]===

===Save a Screetshot Image===
#Open XV from a dec terminal on a workstation by typing <code>$ xv</code>.
#Open and frame the image, program etc. that you would like to save an image of.
#In XV, click GRAB. You can either autograb the entire screen after a delay or manually grab a desired area.
#After grabbing the desired section, click Save in XV.

===[[#Save_the_Image|Save Image]]===
===[[#Save_for_Animation|Save Frames for an Animation]]===

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===Convert AIM to TIF series===

Use the utility SEQ_TO_IMAGE located in the UT directory. A symbol has been set up to run this called TIF.

<pre>
$ mcr ut:seq_to_image
Program: seq_to_image V1.1b
Input-File []: WISDOM_L_R05.AIM
File Format [TIF]:
Default TIF Names: WISDOM_L_R05_xxxx.TIF

Output-File [WISDOM_L_R05]:
!> Reading AimVersion020
Start Slice [0]:
End Slice [179]: 5
Number of images thereof (count) [6]:
Scale Factor (Integer) [1]:
global_pos (1=true, 0=false) [0]:
Max value to norm to 255 [32767]:
Slice: 0
Slice: 1
Slice: 2
Slice: 3
Slice: 4
Slice: 5
$ dir wisdom*

Directory DISK1:[MICROCT.SCRATCH]

WISDOM_L_R05.AIM;1 WISDOM_L_R05_0000.TIF;1 WISDOM_L_R05_0001.TIF;1
WISDOM_L_R05_0002.TIF;1 WISDOM_L_R05_0003.TIF;1
WISDOM_L_R05_0004.TIF;1 WISDOM_L_R05_0005.TIF;1

Total of 7 files.
$
</pre>

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===Generate TIF (or others) from 3D rendered volume===

This replaces uct_movie that operated on the alpha systems. UCT_3D can be called in batch mode.

A pdf describing this tool is located here: [[Media:UCT_RAY V4.0-1.pdf]]

To interactively declare the desired settings:
<pre>
$ uct_3d_batch
?CT RAY_BATCH V4.0-1

UCT_R: Application initialized
Filename []:
Print-Filename [SYS$SCRATCH:TEMP_3D.PS]:
Ambient (0.0..1.0) [0.200]:
Shadows (0/1) [1]:
Size (1..1024) [1024]:
Elevation (-90..90) [30]:
Rotation (-180..180) [35]:
Copies (0..9) [1]:

</pre>

To apply a saved set of settings, a setup-file can be created by running uct_3d in interactive mode. Select "Presets" from the toolbar and save the settings you desire (e.g. elevation 90, rotation 0).

<pre>
$ uct_3d_batch setup-file [data-file printfile]

Examples:

$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.ps
$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.tif

</pre>

To automatically generate tifs for many files, a script was created to replace PRINT_3D.COM
The script is currently stored in the xtremect2 com directory.

<pre>
@COM:PRINT_REG_TIF.COM

Generates a 3D image from a segmented file.

The outputs include:
- two 3D renderings (TIF)

Use full pathnames for the segmented AIM.

P1 - Segmented AIM

Usage:
@COM:PRINT_REG_TIF.COM DISK2:[MICROCT.DATA.00000379.00001376]C0001234_SEG.AIM
</pre>

This script can be modified to use a custom preset file.

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===Make an Animation===

To calculate an Animation, two (separate) tools of the 3D program are used: the set-up of start and end point of the Animation, and the 'Auto-Print' tool that automatically creates the TIF files for every rendered image.

This is a 'step by step' guide to create an animation using TIFF files:
:* Open your sample in the 3D program.
:* Now, open 'options','Animation'
:* Render your Image the way you want your animation to start. e.g. observer rotation -179 degrees. You may interrupt if you want. If you are satisfied with all the settings (rotation, elevation, transparency, colors etc.) the Click on 'Get Settings A'
:* Then, adjust all the settings for the endpoint of your animation (with the mouse or the sliders) e.g. observer rotation +179, and start the rendering. If satisfied, click 'Get settings B'

Note: To test, put # of views to 5 or 10... You can also interrupt the build-ups for faster viewing.
:* Click the START button again, wait till the build-up of the 3D image is finished.
:* DO NOT HIT 'START CALCULATION' YET!
:* First, you also need to set-up the 'Auto-Print' mode:
:* Go to the 'Print' menu (file --> print), choose print to TIF and to File and enter THE BEGINNING OF A FILENAME, e.g. sys$scratch:test_ (the program will append 0000.TIF, 0001.TIF etc afterwards) Or enter (possibly with middle-mouse-click): "DK0:[MICROCT.DATA.00001234.00003456]ANIMATION_" to have the result go to the measurement directory.
:* Click on the 'Auto-Print' box. Then 'ok'
:* Adjust the number of views (e.g. 200), then click on 'Start Calculation', and it will render. This may well take a long time.
:* Take those TIFF files to your PC, and combine the sequences in the program that you are using to convert the TIFF files to AVI or MOV files (like Windows Movie Maker 2, or Quick Time Pro, or Adobe Premiere etc.)

Notes/Hints:
:* The order in the above list can also be reversed: You can first set up the 'Auto-Print', and then go into the 'Animation' menu, choose start and end settings, and hit 'Start Calculation'
:* The positions A and B can be any: e.g. with subdim, you can first take everything (A), then slide it back to nothing (B).
:* You can even slowly change the color of an object. Or slowly hiding objects: choose 'transparent' for object, but change from 0.0 (A) to 1.0 (B)
:* If you want to create a movie with different sections, e.g. first rotate around, then slowly make bone transparent, then cut in: Do this in multiple sections with the 3D program, e.g. first create Auto-Print files 'rotation_0000 to rotation_0200', then 'transp_0000 to transp_0050', and then 'cut_0000 to cut_0100'. Make sure ALL the settings from the last view of the previous section match those of the first view of the next section so you get smoot transitions.
:* The 'Auto-Print' box is also usable without the 'Animation' Menu: Activate it, Like above, with sys$scratch:test_ only the beginning of filename. 'ok' Then, whenever a 3D image is completely built-up (so when you are happy with a view and you do not interrupt the build-up), automatically a TIF file is generated, numbered sequentially.

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===Combine two volumes to create transparent image===

First create your two start "seg.aim" images
Start by running either the normal eval, or $ voi to get one _seg.aim file of one region

Rename it to a better name in the session manager, e.g. c0001234_all.aim

Then either by choosing different contours, or a different threshold, start the $ voi or the normal evaluation again, which will create another _seg.aim file.

Load them in the 3D viewer ('all files') to check that they look like expected.

Now we will go into IPL and concatenate those two volumes.

<pre>
$ ipl
/read all xx_all.aim
/read trab xx_seg.aim
/transparent
-input_solid trab
-input_transp all
-output out
</pre>

Note: the solid volume is OVERWRITING the transparent input volume, so usually, it
is the smaller (inner) of the two.

<pre>
/write out xxx_transp.aim
/quit
</pre>

Then load the _transp.aim file in 3D, go to 3D program FAQ to see how to change transparency levels in the Display options there.

See IPL FAQ or 3D program FAQ if you need help with these parts.

Step by Step Example: Showing your chosen trab VOI within whole bone
:* $ voi, enter threshold in ipl_voi.com, start 3d eval WITHOUT contours
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_all.aim
:* Start up normal eval program, draw trabecular contours, check threshold in ipl_fixed_batch_v4.com, start 3D eval.
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished

Step by Step Example: Showing high-dense volume surronded by lower density volume

:* Start normal 3D eval with HIGH threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_high.aim
:* If wished: read out 3d result database with $ uct_list
:* Start normal 3D eval with LOW threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished

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==Image Tours==
===XtremeCT Image Tours===

===MicroCT Image Tours===
*Refer to [[Media:Tours_image_gallery.pdf|'''MicroCT Image Gallery''']] with its [[Media:Tours_image_notes.pdf|'''Image Notes''']].
*Refer to [https://youtu.be/tT3dz4VrwfE '''MicroCT Image Tour YouTube Video''']
*Hover over a thumbnail and click on its overlaid description to see the animated GIF or a larger version of the image.

<gallery mode="packed-hover" heights=220px caption="Micro-CT Scans">
Image:MOUSE_SKELETON_PIC01.jpg|[[Media:MOUSE_SKELETON_360.gif|Mouse (38µm)]]
Image:Segmented_Mouse_Femur.jpg|[[Media:Segmented_Mouse_Femur.jpg|Mouse Femur showing Cortical and Trabecular Bone (10µm)]]
Image:LIZARD_WHOLE_VIEW_P1_0044.jpg|[[Media:LIZARD_SKELETON_360.gif|Lizard (88µm)]]
Image:LIZARD_SKULL.jpg|[[Media:LIZARD_SKULL.jpg|Lizard Skull showing Thickness Distribution (25µm)]]
Image:DUCK_BEAK_PIC01.jpg|[[Media:DUCK_BEAK_360.gif|Duck Beak (60µm) Courtesy of Dr. A. Iwaniuk]]
Image:Human_Tooth.jpg|[[Media:Human_Tooth.jpg|Human Tooth (30µm) Courtesy of Dr. C. Stewart]]
Image:PINECONE_TH_PIC05.jpg|[[Media:PINECONE_360.gif|Pinecone showing Thickness Distribution (69µm)]]
Image:SHELL01_SEG_PIC01.jpg|[[Media:SEASHELL_360.gif|Seashell (50µm)]]
Image:TURTLE_SKULL.jpg|[[Media:TURTLE_SKULL_360.gif|Turtle Skull (60µm)]]
Image:SAND_DOLLAR.jpg|[[Media:SAND_DOLLAR.jpg|Sand Dollar (37µm)]]
Image:MOUSE_L1-L6.jpg|[[Media:MOUSE_SPINE_SEG_360.gif|Mouse Spine showing Cortical and Trabecular Bone (10µm)]]
Image:MOLAR.jpg|[[Media:MOLAR.gif|Human Tooth (60µm) Courtesy of Dr. C. Stewart]]
</gallery>

<gallery mode="packed-hover" heights=220px caption="Contrast-Enhanced Micro-CT Scans">
Image:Contrast_mouse_head_XZ_thumb.jpg|[[Media:Contrast mouse head XZ.jpg|Mouse Head (60µm, XZ plane)]]
Image:Contrast_mouse_head_XY_thumb.jpg|[[Media:Contrast mouse head XY.jpg|Mouse Head (60µm, XY plane)]]
Image:Contrast_mouse_head_YZ_thumb.jpg|[[Media:Contrast mouse head YZ.jpg|Mouse Head (60µm, YZ plane)]]
</gallery>

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==Extract Results==
===Automatic Results===
Results are generally automatically extracted after each analysis to the UCT_RESULTS directory. 
The results files have the form of:
*UCT_LIST_*''PROJECT''*.TXT for XtremeCTs: e.g. result file UCT_LIST_KYLA.TXT for the following project.
*UCT_LIST_3DLOG_*''PROJECT''*.TXT for microCTs: e.g. result file UCT_LIST_3DLOG_KYLA.TXT for the following project.
*where ''PROJECT'' is specified in the evaluation tool script setup.
[[File:Script_modify_basic_project.jpg|500px]]

Open the result file and copy and paste it into Excel, e.g.
<pre>
$ dir uct_results:*kyla*
$ eve uct_results:UCT_LIST_3DLOG_KYLA.TXT
</pre>

Or transfer the file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].
*microct/vivact account UCT_RESULTS location: ADISK1:[MICROCT.RESULTS]
*invivo/invitro account UCT_RESULTS location: ADISK1:[BONELAB.RESULTS]

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===Extract Results from XtremeCT Database using UPAT_LIST===
*Run <code>$ UPAT_LIST</code> to take in a range of samples and extract the standard patient results, which may include scans from other projects.

*Run <code>$ @com:EXTRACT_UPAT_LIST</code> to take in a list of sample numbers and extract the standard patient results with follow-ups and append them to a result file.
<pre>
$@COM:EXTRACT_UPAT_LIST P1 P2 P3 P4 P5

P1 = Sample List
P2 = Site (RR, RL, TR, TL, R*, T*, *)
P3 = Number of Follow-Ups (max 19)
P4 = Results Output File
P5 = Eval type (4=XT1, 5=Trab, 6=Cort)
</pre>

An example to extract all sites:
<pre>
$ @com:EXTRACT_UPAT_LIST mysamples.txt * 19 myresults.txt
</pre>

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===Extracts Results from microCT Database using UCT_LIST===
*Run <code>$ UCT_LIST</code> to take in a range of samples and extract the results, by specifying the first and last measurement numbers for the range they want to extract
*This may include scans results from other projects, but you can delete unrelated results that are extracted afterwards.
*The program will output a tab-delimited text file, which can be read into Excel or other analysis programs.
<pre>
$ uct_list

UCT_LIST.EXE Version V5.22
Template-File [UCT_3D_LIST_SHEET]: !Press Enter to use the default results sheet.
Output-File [SYS$SCRATCH:UCT_EVAL.TXT]: !Enter a filename, e.g., BUIE_RESULTS.TXT.
Density units (0 default) [0]: !Press Enter.
From Meas. # [0]: !Enter the first measurement number, e.g., 100.
To Meas. # [0]: !Enter the last measurement number, e.g., 101.

Processing measurement 100
Processing measurement 101
</pre>
*An example output file: [[Media:Buie_results.xlsx|Buie_results.txt]]
*Or Run <code>$ @com:extract_results.com</code>

*References of results template:
:*Formatted [[Media:Results_template_uct_list.xlsx|Excel template 1]] for results extracted with uct_list.
:*Formatted [[Media:Results_template_extract_results.xlsx|Excel template 2]] for results extracted with extract_results.com.
:*In vivo spreadsheet template for UCT data: [[Media:In vivo results template.xls| In vivo results template.xls]]
:*In vitro spreadsheet template for UCT data: [[Media:In vitro results template.xls| In vitro results template.xls]]

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===Understand Morphological Parameters===
*Refer to [[Media:Reference_Document_-_Parameters_from_upat_list.doc|'''Explanation of UPAT_LIST Output''']] to understand the result file.
*Refer to [[Media:Reference_Document_-_Parameters_from_uct_list.doc|'''Explanation of UCT_LIST Output''']] to understand the result file.

All values are determined on a slice-by-slice basis, then averaged over all the slices to calculate morphological results:

:*BV/TV -> Sum all raw data withing the GOBJ and divide by 1200 mg/cc HA
:*Tb.N -> As per standard method
:*Tb.Th and Tb.Sp -> Derived from BV/TV and Tb.N above (semi-derived method)
:*D100 -> Average density of entire cross section
:*DTrab -> Average density of trabecular region
:*Ct.Th -> Cortical area (from seg) divided by circumference (from GOBJ)
:*GOBJ circumference can be determined with /gobj_circum.

<pre>
BV/TV -> VOX-BV/TV
BS/BV -> TRI-BS/BV
Tb.Th -> DT-Tb.Th
Tb.Sp -> DT-Tb.Sp
Tb.N -> DT-Tb.N
ConnD -> Conn-Dens
SMI -> TRI-SMI
DA -> TRI-DA
</pre>

Usually I'd use the names on the left for the plots, but these correspond to the names on the right of the arrow in the Scanco output files.

Note, if you use the TRI-Tb.Th rather than the DT-Tb.Th*, then you are using the derived (plate-model) morphological parameters. These are less accurate than the direct parameters. They are calculated by triangulating the surface (marching cubes) to get BS, and then calculate thickness
Th = 2 * BV / BS, etc...

'''Mean Values'''
<pre>
mean 1: mean of bone AND marrow --> 'apparent density'
mean 2: mean of what was considered bone only (i.e. what was segmented)
'bone tissue density'
</pre>

Note, there are five possible categories for the mean Mu. They are assigned by setting <code>-region_number</code> in the <code>/voxgobj_scanco_param</code> function. The region number is zero-based, so setting it to 0 corresponds to mean1, 1 corresponds to mean2, etc. So, although mean1 and mean2 are typically apparent and tissue density, respectively, this can be adjusted in the IPL script by setting the region_number. Mean3 might be useful for storing cortical bone density, for example.

<pre>
/voxgobj_scanco_param Voxel or Mu Scanco Parameters
-input Gray scale or Segmented AIM object
-gobj_filename GOBJ: input or Automatic
-peel_iter Peel Iterations or Automatic
-region_number Region number for Mu only

! -region_number 0 ! mean1
! -region_number 1 ! mean2
! -region_number 2 ! mean3
! -region_number 3 ! mean4
! -region_number 4 ! mean5
</pre>

What you should also know: because of partial voluming effects, for Mean2, we are DISCARDING the 2 surface voxels of EVERY trabeculae - thus, to get meaningful Mean2, you have to do your scan with the chosen resolution high enough, such that the mean trabeculae is depicted by at the very least 5 pixels, better actually more than 6 pixels thickness. (You can do this check at the end in the XLS sheet: divide DT-Tb.Th* by el-size-mm.x, and you need to get numbers bigger than 6 or 7 or 10 or so.

For parameters such as ConnD where no GOBJ is taken as input, the TV is determined from the processing log stored in an AIM that has previously had a GOBJ applied (stored as the relative region of interest; ROI). So, it is important to apply a GOBJ prior to ConnD measurements to ensure the TV is correctly determined (and not taken as the whole AIM).

'''Trabecular Number (TbN)'''
The epsilon values can be set to account for differences in scanner resolution, and hence 'surface roughness' for individual pixel suppression.

For microct, for good resolution: if there is a pixel 'sticking out' from a flat surface we do not assign that pixel with a thickness value of 1, but we let it 'get eaten' by the bigger sphere that sits in the center of the trabeculae. So this is nice for 'noise' (0.9/1.5).

For XT resolution, where also many 'good' features are just one or two pixels wide, I liked a lower epsilon value better (0.9/0.5).

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==Generate Report==
===Generate Standard Patient Report===
The standard patient reports are extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.
*The number of follow-ups specified will determine if a baseline or follow-up report is generated.

<pre>
$ upat_list

Mode (1 = list, 2 = print, 3 = show) [1]: 2
Patient # (1-3162) [1]: !input the patient's sample number
Site (found RR) [RR]: !RR or RL or TR or TL
Maximum # of follow-ups (0-19) [19]: !0 for baseline report, press return for follow-ups
Template file [default]: !press return to use the default template
Output filename [SYS$SCRATCH:UPAT...]: !default output file (with sample number and the site) goes to sys$scratch
# copies [1]: !the number of printouts, 0 if no printout is desired
</pre>

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===Generate CaMos Patient Report===
The [http://www.camos.org '''CaMos'''] patient report is extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.
*To ensure the report is generated using the appropriate normative results, the patient's sample remarks should be in the form "F-RHRF" where the first character indicates the sex of the individual, otherwise the patient is assumed to be male.
<pre>
$ upat_list

Mode (1 = list, 2 = print, 3 = show) [1]: 2
Patient # (1-3162) [1]: !input the patient's sample number
Site (found RR) [RR]: !RR or RL or TR or TL
Maximum # of follow-ups (0-19) [19]: !0 - 1st scan, 1 - 2nd scan, 2 - 3rd scan...press return for latest scan report
Template file [default]: COM:UPAT_EVAL_CAMOS.PS
Output filename [SYS$SCRATCH:UPAT...]: !default output file (with sample number and the site) goes to sys$scratch
# copies [1]: !the number of printouts, 0 if no printout is desired
</pre>

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===Print out report sheets===

The postscript report sheets can be generated and printed on the command line. For the XtremeCT system, use <code>UPAT_PRINT_LIST.EXE</code> which can be run (using the symbol):
<pre>
$ UPAT_LIST
</pre>

Look in the UU: directory to see options for the template files (UPAT*.TXT) and the postscript output files (*.PS).
:* UU:UPAT_EVAL_FUP05_SCUSA.PS
:* UU:UPAT_EVAL_BASELINE_SCUSA.PS

For other options, see the upat_list help:
<pre>
$ UPAT_LIST -h
</pre>

One particular option that may be useful, is to turn off slice matching:
<pre>
$ UPAT_LIST -nomatch
</pre>

Here is an example of producing a report for the third measurement of TL for a patient, where we want only the most recent results in the report, without slice matching:
<pre>
$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=UU:UPAT_EVAL_BASELINE_SCUSA.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_0fu.ps

$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=DISK1:[MICROCT.COMMANDS]UPAT_EVAL_CAMOS.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_camos.ps
</pre>
The first command line generates a normal Scanco report, and the second command line generates a CAMOS report.

For reports from non-patient measurements (i.e., the vivaCT system or non-patient scans on the XtremeCT), the template files are different (UCT*.TXT) and the postscript outputs are different (UCT*.PS). To print a result sheet use:
<pre>
$ RUN UM:UCT_RAY_BATCH.EXE
</pre>

If you want to create a postscript file, but not send it to the printer, set the number of copies to zero (interactive). Then, find the postscript file from the <code>SYS$SCRATCH</code> directory and transfer it to your PC. You must transfer the postscript file in ASCII mode. The files are typically called TEMP_3D.PS or UPAT_PAT_62_RR.PS. A program such as Adobe Photoshop can convert the postscript file to a different format.

See also our custom scripts:
<pre>
$ @COM:PRINT_2D.COM
$ @COM:PRINT_3D.COM
</pre>

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===Convert PS to PDF report===
The report can be converted to PDF using <code>$ @SCOM:PS_TO_PDF</code> by:

#Follow the instructions above for creating a report, using "2" to print and "0" for the number of copies. (Use the default template file and output filename.)
#Locate the file on the sys$scratch by <code>$ cd sys$scratch</code> and <code>$ dir</code>
#*The file should read "UPAT_PAT_[sample #]_[site].PS;1" (e.g. UPAT_PAT_0010_RL.PS;1)
#*You can view this file on the monitor by typing <code>$ gs UPAT_PAT_0010_RL.PS;1</code>
#Convert the postscript to PDF by typing in the command followed by the .PS file to convert <pre>$ @SCOM:PS_TO_PDF UPAT_PAT_0010_RL.PS;1</pre>
#The PDF file can then be located again in the sys$scratch directory.

You can transfer the result file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].

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=Data Management=
==Trainee’s Data Responsibility==
#Perform '''Contouring and Data Analysis''' on Data Disk ideally 1-2 months after scanning.
#After finished onsite analysis, [[Scanco_User_Instructions#Move_data_from_Data_Disk_to_Project_Disk|'''use Scripts''']] to '''Copy and Rename''' image data (no RSQ, no ISQ, only AIM, SEG.AIM, GOBJ, COM, LOG, PDF, PS ect) to your specific project folder on Project Disk.
#After finished copying all your image data to Project Disk, '''Notify''' lab personal to delete your data on Data Disk by providing a [[Media:Data_Scans_to_delete_template.xlsx|'''Data Scans to Delete Template''']].
#'''Notify''' lab personal to backup your project folder on Project Disk to Winston server on a monthly basis.
#*Only the two most recent backups (A or B version) are kept for each project on Winston:
#:Backup version "_A" for odd months (Jan, Mar, May, Jul, Sep, Nov), e.g. YZHU_A_OTHER_2017-01-12.SAV
#:Backup version "_B" for even months (Feb, Apr, Jun, Aug, Oct, Dec), e.g. YZHU_B_OTHER_2020-04-08.SAV
#When a project is finished, '''Notify''' lab personal to archive your project to HOG server.
#When a trainee is about leaving, '''Notify''' Steve and lab personal to determine either to backup or to archive your project.

[[File:BoneLabDataManagement.JPG|800px]]

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==Move data from Data Disk to Project Disk==
This is generally done after onsite analysis (i.e. autocontour, cortical porosity, FE etc.) is done. Examples of this can be found in DISK3:[MICROCT.PROJECTS.GRACE.COM] 
1. Go to the specific project's .COM directory, for example:
<pre>
$ cd DISK3:[MICROCT.PROJECTS.GRACE.COM]
</pre>
2. Create a script that will move all IMA (i.e. .AIM, .GOBJ, _SEG.AIM, _CORTEX.AIM, _LHTH_DTN.AIM) to the .MODELS directory for the project. You will use the rename_to_models.com script to generate this script. To move Grace data for example, with a measurement range of 2684 to 2685, you would use:
$ @com:rename_to_models.com meas#1:meas#2 DESTINATION DIR
$ @com:rename_to_models.com 2684:2685 DISK3:[MICROCT.PROJECTS.GRACE.MODELS]

3.This will create a file named RENAME_ALL.COM to the project's COM directory. You will now have to open the RENAME_ALL.COM file and add site + other details into the script. Following the same example as above, it should look like this:
$ eve RENAME_ALL.COM ! to open the file using a text editor
$ COPY DISK2:[MICROCT.DATA.00000700.00002684]C0002040.AIM -
DISK3:[MICROCT.PROJECTS.GRACE.MODELS]GRACE_020_00MTH_RR.AIM
$! DELETE/CONFIRM DISK2:[MICROCT.DATA.00000700.00002684]C0002040.AIM;1
$ COPY DISK2:[MICROCT.DATA.00000700.00002685]C0002041.AIM -
DISK3:[MICROCT.PROJECTS.GRACE.MODELS]GRACE_020_00MTH_RL.AIM
$! DELETE/CONFIRM DISK2:[MICROCT.DATA.00000700.00002685]C0002041.AIM;1
4. You also need to copy the rest of the standard patient image files (i.e. .AIM, .GOBJ, _SEG.AIM, _CORTEX.AIM, _LHTH_DTN.AIM) which is easily done by copying the above lines and replacing .AIM with the respective files.

[[Image:Bones2.jpg|20px]] Warning: Always use the same account consistently to create all files and subfolders within their Project folder, otherwise you way miss data when doing Project Backup or Archive!

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=Import and Export=
==Import Foreign Data to Scanco System==
Only RSQ and ISQ files can be imported into the database, however it is possible to convert other types of data into ISQ files (i.e., stacks of BMPs into ISQ).

PART 1:

After transfering your data to the VMS system (use the data disk <code>disk2</code>, NOT the user disk <code>disk1</code>), use the IPL commands <code>/import_freeformat</code> or <code>/read_aim function</code> to import your data for conversion to an ISQ.

For AIM files, navigate to the location of the AIM file. Then open IPL by:

<pre>$ IPL</pre>

In IPL, read in the .AIM file:

<pre>ipl> read in [.AIM file]</pre>

IPL will do the following:

<pre>ipl> read in STUDYID_001_RL.AIM

/read
-name in
-filename STUDYID_001_RL.AIM
!> Reading AimVersion020

!% /read completed: CPU: 00:01.03 ELAP: 00:01.55 </pre>

For DICOM files, start IPL and run the <code>/dicom</code> function to import. For DICOM, if your object is a single 3D file (-multifile false) or many many individual slice files (-multifile true, and give beginning of filenames, and –extension).

There may be requests by IPL to convert your data to <code>signed short</code> or <code>signed char</code> from other data types. Obey these requests and do it by running the <code>/convert_unsigned</code> function.

Then, write the ISQ file using either the "toisq" or "from_aim" commands:
<pre>ipl> toisq
-aim_name [in] >[leave blank as you defined “in” as .AIM file.]
-isq_filename [default_file_name] > C0001234.ISQ [Create a 1 letter and 7 digit file name]
-square_flag [true] > false
-original_position [true] > false

ipl>toisq_from_aim
-aim_name in
-isq_filename C0001234.ISQ
-square_flag false
-original_position false

!% Dimensions of ISQ file: dim.x dim.y dim.z 558 638 168
Write_ctdata_headerext_new: no mhext found. Init mhext.
Extended header successfully added of type 8

!% Writing ISQ slice 167 (Done: 168/168)

!% /toisq_from_aim completed: CPU: 00:05.12 ELAP: 00:10.47 </pre>

Type ipl>help toisq [or ipl>help from_aim] to see details of the command.

This writes the ISQ file. Make note of the ISQ file name.

Remember, the ISQ name must be 8 characters long (1 character followed by seven digits)!!! The letters and numbers can be chosen freely.

Exit IPL:

<pre>ipl>quit</pre>

PART 2:

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

The measurement can be verified by looking at the Header Information. (File, Header)

If you only needed to view the ISQ, delete the file when finished by:

<pre>$ dir/sincet
$del [.ISQ file]</pre>

PART 3:

To use the ISQ further (e.g. for evaluations, contouring, etc.) create a sample in the database and write down the sample and measurement number. Then, run:

<pre>$ run um:uct_import ! will import both RSQ and ISQ (modify patient index, etc)</pre>

and give the new ISQ file, the new sample-number and check that the feedback is correct (i.e., that the name from the database is matching the name from the ISQ file header). If the Patient Name in the ISQ header doesn't match the measurement database Patient Name (very likely), then upon importing the RSQ/ISQ the headers will be updated to the new Patient Name.

Operator and controlfile can be left 0 if you want. However, controlfile should be set appropriately if the data being imported is for the XtremeCT patient database.

If you are also importing the RSQ, put it in the same directory as the ISQ.

Then it changes the sample and measurement number in the ISQ file, makes the correct directory on <code>DK0</code>, and gives you the line on the screen of how to rename the file to the correct, new directory. Take this line and use it on the command line. Done!

You can now use the normal <code>uct_evaluation</code> program with this file. If the control file was set properly, then the evaluation will be done correctly (i.e., for XtremeCT patient measurements).

Note: Any AIMs created from the original ISQ should be recreated. So, it is important that you re-evaluate your newly imported ISQ. It is OK to move the GOBJ from the old directory to the same directly as the newly imported ISQ (it does not have a 'registry' in the database).

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==Import DICOM to Scanco System==
#Load MRI's or CT's DICOM data in Osirix
#Export from Osirix
#*Click export button in top left in osirix.
#*Select "flat" and "decompress all DICOM files"
#Copy files to correct folder in scanco system
#*Use Fillezilla or FTP (make sure it's set to binary mode)
#Use IPL to convert dicom to aim or isq

<pre>
/dicom_to_aim
-aim_name in
-dicom_filename IM-0001-0001.DCM ! Note - choose the first filename of the series
-multifiles true

/convert_unsigned
-input in
-shift_flag false
-divide_by_2 true

/write_v020
-name in
-filename PREOA_023_L_MR.aim
-compress_type bin
-version_020 true

/toisq_from_aim
-aim_name in
-isq_filename MROA023L.isq
-square_flag true
-original_position true''

</pre>

5. Delete dicoms

<pre>
/del *.dcm;1
</pre>

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==Import Xradia *.bin to Scanco System==
Xradia scanner exports a *.bin image that is:

- 16-bit unsigned ! This is "short" (8-bit is char - we don't want this for a grey-scale image)
- 2 bytes per voxel
- little endian notation

To upload this binary image to Scanco database, the steps are as follows:

#Ftp the *.bin to Scanco system using binary transfer (not ascii)
#Convert it to an AIM or ISQ in IPL

$ipl

/import_freeformat
-internal_name in
-file_name BMLPL_006.BIN
-sample_name BMLPL_006
-data_offset 0
-data_dim 1000 1024 1016 !dimensions from header file
-data_el_size 0.013 0.013 0.013 !voxel size from header file
-bytes_per_voxel 2
-data_endian little_endian
-data_type integer
-signed_type unsigned !correct
-multifiles false

/convert_unsigned
-input in
-shift_flag true !shift_flag = TRUE will produce an ISQ/AIM with negative values which may not be visualized properly using uct_evaluation, but keeps the original image resolution.
-divide_by_2 false !divide_by_2 = TRUE will down grade image resolution, but all positive values in an ISQ/AIM will be visualized properly using uct_evaluation.

/write_v020
-name in
-filename test.aim
-compress_type bin
-version_020 true

/from_aim_to_isq
-aim_name in
-isq_filename bmlpl006.isq !ISQ name requires 8 characters
-square_flag true
-original_position true

quit

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

Alternatively the image can be converted to a 16-bit signed in ImageJ (and cropped) before importing to ipl. It then becomes:

- 16-bit signed
- 2 bytes per voxel
- big endian notation

It can then be imported into ipl without the need to run <code>/convert_unsigned</code>.

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==Get Your Files==
===MAC/Linux Options===
====Fetch====
#Download and install [http://fetchsoftworks.com/fetch/|'''Fetch''']
#*This program is free for university staff and students.
#Fill out [http://fetchsoftworks.com/fetch/free|'''a form'''].

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====FTP from Terminal====
#Open a terminal
#*MAC: open the "Applications" folder, choose "Utilities", then "Terminal".
#Navigate to where you want to transfer the files to.
#Connect to the micro-CT ftp server using the ftp command in the terminal:
#*Login with the micro-CT user account and password.
#Navigate to the directory of interest on the micro-CT system.
#*Logicals such as "ur" can be used as short cuts. Whole directory names must be used.
#Set a filename mapping convention to remove OpenVMS version numbers.
#*The command <code>ftp> nmap $1;$2 $1</code> sets anything before the version number to parameter $1 and anything after the version number to $2. The file output will be set to $1, therefore the version number will not be kept.
#Set the file transfer mode.
#*[[File:Important.JPG|20px]] If you transfer an .AIM file in ascii mode, you will receive a "mesh generation" errors and "material ID out of range" message.
#Transfer your files.
#*Option: Turn off prompt so does not ask you whether or not to transfer each file.
#*If you do not turn off the prompt prior to transferring the files, press "a" (for all) to transfer all files at once.
#Exit FTP.

<pre>
$ FTP 136.159.74.231 !Connect to an FTP Server. Need to input user name and password.
$ FTP emily.ucalgary.ca !Connect to an FTP Server. Need to input user name and password.
$ FTP microct@emily.ucalgary.ca !Connect to an FTP Server. Need to input password.

FTP> cd ur !Navigate to the directory containing the target files.
FTP> cd sys$scratch !Navigate to the directory containing the target files.

FTP> nmap $1;$2 $1 !Set a filename mapping convention to remove OpenVMS version numbers.

FTP> bin !Set transfer mode to binary (.aim, .gobj, .isq, and most image file types).
FTP> ascii !Set transfer mode to ascii (.txt, .log, .com, .ps, .pdf and all other files in general).

FTP> put test.aim !Put the file
FTP> get test.aim !Get the file

FTP> prompt !Interactive mode off before transferring multiple files without having to be prompted.
FTP> mput *.aim !Put all files with the .aim extension on the FTP server (mput = multiple put).
FTP> mget *.aim !Get all files with the .aim extension from the FTP server (mget = multiple get).
FTP> mget *.aim; !Transfer the latest version of all aim files in a directory.

FTP> quit !Disconnect from the FTP Server.
</pre>

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===Windows Options===
====Scanco Medical µCT FTP====
#Downlod '''Scanco Medical MicroCT FTP 3.4''' from BoydDrive:\\04 - Resources\04 - Software\Scanco Medical MicroCT FTP 3.4\
#Install the software using the default parameters.
#Click on FTP Connection and input the host to connect to, the username, password.
#Give this profile a name.
#:[[File:Microct_FTP_pic01.jpg|600px]]
#Click on the options tab to set the locations to connect to (e.g., project disk, scratch) and the location on your computer to transfer files to.
#:[[File:Microct_FTP_pic02.jpg|600px]]
#Go back to FTP Connection and press the Connect button.
#*If you are connecting from off campus to the XtremeCT you will need to use the VPN to gain access through the firewall.
#Use the left tree to navigate folders.
#*Use the file filter to search for specific file types or file names (bottom left).
#Select files to download and press the Download Selected Files button (bottom right).
#:[[File:Microct_FTP_pic03.jpg|600px]]
#Press the Exit button to disconnect.

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====Filezilla====
#Download '''Filezilla 2.2.32''' from BoydDrive:\\04 - Resources\04 - Software\Filezilla 2.2.32\
#*This version of Filezilla will remove the OpenVMS version number from files, the new version will not!
#*The left side of the program shows your computer, the right side will show the micro-CT system once you have connected.
#:[[File:Filezilla_pic01.jpg|500px]]
#On the top menu, choose "File", then "Site Manager".
#Create a "New Site" for all the directories that you frequently access.
#*Give the site a meaningful name.
#*For the host, you may connect to "emily.ucalgary.ca" or "sceval.ucalgary.ca".
#*For the logon type choose "Normal" and input the micro-CT user name and password.
#:[[File:Filezilla_pic02.jpg|400px]]
#Click on the "Advanced..." button to set the default remote directory (i.e., on the micro-CT system).
#Set the default local directory if there is a specific location you plan to always transfer files to.
#Setup any additional sites you want then press "Save and Exit".
#:[[File:Filezilla_pic03.jpg|300px]]
#To connect to a session, hold the left mouse button down over the arrow next to the site manager button (computer icon under "File") to bring up your list of sites. Highlight the site of interest then release the mouse button to connect.
#Once connected, you can drag and drop files from the remote site to your local computer.

;*Common FTP locations
{| class="wikitable"
|-
! scope="col"| Account
! scope="col"| Location
! scope="col"| Path
|-
| microct / vivact || Data Disk ||DISK2:[MICROCT.DATA]
|-
| microct / vivact || Projects Disk ||DISK3:[MICROCT.PROJECTS]
|-
| microct / vivact || Scratch Disk ||ADISK1:[MICROCT.SCRATCH]
|-
| invivo / invitro || Data Disk ||DISK4:[BONELAB.DATA]
|-
| invivo / invitro || Projects Disk ||DISK5:[BONELAB.PROJECTS]
|-
| invivo / invitro || Scratch Disk ||ADISK1:[BONELAB.SCRATCH]
|}

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=Remote Access=

== VPN Setup ==

Access to the OpenVMS workstations from campus does not require VPN setup; however, to access from off the campus requires establishing a VPN connection prior to connecting.

*The VPN server is: gpvpn2.ucalgary.ca

*The client needed for VPN connection is '''FortiClient SSL''' which is available through [https://ucalgary.service-now.com/it| UofC IT Service Request] "Order Something".

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== Setup for MAC/Linux ==

=== Terminal and XQuartz ===
You need following to access the MicroCT system remotely.
#'''Terminal''': an SSH client
#*Preinstalled in MAC/Linux.
#'''XQuartz''': an X server for X11 forwarding
#*X11 was previously distributed with Mac OSX but has since stopped.
#*Check if preinstalled in MAC: open the "Applications" folder, choose "Utilities", there should be a file called "XQuartz". No need to open.
#*If not preinstalled, download the most recent [https://www.xquartz.org/ '''XQuartz.dmg'''].
#*Once downloaded, double click the .dmg file to follow the instructions and install.
 
;SSH from terminal
#Open a terminal.
#*MAC: Open the "Applications" folder, choose "Utilities", then "Terminal".
#Type <pre>$ ssh xtremect2@emily.ucalgary.ca -Y</pre>
#*The -Y flag activates X11 forwarding.
#Or type <pre>$ ssh -Y -p22 -c 3des-cbc -o KexAlgorithms=+diffie-hellman-group1-sha1 -o HostKeyAlgorithms=+ssh-dss xt2recalib@emily.ucalgary.ca </pre>
#*Type <pre>$ alias xt2recalib='<ssh command above>'</pre> allows you to only type <pre>"$ xt2recalib"</pre> in the terminal from here on out to access the MicroCT system.
#You're good to go!

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== Setup for Windows ==
=== MobaXterm ===

There is only one program required to access MicroCT remotely: MobaXterm. It will act as both an SSH client and as an X server.

*Download [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Home Edition (Portable Edition)]
 
;Configure MobaXterm
*Run the .exe file after downloading MobaXterm.
:[[File:MobaXterm_init.PNG|500px]]

*Click on "Sessions" -> "User Sessions" and choose "SSH" in the top left of the "Session settings" window.
*Input your host info into the "Remote host" dialogue box such as "emily.ucalgary.ca", check on "Specify username" and input your username such as "xt2recalib" and ensure "X-11 Forwarding" is checked in "Advanced SSH Settings" tab, and click OK.
:[[File:MobaXterm_SSH.PNG|500px]]
 
;Start the session
*Launch the MobaXterm client and under "Sessions" -> "User session" you should have something titled "xt2recalib@emily.ucalgary.ca".
*Double click that session and you're good to go!
:[[File:MobaXterm_Session.PNG|500px]]

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=== PuTTY and Xming ===
There are two programs required:
#'''PuTTY''': an SSH client
#*Download [http://www.chiark.greenend.org.uk/~sgtatham/putty/ '''PuTTY'''] or from BoydDrive:\\04 - Resources\04 - Software\PuTTY.
#'''Xming''': an X server
#*Download [https://sourceforge.net/projects/xming/files/latest/download?source=files '''Xming 6.9.0.31''']
#*Download [https://sourceforge.net/projects/xming/files/Xming-fonts/7.5.0.93/Xming-fonts-7-5-0-93-setup.exe/download '''Xming Fonts''']
 
;Configure PuTTY
*Under categories, expand the "Connection" and "SSH" trees. Click on "X11" and check the "Enable X11forwarding" box.
:[[File:Putty1.png|400px]]
*Under categories, now choose "Sessions".
*Under host name, put in "emily.ucalgary.ca". Choose "SSH" for the connection type.
*Under Saved Sessions, give the session a name (e.g., Emily). Click the "Save" button.
:[[File:Putty2.png|400px]]
 
;Start the Session
*Launch the Xming program, nothing should open except the Xming icon on the task bar.
*Open PuTTY. Double-click on the saved session, which will open a DEC terminal.
*Any program that you run remotely will be displayed by Xming.

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==Remote Access FAQ==
=== MAC Open SSH Authentication Issue ===
You might get an error similar to the following especially after a recent OS update:
Unsupported KEX algorithm "+diffie-hellman-group1-sha1"
command-line line 0: Bad SSH2 KexAlgorithms '+diffie-hellman-group1-sha1
This is not Apple’s fault, it’s OpenSSH version 7. SHA1 is weak, so support for it has been removed. Which is fine, but VMS clients are probably using RSA/SHA1. So until they’re all updated (i.e. never!) we need to re-enable SHA1.

Open a terminal windows and execute the following:
sudo nano /etc/ssh/ssh_config
ENTER YOUR PASSWORD

Locate the line ‘# MACs hmac-md5,hmac-sha1,umac-64@openssh.com,hmac-ripemd160′ and remove the Hash/Pound sight from the beginning.

Locate the line ‘# Ciphers aes128-ctr,aes192-ctr,aes256-ctr,aes128-cbc,3des-cbc’ and remove the Hash/Pound sight from the beginning.

Then paste the following on the end;

HostkeyAlgorithms ssh-dss,ssh-rsa
KexAlgorithms +diffie-hellman-group1-sha1
There’s no reason to reboot, it should work straight away.
 

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=== SSH Speed Issues ===
 
If you notice that the remote display is quite slow, you may prefer to enter the 'manual' X display redirection after connecting with ssh. 
 
The steps to enter the 'manual' X display redirection are outlined in one of Scanco's FAQs found [http://www.scanco.ch/en/support/customer-login/faq-customers/faq-customers-general.html here]. 
Click the "Remote Graphical Access from your PC to the MicroCT" tab (5th tab) and scroll down to "SSH Speed Issue" for more information.

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=== MobaXterm Backspace Issue ===
If the Backspace/Delete key doesn't work on your MobaXterm

#Right-click on a session name on the left column and click "Edit session"
#:[[File:MobaXterm1.png|500px]]
#: 
#Under "SSH" page "Terminal settings" tab, toggle off "Backspace sends ^H" and "Save"
#:[[File:MobaXterm2.JPG|500px]]

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Scanco User Instructions

2021-05-07T18:48:06Z

Yingzhu: /* Import MRI/DICOM to Scanco System */

=OpenVMS Basics=
The micro-CT scanners in the lab are manufactured by [http://www.scanco.ch Scanco Medical] and most analyses are performed using their custom software. The micro-CT workstations run OpenVMS as its operating system and it is useful to learn some basic commands.

==OpenVMS Beginner's Reference==
OpenVMS (informally known as VMS) is a high-end computer server operating system with reliable, multitasking, real-time and batch processing. OpenVMS supports computer clustering via a LAN, enabling computers to share resources such as processors and disks to balance workload efficiently.

*[http://saf.bio.caltech.edu/vms_beginners_faq.html '''OpenVMS Beginner's FAQ''']

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==Session Manager==

The session manager automatically starts after a user logs in locally. For remote sessions, the session manager can be started with the command <code>$ vue </code>.

[[Image:SessionManager.jpg|600px]]

===Session===
Here you will find an option to "End Session", which you should do when you are finished using a workstation. You can click "Work in Progress..." when you have to leave in the middle of a session without logging out but showing a work in progress screen to other users to prevent interference.

===Views (directory shortcuts)===
The session manager is a graphical user interface that can be used to navigate directories (left side of session manager) and open files (right side of session manager). There are shortcuts to key directories under "Views". Single-click on a directory to list its subdirectories and files. Double-click on a file to open it.

===Commands and Utilities===
Under commands you will find tools such as copy, delete, and rename; however, it is much more practical to do these sorts of operations from a DEC terminal.

===Applications===
Under applications you can launch various applications including:
*DECterm: opens a DEC terminal
*MICROCT: opens the micro-ct control panel (buttons for Scanco Medical programs)
*Mozilla/Netscape: opens a web browser
*XV: opens a screen capture program

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==DEC Terminal and Digital Command Language (DCL)==
This is a DEC terminal: Commands issued in a DEC terminal are DCL commands.

[[Image:decterm.jpg|600px]]

===Copy and paste using the mouse in DEC terminal===
In the DEC terminal, you can highlight text by holding down and moving the mouse. Highlighted text can be pasted into applications or in the terminal using the middle mouse button. You can also highlight files in the Session Manager and paste the filename (with its full path) using the middle mouse button.

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===What is a symbol===
DCL can store information such as strings or integers in "symbols". DCL can also manipulate these symbols to create other symbols.
Symbols are primarily used to define short strings that replace long commands, perform certain calculations and replacements within DCL
procedures, hold status information.
<pre>
$ UR == "SET DEFAULT DISK4:[BONELAB.PROJECTS]" !A short hand to change locations to the project disk.
$ UR :== SET DEFAULT DISK4:[BONELAB.PROJECTS] !Another way to define the symbol without quotations.
$ x == 3 !Store the value 3 in the symbol x.
$ SHOW SYMBOL x !Displays the value of the specified symbol, x.
$ DELETE/SYMBOL/GLOBAL x !Deletes the specified symbol, x.
</pre>
Selected symbols on the Scanco system:
<pre>
$ UD !Changes to the data directory.
$ UR !Changes to the projects directory.
$ DISKS !Shows the current disk usage.
$ DEC !Opens a new DEC terminal.
$ EVE file.txt !Opens the file in the text editor.
$ AIX file.aim !Shows the processing log for an aim file.
$ AIX -L file.aim !The "-L" is used to show the full processing log.
$ QUE !Shows all entries in the queue.
$ GS file.ps or file.pdf !Opens *.ps and *.pdf files in GhostScript.
$ CTHEADER file.isq or file.rsq !Shows scan information for an *.isq or *.rsq file.
</pre>

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===What is a logical===
Logical names are strings, like symbols, but can be passed into programs whereas symbols can usually only be interpreted by the command line interpreter. For example, if the logical name UD was defined to be DISK2:[XTREMECT2.DATA] then UD: could be used as a substitute when entering the path to search for files from within a program.
<pre>
$ DEFINE UD DISK2:[XTREMECT2.DATA] !Defines a logical ud to point to the data directory.
$ DEFINE uct_default_isq myfile.isq !Defines the default isq file for Scanco Medical programs. The isq filename must contain the full path to the file to be evaluated, whereas the path can be left out if you just want to contour the scan.
</pre>
Selected logicals on the micro-CT system:
<pre>
COM !Logical pointing to the commands directory IDISK1:[XTREMECT2.COMMANDS]
UD !Logical pointing to the data directory DISK2:[XTREMECT2.DATA]
UD6 !Logical pointing to the data directory DISK6:[XTREMECT2.DATA]
UR !Logical pointing to the projects directory DISK4:[BONELAB.PROJECTS]
UE !Logical pointing to the evaluation script directory MICROCT_ROOT:[EVAL]
UU !Logical pointing to the templates directory MICROCT_ROOT:[UIL]
UCT_RESULTS !Logical pointing to the results directory MICROCT_USER:[RESULTS]
</pre>

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===Arithmetic operations===
{| class="wikitable"
|style="width: 10%"|Addition ||style="width: 5%;text-align:center;"| + ||The plus sign (+) adds two numbers.
|-
|style="width: 10%"|Subtraction ||style="width: 5%;text-align:center;"| - ||The minus sign (-) subtracts the second specified number from the first specified number.
|-
|style="width: 10%"|Multiplication ||style="width: 5%;text-align:center;"| * ||The asterisk (*) multiplies two numbers.
|-
|style="width: 10%"|Division ||style="width: 5%;text-align:center;"| / ||The slash (/) divides the first specified number by the second specified number. If a number does not divide evenly, the remainder is lost. No rounding takes place.
|}

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===Logical expressions===
{| class="wikitable" style="width: 100%;"
|style="width: 10%"|And||.AND.||The operator .AND. combines two logical values as follows
true .AND. true = true true .AND. false = false false .AND. true = false false .AND. false = false
|-
|style="width: 10%"|Or||.OR.||The operator .OR. combines two logical values as follows
true .OR. true = true true .OR. false = true false .OR. true = true false .OR. false = false
|-
|style="width: 10%"|Not||.NOT.||The operator .NOT. reverses the bit configuration of a logical value. A true value becomes false and a false value becomes true.
|}

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===Numeric comparisons===
{| class="wikitable"
|style="width: 15%"|Equal to||style="width: 5%;text-align:center;"|.EQ.||Compares one number to another for equality.
|-
|style="width: 15%"|Not equal||style="width: 5%;text-align:center;"|.NE.||Compares one number to another for inequality.
|-
|style="width: 15%"|Greater than||style="width: 5%;text-align:center;"|.GT.||Compares one number to another for a greater value in the first number.
|-
|style="width: 15%"|Greater than or equal to||style="width: 5%;text-align:center;"|.GE.||Compares one number to another for greater or equal value in the first number.
|-
|style="width: 15%"|Less than or equal to||style="width: 5%;text-align:center;"|.LE.||Compares one number to another for a lesser or equal value in the first number.
|-
|style="width: 15%"|Less than||style="width: 5%;text-align:center;"|.LT.||Compares one number to another for a lesser value in the first number.
|}

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===String comparisons===
The operators for string comparisons are the same as for numeric comparisons with an added "S" for string.
{| class="wikitable"
|style="width: 15%"|Equal to||style="width: 5%;text-align:center;"|.EQS.||Compares one character string to another for equality.
|-
|style="width: 15%"|Not equal||style="width: 5%;text-align:center;"|.NES.||Compares one character string to another for inequality.
|-
|style="width: 15%"|Greater than||style="width: 5%;text-align:center;"|.GTS.||Compares one character string to another for a greater value in the first specified string.
|-
|style="width: 15%"|Greater than or equal to||style="width: 5%;text-align:center;"|.GES.||Compares one character string to another for greater or equal value in the first specified string.
|-
|style="width: 15%"|Less than or equal to||style="width: 5%;text-align:center;"|.LES.||Compares one character string to another for a lesser or equal value in the first specified string.
|-
|style="width: 15%"|Less than||style="width: 5%;text-align:center;"|.LTS.||Compares one character string to another for a lesser value in the first specified string.
|}

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==DCL Programming Guide==
The OpenVMS systems allow for scripts to be written in a language called '''DCL (DIGITAL Command Language)'''. It was not designed to be more difficult than other scripting languages, but learning any new programming language comes with its learning curve.

*DCL has 243 commands, but most programs can be written with a base set of about 20 commands. The goal of this section is to provide a convenient reference for these commonly-used commands.

It is recommended to open a text editor, enter the whole series of commands, and then run them as a whole program. The terminal on OpenVMS is technically a DCL interpreter, so these commands could be typed in sequence into a terminal with the same result. Typing code interactively is helpful when testing a small code snippet in more detail.

===Your First DCL Script===
Ever since Kernighan and Ritchie wrote the book "The C Programming Language", it has been custom to start with a program that prints the text "Hello, world" to the screen. Open a text editor (for example "EVE") and enter the text below.
<pre>
$! My First DCL Script
$ mymessage = "Hello, world"
$ WRITE SYS$OUTPUT mymessage
$ EXIT
</pre>
Now save the file as HELLO1.COM, and run it using <pre>$ @HELLO1.COM</pre>

Several things are happening in the above program:
*'''Comment !''': The exclamation mark can appear anywhere on the line, and everything following the mark will be treated as a comment.
*'''Variable''': "mymessage" variable is populated with the string "Hello, world", which can be used in the rest of the script.
*'''Command''' "WRITE" send text to various places, in this case to "SYS$OUTPUT", that is to the standard output (i.e. screen).
*'''EXIT''' command tells the DCL interpreter that the script is done and we should exit.
*Commands in DCL are '''NOT case sensitive''', so the command "write sys$output mymessage" would produce the exact same result, but by convention we write commands in all uppercase.

*'''Special Comment !!''' automatically prints the contents of the comment to the screen/logfile. It is useful when you want to know what part of the script you are in.

===Basic Arithmetic===
The DCL language supports several types of data in variables. In the "Hello, world" example above, we saw how to store a string in a variable. We could have stored an integer, that is a positive or negative whole number, in the variable, and done some basic math.
*Refer to [[Scanco_User_Instructions#Arithmetic_operations|'''Arithmetic Operations''']], For example:
<pre>
$ i = 1
$ WRITE SYS$OUTPUT i+1
$ j = 3
$ k = j * (i + 1)
$ WRITE SYS$OUTPUT k
$ WRITE SYS$OUTPUT (k / 4)
$ WRITE SYS$OUTPUT 2 + 2 * 2
$ EXIT
will return:

2
6
1
6
</pre>
Two things are worth noting.
*Because we are limited to integers, division of 6 / 4 needs to return an integer (1.5 is not an integer); the value is truncated, which means rounding is always done toward zero.
*Order of operations is done in the "correct" order, and not left-to-right, so "2 + 2 * 2" is interpreted as "2 + (2 * 2)".

===Conditional Statements===
Sooner or later, you will want to run a program with some logic. The general syntax is:
<pre>
IF [condition]
THEN
[do something]
ELSE
[do something else]
ENDIF
</pre>
*The "ELSE" component is optional.
*If you need a very simple if..then with only one command, it can be written on one line without the "ENDIF":
<pre>
IF [condition] THEN [do something]
</pre>
*Refer to [[Scanco_User_Instructions#Numeric_comparisons|'''Numeric Comparisons''']], [[Scanco_User_Instructions#String_comparisons|'''String Comparisons''']] and [[Scanco_User_Instructions#Logical_expressions|''' Logical Expressions''']] for all possible logical operators (very similar to Fortran).

===Loops===
Most programming languages have 3 kinds of loops:
*Precondition Loops: Condition is tested at the beginning of the loop
*Postcondition Loops: Condition is tested after the loop has executed at least once
*Iterative Loops: A variable changes in a predetermined fashion each time the loop is called.

DCL has none of these. Instead, it has the concept of a "label" and the "GOTO" command. A loop in DCL would look like this:
<pre>
$ i = 1
$loop1:
$ IF i .GE. 10 THEN GOTO exitloop1
$ WRITE SYS$OUTPUT i
$ i = i + 1
$ GOTO loop1
$exitloop1:
$ EXIT
</pre>
This program will print the numbers from 1 to 10 in sequence.

===Subroutines===
Most programming languages allow to define a set of commands that can be called from various parts of the program.
*In DCL, the subroutine can be defined anywhere in the file (unlike C or Python, where the definition must precede the call).
<pre>
$ CALL mycustomsub Joe
$ CALL mycustomsub Mary
$ EXIT
$mycustomsub: SUBROUTINE
$ WRITE SYS$OUTPUT "Hello, ", P1, "!"
$ EXIT
$ ENDSUBROUTINE
</pre>

The first line calls a subroutine named "mycustomsub", which jumps execution to the 4th line. The parameters after the name of the function get copied over to local variables named "P1", "P2", "P3" etc. (in this example, only one parameter, but the maximum is 8) that are available to the subroutine. Note that the command "WRITE" accepts several arguments separated by commas, which get printed on one line.
*The subroutine should be terminated with the command "EXIT" followed by "ENDSUBROUTINE".
*Note that the parameters get passed literally to the subroutine, that is the subroutine gets the text "Joe", and not the contents of a variable named "Joe".
*To force symbol substitution, the parameter would need to be enclosed in single quotes.
<pre>
$ Joe = "Joe Smith"
$ Mary = "Mary Jane"
$ CALL mycustomsub 'Joe'
$ CALL mycustomsub 'Mary'
$ EXIT
$mycustomsub: SUBROUTINE
$ WRITE SYS$OUTPUT "Hello, ", P1, "!"
$ EXIT
$ ENDSUBROUTINE
</pre>

===Reading from files===
Sometimes you have a list of files (for example Micro-CT scans) that are to be processed in a certain way. The obvious way is to copy-paste the code several times, changing only the name of the file, but this is error-prone and inefficient.
*A better way is to put the list of models into a text file, and then call a subroutine on each model file. For example:
<pre>
$ CLOSE/NOLOG foo
$ OPEN/READ foo DISK3:[MICROCT.PROJECTS.OWOC.COM]MYLIST.TXT
$read_loop:
$ READ/END=done foo myline
$ CALL process_me 'myline'
$ GOTO read_loop
$done:
$ CLOSE/NOLOG foo
$ EXIT
$process_me: SUBROUTINE
$ scriptname = DISK3:[MICROCT.PROJECTS.OWOC.COM]MYSCRIPT.COM
$ SUBMIT/NOPRINT/QUE=SYS$FAST/PARAM='P1' 'scriptname'
$ EXIT
$ ENDSUBROUTINE
</pre>
*The first line closes the file handle, in case it was left open in a previous script.
*The second opens the file "MYLIST.TXT" for reading, and assigns the open file a handle named "foo".
*A loop reads the file line-by-line, calling a subroutine with the contents of each line.
*When the end of the file is reached, the file is closed and the script exits.

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==List of basic commands==
<pre>
$ VUE !Start the session manager. Press enter after to regain prompt.
$ DEC !Open a new DEC terminal
$ UCT !Open the micro-CT control panel.
$ UCT_SAMPLE !Start µCT Samples.
$ UCT_MEASUREMENT !Start µCT Tomography.
$ UCT_EVALUATION !Start µCT Evaluation Program.
$ UCT_3D !Start µCT Ray.
$ UCT_BACKUP !Start µCT Disk-Utility.
$ CD UD !Change location to the data directory.
$ CD UR !Change location to the projects directory.
$ CD SYS$SCRATCH !Change location to the scratch directory.
$ CD UCT_RESULTS !Change location to the results directory.
$ DIR UE !List files in the evaluation directory.
$ DIR UU !List files in the templates directory.
$ DIR COM !List files in the commands directory.
$ UCT_LIST !Extract results from the database.
$ AIX -L !View the header of an AIM file.
$ CTHEADER !View the header of an RSQ or ISQ file.
$ EVE !Start the text editor.
$ DISKS !Show the current disk usage (all hard drives).
$ LOGOUT !End a session. For remote sessions, logout from the main (initial) login terminal.
</pre>

===How to move to a different directory===
Use the SET DEFAULT command. You can use an absolute directory path or a relative directory path.
<pre>
$ SET DEFAULT disk:[dir.subdir] !Moves to specified path.
$ SET DEFAULT [.subdir] !Moves one level into subdirectory subdir.
</pre>

Use the CD (i.e., change directory) command (this calls the script $ @SCOM:CD.COM).
<pre>
$ CD subdir !Moves into subdirectory subdir.
$ CD subdir1 subdir2 !Moves into subdirectory subdir1, then into subdir2.
$ CD .. !Moves up one level (i.e., out of one directory).
</pre>

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===How to list the files in a directory===
Use the DIRECTORY command, which may be abbreviated to DIR.
<pre>
$ DIR !List everything in the current directory.
$ DIR disk:[dir.subdir] !Lists everything in the specified directory.
$ DIR disk:[dir.subdir...] !Lists everything in the specified directory and subdirectories.
$ DIR/COL=1 *.aim !Lists all files with the extension .aim in a single column.
$ DIR /VERSIONS=1 !Show only the newest version of each file in the directory.
$ DIR/SINCE=TODAY !Lists all files created today.
$ DIR [...*.aim] !The "..." indicates to do so recursively (i.e., counting all files in all subdirectories).
$ DIR/SIZE !Lists each file and its size.
$ dir/size/grand_total [.subdir...] !List the total size of all files in the SUBDIR directory.
$ HELP DIR !More information on the DIRECTORY command.
</pre>

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===How to copy files===
Use the COPY or BACKUP command.
<pre>
$ COPY file1.ext disk:[dir.subdir1]file2.ext !Make a copy of file1.ext to another location and call it file2.ext
$ COPY *.aim;* disk:[dir.subdir1] !Copy all .aim files (including all versions) to another location keeping the same name.
$ HELP COPY !More information on the COPY command.
</pre>
<pre>
$ BACKUP/VERIFY [.subdir1...]*.*;* [.subdir2...] !Copy entire directory SUBDIR1, including all subdirectories and files, into SUBDIR2.
$ BACKUP/VERIFY [.subdir1...]*.*;* []subdir1.sav/SAVE !Copy entire directory SUBDIR1, including all subdirectories and files, into a save set. The save set could be transferred and unpacked on another OpenVMS machine.
$ HELP BACKUP !More information on the BACKUP command.
</pre>

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===How to delete files===
Use the DELETE command, which may be abbreviated to DEL.
<pre>
$ DEL myfile.txt; !Delete the most recent version of myfile.txt.
$ DEL myfile.txt;* !Delete all versions of myfile.txt.
$ HELP DELETE !More information on the DELETE command.
</pre>
[[Image:Bones2.jpg|20px]] Warning: Extreme caution!
<pre>
$ DEL *.*;* !Delete everything in the current directory!
</pre>

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===How to create a directory===
Use the CREATE/DIR command.
<pre>
$ CREATE/DIR [.subdir] !Creates a subdirectory named subdir.dir in the current directory.
$ CREATE/DIR disk:[dir.subdir] !Creates the subdirectory subdir at the specified path.
</pre>

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===How to rename files and directories===
Use the RENAME command.
<pre>
$ SET FILE/PROTECTION=O:RWED olddir.dir !Sets protections so you can rename the directory.
$ RENAME oldfile.ext newfile.ext !Renames oldfile.ext to newfile.ext.
</pre>

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===How to check the queue===
Use the SHOW QUEUE command, which may be abbreviated to SH QUE.
<pre>
$ SHOW QUEUE !Shows all the queues, there are many!
$ SH QUE *FAST !Shows all queues whose names end with "fast", these are used for evaluations.
$ SH QUE *SLOW !Shows all queues whose names end with "slow", these are used for reconstructions.
$ SH QUE *FAST/ALL !By default you are only shown queue entries for the user you are logged in as. To show jobs for all users, use the /ALL qualifier.
$ SH QUE *FAST/BY=EXE/ALL !Show only jobs that are currently executing for all users.
</pre>

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===How to get queue information===
Use the SHOW ENTRY command to obtain information about batch jobs in the queues.
<pre>
$ SHOW ENTRY !Shows all the batch jobs for your user, there may be lots!
$ SHOW ENTRY 251 !Shows information for batch job number 251.
$ SHOW ENTRY 251/FULL !Shows detailed information for batch job number 251.
$ SHOW ENTRY/ALL !Shows all the batch jobs for all users.
</pre>

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=Micro-Computed Tomography (µCT) Basics=

==User Tutorials==
For Scanco MicroCT Systems and Software:
:*[[Media:Microct-v14.pdf | '''Scanco MicroCT Systems and Software''']]

For XtremeCT II and I:
:*[[Media:SOP Berlin V1.0.pdf | '''Scanco XtremeCT I SOP (Berlin)''']]
:*[[Media:XtremectIIB-v4-us.pdf | '''Scanco XtremeCT II Specs''']]

For MicroCT35, VivaCT40 and VivaCT80:
:*[[Media:ScancoMicro-CT_User_Policy_Guidelines_19052005.pdf| '''MicroCT User Policy & Guidelines''']]
:*[[Media:MicroCT_Starter_Package.pdf | '''MicroCT Starter Package''']] and its [[Media:Microctstarterpackagejun2012.docx| '''Word format''']].
:*[[Media:Scanco-training-uct35-and-vivact40.pdf | '''MicroCT Customer Training Guide''']]
:*[[Media:Vivact_80_v3-nomarks.pdf | '''VivaCT 80 Specifications''']]

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==Micro-CT Image Basics==
Computed tomography is a non-destructive x-ray imaging modality that enables three-dimensional (3D) virtual models of an object to be created, which can be subsequently visualized and analyzed. Micro-CT refers to CT in which the [http://www.scanco.ch/index.php?id=faq_general#c779 resolution] lies in the micro-scale, which is achieved with a high-resolution x-ray detector and a field of view that is much smaller than conventional CT. Structural detail provided by CT depends on differences in x-ray attenuation properties. Components with very different x-ray attenuation properties, for example air, soft tissue, and bone, can be differentiated in a CT scans whereas different types of soft tissues, for example muscle and cartilage, do not have sufficient differences in attenuation to be distinguish.

===Dark Field===
Detector response with x-rays off. Enables corrections of non-uniformities of the detector. Acquired automatically by the scanning software before each scan.

[[File:Dark_field_single.img_assist_custom-400x97.jpg|400px]]

===Bright Field===
Detector response with x-rays on but no sample. Enables corrections of non-uniformities of the x-ray beam. Acquired automatically by the scanning software before each scan.

[[File:Bright_field_single.jpg|400px]]

===Raw Projection===
A raw x-ray projection of a mouse leg. The darker regions correspond with higher x-ray attenuation. The discontinuities result from overlaps where the detector was shifted to acquire the large region of interest (3x2 detector frames in this example). Projections are acquired at many incremental rotations around the sample.

[[File:Raw_projection_notes.jpg|400px]]

===Sinogram===
The sinogram is a different representation of the projection data. The sinogram represents the attenuation values of one row of the detector at each rotational increment around the sample.

[[File:Sinogram.jpg|400px]]

===Attenuation Projection===
Accounting for the inhomogeneities of the detector and beam, we can calculate the x-ray attenuation caused by the sample. Bright regions correspond with higher attenuation.

[[File:Attenuation_projection.jpg|400px]]

===Reconstructed Image===
From the attenuation projections, the original structure can be calculate using filtered back projection.

*[https://youtu.be/DBLYSETYbe8 CT Back-projection Reconstruction]
*[https://youtu.be/NWeM35_KR2w CT Reconstruction of a Head]

[[File:Reconstruction_xy_yz_planes.jpg|400px]]

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==Image Data==
===Image Data Type===
====Binary Images====
Binary images are images whose pixels contain only two possible intensity values (off-on, or black-white B&W). The off or black value is usually 0 and the on or white value is usually 1 (1-bit pixel) or 255 (8-bit pixel). This type of image is commonly used as a multiplier to mask regions within another image.

====Grayscale Images====
Grayscale images represent intensities. Pixels range from least intense (black) to most intense (white). Pixel values usually range from 0 to 255 or are scaled to this range when displayed.

====Indexed Images====
An indexed image uses direct mapping of pixel values to colormap values. Instead of intensities, a pixel value within an indexed image relates to a color value within a color lookup table. An indexed image consists of a data matrix and a colormap matrix. The data matrix can be of class uint8, uint16, or double. The colormap matrix is an m-by-3 array of class double containing floating-point values in the range [0,1]. Each row of map specifies the red, green, and blue components of a single color. Since indexed images reference color tables composed of up to 256 colors, the data values of these images are usually scaled to range from 0 to 255.

====RGB Images====
Within the three-dimensional array of an RGB image, two of the dimensions specify the location of a pixel within an image. The other dimension specifies the color of each pixel. The color dimension always has a size of 3 and is composed of the red, green, and blue color bands (channels) of the image.

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===Image Data Pixel Values===
The image data type is determined by the pixel depth in bits per channel, or bit depth. Bit depth for each channel can be 8, 16, 32 or 64. The data may be signed, unsigned (u), floating-point (f), real or complex (c) for some arithmetic functions, where each channel value is represented by two numbers: real and imaginary part. All channels in an image must have the same data type.

{| class="wikitable"
|-
! scope="col"| Image Data Type
! scope="col"| Name
! scope="col"| Byte
! scope="col"| Value Range
! scope='col'| Comments
|-
! scope="row"| char
| 8-bit signed integer
| 1
| -128 ~ 127
| Scanco SEG.AIM, GOBJ
|-
! scope="row"| uchar
| 8-bit unsigned integer
| 1
| 0 ~ 255
|
|-
! scope="row"| int
| 16-bit signed integer
| 2
| −32768 ~ 32767
| Scanco grey-scaled images, ISQ, AIM
|-
! scope="row"| uint
| 16-bit unsigned integer
| 2
| 0 ~ 65535
| Converted format of Scanco grey-scaled images
|-
! scope="row"| long
| 32-bit signed integer
| 4
| −2^31 ~ 2^31 - 1
|
|-
! scope="row"| ulong
| 32-bit unsigned integer
| 4
| 0 ~ 2^32 - 1
|
|-
! scope="row"| float
| floating point
| 4
| ±3.40282347 E+38
| 32-bit single-precision with 6~7 significant digits
|-
! scope="row"| long64
| 64-bit signed integer
| 8
| −2^63 ~ 2^63 - 1
|
|-
! scope="row"| ulong64
| 64-bit unsigned integer
| 8
| 0 ~ 2^64 - 1
|
|-
! scope="row"| double
| double precision floating point
| 8
| ±1.79769313486231570 E+308
| 64-bit double-precision with 15~16 significant digits
|-
! scope="row"| complex
| floating point complex
| 8
| same as floating-point
| same as floating-point
|-
! scope="row"| dcomplex
| double precision complex
| 16
| same as double-precision
| same as double-precision
|}

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===Scanco Image File Types===

{| class="wikitable"
! scope="col"| Extension
! scope="col", style="width: 65%"| Description
! scope="col"| Creation
! scope="col"| Opens with
|-
! scope="row"| RSQ
| '''R'''aw '''S'''e'''Q'''uence data. This is the raw data collected after the scan. This file contains the bright and dark field corrections and the raw projections. || created with scan || $ x
|-
! scope="row"| ISQ
| '''I'''mage '''S'''e'''Q'''uence data. This is the reconstructed 3D image, which you see in the µCT Evaluation Program. || created from RSQ
| $ uct_evaluation
$ x
|-
! scope="row"| AIM
| '''A'''ny '''IM'''age data. This is a binary raw data format (16-bit signed data, little endian) 3D discretized data you see using the µCT Ray Program and used for the analysis. The AIM file is a volume of interest isolated from the ISQ file. || extracted from ISQ
|$ uct_3d
$ uct_evaluation
|-
! scope="row"| GOBJ
| '''G'''raphical '''OBJ'''ect data. These are the green contours in the µCT Evaluation Program, which are used to isolate regions of interest from an AIM file for analysis. || extracted from ISQ/AIM || $ uct_evaluation
|-
! scope="row"| SCV
| '''SC'''out '''V'''iew || created with scan || $ x
|-
! scope="row"| RAD
| Scout View || created with scan || $ x
|-
! scope="row"| RSW
| raw data (RSQ) || created with scan || $ x
|-
! scope="row"| IMA
| image data (AIM, ISQ, GOBJ)|| created from RSQ || $ uct_evaluation
|}
*Refer to [[Media:Aimpack_documentation.pdf|'''Scanco Aim Format''' ]] or its [[Media:Scanco_Aim_File_Format.doc|'''Doc Format''']] for its header info.

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==Scanco Medical Micro-CT Software==
In the bottom left hand corner of the micro-CT workstation desktop is the micro-CT control panel, from which the micro-CT programs can be launched. The standard operating procedure for scanning a samples involves proceeding through the programs in the control panel from left to right:
<pre>
$ UCT_SAMPLE !Samples: Registering a sample
$ UCT_MEASUREMENT !Tomography: Scanning
$ UCT_EVALUATION !Evaluation: Evaluating the scan
$ UCT_3D !Ray: Viewing the 3D scan
$ UCT_BACKUP !Disk-Utility: Archiving the data
</pre>
You must specify an operator in the control panel to use the scanning and evaluation programs.
* XtremeCT
[[File:XCTcontrol_panel.img_assist_custom-302x100.jpg|300px]]
* MicroCT35, VivaCT40 and VivaCT80
[[File:Uct35_control_panel.jpg|300px]]
[[File:VivaCT40_control_panel.jpg|300px]]
[[File:VivaCT80_control_panel.jpg|300px]]

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===µCT Samples===
The µCT-Samples program is used to register new samples to be scanned and update sample names (e.g., to correct a sample name). To start the program type <code>$ uct_sample</code> in a DEC terminal, or use the sample button.

[[File:Xtremect_button_samples.jpg|40px]]
[[File:Uct_sample_uct35.jpg|40px]]
[[File:Uct_sample_vivact40.jpg|40px]]

#'''Prepare Sample Names''' according to [[Scanco_User_Instructions#Sample_Name_Convention|'''Sample Name Convention''']]
#'''Register Sample Names'''
#*Create a new sample by clicking “New” and typing in your sample name where it says “Name.” “Save” the sample.
#*You are now given a sample number. Record the sample number on the log sheet.
#:[[File:Uct_sample_pic01.jpg|500px]]
#'''Create Additional Sample Names Using Copy and Paste'''
#*If you have many samples to register, you can copy and paste part of the sample name you just created. Highlight the part of the sample name you want to copy by holding down the left mouse button while dragging the mouse, then release the mouse button.
#:[[File:Uct_sample_pic02.jpg|500px]]
#*Paste the highlighted text into a DEC terminal by pressing the middle mouse button. Now highlight the text in the DEC term.
#:[[File:Uct_sample_pic03.jpg|300px]]
#*Go back to the µCT-sample window, click "New", and paste the information next to "Name" using the middle mouse button. Update the name as required and "Save."
#'''Add Additional Sample Details'''
#*When a patient comes in for their first scan, you need to update their sample with their date of birth, sex, and hand/foot dominance.
#*Use the "Find..." button to search for a sample that has already been registered. You can search by sample number or by project name (e.g., CAMOS).
#*Date of birth: DD/MMM/YYYY. Example: 14/JAN/1951
#*Remarks: include the sex and hand/foot dominance. Example: F-RHRF for female that is right hand dominant and right foot dominant

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===µCT Tomography===
The µCT-Tomography program is used to perform a scan. To start the program type <code>$ uct_measurement</code> in a DEC terminal on the scanner computer (remote access does not allow this functionality), or use the scanner button. If you use the button, you must specify an operator prior to using the program.

[[File:Xtremect_button_scan.jpg|40px]]
[[File:Uct_measurement_uct35.jpg|40px]]
[[File:Uct_measurement_vivact40.jpg|40px]]
[[File:VivaCT80_scan.jpg|40px]]

[[File:Uct_tomography_pic00.jpg|600px]]

#'''Select Sample'''
#*When the µCT-Tomography program is first started, you will be prompted to enter the sample name or number of the specimen you are about to scan.
#*If you have not registered your sample, press "Cancel" to close the select sample box, then press "New..." in the measurement sample box to register a new sample (see [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT-Samples''']]).
#*Once you have entered your sample information, the measurement sample box will show details for that sample, including the sample name and scan (measurement) history.
#:[[File:Uct_tomography_pic01.jpg|400px]]
#*After your first scan you will need to press the "Other..." button to open the sample selection box and find your next sample.
#'''Select a Controlfile'''
#*The controlfile contains scan parameters such as the x-ray energy, current, and more (see [[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29 controlfiles |'''Controlfiles''']]).
#*Once the controlfile is setup, you need only to select it. If there are many controlfiles, you may want to search for yours using the file filter by entering part of the name or number in the white box and pressing enter; if you do this, you still must click on the controlfile so that it is highlighted in black as shown below.
#:[[File:Uct_tomography_pic02.jpg|400px]]
#'''Precalibrate'''
#*Calibrations are done before loading your patient/animal and scanning for quality control and to reduce the time the patient/animal is under preparation/anaesthesia. Start the calibration by pressing the "Precalibrate" button.
#:[[File:Uct_tomography_pic03.jpg|400px]]
#*Press "Start Calibration". The calibration will start with an "X-Ray Warmup", followed by "Measuring Dark" and "Measuring I0" and usually takes about 2-3 minutes to complete.
#:[[File:Precalibrate.jpg|300px]]
#*The precalibration is good for 15~20 min. The time remaining is shown on the "Precalibrate" button.
#:[[File:Uct_tomography_pic5.jpg|400px]]
#*The precalibrate option cannot be used with batch measurements, and it's not available for MicroCT35 which is not intended for invivo/live scan.
#'''Load and Position the Patient/Sample'''
#*Instruct the patient to remove any jewelry in the scan areas (wrist/ankle/knee/elbow ect). With the patient seated, put the wrist/ankle/knee/elbow into the appropriate cast. Different pads with different sizes can be used to fit the patient.
#*For invivo/invitro samples, prepare your sample in terms of orientation, immobilization, hydration ect.
#*After the precalibration is complete, you can now open the bore cover and insert the patient's wrist/ankle/knee/elbow or sample into the scanner. Gently move the wrist/ankle/knee/elbow or sample into the scanner until you can snap in the cast at the gantry. Check that the cast is positioned correctly and the patient/sample is comfortable.
#*Close the bore cover.
#'''Scout-View'''
#*A scout-view is similar to a 2D x-ray image and allows the user to set where to start and stop the scan.
#*After loading your sample, press the "Scout-View..." button to bring up the scout-view window.
#*The start position (top of the scanner) and end position (bottom of the scanner) can be modified to zoom in on the region of interest.
#*The angle of the scout view can also be changed to see the object in a different orientation.
#*Once pressed the "Scout-View" button but the scout view is found not in an appropriate position, press "Cancel", modify the start position, end position, or angle and press "Scout-View" again.
#:[[File:Scout_view_window.jpg|400px]]
#*Scout view image is displayed in the top right hand corner of the program and will start by showing the right half of the image, followed by the left half of the image.
#'''Set Reference Line and Launch a Scan'''
#*A reference line (solid green line) is placed to set the scan region (green block).
#*Press the "Reference-Line" button to show the reference line and default scan region over the scout view.
#*To change the number of slices to scan, move the reference line to the top of the scan region, then hold down the shift button while dragging the mouse to extend the scan region and press the left mouse button to set the reference line.
#*To centre the scan region between two reference lines, move the reference line to the top of the scan region, then hold down the alt key while dragging the mouse until the second green reference line is in place, then press the left mouse button to set while still holding down the alt key!
#:[[File:Uct_tomography_pic06.jpg|700px]]
#*For a single scan, select "OK", "Scan" and "Start Measurement". Record measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']].
#*For a batch scan which is only available on microCTs, select "Batch Measurement" and record the measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']]. You may now setup a new scan (select new sample and controlfile, perform scout, etc). When you have finished setting up all scans, press "Start Batch Scans." (See [[Scanco_User_Instructions&action=edit&section=48#Perform_Batch_Scans|'''Perform Batch Scans''']] for detailed instructions)
#'''Cancel or Reposition a Scan'''
#*If you need to interrupt a scan, press the cancel button and restart the scan or if you do not want to rescan then "unload" the scanner.
#*If you have not started a scan and need to reposition the patient, you also must "unload" the scanner.
#'''Remove Patient/Sample from Scanner'''
#*After the scanning is complete, open the bore cover and slide the patient's wrist/ankle/knee/elbow or sample out of the scanner. Release the cast by pushing down the cast release handle.

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===µCT Evaluation Program===
The µCT Evaluation Program is used to evaluate a scan. To start the program type <code>$ uct_evaluation</code> in a DEC terminal, or use the graph button. If you use the button, you must specify an operator prior to using the program.

[[File:Uct_evaluation.jpg|40px]]

[[File:Uct_evaluation_pic01.jpg|600px]]

#'''Find Your Sample'''
#:Enter the first part of your sample name in the file filter box and press enter. The samples are shown in the left hand box. The measurement box on the right shows scans for the selected sample (highlighted in black). Select a measurement and press "OK."
#:[[File:Uct_evaluation_pic02.jpg|500px]]
#'''Draw Contours (If Applicable)'''
#*Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
#*Contours must always be drawn COUNTER-CLOCKWISE!!!
#*[[Media:Contouring-tools.pdf |'''Contouring tools reference sheet''']]
#*For this sample, we are only interested in viewing the object in 3D and drew contours to isolate the bone and soft tissue from the sample tube.
#:[[File:Uct evaluation pic03.jpg|600px]]
#'''Evaluate'''
#*Scanco Medical provides several standard evaluation scripts. Open the 3D-Evaluation menu either using the "T..." button or from the top menu by going to "Tasks" and "Evaluation 3D...". If you set a default evaluation script in your scanning controlfile, it will be listed under "Task/Evaluation."
#:[[File:Uct_evaluation_pic04.jpg|400px]]
#*If you want to run a different evaluation press "Select...", highlight the evaluation script of interest, and press "OK".
#:[[File:Uct_evaluation_pic05.jpg|400px]]
#*When the 3D-Evaluation window is activated, a white box will appear on your reconstructed image. The white box is the region of interest that will be "cut out" of the full scan. If you have drawn contours, the white box will automatically be adjusted to fit the contours. Adjust the box if necessary by grabbing one of the white handles; use the left mouse button to move the box and the right mouse button to resize. The box can also be resized using the "VOI Start" and "Dimensions" in the 3D-Evaluation window.
#*For most evaluation scripts, you will be required to specify parameters for a Gaussian filter, to reduce noise, and a threshold, to isolate your object (e.g., bone) from the background. Check that the parameters used provide a good representation of your scanned sample by flipping back and forth between the segmented and grayscale image using the "Preview" and "Grayscale" buttons.
#:[[File:Uct_evaluation_pic06.jpg|400px]]
#*When you are satisfied with the segmentation parameters, press "Start Evaluation", which will submit the job to the queue.

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===µCT Ray===
The µCT Ray program is used to view scanned objects in 3D, create images, and create image sequences for animations. To start the program type <code>$ uct_3d</code> in a DEC terminal, or use the 3D object button.

[[File:Uct_3d.jpg|40px]]

[[File:Uct_3d_pic01.jpg|600px]]

#'''Select and Render Your Sample'''
#*'''Select:''' If you have used the default Scanco Medical scripts, then
#:*If your data is on the "data disk" and you can search for your files using the file filter to select a sample and measurement then press "OK". To open a new file, File --> Open.
#:*If your data is not in the standard location (e.g., it was copied to the projects disk), then use File --> Read and navigate to find the file to open.
#:*Alternatively you can start the program with a file to open <code>$ uct_3d myfile_seg.aim</code>
#: 
#*'''Rendering:'''
#:*Use a single click of the left mouse button to start or to stop rendering the sample.
#:*You can also use the "Start" and "Stop" buttons at the bottom of the options on the left.
#:*You must stop rendering to change viewing options on the left.
#: 
#*'''Change View:'''
#:*To adjust the view, move the "Rotation" and "Elevation" slider bars in the options on the left.
#:*The slider bar is located above its label.
#:[[File:Uct_3d_pic02.jpg|600px]]
#: 
#*'''Change Colours''' (Object and Background):
#:*From the top menu choose "Options" then "Object/Display Properties...".
#:*A segmented image typically only has two values, 0 (black, background) and 127 (white, object). To change the colour of the object only, we need to set the value 127 to a specific colour.
#:*In this example, the slider bar value "1" corresponds with the value 127 and we will set both slider bars to "1" so that we are adjusting values "127 ... 127", in other words, only value "127".
#:*Under "Surface" click on the "white box" to open the "Color Mixing" window.
#:*Choose the new colour for the object (e.g., orange) and press "OK."
#:*Close the "Object Properties" window or move it to the side.
#:*Now re-render the object with a single click of the left mouse button.
#:[[File:Uct_3d_pic03.jpg|300px]] [[File:Uct_3d_pic04.jpg|300px]]
#: 
#*'''Cutplane (left options) and Subdim (top menu):''' 
#:*The cutplane and subdim functions allow you to show a cross-section of your object.
#:*The subdim function tends to work better than the cutplane but is limited to axes of the scan.
#:[[File:Uct_3d_pic05.jpg|600px]]
#: 
#'''Print an Image to File'''
#*An image must be fully rendered in order to be saved.
#*From the top menu choose "File" then "Print". Set the print format to "TIFF" and the directory to "Scratch/Temp" (or another location using the "Specify in Filename" option).
#*Change the filename to something meaningful then press "OK."
#:[[File:Uct_3d_pic06.jpg|300px]]
#: 
#'''Auto-Print Images for an Animation'''
#*Creating an animation involves saving a sequence of rendered images, which can then be compiled into an animated GIF or other video format using various software packages (e.g., Photoshop, Quicktime Pro).
#*From the top menu choose "Options" and "Animation..." to open the Animation Settings window. Set the viewing parameters for the start of the animation, fully render the image, then press the "Get Settings A" button.
#*Set the parameters for the end of the animation, fully render the image, then press the "Get Settings B" button.
#*Set the number of frames you want, the higher the number frames, the smoother the animation will be, but also the larger the file size.
#*Now setup the auto-print feature. From the top menu choose "File", then "Print". Choose "TIFF" for the print format, and the "Scratch/Temp" for the directory (or use the "Specify in Filename"). Specify a filename prefix, to which numbers will be appended for the image sequence.
#*Activate the "Auto-Print" feature. Press "OK" then press the "Start Calculation" button on the Animation Settings window.
#*Do not interrupt the program while the frames are being rendered and saved. When the program is done rendering all the frames, transfer them to your computer to compile into an animation.
#:[[File:Uct_3d_pic07.jpg|200px]] [[File:Uct_3d_pic08.jpg|300px]]

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===XImage===
The XImage program is used to view the raw data (RSQ file) and scout view. To start the program type <code>$ run um:ximage</code> or <code>$ x </code>in a DEC terminal.

When loading an RSQ, the default view (XY plane) is of the sinogram.

[[File:Ximage_1.jpg|600px]]

To view the attenuations, choose the XZ plane. The first slice in this orientation is the dark field, the second slice is the bright field , and slices three and onward are the raw projections (attenuations).

[[File:Ximage_2.jpg|600px]]

To view the corrected projections, from the Evaluations menu, choose Projection Mode.

[[File:Ximage_3.jpg|400px]]

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=Scanning=
==Sample Name Convention==
*At the Bone Imaging Laboratory, all sample naming must conform to the following format
:'''PROJECT IDENTIFIER _ SAMPLE DETAILS'''
*In CAPITAL LETTERS (filenames are case sensitive, so this makes it easy to remember how you input your sample name)
*No special characters (spaces, /, %, etc.) as further evaluations will not work if spaces are present.
:Examples: CAMOS_771, TESTS_0001, TESTS_0002, TESTS_0003

==Register Samples for Scanning==
*Although samples can be registered immediately prior to a scan, it is much more efficient to register all your samples beforehand.
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT Samples''']] for instructional details.

==Log Sheets==
*Log sheets are used to record important information about scans that are performed, such as sample and measurement numbers ect.
*Log sheets are to remain in the lab. If you would like a copy of your log sheets, please make a photocopy or print two copies to record the scan information.
*Use the PDF file to print blank log sheets. Use the Excel file to make your own custom log sheet.

#Bone Lab for General Patients
#*[[Media:XCT_II_Log_(Studies).pdf|'''XCT II Log Sheet for Studies''']]
#*[[Media:XCT_II_Log_(Miscellaneous).pdf|'''XCT II Log Sheet for Miscellaneous''']]
#MicroCT Lab for General Non-Patients
#*[[Media:UCT_log_sheet_general.pdf|'''MicroCT Log Sheet for Studies (PDF)''']]
#*[[Media:UCT_log_sheet_general.xlsx|'''MicroCT Log Sheet for Studies (Excel)''']]

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==Patient Casts and Sample Holders==
===Patient Casts for XtremeCTs===

===Sample Holders and Scan SOP for microCTs===
====Ex Vivo Sample Holders====
*Ex vivo and inanimate samples are scanned in sample holder tubes. These tubes come in a variety of diameters. It is extremely important that the tube diameter corresponds to, or is smaller than, the field of view (FOV) set in your scanning control file.

*Biological tissues should be hydrated and wrapped in plastic wrap to prevent drying of the sample. Your sample should then be secured in the sample holder using foam to prevent it from shifting around during scanning, which would lead to poor image quality.

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=====Chemical Resistivity of Sample Holders=====
*White tube sample holders are made of PMMA (poly-methyl-methacrylate).
*Yellow tube samples holders are made of PEI (poly-ether-imide).
*Use the yellow tubes if you will need to disinfect the sample holder after scanning.

{| class="wikitable"
!colspan="3"|Thermal and chemical compatibility of sample holders
|-
! scope="col"| Properties
! scope="col"| White Tubes (PMMA)
! scope="col"| Yellow Tubes (PEI)
|-
! scope="row"| Max. Temperature
| +85°C
| +170°C
|-
! scope="row"| Sterilization Steam Autoclave
|non resistant
|resistant (138°C for 20 Min. at 1 bar)
|-
! scope="row"| Water
|resistant
|resistant
|-
! scope="row"| Inorganic Acids
|limited resistance
|resistant
|-
! scope="row"| Inorganic Bases
|non resistant
|limited resistance
|-
! scope="row"| Aldehydes (Formaldehyde)
|limited resistance only in diluted form
|resistant
|-
! scope="row"| Alcohols
|limited resistance
|resistant
|-
! scope="row"| Bleach
|non resistant
|resistant
|}

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=====Mounting of Sample Holders=====
[[File:Uct35_holder.jpg|thumb|right|100px|µCT35 setup]]
*The spindle (metal bit) of the sample holder has a slot, which must be aligned in the scanner or adapter plate.
*The sample holder sits vertically in the µCT35 while horizontally in the VivaCT80 and VivaCT40.
*For the vivaCT40, attach the adapter plate for the tube sample holders to one of the animal bed. The tube sample holders are held horizontally in the vivaCT 40.
:[[File:Vivact40_holder.jpg|thumb|none|700px|VivaCT40 setup]]

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=====Ex vivo rodent scanning SOP=====
*Refer to [[Media:Ex_vivo_scan_sop.pdf|'''Ex Vivo Rodent Scanning''']] for its scan SOP.
*Refer to [[Media:Ex_vivo_scan_sop.docx|'''Ex Vivo Rodent Scanning in docx''']] for its Word version.

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====In Vivo Sample Fixtures and Anesthetic System====
*[[Media:VivaCT40_Anaesthetic_System.pdf |'''Anaesthetic System''']] : You must receive training to use the anaesthetic system.
*[[Media:VivaCT40_Mouse_and_Rat_Tibia_Fixture.pdf |'''Mouse/Rat Tibia Fixture''']]
*[[Media:VivaCT40_Mouse_Lower_Body_Fixture.pdf|'''Mouse Lower Body Fixture''']]
*[[Media:VivaCT40_Mouse_Whole_Body_Tube.pdf|'''Mouse Whole Body Tube''']]

=====In vivo rodent scanning SOP=====
*Refer to [[Media:In_vivo_scan_sop.pdf|'''In vivo rodent scanning''']] for its scan SOP.
*Refer to [[Media:In_vivo_scan_sop.docx|'''In vivo rodent scanning in docx''']] for its Word version.

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====Align whole body device in FOV====

It's important to have your whole sample in the field of view for accurate density measurements.
* Refer to [[Media:wholebody.pdf |'''Align the device''']] for detailed instructions.

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==Scan Parameters (Controlfiles)==

:{| class="wikitable" style="text-align:center;"
|-
! scope="row"| Manufacturer
| colspan="5"|[http://www.scanco.ch '''Scanco Medical AG''']
| [https://www.zeiss.com/microscopy/int/products/x-ray-microscopy.html '''Carl Zeiss X-ray Microscopy''']
|-
! scope="col" rowspan="2"| Model
! scope="col"| XtremeCT II || XtremeCT I || VivaCT80 || VivaCT40 || µCT35 || Xradia 520 Versa
|-
|[[File:XtremeCT.jpg|150px]]
|[[File:XtremeCT.jpg|150px]]
|[[File:VivaCT80.jpg|120px]]
|[[File:VivaCT40.jpg|135px]]
|[[File:UCT35.JPG|150px]]
|[[File:Xradia-520-versa-small.jpg|160px]]
|-
! scope="row"| Application
|colspan="2"| Clinical studies for human extremities in vivo
Horizontal static patient setup
|colspan="2"| Preclinical in vivo animal studies
Horizontal static animal setup
|colspan="2"| High resolution ex vivo specimen scans
Vertical rotational sample setup
|-
! scope="row"| E (KVp)
| 68 || 60
|colspan="3"| 45, 55, 70
| 30 ~ 160
|-
! scope="row"| Power (W)
| 100 || 54
|colspan="3"| 4, 8
|4 ~ 10
|-
! scope="row"| Filter
| Fixed 0.2mm Cu + 1mm Al
(Equivalent 6.7mm Al)
| Fixed 0.1mm Cu + 0.6mm Al
| Default 0.5mm Al,
Air, 0.1mm Al, 0. mm Cu
| Fixed 0.5mm Al
| Fixed 0.5mm Al
| Air, LE1~LE6, HE1~HE6,
customizable filter
|-
! scope="row"| FOV (⌀ * L) (mm^2)
| 140 ⌀ * 200 L
| 126 ⌀ * 150 L
| 31.9 ~ 80 ⌀ * 145 L
| 21.5 ~ 38.9 ⌀ * 148 L
| 7.2 ~ 38 ⌀ * 140 L
(75 L standard)
| 90 ⌀ * 100 L
|-
! scope="row"| Image Matrix
| 4608*4608 ~ 512*512
| 3072*3072 ~ 512*512
| 4096*4096 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
|-
! scope="row"| Voxel Size (µm)
| Standard 60.7
(30.3 ~ 273.4)
| Standard 82.0
(41.0 ~ 246.0)
| 5 ~ 156
| 10.5 ~ 76
| 3.5 ~ 74
| 0.7 ~ 50
|-
! scope="row"| Sample Image
|[[File:XCT2_human_distal_femur.png|160px]]
human distal femur
|[[File:XCT1_human_distal_tibia.JPG|160px]]
human distal tibia
|[[File:VivaCT80_Rat_distal_femur.JPG|160px]]
rat distal femur
|[[File:Vivact40_in-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Uct35_ex-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Xradia_mouse_distal_femur.png|160px]]
mouse distal femur
|}

Controlfiles are used to specify the parameters for the scans. Once your controlfile is setup, you should not modify it over the course of your project.

[[File:XCT2 ControlFile.JPG|right|600px]]

*'''Control File Name''': Specify a meaningful name so that others can reuse yours.

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===General Settings===
*'''Holder Type''': Choose the used holder type for XtremeCT II from Standard Casts, Knee Cast and Elbow Cast. No option for XtremeCT I scanner. For microCTs, Choose the used sample holder type with the correct diameter.

*'''Mode of operation''': Default is continuous operation for all scanners. Gated operation mode is available for VivaCT80 and VivaCT40 scanners.

*'''Evaluation Script''': This sets the default evaluation script used for the analysis. You can manually select a different script from the evaluation program.

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===X-ray Settings===
*'''Tube Energy (KVp)''': Fixed energy for XtremeCTs while having 3 options for each of microCTs: Use the 70 KVp for most samples, use the 55 or 45 KVp for low density objects (e.g., soft tissue) or specimens with a diameter less than 20 mm. Lower energies provide better contrast while higher energies provide better signal to noise (SNR).

*'''Tube Current (µA)''': Fixed current for XtremeCTs while having 2 options for each of energy settings of each microCTs: Use the higher current except when the voxel size is set for the best resolution of the scanner. The higher current will yield better SNR but a larger spot size.

:{| class="wikitable" style="text-align:center;"
|-
! scope="col"|
! scope="col"| XtremeCT II
! scope="col"| XtremeCT I
! colspan="3"| vivaCT80，vivaCT40， µCT35
|-
! scope="row"| E (KVp)
| 68
| 60
| 70
| 55
| 45
|-
! scope="row"| I (µA)
| 1470
| 900
| 114, 57
| 145, 72
| 177, 88
|-
! scope="row"| Power (W)
| 100
| 54
|colspan="3"| 8, 4
|}

*'''Filter''': Fixed filter settings for all scanners except VivaCT 80 has 4 filter options.

*'''Calibration''': This sets the mu scaling factor, density and beam hardening correction used for the reconstruction. For standard patient scans use 200 mg HA/cm3. For ex vivo bone scans, use 1200 mg HA/cm3, for soft tissue use the plexi scaling, and for non-biological tissues use the aluminum scaling.

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===Scout-View Settings===
Normally you will want to enable this and here you can specify the default start and end position, and scout-view angle, which you may override for each scan.

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===CT Scan Settings===

*'''Resolution''': This setting includes the reconstruction matrix size (2048x2048, 1536x1536, 1024x1024, or 512x512) and the number of projections per 180°. The lower the resolution setting, the better the SNR and larger the voxel size.

*'''FOV / Diameter''': This field of view must fully contain the sample holder for accurate density measurements. Fixed FOV for XtremeCTs while having 5 options for each of microCTs: If you choose a smaller FOV than the sample holder, the scan may be aborted to prevent damage to the scanner. For the best resolution, you should choose the smallest holder that contains your sample.

*'''Voxel Size''': The nominal isotropic voxel size is determined by the FOV and the reconstruction matrix.

*'''Number of Slices''': You can specify a specific number of slices or image stacks to acquire (1x110 = 1 image stacks of 110 slices). The scan time increases with each image stack, therefore pay attention to the stack boundaries (e.g., 111 slices will take 2x longer to scan than 110 slices).

*'''Rel Position of First Slice''': This option enables you to offset the scan region from the reference line. This is useful for scanning a region a specific distance from the growth plate or centering the scan region around the reference line. If you disable the scout view, then the position is relative to the absolute 0 position of the scanner (top of the sample holder for the µCT35 and towards the back of the scanner for the vivaCT40).

*'''Integration Time''': The higher the integration time, the better the SNR and longer the scan time. Use 100 ms for patient scans and higher values for ex vivo scans of better image quality. To get the highest integration time, uncheck the "Continuous ROT" button. For standard microCT measurements, use ~400 ms for the µCT35 and ~200 ms for the vivaCT40. The maximum integration time is scanner-specific and limited to prevent saturation of its detector.

*'''Average Data''': This is often referred to as frame averaging and is used to improve a scan's SNR. Multiply the average data value by the integration time to calculate the effective integration time. Only use this if the integration time is maxed out.

*'''Measurement Time''': This is the estimated scan time without the time performing the scout view or warm-up of the scanner.

*'''CTDIvol''': Computed Tomography Dose Index (CTDI) is a standardized measure of radiation dose output of a CT scanner for scanner settings' comparison purposes only, and it represents the average absorbed dose along the longitudinal axis from a series of contiguous CT exposures. Volumetric CTDI is the ratio of the weighted-CTDI to the level of overlap between slices (pitch). CTDIvol has no consideration of real scan length and does not represent actual dose administered to the patient.
:[[File:CTDI.JPG|600px]]

*'''DLP''': Dose Length Product DLP = CTDIvol * Scan Length in unit of mGy-cm.

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====XtremeCT II Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 4608
| 2304
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 3000
| 900
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 140 mm
| 30.3
| 60.7
| 91.1
| 136.7
| 273.4
|-
! colspan="2"| Slices/Stack
| 338
| 168
| 112
| 74
| 37
|-
! colspan="2"| Stack Thickness (mm)
| 10.24
| 10.20
| 10.20
| 10.12
| 10.12
|-
! colspan="2"| Time/Stack (min, at 43 ms Integration Time)
| 8.1
| 2.0
| 2.0
| 1.4
| 0.7
|-
! colspan="2"| Time Current Product (mAs)
| 238
| 71
| 59
| 40
| 20
|-
! colspan="2"| CTDIvol (mGy)
| 37.4
| 11.2
| 9.3
| 6.4
| 3.2
|-
! colspan="2"| DLP (mGycm)
| 38.3
| 11.4
| 9.5
| 6.4
| 3.2
|}

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====XtremeCT I Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 3072
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 126 mm
| 41
| 82
| 123
| 246
|-
! colspan="2"| Slices/Stack
| 221
| 110
| 73
| 36
|-
! colspan="2"| Stack Thickness (mm)
| 9.06
| 9.02
| 8.98
| 8.86
|-
! colspan="2"| Time/Stack (min, at 100 ms Integration Time)
| 3.7
| 2.8
| 1.9
| 1.0
|-
! colspan="2"| Time Current Product (mAs)
| 114
| 86
| 57
| 29
|-
! colspan="2"| CTDIvol (mGy)
| 7.3
| 5.5
| 3.6
| 1.9
|}

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====VivaCT80 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 3072
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1500
| 1000
| 500
| 250
| 125
|-
! rowspan="6"| Voxel Size (µm)
! scope="row"| FOV/Diameter 31.9 mm
| 10.4
| 15.6
| 31.9
| 31.2
| 62.4
|-
! scope="row"| FOV/Diameter 35.9 mm
| 11.6
| 17.5
| 35
| 35
| 70.1
|-
! scope="row"| FOV/Diameter 39.9 mm
| 13
| 19.5
| 39
| 39
| 78
|-
! scope="row"| FOV/Diameter 49.8 mm
| 16.1
| 24.2
| 48.5
| 48.5
| 97.1
|-
! scope="row"| FOV/Diameter 63.9 mm
| 20.8
| 31.2
| 62.4
| 62.4
| 124.8
|-
! scope="row"| FOV/Diameter 79.9 mm
| 26
| 39
| 78
| 78
| 156
|-
! colspan="2"| Slices/Stack
| 333 ~ 328
| 222 ~ 219
| 111 ~ 109
| 111 ~ 109
| 55 ~ 54
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 14.9
| 10.0
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 73
| 48
| 24
| 12
| 6
|}

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====VivaCT40 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 21.5 mm
| 10.5
| 21
| 21
| 42
|-
! scope="row"| FOV/Diameter 25.6 mm
| 12.5
| 25
| 25
| 50
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 35.8 mm
| 17.5
| 35
| 35
| 70
|-
! scope="row"| FOV/Diameter 38.9 mm
| 19
| 38
| 38
| 76
|-
! colspan="2"| Slices/Stack
| 213
| 106
| 106
| 53
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 9.9
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 61
| 31
| 15
| 8
|}

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====µCT35 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 7.2 mm
| 3.5
| 7
| 7
| 14
|-
! scope="row"| FOV/Diameter 12.3 mm
| 6
| 12
| 12
| 24
|-
! scope="row"| FOV/Diameter 20.5 mm
| 10
| 20
| 20
| 40
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 37.9 mm
| 18.5
| 37
| 37
| 74
|-
! colspan="2"| Slices/Stack
| 232 ~ 235
| 116 ~ 117
| 116 ~ 117
| 58
|-
! colspan="2"| Time/Stack (min, at 400 ms Integration Time)
| 23.9
| 12.3
| 6.5
| 3.5
|-
! colspan="2"| Time Current Product (mAs)
| 119
| 60
| 30
| 15
|}

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===Advanced Settings===
*'''Number of Det-lines (for Scout-View)''': Defines how many lines on the detector shall be used during the Scout-View. Using all available lines provides faster Scout-Views but some faint horizontal lines might be seen between the stacks. Limit the number of lines to a small number to obtain Scout-Views without these artifacts but the time of the Scout-View will increase.

*'''Number of Det-lines (for CT-scan)''': Defines how many lines on the detector should be used. This number influences the number of slices within a stack. Limit the number of detection lines if you see residual cone beam artifacts.

*'''FOV/Scan Diameter''': Chose the diameter of the FOV. This action is cropping the area of the detector.

*'''Software binning''': factor of the pixels on the detector.

*'''Hardware binning''':

*'''Samples''': number of (possibly binned) pixels on the detector that are used for each slice (note: this number is given for the whole FOV).
*'''Proj/180°''': number of projections taken per 180° turn of the sample.

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===Reconstruction===

*After each image stack is acquired, it is automatically submitted to the queue (sys$slow) for reconstruction. The reconstruction for each image stack is split into four jobs to make efficient use of processors.
*The reconstruction time depends on the resolution setting, with low resolution scans reconstructing faster than high resolution scans. Normally scans are reconstructed within a day or two.
*It is possible to resubmit a scan for reconstruction (refer to [[Scanco_Administration#Reconstruction | '''Scanco Administration's Reconstruction''']]) for details. This may be necessary or desirable for several reasons:
#The sample did not reconstruct properly (e.g., due to a power failure)
#To reconstruct the object at an angle (e.g., so that the anterior surface of a bone is always in the same direction).
#A new beam hardening correction was applied to the sample
#The scaling was changed for the sample to change the brightness

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==Perform a Scan==
===Perform a Single Scan===
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] for instructional details.

===Perform Batch Scans===
*Batch scan mode is only available on microCT scanners.
*Batch scans can be setup for different regions of interest (ROI) within a sample or for different samples contained within a sample holder.

#'''Setup the First Scan'''
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] to use the "Other..." button to find your sample number, choose a controlfile, perform a scout view (a mouse's whole body in this example), use the reference line to setup the first scan region (mouse skull in this example).
#*To add a batch scan press the "Batch Measurement" button.
#:[[File:Batch_scan_01.preview.jpg|600px]]
#*An information window is displayed with the scan measurement number. Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']] then press "OK" to close the window. An entry is also added to the measurement history for the sample.
#:[[File:Batch_scan_02.preview.jpg|600px]]
#'''Setup the Next Scan'''
#*Using the "Other..." button, find your next sample number, choose a new control file (if desired).
#*If the next region of interest or sample is not in view of the current scout view, adjust the parameters of the scout view and obtain a new one.
#*Use the reference line to set a new scan region (upper limbs in this example).
#*To add a batch scan press the "Batch Measurement" button.
#*As the first scan, a measurement number is assigned for this new scan. Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']].
#:[[File:Batch_scan_03.preview.jpg|600px]]
#*Repeat this process until you have added all your scans.
#'''Start the Batch Scans'''
#:There are two ways to start a batch scan:
##Click the "Start Batch Scans" button: the program will automatically close so that control of the scanner can be allotted to the queue.
##Exit the scanning program.
#:[[File:Batch_scan_04.preview.jpg|600px]]
#'''Check the Queue'''
#*Batch jobs will be submitted to the SCEVA2_BATCH queue for µCT35 or SC5019_BATCH queue for vivaCT40.
#*Initially the jobs will show up as temporary (TMP) jobs:
#:[[File:Batch_scan_05.preview.jpg]]
#*After about 30 seconds, the sample number will show up in entrie names:
#:[[File:Batch_scan_06.preview.jpg]]
#'''Request an Email Notification'''
#*There is a script in the commands (com) directory that will put an entry into the batch queue to send an email. Run the script and input parameters (queue and email) as prompted.
#:[[File:Batch_scan_07.preview.jpg]]
#'''Cancel a Batch Scan'''
#*For errors made during batch scan setup, to cancel a scan in progress, or to cancel a pending scan.
#:[[File:Batch_scan_08.preview.jpg]]
#*If you cancel all the scans and the scanner door does not unlock automatically (µCT 35 only), then start the measurement program and the scanner will unload, unlocking the door.

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==Action on Image Artifacts==
===Rescan for===
*'''Motion Artifacts'''
*'''Sample Out of the Field of View'''

===Contact Scanco Medical for===
*'''Ring Artifacts''' (Bad Detector)
:*Ring artifacts are caused by a faulty detector pixel and show up in the reconstructed image as a full or partial white circle.
:*When noticed, please notify lab technicians who will contact Scanco Medical to perform a "Pixel Correction", which will correct this artifact for future scans and can be used to update previous scans.
:*You should not rescan the sample if there is a ring artifact.
<div><ul>
<li style="display: inline-block;"> [[File:Ring_artifact.jpg|thumb|none|350px|Image with Ring Artifact]] </li>
<li style="display: inline-block;"> [[File:Ring_artifact_corrected.jpg|thumb|none|350px|Same Image after with Detector Correction]]</li>
</ul></div>

*'''Bad Centre Calibration Values'''
*'''Defective Shutter Artifact'''

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=Evaluation=
==Evaluate a Scan==
*To evaluate a scan, refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.

===Open default ISQ===
You can load a defual ISQ usig uct_evaluation program:

<pre>
$ def uct_default_isq DISK3:[MICROCT.PROJECTS.VALIDATION.MODELS]C0000123.ISQ ! or
$ def uct_default_isq DISK2:[MICROCT.DATA.00001234.00005678]C0003456.ISQ
$ uct_evaluation
</pre>

Hit <code>cancel</code> when asked files to load, and the file you just set as default will be loaded.

*Use the whole pathname for ISQ.
*If you don't import your data into the system, you cannot store your evaluation results in the measurement database. You will have to use the LOG file to access your results.
*Only start a 3D evaluation if and only if the sample (patient) and measurement index are correct in the ISQ full path! Also, no results will be stored in the database unless the ISQ header info (samp/meas) is correct.
*Many of the UCT_xxx.COM scripts use the whole filename to extract the sample and measurement numbers, so it is possible that some evaluations will not run. UCT_xxx_BATCH_V4.COM is an example of an evaluation that will not run, but UCT_CUTOUT.COM will run (doesn't need any sample/meas info).

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==Draw Contours==
*Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
*Contouring is the first step in the analysis process, which allows you to segment the desired bone from surrounding tissues.

===Contouring Tools Reference Sheet===
*[[Media:Contouring-tools.pdf |'''Contouring Tools Reference Sheet''']]
*Contours must always be drawn COUNTER-CLOCKWISE!!!

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===Contour and Run the Standard Patient Evaluation===
The following instructions are for contouring standard patient radius and tibias.

#Open the Evaluation Program and select your sample.
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.
#Zoom into the desired bone (Radius or Tibia)
#*Using the zoom menu from the top panel, zoom into the Radius or Tibia.
#*Usually 3x zoom is appropriate.
#Draw contours roughly around the bone.
#*Select the first contouring tool (top left button) and draw COUNTER-CLOCKWISE.
#Automatically generate contours for all slices in the scan.
#*Double click the image to bring up the contouring window.
#*Double click again and the program will attempt to snap the contour to the bone. Double click again if needed.
#*Select Forwards, and then Iterate Forwards to have the evaluation program automatically segment the bone.
#Modify any contours as needed.
#*Select the second contouring tool (2nd button from top) to fix any "wrong" contours.
#*Draw COUNTER-CLOCKWISE!!
#*If many contours cannot be automatically generated correctly i.e. cortical bone is porous and evaluation program misses a lot of bone, it may be better to use the Range/Morph function rather than fixing each individual slice.
##This is done by first clearing all the breakpoints (Clear all BP in contouring window). The boxes will now become red.
##Manually fix the slice that does not have the correct contour automatically drawn, skip a few slices and manually fix that slice as well. The slices that you have fixed will turn green, indicating that it is a breakpoint (BP).
##Now you can morph between the two breakpoints (BP, green boxes) you have just created. Select the BP with the higher slice number, select range (first column on left) from the contouring window, followed by morph (second column from left).
#Save Contour (.GOBJ): Make sure you save your work!
#Run the 3D Standard Evaluation for your specific project (and timepoint).
#*Select 3D evaluation under Tasks to bring up the window. You'll then need to Select... the evaluation specific for your project.
#*There are a variety of evaluations to choose from, you can search for your project's evaluation script by typing in the name of your project in the filter window.
#Check the queue to ensure that the evaluation is running properly.
#*Type <code>$ show que</code> in a terminal window will allow you to see all running processes.

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===Correct Trabecular Contours and Run the Cortical Evaluation===
Once the standard evaluation has been completed, an auto-segmentation process is completed to segment the cortical from the trabecular bone. However, the auto-segmentation is not always accurate, and hence the contour (TRAB.GOBJ) will need to be checked.

#Load TRAB.GOBJ by selecting File, then load GOBJ from the top panel.
#*You will now see a list of all GOBJ files pertaining to your sample. You'll need to load the TRAB.GOBJ.
#*When the TRAB.GOBJ has loaded, you will see that the loaded contour is between the cortical and trabecular bone.
#Correct contours as needed
#*Can manually adjust the slices or use the Range/Morph function.
#*Remember to draw COUNTER-CLOCKWISE!
#Run the 3D cortical evaluation for your specific project (and timepoint, if relevant).
#*Select 3D evaluation under Tasks to select the appropriate evaluation script.

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==Evaluation Scripts==
===Scanco Standard Evaluation Scripts===
The following are descriptions of some of the standard evaluation scripts provided by Scanco Medical.

*'''3D Segmentation of VOI, 1 solid object'''
:Produces a 3D segmented (binary) object with values 0 (background, hidden) and 127 (solid). Input Gaussian filtering and threshold parameters. Draw contour to isolate the object of interest (optional).

*'''3D Seg. of 2 VOIs: solid dense in transparent low dens obj'''
:Produces a 3D segmented object with values -1 (transparent), 0 (background, hidden), and 127 (solid). Input two sets of Gaussian filtering and threshold parameters (input the second set by pressing the red 2 button). The preview shows the solid object in white and the transparent object in red. Draw one contour to isolate the object of interest (optional). This script is useful for showing soft tissue and bone.

*'''Bone Trab. Morphometry (3D Seg, 3D Calc, Print Sheet)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour to isolate the trabecular bone. Performs model-independent (direct) measurements on the trabecular region. Outputs: BV, TV, BV/TV, TbBMD, TbTMD, BS, SMI, DA, ConnD, TbTh, TbThSD, TbSp, TbSpSD, TbN, and Tb1/NSD.

*'''BV/Density only Bone Eval. (3D Seg, BV and Dens Calc, Print)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour to isolate the region of interest. Outputs: BV, TV, BV/TV, BMD, and TMD.

*'''Bone Midshaft Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour on the outer surface of the bone. Outputs: BV, TV, BV/TV, BMD, TMD, and moment of inertia parameters.

*'''Bone Midshaft more than e.g. 50 slices Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour on the outer surface of the bone. If you wish to exclude the medullary area from the analysis, then draw a counterclockwise contour on the outer surface of the bone and a clockwise contour on the inner surface of the bone. Performs direct measurements in addition to the standard midshaft analysis. Outputs: BV, TV, BV/TV, BMD, TMD, moment of inertia parameters, Th, and Sp.

*'''Convert to TIFF'''
:Converts the grayscale data to TIFF slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Convert to DICOM'''
:Converts the grayscale data to DICOM slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Reformat to Axial Cuts'''
:Flips the dataset from the XY plane to the XZ or YZ planes (specify in the advanced options for the script). This is useful if you want to contour your sample in a different plane. The flipped sample is imported as a new measurement under the same sample number as the original data.

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===Understanding Evaluation Scripts===
Following are some example evaluation scripts full of comments to promote understanding:
*[[Media:IPLV6_VOI.pdf|IPLV6_VOI script]]
*[[Media:IPLV6_MIDSHAFT.pdf|IPLV6_MIDSHAFT script]]
*[[Media:IPLV6_TRABECULAR_BONE.pdf|IPLV6_TRABECULAR_BONE script]]

===Setup Customized Evaluation Scripts===
To setup an evaluation script customized to your project, in the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']]:
*Choose "Scripts" then "Import from" then "TEMPLATES", pick a Scanco Standard Evaluation Scripts and Save.
*Choose "Scripts" then "Modify". Choose the script that was just imported and click "OK", Change the name of the script.
*Modify the default segmentation and other parameters for the script. When finished making changes press "Save" then "OK".

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==Image Processing Language (IPL) Scripting==
The following documentations related to IPL scripting, as it applies to image analysis was compiled by Jan Owoc in July 2013 based on numerous sources including own experience.

===Your First IPL Script===
*'''Prerequisite''': you are familiar with navigating the VMS system.
*'''"$" or "ipl>"''': the DCL and IPL prompts respectively, and you should only type the text after the prompt.
*If you FTP the file to the OpenVMS system, ensure you use "binary" to transfer the file.
You can run these commands on almost any greyscale AIM file. Example file here: MJ7101.AIM

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====Interactive IPL====
*Command <code>$ ipl</code> starts IPL interactively, that is you see the result of each command as you run it.
*While it is useful for testing, running large scripts interactively may interfere with others using the computer.
 
*'''Reading an AIM file'''
:Before you can run any analysis on the AIM file, you need to read it into IPL and assign it a file handle. This is done using the command <pre>ipl> read in MJ7101.AIM</pre>
:A fraction of a second later, the file should have been read into memory and assigned the internal name "in". If we want to do some basic density calculations on it, we can use the command<pre>ipl> vox_ in 0</pre>
:*IPL, much like DCL, will automatically complete the command if it is given enough characters.
:The "vox_" was expanded to the command "vox_scanco_param" (calculates voxel-counting parameters) and told you that the mean density of the cube is 114 mg HA/cm3 and a standard deviation of 283 mg HA/cm3.
:The argument "in" is the internal name of the image.
:The argument "0" is the region. The command vox_scanco_param supports several numbered regions if, for example, you wanted to separately compute the density for the trabecular region and the cortical region.
 
*'''Segmenting an AIM file'''
:Some parameters, like average density, are computed from the [[Scanco_User_Instructions#Grayscale_Images|'''Greyscale Image''']]. Other parameters, like the trabecular number, require an image that has been segmented to [[Scanco_User_Instructions#Binary_Images|'''Binary Images''']], that is converted into "bone" and "not bone".
:There are many ways to separate bone from non-bone, and parameters that work well for one dataset will not generally work for images of different samples, or acquired at different resolutions.
:One of the simplest segmentation methods "seg_gauss" is to apply Gaussian smoothing to the sample, to eliminate the noise present in the image, followed by a semi-arbitrary threshold that preserves the trabecular structure.
<pre>
ipl> seg_gauss in seg

-sigma [1.000000] >
-support [2] >
-lower_in_perm_aut_al [300.000000] >
-upper_in_perm_aut_al [100000.000000] >
-value_in_range [127] >
-unit [0] > 2
</pre>
:seg_gauss expects 8 parameters, and we have provided only 2. It will now prompt us for the remaining 6 one-by-one.
:Leave everything at the defaults (simply hit "Enter") except the unit, which we will change to "2".
:For young human trabecular bone from the distal tibia scanned at 20 um in the uCT 35, but then downscaled to 80 um, the above parameters give a reasonable representation of the trabecular structure. With other bones at other resolution, you may need to change the sigma, the support, and the lower threshold.
:The unit of "2" simply means that we are working in units of mg HA/cm3.
:Now that the cube is segmented, we can run the same voxel-counting command as above and obtain more information. <pre>ipl> vox_ seg 0</pre>
:We now know that our combination of smoothing and threshold resulted in an object volume of 103 mm3 (i.e. volume of bone) and a bone volume ratio of 22.88%.
 
*'''Writing out a file'''
:we can write the segmented file out for future use. Accept the defaults for the remaining arguments. <pre>ipl> write seg MJ7101_SEG.AIM</pre>
:Now you can quit IPL and verify that the segmented file has been written out. <pre>ipl> quit</pre>

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====Batch IPL====
*Command <code>$ ipl_batch</code> starts IPL inside a script that would be submitted to a queue.
While the following code is likely to work, it is not very readable:
<pre>
$ IPL_BATCH
read in MJ7101.AIM
vox_ in
seg_gauss in seg 1 2 300 100000 127 2
vox_ seg
write seg MJ7101_SEG.AIM
..
$ EXIT
</pre>
*Instead, it is recommended that you copy and paste the "pretty" output of the command after you have run it once interactively.
*Values that are likely to change should be variables, defined at the top of the script.
*To substitute a variable from DCL into IPL, use a double-quote character before the variable name, as shown in the example below.
Copy and paste the below into a text editor.
<pre>
$ modelname :== MJ7101.AIM
$ threshold == 300
$ outputfile :== MJ7101_SEG.AIM
$
$ IPL_BATCH

/read
-name in
-filename "modelname

/vox_scanco_param
-input in

/seg_gauss
-input in
-output seg
-sigma 1.000000
-support 2
-lower_in_perm_aut_al "threshold
-value_in_range 127
-unit 2

/vox_scanco_param
-input seg

/write
-name seg
-filename "outputfile

..
$ EXIT
</pre>
Now, it is clear what the full names of the commands are, and what the parameters mean.
*If a parameter isn't important and can be left at the default (for example the region number during vox_scanco_param), you can leave it out of the file.
Save the file as MYSCRIPT.COM and run it using <code>@MYSCRIPT.COM</code>.

 
*'''Submitting to the queue'''
:As mentioned in the introduction, running IPL interactively on larger models negatively impacts other users of the system. Copying the commands to a file and running it from the command line has the same effect.
:*The correct way to run larger scripts is to submit the job to the queue. <pre>SUBMIT/QUE=SYS$FAST MYSCRIPT.COM</pre>

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===IPL Reference===
*[[Media:SCANCO_-_Software_-_IPL_instruction_manual_0.pdf|'''Official Scanco IPL Documentation''']]
*[[Media:scanco-software-ipl-instruction-manual.pdf|'''Scanco IPL Manual]]

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====Standard Read Write etc. Functions====
*'''/read''': Reads a file into ipl and gives the file an internal name
*'''/aim_read''':
*'''/read_versatile''':
*'''/write_v020''': Writes an aim file to the directory in which ipl is open (or specified directory if in a script)
*'''/write_new''':
*'''/write_part''':
*'''/copy''': Copies an internal file (a file that is already in the ipl system) and allows the copy to be given a new name.
*'''/delete''': Deletes an internal file (a file that is already in the ipl system)
*'''/rename''': Changes the name of the file (input is the old name and output the new name)
*'''/list''':
*'''/options''':
*'''/release_history''':
*'''/commands_write_log''':

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====Segmentation Functions====
*'''/gauss_lp''': Applies a low pass gaussian filter with specified sigma and support values
*'''/fft_laplace_hamming''':
*'''/median_filter''': Applies a low pass median filter to reduce unwanted noise in an image
*'''/seg_gauss''': Segments aim files using the input sigma of gauss and the filter support for gauss. A threshold can also be applied using this function.
*'''/threshold''': Removes data outside of the specified range
*'''/absolute_threshold''':
*'''/adaptive_threshold''':
*'''/adaptive_iter_threshold''':
*'''/matching_threshold''':

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====Gobj and Masking Functions====
*'''/gobj_maskaimpeel_ow''': Cuts an aim file with a gobj so that only the portion of the aim within the gobj remains. Peel_iter value used to specify the number of pixels within the gobj the function will need to cut.
*'''/gobj_to_aim''': Reads a gobj file from the directory and makes an aim file (the aim file is in ipl, to output it to the directory use write).
*'''/togobj_from_aim''': Takes an aim file and writes a gobj file (the gobj is output to directory).
*'''/gobj_circumf_area''':
*'''/gobj_join''':
*'''/gobj_join_consec''':
*'''/gobj_scale''':
*'''/gobj_isotrop''':
*'''/cortex_maskoff''':
*'''/peel3d''':

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====Voxel-Counting, Density and Triangulation Functions====
*'''/db_scanco_activate''':
*'''/db_clear_eval''':
*'''/db_calib_unit_fill''':
*'''/db_set_mean_accur''':
*'''/voxgobj_scanco_param''': Inputs an aim file and a gobj and provides information (including total volume, object volume and the mean value of the points) on the region within the gobj.
*'''/vox_scanco_param''': Inputs an aim and provides information including total volume, object volume and the mean value of the points.
*'''/tri_da_metric_db''':
*'''/tri_direc_distr''':
*'''/connectivity''': Receives a component labelled aim object and calculates the connectivity of the labelled components.
*'''/conn_nocl''':
*'''/conn_bgcl''':
*'''/fractal_dimension''':

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====Distance Transformation (Sphere Filling) Functions====
*'''/dt_object_param''':
*'''/dt_ow_object_param''':
*'''/dt_background_param''':
*'''/dt_mat_param''':
*'''/dt_cortex_obj_param''':
*'''/dt_value_output''':
*'''/dt_mat_output''':

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====Statistical Functions====
*'''/examine''': Receives an AIM object and outputs specified information based on the item input.
*'''/histo''':
*'''/moment2d_of_inertia''':
*'''/moment3d_of_inertia''':
*'''/zmeanmax''':

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====Voxelsize-Scaling Functions====
*'''/isotrop''':
*'''/scale_elsize''':
*'''/ipscale_elsize''':
*'''/noipscale_elsize''':
*'''/scale_ow_elsize_noip''':

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====Component Labeling Functions====
*'''/cl_ow_rank_extract''': Receives AIM file and over writes it with an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl_rank_extract''': Receives AIM file and outputs an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl26_rank_extract''':
*'''/cl_image''':
*'''/cl_extract''':
*'''/cl_slicewise_extractow''':
*'''/cl_nr_extract''':

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====Add, Concat, Cut etc. Functions====
*'''/add_aims''': Adds the values of two AIM images in a 3D space.
*'''/add_constant_ow''':
*'''/border_change''':
*'''/bounding_box_cut''': Cuts extra space out of an aim file so that only the region with the data remains. A border can be added to the image using the border input.
*'''/concat''': Takes two aim files and combines them. The data from both aims or just the common region can be kept. To add the images add_not_overlay is set to true (for example if image 1 has a value of 41 and image 2 has a value of 82, the combined value will be 123).
*'''/concat_adapt''':
*'''/divide_volumes''':
*'''/fill_min_max_ow''':
*'''/header_geo_set''':
*'''/header_log_set''':
*'''/header_calib_ov''':
*'''/invert_ow''':
*'''/mult_constant_ow''':
*'''/multiply_volumes''':
*'''/sqr_to_float''':
*'''/sqrt_to_float''':
*'''/offset_add''':
*'''/offset_set''':
*'''/clear_offset''':
*'''/fill_offset_mirror''':
*'''/fill_offset_duplicate''':
*'''/set_value''': Sets the values of the object and background of an aim file to chosen values
*'''/sub_get''': Extract a portion of an image 
**-pos corresponds to x,y,z origin -1 -1 -1 maintains the original coordinates 
**-dim corresponds to x,y,z dimensions -1 -1 -1 maintains the original dimensions (within maximum range) 
**indexing starts at 0 instead of 1
*'''/sub_pick''':
*'''/subtract_aims''': Subtracts one aim from another and outputs the remaining region.
*'''/sup_divide''':
*'''/transparent_concat''':

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====Erosion Dilation Open Close Functions====
*'''/erosion''':
*'''/dilation''':
*'''/open''':
*'''/close''':
*'''/erosion_dilat_variable''':

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====Import Export Conversion Norming Functions====
*'''/import_freeformat''':
*'''/dicom_to_aim''':
*'''/todicom_from_aim''':
*'''/dicom_list_series''':
*'''/isq_to_aim''':
*'''/isq_gobjfit_to_aim''':
*'''/toisq_from_aim''': Writes an isq file to the directory ipl is open in (or specified directory) from an aim file. The isq name should be 8 characters long.
*'''/mesh''':
*'''/msq_from_aim''':
*'''/rsq_to_aim''':
*'''/stl_tri''':
*'''/convert_to_type''':
*'''/convert_unsigned''':
*'''/norm_max''':

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====Functions for Root Canal Evaluations====
*'''/separ_roots''':
*'''/calc_ctr_mass_list''':
*'''/calc_ctr_mass_diff''':
*'''/treated_surf''':
*'''/match_cut''':
*'''/match_cut_adapt''':

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====Miscellaneous Functions====
*'''/align_z''':
*'''/dcl''':
*'''/flip_aim''':
*'''/growback_to_orig''':
*'''/turn3d''':
*'''/turn2d''':
*'''/upat_filldb''': Fill special Upat DB for patient (radius/tibia) evaluation
*'''/xray''':

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====Obsolete, Experimental and Duplicate Functions====
*'''/curv_tri''':
*'''/cut2D_shape_ow''':
*'''/join_uncompress''':
*'''/mil_param''':
*'''/milv1_param''':
*'''/gauss_seg''': duplicate of /seg_gauss
*'''/from_aim_to_isq''': The function toisq_from_aim will also convert an aim to an isq
*'''/local_threshold''':
*'''/edge_canny''':
*'''/sobel_grad''':
*'''/hysteresis_thresholg''':

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====Functions only available in iplfe====
*'''/register''': Registers two aim files and output a transformation matrix of the transformation to moving input 2 into the space of input 1. Gobjs can be input (registration is more successful with gobjs). Orientation search can be done with masscenter, and/or moment of inertia (MoI), or degree intervals.
*'''/transform''': Transforms an aim file using a transformation matrix (a text file of the matrix can be input). Interpolation options are nearest neighbor, linear, and cubic interpolation. The inverse of the transform provided can be done by setting Tmat_invert to true.
*'''/fe_solveD''': A number of finite element functions are available in iplfe, not all are listed here

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=Results=

==Images and Animations==
Refer to [[Scanco_User_Instructions#.C2.B5CT_Ray|'''µCT Ray''']] for detailed instructions.

===[[#Change_the_View|Change View]]===
===[[#Change_the_Colours|Change Object Colors]]===
===[[#Cutplane_and_Subdim|Show a Section-View of an Object]]===

===Save a Screetshot Image===
#Open XV from a dec terminal on a workstation by typing <code>$ xv</code>.
#Open and frame the image, program etc. that you would like to save an image of.
#In XV, click GRAB. You can either autograb the entire screen after a delay or manually grab a desired area.
#After grabbing the desired section, click Save in XV.

===[[#Save_the_Image|Save Image]]===
===[[#Save_for_Animation|Save Frames for an Animation]]===

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===Convert AIM to TIF series===

Use the utility SEQ_TO_IMAGE located in the UT directory. A symbol has been set up to run this called TIF.

<pre>
$ mcr ut:seq_to_image
Program: seq_to_image V1.1b
Input-File []: WISDOM_L_R05.AIM
File Format [TIF]:
Default TIF Names: WISDOM_L_R05_xxxx.TIF

Output-File [WISDOM_L_R05]:
!> Reading AimVersion020
Start Slice [0]:
End Slice [179]: 5
Number of images thereof (count) [6]:
Scale Factor (Integer) [1]:
global_pos (1=true, 0=false) [0]:
Max value to norm to 255 [32767]:
Slice: 0
Slice: 1
Slice: 2
Slice: 3
Slice: 4
Slice: 5
$ dir wisdom*

Directory DISK1:[MICROCT.SCRATCH]

WISDOM_L_R05.AIM;1 WISDOM_L_R05_0000.TIF;1 WISDOM_L_R05_0001.TIF;1
WISDOM_L_R05_0002.TIF;1 WISDOM_L_R05_0003.TIF;1
WISDOM_L_R05_0004.TIF;1 WISDOM_L_R05_0005.TIF;1

Total of 7 files.
$
</pre>

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===Generate TIF (or others) from 3D rendered volume===

This replaces uct_movie that operated on the alpha systems. UCT_3D can be called in batch mode.

A pdf describing this tool is located here: [[Media:UCT_RAY V4.0-1.pdf]]

To interactively declare the desired settings:
<pre>
$ uct_3d_batch
?CT RAY_BATCH V4.0-1

UCT_R: Application initialized
Filename []:
Print-Filename [SYS$SCRATCH:TEMP_3D.PS]:
Ambient (0.0..1.0) [0.200]:
Shadows (0/1) [1]:
Size (1..1024) [1024]:
Elevation (-90..90) [30]:
Rotation (-180..180) [35]:
Copies (0..9) [1]:

</pre>

To apply a saved set of settings, a setup-file can be created by running uct_3d in interactive mode. Select "Presets" from the toolbar and save the settings you desire (e.g. elevation 90, rotation 0).

<pre>
$ uct_3d_batch setup-file [data-file printfile]

Examples:

$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.ps
$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.tif

</pre>

To automatically generate tifs for many files, a script was created to replace PRINT_3D.COM
The script is currently stored in the xtremect2 com directory.

<pre>
@COM:PRINT_REG_TIF.COM

Generates a 3D image from a segmented file.

The outputs include:
- two 3D renderings (TIF)

Use full pathnames for the segmented AIM.

P1 - Segmented AIM

Usage:
@COM:PRINT_REG_TIF.COM DISK2:[MICROCT.DATA.00000379.00001376]C0001234_SEG.AIM
</pre>

This script can be modified to use a custom preset file.

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===Make an Animation===

To calculate an Animation, two (separate) tools of the 3D program are used: the set-up of start and end point of the Animation, and the 'Auto-Print' tool that automatically creates the TIF files for every rendered image.

This is a 'step by step' guide to create an animation using TIFF files:
:* Open your sample in the 3D program.
:* Now, open 'options','Animation'
:* Render your Image the way you want your animation to start. e.g. observer rotation -179 degrees. You may interrupt if you want. If you are satisfied with all the settings (rotation, elevation, transparency, colors etc.) the Click on 'Get Settings A'
:* Then, adjust all the settings for the endpoint of your animation (with the mouse or the sliders) e.g. observer rotation +179, and start the rendering. If satisfied, click 'Get settings B'

Note: To test, put # of views to 5 or 10... You can also interrupt the build-ups for faster viewing.
:* Click the START button again, wait till the build-up of the 3D image is finished.
:* DO NOT HIT 'START CALCULATION' YET!
:* First, you also need to set-up the 'Auto-Print' mode:
:* Go to the 'Print' menu (file --> print), choose print to TIF and to File and enter THE BEGINNING OF A FILENAME, e.g. sys$scratch:test_ (the program will append 0000.TIF, 0001.TIF etc afterwards) Or enter (possibly with middle-mouse-click): "DK0:[MICROCT.DATA.00001234.00003456]ANIMATION_" to have the result go to the measurement directory.
:* Click on the 'Auto-Print' box. Then 'ok'
:* Adjust the number of views (e.g. 200), then click on 'Start Calculation', and it will render. This may well take a long time.
:* Take those TIFF files to your PC, and combine the sequences in the program that you are using to convert the TIFF files to AVI or MOV files (like Windows Movie Maker 2, or Quick Time Pro, or Adobe Premiere etc.)

Notes/Hints:
:* The order in the above list can also be reversed: You can first set up the 'Auto-Print', and then go into the 'Animation' menu, choose start and end settings, and hit 'Start Calculation'
:* The positions A and B can be any: e.g. with subdim, you can first take everything (A), then slide it back to nothing (B).
:* You can even slowly change the color of an object. Or slowly hiding objects: choose 'transparent' for object, but change from 0.0 (A) to 1.0 (B)
:* If you want to create a movie with different sections, e.g. first rotate around, then slowly make bone transparent, then cut in: Do this in multiple sections with the 3D program, e.g. first create Auto-Print files 'rotation_0000 to rotation_0200', then 'transp_0000 to transp_0050', and then 'cut_0000 to cut_0100'. Make sure ALL the settings from the last view of the previous section match those of the first view of the next section so you get smoot transitions.
:* The 'Auto-Print' box is also usable without the 'Animation' Menu: Activate it, Like above, with sys$scratch:test_ only the beginning of filename. 'ok' Then, whenever a 3D image is completely built-up (so when you are happy with a view and you do not interrupt the build-up), automatically a TIF file is generated, numbered sequentially.

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===Combine two volumes to create transparent image===

First create your two start "seg.aim" images
Start by running either the normal eval, or $ voi to get one _seg.aim file of one region

Rename it to a better name in the session manager, e.g. c0001234_all.aim

Then either by choosing different contours, or a different threshold, start the $ voi or the normal evaluation again, which will create another _seg.aim file.

Load them in the 3D viewer ('all files') to check that they look like expected.

Now we will go into IPL and concatenate those two volumes.

<pre>
$ ipl
/read all xx_all.aim
/read trab xx_seg.aim
/transparent
-input_solid trab
-input_transp all
-output out
</pre>

Note: the solid volume is OVERWRITING the transparent input volume, so usually, it
is the smaller (inner) of the two.

<pre>
/write out xxx_transp.aim
/quit
</pre>

Then load the _transp.aim file in 3D, go to 3D program FAQ to see how to change transparency levels in the Display options there.

See IPL FAQ or 3D program FAQ if you need help with these parts.

Step by Step Example: Showing your chosen trab VOI within whole bone
:* $ voi, enter threshold in ipl_voi.com, start 3d eval WITHOUT contours
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_all.aim
:* Start up normal eval program, draw trabecular contours, check threshold in ipl_fixed_batch_v4.com, start 3D eval.
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished

Step by Step Example: Showing high-dense volume surronded by lower density volume

:* Start normal 3D eval with HIGH threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_high.aim
:* If wished: read out 3d result database with $ uct_list
:* Start normal 3D eval with LOW threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished

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==Image Tours==
===XtremeCT Image Tours===

===MicroCT Image Tours===
*Refer to [[Media:Tours_image_gallery.pdf|'''MicroCT Image Gallery''']] with its [[Media:Tours_image_notes.pdf|'''Image Notes''']].
*Refer to [https://youtu.be/tT3dz4VrwfE '''MicroCT Image Tour YouTube Video''']
*Hover over a thumbnail and click on its overlaid description to see the animated GIF or a larger version of the image.

<gallery mode="packed-hover" heights=220px caption="Micro-CT Scans">
Image:MOUSE_SKELETON_PIC01.jpg|[[Media:MOUSE_SKELETON_360.gif|Mouse (38µm)]]
Image:Segmented_Mouse_Femur.jpg|[[Media:Segmented_Mouse_Femur.jpg|Mouse Femur showing Cortical and Trabecular Bone (10µm)]]
Image:LIZARD_WHOLE_VIEW_P1_0044.jpg|[[Media:LIZARD_SKELETON_360.gif|Lizard (88µm)]]
Image:LIZARD_SKULL.jpg|[[Media:LIZARD_SKULL.jpg|Lizard Skull showing Thickness Distribution (25µm)]]
Image:DUCK_BEAK_PIC01.jpg|[[Media:DUCK_BEAK_360.gif|Duck Beak (60µm) Courtesy of Dr. A. Iwaniuk]]
Image:Human_Tooth.jpg|[[Media:Human_Tooth.jpg|Human Tooth (30µm) Courtesy of Dr. C. Stewart]]
Image:PINECONE_TH_PIC05.jpg|[[Media:PINECONE_360.gif|Pinecone showing Thickness Distribution (69µm)]]
Image:SHELL01_SEG_PIC01.jpg|[[Media:SEASHELL_360.gif|Seashell (50µm)]]
Image:TURTLE_SKULL.jpg|[[Media:TURTLE_SKULL_360.gif|Turtle Skull (60µm)]]
Image:SAND_DOLLAR.jpg|[[Media:SAND_DOLLAR.jpg|Sand Dollar (37µm)]]
Image:MOUSE_L1-L6.jpg|[[Media:MOUSE_SPINE_SEG_360.gif|Mouse Spine showing Cortical and Trabecular Bone (10µm)]]
Image:MOLAR.jpg|[[Media:MOLAR.gif|Human Tooth (60µm) Courtesy of Dr. C. Stewart]]
</gallery>

<gallery mode="packed-hover" heights=220px caption="Contrast-Enhanced Micro-CT Scans">
Image:Contrast_mouse_head_XZ_thumb.jpg|[[Media:Contrast mouse head XZ.jpg|Mouse Head (60µm, XZ plane)]]
Image:Contrast_mouse_head_XY_thumb.jpg|[[Media:Contrast mouse head XY.jpg|Mouse Head (60µm, XY plane)]]
Image:Contrast_mouse_head_YZ_thumb.jpg|[[Media:Contrast mouse head YZ.jpg|Mouse Head (60µm, YZ plane)]]
</gallery>

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==Extract Results==
===Automatic Results===
Results are generally automatically extracted after each analysis to the UCT_RESULTS directory. 
The results files have the form of:
*UCT_LIST_*''PROJECT''*.TXT for XtremeCTs: e.g. result file UCT_LIST_KYLA.TXT for the following project.
*UCT_LIST_3DLOG_*''PROJECT''*.TXT for microCTs: e.g. result file UCT_LIST_3DLOG_KYLA.TXT for the following project.
*where ''PROJECT'' is specified in the evaluation tool script setup.
[[File:Script_modify_basic_project.jpg|500px]]

Open the result file and copy and paste it into Excel, e.g.
<pre>
$ dir uct_results:*kyla*
$ eve uct_results:UCT_LIST_3DLOG_KYLA.TXT
</pre>

Or transfer the file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].
*microct/vivact account UCT_RESULTS location: ADISK1:[MICROCT.RESULTS]
*invivo/invitro account UCT_RESULTS location: ADISK1:[BONELAB.RESULTS]

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===Extract Results from XtremeCT Database using UPAT_LIST===
*Run <code>$ UPAT_LIST</code> to take in a range of samples and extract the standard patient results, which may include scans from other projects.

*Run <code>$ @com:EXTRACT_UPAT_LIST</code> to take in a list of sample numbers and extract the standard patient results with follow-ups and append them to a result file.
<pre>
$@COM:EXTRACT_UPAT_LIST P1 P2 P3 P4 P5

P1 = Sample List
P2 = Site (RR, RL, TR, TL, R*, T*, *)
P3 = Number of Follow-Ups (max 19)
P4 = Results Output File
P5 = Eval type (4=XT1, 5=Trab, 6=Cort)
</pre>

An example to extract all sites:
<pre>
$ @com:EXTRACT_UPAT_LIST mysamples.txt * 19 myresults.txt
</pre>

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===Extracts Results from microCT Database using UCT_LIST===
*Run <code>$ UCT_LIST</code> to take in a range of samples and extract the results, by specifying the first and last measurement numbers for the range they want to extract
*This may include scans results from other projects, but you can delete unrelated results that are extracted afterwards.
*The program will output a tab-delimited text file, which can be read into Excel or other analysis programs.
<pre>
$ uct_list

UCT_LIST.EXE Version V5.22
Template-File [UCT_3D_LIST_SHEET]: !Press Enter to use the default results sheet.
Output-File [SYS$SCRATCH:UCT_EVAL.TXT]: !Enter a filename, e.g., BUIE_RESULTS.TXT.
Density units (0 default) [0]: !Press Enter.
From Meas. # [0]: !Enter the first measurement number, e.g., 100.
To Meas. # [0]: !Enter the last measurement number, e.g., 101.

Processing measurement 100
Processing measurement 101
</pre>
*An example output file: [[Media:Buie_results.xlsx|Buie_results.txt]]
*Or Run <code>$ @com:extract_results.com</code>

*References of results template:
:*Formatted [[Media:Results_template_uct_list.xlsx|Excel template 1]] for results extracted with uct_list.
:*Formatted [[Media:Results_template_extract_results.xlsx|Excel template 2]] for results extracted with extract_results.com.
:*In vivo spreadsheet template for UCT data: [[Media:In vivo results template.xls| In vivo results template.xls]]
:*In vitro spreadsheet template for UCT data: [[Media:In vitro results template.xls| In vitro results template.xls]]

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===Understand Morphological Parameters===
*Refer to [[Media:Reference_Document_-_Parameters_from_upat_list.doc|'''Explanation of UPAT_LIST Output''']] to understand the result file.
*Refer to [[Media:Reference_Document_-_Parameters_from_uct_list.doc|'''Explanation of UCT_LIST Output''']] to understand the result file.

All values are determined on a slice-by-slice basis, then averaged over all the slices to calculate morphological results:

:*BV/TV -> Sum all raw data withing the GOBJ and divide by 1200 mg/cc HA
:*Tb.N -> As per standard method
:*Tb.Th and Tb.Sp -> Derived from BV/TV and Tb.N above (semi-derived method)
:*D100 -> Average density of entire cross section
:*DTrab -> Average density of trabecular region
:*Ct.Th -> Cortical area (from seg) divided by circumference (from GOBJ)
:*GOBJ circumference can be determined with /gobj_circum.

<pre>
BV/TV -> VOX-BV/TV
BS/BV -> TRI-BS/BV
Tb.Th -> DT-Tb.Th
Tb.Sp -> DT-Tb.Sp
Tb.N -> DT-Tb.N
ConnD -> Conn-Dens
SMI -> TRI-SMI
DA -> TRI-DA
</pre>

Usually I'd use the names on the left for the plots, but these correspond to the names on the right of the arrow in the Scanco output files.

Note, if you use the TRI-Tb.Th rather than the DT-Tb.Th*, then you are using the derived (plate-model) morphological parameters. These are less accurate than the direct parameters. They are calculated by triangulating the surface (marching cubes) to get BS, and then calculate thickness
Th = 2 * BV / BS, etc...

'''Mean Values'''
<pre>
mean 1: mean of bone AND marrow --> 'apparent density'
mean 2: mean of what was considered bone only (i.e. what was segmented)
'bone tissue density'
</pre>

Note, there are five possible categories for the mean Mu. They are assigned by setting <code>-region_number</code> in the <code>/voxgobj_scanco_param</code> function. The region number is zero-based, so setting it to 0 corresponds to mean1, 1 corresponds to mean2, etc. So, although mean1 and mean2 are typically apparent and tissue density, respectively, this can be adjusted in the IPL script by setting the region_number. Mean3 might be useful for storing cortical bone density, for example.

<pre>
/voxgobj_scanco_param Voxel or Mu Scanco Parameters
-input Gray scale or Segmented AIM object
-gobj_filename GOBJ: input or Automatic
-peel_iter Peel Iterations or Automatic
-region_number Region number for Mu only

! -region_number 0 ! mean1
! -region_number 1 ! mean2
! -region_number 2 ! mean3
! -region_number 3 ! mean4
! -region_number 4 ! mean5
</pre>

What you should also know: because of partial voluming effects, for Mean2, we are DISCARDING the 2 surface voxels of EVERY trabeculae - thus, to get meaningful Mean2, you have to do your scan with the chosen resolution high enough, such that the mean trabeculae is depicted by at the very least 5 pixels, better actually more than 6 pixels thickness. (You can do this check at the end in the XLS sheet: divide DT-Tb.Th* by el-size-mm.x, and you need to get numbers bigger than 6 or 7 or 10 or so.

For parameters such as ConnD where no GOBJ is taken as input, the TV is determined from the processing log stored in an AIM that has previously had a GOBJ applied (stored as the relative region of interest; ROI). So, it is important to apply a GOBJ prior to ConnD measurements to ensure the TV is correctly determined (and not taken as the whole AIM).

'''Trabecular Number (TbN)'''
The epsilon values can be set to account for differences in scanner resolution, and hence 'surface roughness' for individual pixel suppression.

For microct, for good resolution: if there is a pixel 'sticking out' from a flat surface we do not assign that pixel with a thickness value of 1, but we let it 'get eaten' by the bigger sphere that sits in the center of the trabeculae. So this is nice for 'noise' (0.9/1.5).

For XT resolution, where also many 'good' features are just one or two pixels wide, I liked a lower epsilon value better (0.9/0.5).

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==Generate Report==
===Generate Standard Patient Report===
The standard patient reports are extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.
*The number of follow-ups specified will determine if a baseline or follow-up report is generated.

<pre>
$ upat_list

Mode (1 = list, 2 = print, 3 = show) [1]: 2
Patient # (1-3162) [1]: !input the patient's sample number
Site (found RR) [RR]: !RR or RL or TR or TL
Maximum # of follow-ups (0-19) [19]: !0 for baseline report, press return for follow-ups
Template file [default]: !press return to use the default template
Output filename [SYS$SCRATCH:UPAT...]: !default output file (with sample number and the site) goes to sys$scratch
# copies [1]: !the number of printouts, 0 if no printout is desired
</pre>

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===Generate CaMos Patient Report===
The [http://www.camos.org '''CaMos'''] patient report is extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.
*To ensure the report is generated using the appropriate normative results, the patient's sample remarks should be in the form "F-RHRF" where the first character indicates the sex of the individual, otherwise the patient is assumed to be male.
<pre>
$ upat_list

Mode (1 = list, 2 = print, 3 = show) [1]: 2
Patient # (1-3162) [1]: !input the patient's sample number
Site (found RR) [RR]: !RR or RL or TR or TL
Maximum # of follow-ups (0-19) [19]: !0 - 1st scan, 1 - 2nd scan, 2 - 3rd scan...press return for latest scan report
Template file [default]: COM:UPAT_EVAL_CAMOS.PS
Output filename [SYS$SCRATCH:UPAT...]: !default output file (with sample number and the site) goes to sys$scratch
# copies [1]: !the number of printouts, 0 if no printout is desired
</pre>

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===Print out report sheets===

The postscript report sheets can be generated and printed on the command line. For the XtremeCT system, use <code>UPAT_PRINT_LIST.EXE</code> which can be run (using the symbol):
<pre>
$ UPAT_LIST
</pre>

Look in the UU: directory to see options for the template files (UPAT*.TXT) and the postscript output files (*.PS).
:* UU:UPAT_EVAL_FUP05_SCUSA.PS
:* UU:UPAT_EVAL_BASELINE_SCUSA.PS

For other options, see the upat_list help:
<pre>
$ UPAT_LIST -h
</pre>

One particular option that may be useful, is to turn off slice matching:
<pre>
$ UPAT_LIST -nomatch
</pre>

Here is an example of producing a report for the third measurement of TL for a patient, where we want only the most recent results in the report, without slice matching:
<pre>
$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=UU:UPAT_EVAL_BASELINE_SCUSA.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_0fu.ps

$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=DISK1:[MICROCT.COMMANDS]UPAT_EVAL_CAMOS.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_camos.ps
</pre>
The first command line generates a normal Scanco report, and the second command line generates a CAMOS report.

For reports from non-patient measurements (i.e., the vivaCT system or non-patient scans on the XtremeCT), the template files are different (UCT*.TXT) and the postscript outputs are different (UCT*.PS). To print a result sheet use:
<pre>
$ RUN UM:UCT_RAY_BATCH.EXE
</pre>

If you want to create a postscript file, but not send it to the printer, set the number of copies to zero (interactive). Then, find the postscript file from the <code>SYS$SCRATCH</code> directory and transfer it to your PC. You must transfer the postscript file in ASCII mode. The files are typically called TEMP_3D.PS or UPAT_PAT_62_RR.PS. A program such as Adobe Photoshop can convert the postscript file to a different format.

See also our custom scripts:
<pre>
$ @COM:PRINT_2D.COM
$ @COM:PRINT_3D.COM
</pre>

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===Convert PS to PDF report===
The report can be converted to PDF using <code>$ @SCOM:PS_TO_PDF</code> by:

#Follow the instructions above for creating a report, using "2" to print and "0" for the number of copies. (Use the default template file and output filename.)
#Locate the file on the sys$scratch by <code>$ cd sys$scratch</code> and <code>$ dir</code>
#*The file should read "UPAT_PAT_[sample #]_[site].PS;1" (e.g. UPAT_PAT_0010_RL.PS;1)
#*You can view this file on the monitor by typing <code>$ gs UPAT_PAT_0010_RL.PS;1</code>
#Convert the postscript to PDF by typing in the command followed by the .PS file to convert <pre>$ @SCOM:PS_TO_PDF UPAT_PAT_0010_RL.PS;1</pre>
#The PDF file can then be located again in the sys$scratch directory.

You can transfer the result file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].

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=Data Management=
==Trainee’s Data Responsibility==
#Perform '''Contouring and Data Analysis''' on Data Disk ideally 1-2 months after scanning.
#After finished onsite analysis, [[Scanco_User_Instructions#Move_data_from_Data_Disk_to_Project_Disk|'''use Scripts''']] to '''Copy and Rename''' image data (no RSQ, no ISQ, only AIM, SEG.AIM, GOBJ, COM, LOG, PDF, PS ect) to your specific project folder on Project Disk.
#After finished copying all your image data to Project Disk, '''Notify''' lab personal to delete your data on Data Disk by providing a [[Media:Data_Scans_to_delete_template.xlsx|'''Data Scans to Delete Template''']].
#'''Notify''' lab personal to backup your project folder on Project Disk to Winston server on a monthly basis.
#*Only the two most recent backups (A or B version) are kept for each project on Winston:
#:Backup version "_A" for odd months (Jan, Mar, May, Jul, Sep, Nov), e.g. YZHU_A_OTHER_2017-01-12.SAV
#:Backup version "_B" for even months (Feb, Apr, Jun, Aug, Oct, Dec), e.g. YZHU_B_OTHER_2020-04-08.SAV
#When a project is finished, '''Notify''' lab personal to archive your project to HOG server.
#When a trainee is about leaving, '''Notify''' Steve and lab personal to determine either to backup or to archive your project.

[[File:BoneLabDataManagement.JPG|800px]]

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==Move data from Data Disk to Project Disk==
This is generally done after onsite analysis (i.e. autocontour, cortical porosity, FE etc.) is done. Examples of this can be found in DISK3:[MICROCT.PROJECTS.GRACE.COM] 
1. Go to the specific project's .COM directory, for example:
<pre>
$ cd DISK3:[MICROCT.PROJECTS.GRACE.COM]
</pre>
2. Create a script that will move all IMA (i.e. .AIM, .GOBJ, _SEG.AIM, _CORTEX.AIM, _LHTH_DTN.AIM) to the .MODELS directory for the project. You will use the rename_to_models.com script to generate this script. To move Grace data for example, with a measurement range of 2684 to 2685, you would use:
$ @com:rename_to_models.com meas#1:meas#2 DESTINATION DIR
$ @com:rename_to_models.com 2684:2685 DISK3:[MICROCT.PROJECTS.GRACE.MODELS]

3.This will create a file named RENAME_ALL.COM to the project's COM directory. You will now have to open the RENAME_ALL.COM file and add site + other details into the script. Following the same example as above, it should look like this:
$ eve RENAME_ALL.COM ! to open the file using a text editor
$ COPY DISK2:[MICROCT.DATA.00000700.00002684]C0002040.AIM -
DISK3:[MICROCT.PROJECTS.GRACE.MODELS]GRACE_020_00MTH_RR.AIM
$! DELETE/CONFIRM DISK2:[MICROCT.DATA.00000700.00002684]C0002040.AIM;1
$ COPY DISK2:[MICROCT.DATA.00000700.00002685]C0002041.AIM -
DISK3:[MICROCT.PROJECTS.GRACE.MODELS]GRACE_020_00MTH_RL.AIM
$! DELETE/CONFIRM DISK2:[MICROCT.DATA.00000700.00002685]C0002041.AIM;1
4. You also need to copy the rest of the standard patient image files (i.e. .AIM, .GOBJ, _SEG.AIM, _CORTEX.AIM, _LHTH_DTN.AIM) which is easily done by copying the above lines and replacing .AIM with the respective files.

[[Image:Bones2.jpg|20px]] Warning: Always use the same account consistently to create all files and subfolders within their Project folder, otherwise you way miss data when doing Project Backup or Archive!

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=Import and Export=
==Import Foreign Data to Scanco System==
Only RSQ and ISQ files can be imported into the database, however it is possible to convert other types of data into ISQ files (i.e., stacks of BMPs into ISQ).

PART 1:

After transfering your data to the VMS system (use the data disk <code>disk2</code>, NOT the user disk <code>disk1</code>), use the IPL commands <code>/import_freeformat</code> or <code>/read_aim function</code> to import your data for conversion to an ISQ.

For AIM files, navigate to the location of the AIM file. Then open IPL by:

<pre>$ IPL</pre>

In IPL, read in the .AIM file:

<pre>ipl> read in [.AIM file]</pre>

IPL will do the following:

<pre>ipl> read in STUDYID_001_RL.AIM

/read
-name in
-filename STUDYID_001_RL.AIM
!> Reading AimVersion020

!% /read completed: CPU: 00:01.03 ELAP: 00:01.55 </pre>

For DICOM files, start IPL and run the <code>/dicom</code> function to import. For DICOM, if your object is a single 3D file (-multifile false) or many many individual slice files (-multifile true, and give beginning of filenames, and –extension).

There may be requests by IPL to convert your data to <code>signed short</code> or <code>signed char</code> from other data types. Obey these requests and do it by running the <code>/convert_unsigned</code> function.

Then, write the ISQ file using either the "toisq" or "from_aim" commands:
<pre>ipl> toisq
-aim_name [in] >[leave blank as you defined “in” as .AIM file.]
-isq_filename [default_file_name] > C0001234.ISQ [Create a 1 letter and 7 digit file name]
-square_flag [true] > false
-original_position [true] > false

ipl>toisq_from_aim
-aim_name in
-isq_filename C0001234.ISQ
-square_flag false
-original_position false

!% Dimensions of ISQ file: dim.x dim.y dim.z 558 638 168
Write_ctdata_headerext_new: no mhext found. Init mhext.
Extended header successfully added of type 8

!% Writing ISQ slice 167 (Done: 168/168)

!% /toisq_from_aim completed: CPU: 00:05.12 ELAP: 00:10.47 </pre>

Type ipl>help toisq [or ipl>help from_aim] to see details of the command.

This writes the ISQ file. Make note of the ISQ file name.

Remember, the ISQ name must be 8 characters long (1 character followed by seven digits)!!! The letters and numbers can be chosen freely.

Exit IPL:

<pre>ipl>quit</pre>

PART 2:

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

The measurement can be verified by looking at the Header Information. (File, Header)

If you only needed to view the ISQ, delete the file when finished by:

<pre>$ dir/sincet
$del [.ISQ file]</pre>

PART 3:

To use the ISQ further (e.g. for evaluations, contouring, etc.) create a sample in the database and write down the sample and measurement number. Then, run:

<pre>$ run um:uct_import ! will import both RSQ and ISQ (modify patient index, etc)</pre>

and give the new ISQ file, the new sample-number and check that the feedback is correct (i.e., that the name from the database is matching the name from the ISQ file header). If the Patient Name in the ISQ header doesn't match the measurement database Patient Name (very likely), then upon importing the RSQ/ISQ the headers will be updated to the new Patient Name.

Operator and controlfile can be left 0 if you want. However, controlfile should be set appropriately if the data being imported is for the XtremeCT patient database.

If you are also importing the RSQ, put it in the same directory as the ISQ.

Then it changes the sample and measurement number in the ISQ file, makes the correct directory on <code>DK0</code>, and gives you the line on the screen of how to rename the file to the correct, new directory. Take this line and use it on the command line. Done!

You can now use the normal <code>uct_evaluation</code> program with this file. If the control file was set properly, then the evaluation will be done correctly (i.e., for XtremeCT patient measurements).

Note: Any AIMs created from the original ISQ should be recreated. So, it is important that you re-evaluate your newly imported ISQ. It is OK to move the GOBJ from the old directory to the same directly as the newly imported ISQ (it does not have a 'registry' in the database).

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==Import MRI DICOM to Scanco System==
#Load MR data in Osirix
#Export from Osirix
#*Click export button in top left in osirix.
#*Select "flat" and "decompress all DICOM files"
#Copy files to correct folder in scanco system
#*Use Fillezilla or FTP (make sure it's set to binary mode)
#Use IPL to convert dicom to aim or isq

<pre>
/dicom_to_aim
-aim_name in
-dicom_filename IM-0001-0001.DCM ! Note - choose the first filename of the series
-multifiles true

/convert_unsigned
-input in
-shift_flag false
-divide_by_2 true

/write_v020
-name in
-filename PREOA_023_L_MR.aim
-compress_type bin
-version_020 true

/toisq_from_aim
-aim_name in
-isq_filename MROA023L.isq
-square_flag true
-original_position true''

</pre>

5. Delete dicoms

<pre>
/del *.dcm;1
</pre>

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==Import Xradia *.bin to Scanco System==
Xradia scanner exports a *.bin image that is:

- 16-bit unsigned ! This is "short" (8-bit is char - we don't want this for a grey-scale image)
- 2 bytes per voxel
- little endian notation

To upload this binary image to Scanco database, the steps are as follows:

#Ftp the *.bin to Scanco system using binary transfer (not ascii)
#Convert it to an AIM or ISQ in IPL

$ipl

/import_freeformat
-internal_name in
-file_name BMLPL_006.BIN
-sample_name BMLPL_006
-data_offset 0
-data_dim 1000 1024 1016 !dimensions from header file
-data_el_size 0.013 0.013 0.013 !voxel size from header file
-bytes_per_voxel 2
-data_endian little_endian
-data_type integer
-signed_type unsigned !correct
-multifiles false

/convert_unsigned
-input in
-shift_flag true !shift_flag = TRUE will produce an ISQ/AIM with negative values which may not be visualized properly using uct_evaluation, but keeps the original image resolution.
-divide_by_2 false !divide_by_2 = TRUE will down grade image resolution, but all positive values in an ISQ/AIM will be visualized properly using uct_evaluation.

/write_v020
-name in
-filename test.aim
-compress_type bin
-version_020 true

/from_aim_to_isq
-aim_name in
-isq_filename bmlpl006.isq !ISQ name requires 8 characters
-square_flag true
-original_position true

quit

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

Alternatively the image can be converted to a 16-bit signed in ImageJ (and cropped) before importing to ipl. It then becomes:

- 16-bit signed
- 2 bytes per voxel
- big endian notation

It can then be imported into ipl without the need to run <code>/convert_unsigned</code>.

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==Get Your Files==
===MAC/Linux Options===
====Fetch====
#Download and install [http://fetchsoftworks.com/fetch/|'''Fetch''']
#*This program is free for university staff and students.
#Fill out [http://fetchsoftworks.com/fetch/free|'''a form'''].

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====FTP from Terminal====
#Open a terminal
#*MAC: open the "Applications" folder, choose "Utilities", then "Terminal".
#Navigate to where you want to transfer the files to.
#Connect to the micro-CT ftp server using the ftp command in the terminal:
#*Login with the micro-CT user account and password.
#Navigate to the directory of interest on the micro-CT system.
#*Logicals such as "ur" can be used as short cuts. Whole directory names must be used.
#Set a filename mapping convention to remove OpenVMS version numbers.
#*The command <code>ftp> nmap $1;$2 $1</code> sets anything before the version number to parameter $1 and anything after the version number to $2. The file output will be set to $1, therefore the version number will not be kept.
#Set the file transfer mode.
#*[[File:Important.JPG|20px]] If you transfer an .AIM file in ascii mode, you will receive a "mesh generation" errors and "material ID out of range" message.
#Transfer your files.
#*Option: Turn off prompt so does not ask you whether or not to transfer each file.
#*If you do not turn off the prompt prior to transferring the files, press "a" (for all) to transfer all files at once.
#Exit FTP.

<pre>
$ FTP 136.159.74.231 !Connect to an FTP Server. Need to input user name and password.
$ FTP emily.ucalgary.ca !Connect to an FTP Server. Need to input user name and password.
$ FTP microct@emily.ucalgary.ca !Connect to an FTP Server. Need to input password.

FTP> cd ur !Navigate to the directory containing the target files.
FTP> cd sys$scratch !Navigate to the directory containing the target files.

FTP> nmap $1;$2 $1 !Set a filename mapping convention to remove OpenVMS version numbers.

FTP> bin !Set transfer mode to binary (.aim, .gobj, .isq, and most image file types).
FTP> ascii !Set transfer mode to ascii (.txt, .log, .com, .ps, .pdf and all other files in general).

FTP> put test.aim !Put the file
FTP> get test.aim !Get the file

FTP> prompt !Interactive mode off before transferring multiple files without having to be prompted.
FTP> mput *.aim !Put all files with the .aim extension on the FTP server (mput = multiple put).
FTP> mget *.aim !Get all files with the .aim extension from the FTP server (mget = multiple get).
FTP> mget *.aim; !Transfer the latest version of all aim files in a directory.

FTP> quit !Disconnect from the FTP Server.
</pre>

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===Windows Options===
====Scanco Medical µCT FTP====
#Downlod '''Scanco Medical MicroCT FTP 3.4''' from BoydDrive:\\04 - Resources\04 - Software\Scanco Medical MicroCT FTP 3.4\
#Install the software using the default parameters.
#Click on FTP Connection and input the host to connect to, the username, password.
#Give this profile a name.
#:[[File:Microct_FTP_pic01.jpg|600px]]
#Click on the options tab to set the locations to connect to (e.g., project disk, scratch) and the location on your computer to transfer files to.
#:[[File:Microct_FTP_pic02.jpg|600px]]
#Go back to FTP Connection and press the Connect button.
#*If you are connecting from off campus to the XtremeCT you will need to use the VPN to gain access through the firewall.
#Use the left tree to navigate folders.
#*Use the file filter to search for specific file types or file names (bottom left).
#Select files to download and press the Download Selected Files button (bottom right).
#:[[File:Microct_FTP_pic03.jpg|600px]]
#Press the Exit button to disconnect.

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====Filezilla====
#Download '''Filezilla 2.2.32''' from BoydDrive:\\04 - Resources\04 - Software\Filezilla 2.2.32\
#*This version of Filezilla will remove the OpenVMS version number from files, the new version will not!
#*The left side of the program shows your computer, the right side will show the micro-CT system once you have connected.
#:[[File:Filezilla_pic01.jpg|500px]]
#On the top menu, choose "File", then "Site Manager".
#Create a "New Site" for all the directories that you frequently access.
#*Give the site a meaningful name.
#*For the host, you may connect to "emily.ucalgary.ca" or "sceval.ucalgary.ca".
#*For the logon type choose "Normal" and input the micro-CT user name and password.
#:[[File:Filezilla_pic02.jpg|400px]]
#Click on the "Advanced..." button to set the default remote directory (i.e., on the micro-CT system).
#Set the default local directory if there is a specific location you plan to always transfer files to.
#Setup any additional sites you want then press "Save and Exit".
#:[[File:Filezilla_pic03.jpg|300px]]
#To connect to a session, hold the left mouse button down over the arrow next to the site manager button (computer icon under "File") to bring up your list of sites. Highlight the site of interest then release the mouse button to connect.
#Once connected, you can drag and drop files from the remote site to your local computer.

;*Common FTP locations
{| class="wikitable"
|-
! scope="col"| Account
! scope="col"| Location
! scope="col"| Path
|-
| microct / vivact || Data Disk ||DISK2:[MICROCT.DATA]
|-
| microct / vivact || Projects Disk ||DISK3:[MICROCT.PROJECTS]
|-
| microct / vivact || Scratch Disk ||ADISK1:[MICROCT.SCRATCH]
|-
| invivo / invitro || Data Disk ||DISK4:[BONELAB.DATA]
|-
| invivo / invitro || Projects Disk ||DISK5:[BONELAB.PROJECTS]
|-
| invivo / invitro || Scratch Disk ||ADISK1:[BONELAB.SCRATCH]
|}

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=Remote Access=

== VPN Setup ==

Access to the OpenVMS workstations from campus does not require VPN setup; however, to access from off the campus requires establishing a VPN connection prior to connecting.

*The VPN server is: gpvpn2.ucalgary.ca

*The client needed for VPN connection is '''FortiClient SSL''' which is available through [https://ucalgary.service-now.com/it| UofC IT Service Request] "Order Something".

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== Setup for MAC/Linux ==

=== Terminal and XQuartz ===
You need following to access the MicroCT system remotely.
#'''Terminal''': an SSH client
#*Preinstalled in MAC/Linux.
#'''XQuartz''': an X server for X11 forwarding
#*X11 was previously distributed with Mac OSX but has since stopped.
#*Check if preinstalled in MAC: open the "Applications" folder, choose "Utilities", there should be a file called "XQuartz". No need to open.
#*If not preinstalled, download the most recent [https://www.xquartz.org/ '''XQuartz.dmg'''].
#*Once downloaded, double click the .dmg file to follow the instructions and install.
 
;SSH from terminal
#Open a terminal.
#*MAC: Open the "Applications" folder, choose "Utilities", then "Terminal".
#Type <pre>$ ssh xtremect2@emily.ucalgary.ca -Y</pre>
#*The -Y flag activates X11 forwarding.
#Or type <pre>$ ssh -Y -p22 -c 3des-cbc -o KexAlgorithms=+diffie-hellman-group1-sha1 -o HostKeyAlgorithms=+ssh-dss xt2recalib@emily.ucalgary.ca </pre>
#*Type <pre>$ alias xt2recalib='<ssh command above>'</pre> allows you to only type <pre>"$ xt2recalib"</pre> in the terminal from here on out to access the MicroCT system.
#You're good to go!

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== Setup for Windows ==
=== MobaXterm ===

There is only one program required to access MicroCT remotely: MobaXterm. It will act as both an SSH client and as an X server.

*Download [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Home Edition (Portable Edition)]
 
;Configure MobaXterm
*Run the .exe file after downloading MobaXterm.
:[[File:MobaXterm_init.PNG|500px]]

*Click on "Sessions" -> "User Sessions" and choose "SSH" in the top left of the "Session settings" window.
*Input your host info into the "Remote host" dialogue box such as "emily.ucalgary.ca", check on "Specify username" and input your username such as "xt2recalib" and ensure "X-11 Forwarding" is checked in "Advanced SSH Settings" tab, and click OK.
:[[File:MobaXterm_SSH.PNG|500px]]
 
;Start the session
*Launch the MobaXterm client and under "Sessions" -> "User session" you should have something titled "xt2recalib@emily.ucalgary.ca".
*Double click that session and you're good to go!
:[[File:MobaXterm_Session.PNG|500px]]

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=== PuTTY and Xming ===
There are two programs required:
#'''PuTTY''': an SSH client
#*Download [http://www.chiark.greenend.org.uk/~sgtatham/putty/ '''PuTTY'''] or from BoydDrive:\\04 - Resources\04 - Software\PuTTY.
#'''Xming''': an X server
#*Download [https://sourceforge.net/projects/xming/files/latest/download?source=files '''Xming 6.9.0.31''']
#*Download [https://sourceforge.net/projects/xming/files/Xming-fonts/7.5.0.93/Xming-fonts-7-5-0-93-setup.exe/download '''Xming Fonts''']
 
;Configure PuTTY
*Under categories, expand the "Connection" and "SSH" trees. Click on "X11" and check the "Enable X11forwarding" box.
:[[File:Putty1.png|400px]]
*Under categories, now choose "Sessions".
*Under host name, put in "emily.ucalgary.ca". Choose "SSH" for the connection type.
*Under Saved Sessions, give the session a name (e.g., Emily). Click the "Save" button.
:[[File:Putty2.png|400px]]
 
;Start the Session
*Launch the Xming program, nothing should open except the Xming icon on the task bar.
*Open PuTTY. Double-click on the saved session, which will open a DEC terminal.
*Any program that you run remotely will be displayed by Xming.

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==Remote Access FAQ==
=== MAC Open SSH Authentication Issue ===
You might get an error similar to the following especially after a recent OS update:
Unsupported KEX algorithm "+diffie-hellman-group1-sha1"
command-line line 0: Bad SSH2 KexAlgorithms '+diffie-hellman-group1-sha1
This is not Apple’s fault, it’s OpenSSH version 7. SHA1 is weak, so support for it has been removed. Which is fine, but VMS clients are probably using RSA/SHA1. So until they’re all updated (i.e. never!) we need to re-enable SHA1.

Open a terminal windows and execute the following:
sudo nano /etc/ssh/ssh_config
ENTER YOUR PASSWORD

Locate the line ‘# MACs hmac-md5,hmac-sha1,umac-64@openssh.com,hmac-ripemd160′ and remove the Hash/Pound sight from the beginning.

Locate the line ‘# Ciphers aes128-ctr,aes192-ctr,aes256-ctr,aes128-cbc,3des-cbc’ and remove the Hash/Pound sight from the beginning.

Then paste the following on the end;

HostkeyAlgorithms ssh-dss,ssh-rsa
KexAlgorithms +diffie-hellman-group1-sha1
There’s no reason to reboot, it should work straight away.
 

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=== SSH Speed Issues ===
 
If you notice that the remote display is quite slow, you may prefer to enter the 'manual' X display redirection after connecting with ssh. 
 
The steps to enter the 'manual' X display redirection are outlined in one of Scanco's FAQs found [http://www.scanco.ch/en/support/customer-login/faq-customers/faq-customers-general.html here]. 
Click the "Remote Graphical Access from your PC to the MicroCT" tab (5th tab) and scroll down to "SSH Speed Issue" for more information.

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=== MobaXterm Backspace Issue ===
If the Backspace/Delete key doesn't work on your MobaXterm

#Right-click on a session name on the left column and click "Edit session"
#:[[File:MobaXterm1.png|500px]]
#: 
#Under "SSH" page "Terminal settings" tab, toggle off "Backspace sends ^H" and "Save"
#:[[File:MobaXterm2.JPG|500px]]

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Scanco User Instructions

2021-05-07T18:47:44Z

Yingzhu: /* Import MRI to Scanco System */

=OpenVMS Basics=
The micro-CT scanners in the lab are manufactured by [http://www.scanco.ch Scanco Medical] and most analyses are performed using their custom software. The micro-CT workstations run OpenVMS as its operating system and it is useful to learn some basic commands.

==OpenVMS Beginner's Reference==
OpenVMS (informally known as VMS) is a high-end computer server operating system with reliable, multitasking, real-time and batch processing. OpenVMS supports computer clustering via a LAN, enabling computers to share resources such as processors and disks to balance workload efficiently.

*[http://saf.bio.caltech.edu/vms_beginners_faq.html '''OpenVMS Beginner's FAQ''']

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==Session Manager==

The session manager automatically starts after a user logs in locally. For remote sessions, the session manager can be started with the command <code>$ vue </code>.

[[Image:SessionManager.jpg|600px]]

===Session===
Here you will find an option to "End Session", which you should do when you are finished using a workstation. You can click "Work in Progress..." when you have to leave in the middle of a session without logging out but showing a work in progress screen to other users to prevent interference.

===Views (directory shortcuts)===
The session manager is a graphical user interface that can be used to navigate directories (left side of session manager) and open files (right side of session manager). There are shortcuts to key directories under "Views". Single-click on a directory to list its subdirectories and files. Double-click on a file to open it.

===Commands and Utilities===
Under commands you will find tools such as copy, delete, and rename; however, it is much more practical to do these sorts of operations from a DEC terminal.

===Applications===
Under applications you can launch various applications including:
*DECterm: opens a DEC terminal
*MICROCT: opens the micro-ct control panel (buttons for Scanco Medical programs)
*Mozilla/Netscape: opens a web browser
*XV: opens a screen capture program

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==DEC Terminal and Digital Command Language (DCL)==
This is a DEC terminal: Commands issued in a DEC terminal are DCL commands.

[[Image:decterm.jpg|600px]]

===Copy and paste using the mouse in DEC terminal===
In the DEC terminal, you can highlight text by holding down and moving the mouse. Highlighted text can be pasted into applications or in the terminal using the middle mouse button. You can also highlight files in the Session Manager and paste the filename (with its full path) using the middle mouse button.

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===What is a symbol===
DCL can store information such as strings or integers in "symbols". DCL can also manipulate these symbols to create other symbols.
Symbols are primarily used to define short strings that replace long commands, perform certain calculations and replacements within DCL
procedures, hold status information.
<pre>
$ UR == "SET DEFAULT DISK4:[BONELAB.PROJECTS]" !A short hand to change locations to the project disk.
$ UR :== SET DEFAULT DISK4:[BONELAB.PROJECTS] !Another way to define the symbol without quotations.
$ x == 3 !Store the value 3 in the symbol x.
$ SHOW SYMBOL x !Displays the value of the specified symbol, x.
$ DELETE/SYMBOL/GLOBAL x !Deletes the specified symbol, x.
</pre>
Selected symbols on the Scanco system:
<pre>
$ UD !Changes to the data directory.
$ UR !Changes to the projects directory.
$ DISKS !Shows the current disk usage.
$ DEC !Opens a new DEC terminal.
$ EVE file.txt !Opens the file in the text editor.
$ AIX file.aim !Shows the processing log for an aim file.
$ AIX -L file.aim !The "-L" is used to show the full processing log.
$ QUE !Shows all entries in the queue.
$ GS file.ps or file.pdf !Opens *.ps and *.pdf files in GhostScript.
$ CTHEADER file.isq or file.rsq !Shows scan information for an *.isq or *.rsq file.
</pre>

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===What is a logical===
Logical names are strings, like symbols, but can be passed into programs whereas symbols can usually only be interpreted by the command line interpreter. For example, if the logical name UD was defined to be DISK2:[XTREMECT2.DATA] then UD: could be used as a substitute when entering the path to search for files from within a program.
<pre>
$ DEFINE UD DISK2:[XTREMECT2.DATA] !Defines a logical ud to point to the data directory.
$ DEFINE uct_default_isq myfile.isq !Defines the default isq file for Scanco Medical programs. The isq filename must contain the full path to the file to be evaluated, whereas the path can be left out if you just want to contour the scan.
</pre>
Selected logicals on the micro-CT system:
<pre>
COM !Logical pointing to the commands directory IDISK1:[XTREMECT2.COMMANDS]
UD !Logical pointing to the data directory DISK2:[XTREMECT2.DATA]
UD6 !Logical pointing to the data directory DISK6:[XTREMECT2.DATA]
UR !Logical pointing to the projects directory DISK4:[BONELAB.PROJECTS]
UE !Logical pointing to the evaluation script directory MICROCT_ROOT:[EVAL]
UU !Logical pointing to the templates directory MICROCT_ROOT:[UIL]
UCT_RESULTS !Logical pointing to the results directory MICROCT_USER:[RESULTS]
</pre>

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===Arithmetic operations===
{| class="wikitable"
|style="width: 10%"|Addition ||style="width: 5%;text-align:center;"| + ||The plus sign (+) adds two numbers.
|-
|style="width: 10%"|Subtraction ||style="width: 5%;text-align:center;"| - ||The minus sign (-) subtracts the second specified number from the first specified number.
|-
|style="width: 10%"|Multiplication ||style="width: 5%;text-align:center;"| * ||The asterisk (*) multiplies two numbers.
|-
|style="width: 10%"|Division ||style="width: 5%;text-align:center;"| / ||The slash (/) divides the first specified number by the second specified number. If a number does not divide evenly, the remainder is lost. No rounding takes place.
|}

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===Logical expressions===
{| class="wikitable" style="width: 100%;"
|style="width: 10%"|And||.AND.||The operator .AND. combines two logical values as follows
true .AND. true = true true .AND. false = false false .AND. true = false false .AND. false = false
|-
|style="width: 10%"|Or||.OR.||The operator .OR. combines two logical values as follows
true .OR. true = true true .OR. false = true false .OR. true = true false .OR. false = false
|-
|style="width: 10%"|Not||.NOT.||The operator .NOT. reverses the bit configuration of a logical value. A true value becomes false and a false value becomes true.
|}

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===Numeric comparisons===
{| class="wikitable"
|style="width: 15%"|Equal to||style="width: 5%;text-align:center;"|.EQ.||Compares one number to another for equality.
|-
|style="width: 15%"|Not equal||style="width: 5%;text-align:center;"|.NE.||Compares one number to another for inequality.
|-
|style="width: 15%"|Greater than||style="width: 5%;text-align:center;"|.GT.||Compares one number to another for a greater value in the first number.
|-
|style="width: 15%"|Greater than or equal to||style="width: 5%;text-align:center;"|.GE.||Compares one number to another for greater or equal value in the first number.
|-
|style="width: 15%"|Less than or equal to||style="width: 5%;text-align:center;"|.LE.||Compares one number to another for a lesser or equal value in the first number.
|-
|style="width: 15%"|Less than||style="width: 5%;text-align:center;"|.LT.||Compares one number to another for a lesser value in the first number.
|}

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===String comparisons===
The operators for string comparisons are the same as for numeric comparisons with an added "S" for string.
{| class="wikitable"
|style="width: 15%"|Equal to||style="width: 5%;text-align:center;"|.EQS.||Compares one character string to another for equality.
|-
|style="width: 15%"|Not equal||style="width: 5%;text-align:center;"|.NES.||Compares one character string to another for inequality.
|-
|style="width: 15%"|Greater than||style="width: 5%;text-align:center;"|.GTS.||Compares one character string to another for a greater value in the first specified string.
|-
|style="width: 15%"|Greater than or equal to||style="width: 5%;text-align:center;"|.GES.||Compares one character string to another for greater or equal value in the first specified string.
|-
|style="width: 15%"|Less than or equal to||style="width: 5%;text-align:center;"|.LES.||Compares one character string to another for a lesser or equal value in the first specified string.
|-
|style="width: 15%"|Less than||style="width: 5%;text-align:center;"|.LTS.||Compares one character string to another for a lesser value in the first specified string.
|}

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==DCL Programming Guide==
The OpenVMS systems allow for scripts to be written in a language called '''DCL (DIGITAL Command Language)'''. It was not designed to be more difficult than other scripting languages, but learning any new programming language comes with its learning curve.

*DCL has 243 commands, but most programs can be written with a base set of about 20 commands. The goal of this section is to provide a convenient reference for these commonly-used commands.

It is recommended to open a text editor, enter the whole series of commands, and then run them as a whole program. The terminal on OpenVMS is technically a DCL interpreter, so these commands could be typed in sequence into a terminal with the same result. Typing code interactively is helpful when testing a small code snippet in more detail.

===Your First DCL Script===
Ever since Kernighan and Ritchie wrote the book "The C Programming Language", it has been custom to start with a program that prints the text "Hello, world" to the screen. Open a text editor (for example "EVE") and enter the text below.
<pre>
$! My First DCL Script
$ mymessage = "Hello, world"
$ WRITE SYS$OUTPUT mymessage
$ EXIT
</pre>
Now save the file as HELLO1.COM, and run it using <pre>$ @HELLO1.COM</pre>

Several things are happening in the above program:
*'''Comment !''': The exclamation mark can appear anywhere on the line, and everything following the mark will be treated as a comment.
*'''Variable''': "mymessage" variable is populated with the string "Hello, world", which can be used in the rest of the script.
*'''Command''' "WRITE" send text to various places, in this case to "SYS$OUTPUT", that is to the standard output (i.e. screen).
*'''EXIT''' command tells the DCL interpreter that the script is done and we should exit.
*Commands in DCL are '''NOT case sensitive''', so the command "write sys$output mymessage" would produce the exact same result, but by convention we write commands in all uppercase.

*'''Special Comment !!''' automatically prints the contents of the comment to the screen/logfile. It is useful when you want to know what part of the script you are in.

===Basic Arithmetic===
The DCL language supports several types of data in variables. In the "Hello, world" example above, we saw how to store a string in a variable. We could have stored an integer, that is a positive or negative whole number, in the variable, and done some basic math.
*Refer to [[Scanco_User_Instructions#Arithmetic_operations|'''Arithmetic Operations''']], For example:
<pre>
$ i = 1
$ WRITE SYS$OUTPUT i+1
$ j = 3
$ k = j * (i + 1)
$ WRITE SYS$OUTPUT k
$ WRITE SYS$OUTPUT (k / 4)
$ WRITE SYS$OUTPUT 2 + 2 * 2
$ EXIT
will return:

2
6
1
6
</pre>
Two things are worth noting.
*Because we are limited to integers, division of 6 / 4 needs to return an integer (1.5 is not an integer); the value is truncated, which means rounding is always done toward zero.
*Order of operations is done in the "correct" order, and not left-to-right, so "2 + 2 * 2" is interpreted as "2 + (2 * 2)".

===Conditional Statements===
Sooner or later, you will want to run a program with some logic. The general syntax is:
<pre>
IF [condition]
THEN
[do something]
ELSE
[do something else]
ENDIF
</pre>
*The "ELSE" component is optional.
*If you need a very simple if..then with only one command, it can be written on one line without the "ENDIF":
<pre>
IF [condition] THEN [do something]
</pre>
*Refer to [[Scanco_User_Instructions#Numeric_comparisons|'''Numeric Comparisons''']], [[Scanco_User_Instructions#String_comparisons|'''String Comparisons''']] and [[Scanco_User_Instructions#Logical_expressions|''' Logical Expressions''']] for all possible logical operators (very similar to Fortran).

===Loops===
Most programming languages have 3 kinds of loops:
*Precondition Loops: Condition is tested at the beginning of the loop
*Postcondition Loops: Condition is tested after the loop has executed at least once
*Iterative Loops: A variable changes in a predetermined fashion each time the loop is called.

DCL has none of these. Instead, it has the concept of a "label" and the "GOTO" command. A loop in DCL would look like this:
<pre>
$ i = 1
$loop1:
$ IF i .GE. 10 THEN GOTO exitloop1
$ WRITE SYS$OUTPUT i
$ i = i + 1
$ GOTO loop1
$exitloop1:
$ EXIT
</pre>
This program will print the numbers from 1 to 10 in sequence.

===Subroutines===
Most programming languages allow to define a set of commands that can be called from various parts of the program.
*In DCL, the subroutine can be defined anywhere in the file (unlike C or Python, where the definition must precede the call).
<pre>
$ CALL mycustomsub Joe
$ CALL mycustomsub Mary
$ EXIT
$mycustomsub: SUBROUTINE
$ WRITE SYS$OUTPUT "Hello, ", P1, "!"
$ EXIT
$ ENDSUBROUTINE
</pre>

The first line calls a subroutine named "mycustomsub", which jumps execution to the 4th line. The parameters after the name of the function get copied over to local variables named "P1", "P2", "P3" etc. (in this example, only one parameter, but the maximum is 8) that are available to the subroutine. Note that the command "WRITE" accepts several arguments separated by commas, which get printed on one line.
*The subroutine should be terminated with the command "EXIT" followed by "ENDSUBROUTINE".
*Note that the parameters get passed literally to the subroutine, that is the subroutine gets the text "Joe", and not the contents of a variable named "Joe".
*To force symbol substitution, the parameter would need to be enclosed in single quotes.
<pre>
$ Joe = "Joe Smith"
$ Mary = "Mary Jane"
$ CALL mycustomsub 'Joe'
$ CALL mycustomsub 'Mary'
$ EXIT
$mycustomsub: SUBROUTINE
$ WRITE SYS$OUTPUT "Hello, ", P1, "!"
$ EXIT
$ ENDSUBROUTINE
</pre>

===Reading from files===
Sometimes you have a list of files (for example Micro-CT scans) that are to be processed in a certain way. The obvious way is to copy-paste the code several times, changing only the name of the file, but this is error-prone and inefficient.
*A better way is to put the list of models into a text file, and then call a subroutine on each model file. For example:
<pre>
$ CLOSE/NOLOG foo
$ OPEN/READ foo DISK3:[MICROCT.PROJECTS.OWOC.COM]MYLIST.TXT
$read_loop:
$ READ/END=done foo myline
$ CALL process_me 'myline'
$ GOTO read_loop
$done:
$ CLOSE/NOLOG foo
$ EXIT
$process_me: SUBROUTINE
$ scriptname = DISK3:[MICROCT.PROJECTS.OWOC.COM]MYSCRIPT.COM
$ SUBMIT/NOPRINT/QUE=SYS$FAST/PARAM='P1' 'scriptname'
$ EXIT
$ ENDSUBROUTINE
</pre>
*The first line closes the file handle, in case it was left open in a previous script.
*The second opens the file "MYLIST.TXT" for reading, and assigns the open file a handle named "foo".
*A loop reads the file line-by-line, calling a subroutine with the contents of each line.
*When the end of the file is reached, the file is closed and the script exits.

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==List of basic commands==
<pre>
$ VUE !Start the session manager. Press enter after to regain prompt.
$ DEC !Open a new DEC terminal
$ UCT !Open the micro-CT control panel.
$ UCT_SAMPLE !Start µCT Samples.
$ UCT_MEASUREMENT !Start µCT Tomography.
$ UCT_EVALUATION !Start µCT Evaluation Program.
$ UCT_3D !Start µCT Ray.
$ UCT_BACKUP !Start µCT Disk-Utility.
$ CD UD !Change location to the data directory.
$ CD UR !Change location to the projects directory.
$ CD SYS$SCRATCH !Change location to the scratch directory.
$ CD UCT_RESULTS !Change location to the results directory.
$ DIR UE !List files in the evaluation directory.
$ DIR UU !List files in the templates directory.
$ DIR COM !List files in the commands directory.
$ UCT_LIST !Extract results from the database.
$ AIX -L !View the header of an AIM file.
$ CTHEADER !View the header of an RSQ or ISQ file.
$ EVE !Start the text editor.
$ DISKS !Show the current disk usage (all hard drives).
$ LOGOUT !End a session. For remote sessions, logout from the main (initial) login terminal.
</pre>

===How to move to a different directory===
Use the SET DEFAULT command. You can use an absolute directory path or a relative directory path.
<pre>
$ SET DEFAULT disk:[dir.subdir] !Moves to specified path.
$ SET DEFAULT [.subdir] !Moves one level into subdirectory subdir.
</pre>

Use the CD (i.e., change directory) command (this calls the script $ @SCOM:CD.COM).
<pre>
$ CD subdir !Moves into subdirectory subdir.
$ CD subdir1 subdir2 !Moves into subdirectory subdir1, then into subdir2.
$ CD .. !Moves up one level (i.e., out of one directory).
</pre>

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===How to list the files in a directory===
Use the DIRECTORY command, which may be abbreviated to DIR.
<pre>
$ DIR !List everything in the current directory.
$ DIR disk:[dir.subdir] !Lists everything in the specified directory.
$ DIR disk:[dir.subdir...] !Lists everything in the specified directory and subdirectories.
$ DIR/COL=1 *.aim !Lists all files with the extension .aim in a single column.
$ DIR /VERSIONS=1 !Show only the newest version of each file in the directory.
$ DIR/SINCE=TODAY !Lists all files created today.
$ DIR [...*.aim] !The "..." indicates to do so recursively (i.e., counting all files in all subdirectories).
$ DIR/SIZE !Lists each file and its size.
$ dir/size/grand_total [.subdir...] !List the total size of all files in the SUBDIR directory.
$ HELP DIR !More information on the DIRECTORY command.
</pre>

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===How to copy files===
Use the COPY or BACKUP command.
<pre>
$ COPY file1.ext disk:[dir.subdir1]file2.ext !Make a copy of file1.ext to another location and call it file2.ext
$ COPY *.aim;* disk:[dir.subdir1] !Copy all .aim files (including all versions) to another location keeping the same name.
$ HELP COPY !More information on the COPY command.
</pre>
<pre>
$ BACKUP/VERIFY [.subdir1...]*.*;* [.subdir2...] !Copy entire directory SUBDIR1, including all subdirectories and files, into SUBDIR2.
$ BACKUP/VERIFY [.subdir1...]*.*;* []subdir1.sav/SAVE !Copy entire directory SUBDIR1, including all subdirectories and files, into a save set. The save set could be transferred and unpacked on another OpenVMS machine.
$ HELP BACKUP !More information on the BACKUP command.
</pre>

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===How to delete files===
Use the DELETE command, which may be abbreviated to DEL.
<pre>
$ DEL myfile.txt; !Delete the most recent version of myfile.txt.
$ DEL myfile.txt;* !Delete all versions of myfile.txt.
$ HELP DELETE !More information on the DELETE command.
</pre>
[[Image:Bones2.jpg|20px]] Warning: Extreme caution!
<pre>
$ DEL *.*;* !Delete everything in the current directory!
</pre>

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===How to create a directory===
Use the CREATE/DIR command.
<pre>
$ CREATE/DIR [.subdir] !Creates a subdirectory named subdir.dir in the current directory.
$ CREATE/DIR disk:[dir.subdir] !Creates the subdirectory subdir at the specified path.
</pre>

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===How to rename files and directories===
Use the RENAME command.
<pre>
$ SET FILE/PROTECTION=O:RWED olddir.dir !Sets protections so you can rename the directory.
$ RENAME oldfile.ext newfile.ext !Renames oldfile.ext to newfile.ext.
</pre>

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===How to check the queue===
Use the SHOW QUEUE command, which may be abbreviated to SH QUE.
<pre>
$ SHOW QUEUE !Shows all the queues, there are many!
$ SH QUE *FAST !Shows all queues whose names end with "fast", these are used for evaluations.
$ SH QUE *SLOW !Shows all queues whose names end with "slow", these are used for reconstructions.
$ SH QUE *FAST/ALL !By default you are only shown queue entries for the user you are logged in as. To show jobs for all users, use the /ALL qualifier.
$ SH QUE *FAST/BY=EXE/ALL !Show only jobs that are currently executing for all users.
</pre>

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===How to get queue information===
Use the SHOW ENTRY command to obtain information about batch jobs in the queues.
<pre>
$ SHOW ENTRY !Shows all the batch jobs for your user, there may be lots!
$ SHOW ENTRY 251 !Shows information for batch job number 251.
$ SHOW ENTRY 251/FULL !Shows detailed information for batch job number 251.
$ SHOW ENTRY/ALL !Shows all the batch jobs for all users.
</pre>

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=Micro-Computed Tomography (µCT) Basics=

==User Tutorials==
For Scanco MicroCT Systems and Software:
:*[[Media:Microct-v14.pdf | '''Scanco MicroCT Systems and Software''']]

For XtremeCT II and I:
:*[[Media:SOP Berlin V1.0.pdf | '''Scanco XtremeCT I SOP (Berlin)''']]
:*[[Media:XtremectIIB-v4-us.pdf | '''Scanco XtremeCT II Specs''']]

For MicroCT35, VivaCT40 and VivaCT80:
:*[[Media:ScancoMicro-CT_User_Policy_Guidelines_19052005.pdf| '''MicroCT User Policy & Guidelines''']]
:*[[Media:MicroCT_Starter_Package.pdf | '''MicroCT Starter Package''']] and its [[Media:Microctstarterpackagejun2012.docx| '''Word format''']].
:*[[Media:Scanco-training-uct35-and-vivact40.pdf | '''MicroCT Customer Training Guide''']]
:*[[Media:Vivact_80_v3-nomarks.pdf | '''VivaCT 80 Specifications''']]

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==Micro-CT Image Basics==
Computed tomography is a non-destructive x-ray imaging modality that enables three-dimensional (3D) virtual models of an object to be created, which can be subsequently visualized and analyzed. Micro-CT refers to CT in which the [http://www.scanco.ch/index.php?id=faq_general#c779 resolution] lies in the micro-scale, which is achieved with a high-resolution x-ray detector and a field of view that is much smaller than conventional CT. Structural detail provided by CT depends on differences in x-ray attenuation properties. Components with very different x-ray attenuation properties, for example air, soft tissue, and bone, can be differentiated in a CT scans whereas different types of soft tissues, for example muscle and cartilage, do not have sufficient differences in attenuation to be distinguish.

===Dark Field===
Detector response with x-rays off. Enables corrections of non-uniformities of the detector. Acquired automatically by the scanning software before each scan.

[[File:Dark_field_single.img_assist_custom-400x97.jpg|400px]]

===Bright Field===
Detector response with x-rays on but no sample. Enables corrections of non-uniformities of the x-ray beam. Acquired automatically by the scanning software before each scan.

[[File:Bright_field_single.jpg|400px]]

===Raw Projection===
A raw x-ray projection of a mouse leg. The darker regions correspond with higher x-ray attenuation. The discontinuities result from overlaps where the detector was shifted to acquire the large region of interest (3x2 detector frames in this example). Projections are acquired at many incremental rotations around the sample.

[[File:Raw_projection_notes.jpg|400px]]

===Sinogram===
The sinogram is a different representation of the projection data. The sinogram represents the attenuation values of one row of the detector at each rotational increment around the sample.

[[File:Sinogram.jpg|400px]]

===Attenuation Projection===
Accounting for the inhomogeneities of the detector and beam, we can calculate the x-ray attenuation caused by the sample. Bright regions correspond with higher attenuation.

[[File:Attenuation_projection.jpg|400px]]

===Reconstructed Image===
From the attenuation projections, the original structure can be calculate using filtered back projection.

*[https://youtu.be/DBLYSETYbe8 CT Back-projection Reconstruction]
*[https://youtu.be/NWeM35_KR2w CT Reconstruction of a Head]

[[File:Reconstruction_xy_yz_planes.jpg|400px]]

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==Image Data==
===Image Data Type===
====Binary Images====
Binary images are images whose pixels contain only two possible intensity values (off-on, or black-white B&W). The off or black value is usually 0 and the on or white value is usually 1 (1-bit pixel) or 255 (8-bit pixel). This type of image is commonly used as a multiplier to mask regions within another image.

====Grayscale Images====
Grayscale images represent intensities. Pixels range from least intense (black) to most intense (white). Pixel values usually range from 0 to 255 or are scaled to this range when displayed.

====Indexed Images====
An indexed image uses direct mapping of pixel values to colormap values. Instead of intensities, a pixel value within an indexed image relates to a color value within a color lookup table. An indexed image consists of a data matrix and a colormap matrix. The data matrix can be of class uint8, uint16, or double. The colormap matrix is an m-by-3 array of class double containing floating-point values in the range [0,1]. Each row of map specifies the red, green, and blue components of a single color. Since indexed images reference color tables composed of up to 256 colors, the data values of these images are usually scaled to range from 0 to 255.

====RGB Images====
Within the three-dimensional array of an RGB image, two of the dimensions specify the location of a pixel within an image. The other dimension specifies the color of each pixel. The color dimension always has a size of 3 and is composed of the red, green, and blue color bands (channels) of the image.

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===Image Data Pixel Values===
The image data type is determined by the pixel depth in bits per channel, or bit depth. Bit depth for each channel can be 8, 16, 32 or 64. The data may be signed, unsigned (u), floating-point (f), real or complex (c) for some arithmetic functions, where each channel value is represented by two numbers: real and imaginary part. All channels in an image must have the same data type.

{| class="wikitable"
|-
! scope="col"| Image Data Type
! scope="col"| Name
! scope="col"| Byte
! scope="col"| Value Range
! scope='col'| Comments
|-
! scope="row"| char
| 8-bit signed integer
| 1
| -128 ~ 127
| Scanco SEG.AIM, GOBJ
|-
! scope="row"| uchar
| 8-bit unsigned integer
| 1
| 0 ~ 255
|
|-
! scope="row"| int
| 16-bit signed integer
| 2
| −32768 ~ 32767
| Scanco grey-scaled images, ISQ, AIM
|-
! scope="row"| uint
| 16-bit unsigned integer
| 2
| 0 ~ 65535
| Converted format of Scanco grey-scaled images
|-
! scope="row"| long
| 32-bit signed integer
| 4
| −2^31 ~ 2^31 - 1
|
|-
! scope="row"| ulong
| 32-bit unsigned integer
| 4
| 0 ~ 2^32 - 1
|
|-
! scope="row"| float
| floating point
| 4
| ±3.40282347 E+38
| 32-bit single-precision with 6~7 significant digits
|-
! scope="row"| long64
| 64-bit signed integer
| 8
| −2^63 ~ 2^63 - 1
|
|-
! scope="row"| ulong64
| 64-bit unsigned integer
| 8
| 0 ~ 2^64 - 1
|
|-
! scope="row"| double
| double precision floating point
| 8
| ±1.79769313486231570 E+308
| 64-bit double-precision with 15~16 significant digits
|-
! scope="row"| complex
| floating point complex
| 8
| same as floating-point
| same as floating-point
|-
! scope="row"| dcomplex
| double precision complex
| 16
| same as double-precision
| same as double-precision
|}

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===Scanco Image File Types===

{| class="wikitable"
! scope="col"| Extension
! scope="col", style="width: 65%"| Description
! scope="col"| Creation
! scope="col"| Opens with
|-
! scope="row"| RSQ
| '''R'''aw '''S'''e'''Q'''uence data. This is the raw data collected after the scan. This file contains the bright and dark field corrections and the raw projections. || created with scan || $ x
|-
! scope="row"| ISQ
| '''I'''mage '''S'''e'''Q'''uence data. This is the reconstructed 3D image, which you see in the µCT Evaluation Program. || created from RSQ
| $ uct_evaluation
$ x
|-
! scope="row"| AIM
| '''A'''ny '''IM'''age data. This is a binary raw data format (16-bit signed data, little endian) 3D discretized data you see using the µCT Ray Program and used for the analysis. The AIM file is a volume of interest isolated from the ISQ file. || extracted from ISQ
|$ uct_3d
$ uct_evaluation
|-
! scope="row"| GOBJ
| '''G'''raphical '''OBJ'''ect data. These are the green contours in the µCT Evaluation Program, which are used to isolate regions of interest from an AIM file for analysis. || extracted from ISQ/AIM || $ uct_evaluation
|-
! scope="row"| SCV
| '''SC'''out '''V'''iew || created with scan || $ x
|-
! scope="row"| RAD
| Scout View || created with scan || $ x
|-
! scope="row"| RSW
| raw data (RSQ) || created with scan || $ x
|-
! scope="row"| IMA
| image data (AIM, ISQ, GOBJ)|| created from RSQ || $ uct_evaluation
|}
*Refer to [[Media:Aimpack_documentation.pdf|'''Scanco Aim Format''' ]] or its [[Media:Scanco_Aim_File_Format.doc|'''Doc Format''']] for its header info.

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==Scanco Medical Micro-CT Software==
In the bottom left hand corner of the micro-CT workstation desktop is the micro-CT control panel, from which the micro-CT programs can be launched. The standard operating procedure for scanning a samples involves proceeding through the programs in the control panel from left to right:
<pre>
$ UCT_SAMPLE !Samples: Registering a sample
$ UCT_MEASUREMENT !Tomography: Scanning
$ UCT_EVALUATION !Evaluation: Evaluating the scan
$ UCT_3D !Ray: Viewing the 3D scan
$ UCT_BACKUP !Disk-Utility: Archiving the data
</pre>
You must specify an operator in the control panel to use the scanning and evaluation programs.
* XtremeCT
[[File:XCTcontrol_panel.img_assist_custom-302x100.jpg|300px]]
* MicroCT35, VivaCT40 and VivaCT80
[[File:Uct35_control_panel.jpg|300px]]
[[File:VivaCT40_control_panel.jpg|300px]]
[[File:VivaCT80_control_panel.jpg|300px]]

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===µCT Samples===
The µCT-Samples program is used to register new samples to be scanned and update sample names (e.g., to correct a sample name). To start the program type <code>$ uct_sample</code> in a DEC terminal, or use the sample button.

[[File:Xtremect_button_samples.jpg|40px]]
[[File:Uct_sample_uct35.jpg|40px]]
[[File:Uct_sample_vivact40.jpg|40px]]

#'''Prepare Sample Names''' according to [[Scanco_User_Instructions#Sample_Name_Convention|'''Sample Name Convention''']]
#'''Register Sample Names'''
#*Create a new sample by clicking “New” and typing in your sample name where it says “Name.” “Save” the sample.
#*You are now given a sample number. Record the sample number on the log sheet.
#:[[File:Uct_sample_pic01.jpg|500px]]
#'''Create Additional Sample Names Using Copy and Paste'''
#*If you have many samples to register, you can copy and paste part of the sample name you just created. Highlight the part of the sample name you want to copy by holding down the left mouse button while dragging the mouse, then release the mouse button.
#:[[File:Uct_sample_pic02.jpg|500px]]
#*Paste the highlighted text into a DEC terminal by pressing the middle mouse button. Now highlight the text in the DEC term.
#:[[File:Uct_sample_pic03.jpg|300px]]
#*Go back to the µCT-sample window, click "New", and paste the information next to "Name" using the middle mouse button. Update the name as required and "Save."
#'''Add Additional Sample Details'''
#*When a patient comes in for their first scan, you need to update their sample with their date of birth, sex, and hand/foot dominance.
#*Use the "Find..." button to search for a sample that has already been registered. You can search by sample number or by project name (e.g., CAMOS).
#*Date of birth: DD/MMM/YYYY. Example: 14/JAN/1951
#*Remarks: include the sex and hand/foot dominance. Example: F-RHRF for female that is right hand dominant and right foot dominant

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===µCT Tomography===
The µCT-Tomography program is used to perform a scan. To start the program type <code>$ uct_measurement</code> in a DEC terminal on the scanner computer (remote access does not allow this functionality), or use the scanner button. If you use the button, you must specify an operator prior to using the program.

[[File:Xtremect_button_scan.jpg|40px]]
[[File:Uct_measurement_uct35.jpg|40px]]
[[File:Uct_measurement_vivact40.jpg|40px]]
[[File:VivaCT80_scan.jpg|40px]]

[[File:Uct_tomography_pic00.jpg|600px]]

#'''Select Sample'''
#*When the µCT-Tomography program is first started, you will be prompted to enter the sample name or number of the specimen you are about to scan.
#*If you have not registered your sample, press "Cancel" to close the select sample box, then press "New..." in the measurement sample box to register a new sample (see [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT-Samples''']]).
#*Once you have entered your sample information, the measurement sample box will show details for that sample, including the sample name and scan (measurement) history.
#:[[File:Uct_tomography_pic01.jpg|400px]]
#*After your first scan you will need to press the "Other..." button to open the sample selection box and find your next sample.
#'''Select a Controlfile'''
#*The controlfile contains scan parameters such as the x-ray energy, current, and more (see [[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29 controlfiles |'''Controlfiles''']]).
#*Once the controlfile is setup, you need only to select it. If there are many controlfiles, you may want to search for yours using the file filter by entering part of the name or number in the white box and pressing enter; if you do this, you still must click on the controlfile so that it is highlighted in black as shown below.
#:[[File:Uct_tomography_pic02.jpg|400px]]
#'''Precalibrate'''
#*Calibrations are done before loading your patient/animal and scanning for quality control and to reduce the time the patient/animal is under preparation/anaesthesia. Start the calibration by pressing the "Precalibrate" button.
#:[[File:Uct_tomography_pic03.jpg|400px]]
#*Press "Start Calibration". The calibration will start with an "X-Ray Warmup", followed by "Measuring Dark" and "Measuring I0" and usually takes about 2-3 minutes to complete.
#:[[File:Precalibrate.jpg|300px]]
#*The precalibration is good for 15~20 min. The time remaining is shown on the "Precalibrate" button.
#:[[File:Uct_tomography_pic5.jpg|400px]]
#*The precalibrate option cannot be used with batch measurements, and it's not available for MicroCT35 which is not intended for invivo/live scan.
#'''Load and Position the Patient/Sample'''
#*Instruct the patient to remove any jewelry in the scan areas (wrist/ankle/knee/elbow ect). With the patient seated, put the wrist/ankle/knee/elbow into the appropriate cast. Different pads with different sizes can be used to fit the patient.
#*For invivo/invitro samples, prepare your sample in terms of orientation, immobilization, hydration ect.
#*After the precalibration is complete, you can now open the bore cover and insert the patient's wrist/ankle/knee/elbow or sample into the scanner. Gently move the wrist/ankle/knee/elbow or sample into the scanner until you can snap in the cast at the gantry. Check that the cast is positioned correctly and the patient/sample is comfortable.
#*Close the bore cover.
#'''Scout-View'''
#*A scout-view is similar to a 2D x-ray image and allows the user to set where to start and stop the scan.
#*After loading your sample, press the "Scout-View..." button to bring up the scout-view window.
#*The start position (top of the scanner) and end position (bottom of the scanner) can be modified to zoom in on the region of interest.
#*The angle of the scout view can also be changed to see the object in a different orientation.
#*Once pressed the "Scout-View" button but the scout view is found not in an appropriate position, press "Cancel", modify the start position, end position, or angle and press "Scout-View" again.
#:[[File:Scout_view_window.jpg|400px]]
#*Scout view image is displayed in the top right hand corner of the program and will start by showing the right half of the image, followed by the left half of the image.
#'''Set Reference Line and Launch a Scan'''
#*A reference line (solid green line) is placed to set the scan region (green block).
#*Press the "Reference-Line" button to show the reference line and default scan region over the scout view.
#*To change the number of slices to scan, move the reference line to the top of the scan region, then hold down the shift button while dragging the mouse to extend the scan region and press the left mouse button to set the reference line.
#*To centre the scan region between two reference lines, move the reference line to the top of the scan region, then hold down the alt key while dragging the mouse until the second green reference line is in place, then press the left mouse button to set while still holding down the alt key!
#:[[File:Uct_tomography_pic06.jpg|700px]]
#*For a single scan, select "OK", "Scan" and "Start Measurement". Record measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']].
#*For a batch scan which is only available on microCTs, select "Batch Measurement" and record the measurement number on your [[Scanco_User_Instructions#Log_Sheets |'''log sheet''']]. You may now setup a new scan (select new sample and controlfile, perform scout, etc). When you have finished setting up all scans, press "Start Batch Scans." (See [[Scanco_User_Instructions&action=edit&section=48#Perform_Batch_Scans|'''Perform Batch Scans''']] for detailed instructions)
#'''Cancel or Reposition a Scan'''
#*If you need to interrupt a scan, press the cancel button and restart the scan or if you do not want to rescan then "unload" the scanner.
#*If you have not started a scan and need to reposition the patient, you also must "unload" the scanner.
#'''Remove Patient/Sample from Scanner'''
#*After the scanning is complete, open the bore cover and slide the patient's wrist/ankle/knee/elbow or sample out of the scanner. Release the cast by pushing down the cast release handle.

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===µCT Evaluation Program===
The µCT Evaluation Program is used to evaluate a scan. To start the program type <code>$ uct_evaluation</code> in a DEC terminal, or use the graph button. If you use the button, you must specify an operator prior to using the program.

[[File:Uct_evaluation.jpg|40px]]

[[File:Uct_evaluation_pic01.jpg|600px]]

#'''Find Your Sample'''
#:Enter the first part of your sample name in the file filter box and press enter. The samples are shown in the left hand box. The measurement box on the right shows scans for the selected sample (highlighted in black). Select a measurement and press "OK."
#:[[File:Uct_evaluation_pic02.jpg|500px]]
#'''Draw Contours (If Applicable)'''
#*Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
#*Contours must always be drawn COUNTER-CLOCKWISE!!!
#*[[Media:Contouring-tools.pdf |'''Contouring tools reference sheet''']]
#*For this sample, we are only interested in viewing the object in 3D and drew contours to isolate the bone and soft tissue from the sample tube.
#:[[File:Uct evaluation pic03.jpg|600px]]
#'''Evaluate'''
#*Scanco Medical provides several standard evaluation scripts. Open the 3D-Evaluation menu either using the "T..." button or from the top menu by going to "Tasks" and "Evaluation 3D...". If you set a default evaluation script in your scanning controlfile, it will be listed under "Task/Evaluation."
#:[[File:Uct_evaluation_pic04.jpg|400px]]
#*If you want to run a different evaluation press "Select...", highlight the evaluation script of interest, and press "OK".
#:[[File:Uct_evaluation_pic05.jpg|400px]]
#*When the 3D-Evaluation window is activated, a white box will appear on your reconstructed image. The white box is the region of interest that will be "cut out" of the full scan. If you have drawn contours, the white box will automatically be adjusted to fit the contours. Adjust the box if necessary by grabbing one of the white handles; use the left mouse button to move the box and the right mouse button to resize. The box can also be resized using the "VOI Start" and "Dimensions" in the 3D-Evaluation window.
#*For most evaluation scripts, you will be required to specify parameters for a Gaussian filter, to reduce noise, and a threshold, to isolate your object (e.g., bone) from the background. Check that the parameters used provide a good representation of your scanned sample by flipping back and forth between the segmented and grayscale image using the "Preview" and "Grayscale" buttons.
#:[[File:Uct_evaluation_pic06.jpg|400px]]
#*When you are satisfied with the segmentation parameters, press "Start Evaluation", which will submit the job to the queue.

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===µCT Ray===
The µCT Ray program is used to view scanned objects in 3D, create images, and create image sequences for animations. To start the program type <code>$ uct_3d</code> in a DEC terminal, or use the 3D object button.

[[File:Uct_3d.jpg|40px]]

[[File:Uct_3d_pic01.jpg|600px]]

#'''Select and Render Your Sample'''
#*'''Select:''' If you have used the default Scanco Medical scripts, then
#:*If your data is on the "data disk" and you can search for your files using the file filter to select a sample and measurement then press "OK". To open a new file, File --> Open.
#:*If your data is not in the standard location (e.g., it was copied to the projects disk), then use File --> Read and navigate to find the file to open.
#:*Alternatively you can start the program with a file to open <code>$ uct_3d myfile_seg.aim</code>
#: 
#*'''Rendering:'''
#:*Use a single click of the left mouse button to start or to stop rendering the sample.
#:*You can also use the "Start" and "Stop" buttons at the bottom of the options on the left.
#:*You must stop rendering to change viewing options on the left.
#: 
#*'''Change View:'''
#:*To adjust the view, move the "Rotation" and "Elevation" slider bars in the options on the left.
#:*The slider bar is located above its label.
#:[[File:Uct_3d_pic02.jpg|600px]]
#: 
#*'''Change Colours''' (Object and Background):
#:*From the top menu choose "Options" then "Object/Display Properties...".
#:*A segmented image typically only has two values, 0 (black, background) and 127 (white, object). To change the colour of the object only, we need to set the value 127 to a specific colour.
#:*In this example, the slider bar value "1" corresponds with the value 127 and we will set both slider bars to "1" so that we are adjusting values "127 ... 127", in other words, only value "127".
#:*Under "Surface" click on the "white box" to open the "Color Mixing" window.
#:*Choose the new colour for the object (e.g., orange) and press "OK."
#:*Close the "Object Properties" window or move it to the side.
#:*Now re-render the object with a single click of the left mouse button.
#:[[File:Uct_3d_pic03.jpg|300px]] [[File:Uct_3d_pic04.jpg|300px]]
#: 
#*'''Cutplane (left options) and Subdim (top menu):''' 
#:*The cutplane and subdim functions allow you to show a cross-section of your object.
#:*The subdim function tends to work better than the cutplane but is limited to axes of the scan.
#:[[File:Uct_3d_pic05.jpg|600px]]
#: 
#'''Print an Image to File'''
#*An image must be fully rendered in order to be saved.
#*From the top menu choose "File" then "Print". Set the print format to "TIFF" and the directory to "Scratch/Temp" (or another location using the "Specify in Filename" option).
#*Change the filename to something meaningful then press "OK."
#:[[File:Uct_3d_pic06.jpg|300px]]
#: 
#'''Auto-Print Images for an Animation'''
#*Creating an animation involves saving a sequence of rendered images, which can then be compiled into an animated GIF or other video format using various software packages (e.g., Photoshop, Quicktime Pro).
#*From the top menu choose "Options" and "Animation..." to open the Animation Settings window. Set the viewing parameters for the start of the animation, fully render the image, then press the "Get Settings A" button.
#*Set the parameters for the end of the animation, fully render the image, then press the "Get Settings B" button.
#*Set the number of frames you want, the higher the number frames, the smoother the animation will be, but also the larger the file size.
#*Now setup the auto-print feature. From the top menu choose "File", then "Print". Choose "TIFF" for the print format, and the "Scratch/Temp" for the directory (or use the "Specify in Filename"). Specify a filename prefix, to which numbers will be appended for the image sequence.
#*Activate the "Auto-Print" feature. Press "OK" then press the "Start Calculation" button on the Animation Settings window.
#*Do not interrupt the program while the frames are being rendered and saved. When the program is done rendering all the frames, transfer them to your computer to compile into an animation.
#:[[File:Uct_3d_pic07.jpg|200px]] [[File:Uct_3d_pic08.jpg|300px]]

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===XImage===
The XImage program is used to view the raw data (RSQ file) and scout view. To start the program type <code>$ run um:ximage</code> or <code>$ x </code>in a DEC terminal.

When loading an RSQ, the default view (XY plane) is of the sinogram.

[[File:Ximage_1.jpg|600px]]

To view the attenuations, choose the XZ plane. The first slice in this orientation is the dark field, the second slice is the bright field , and slices three and onward are the raw projections (attenuations).

[[File:Ximage_2.jpg|600px]]

To view the corrected projections, from the Evaluations menu, choose Projection Mode.

[[File:Ximage_3.jpg|400px]]

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=Scanning=
==Sample Name Convention==
*At the Bone Imaging Laboratory, all sample naming must conform to the following format
:'''PROJECT IDENTIFIER _ SAMPLE DETAILS'''
*In CAPITAL LETTERS (filenames are case sensitive, so this makes it easy to remember how you input your sample name)
*No special characters (spaces, /, %, etc.) as further evaluations will not work if spaces are present.
:Examples: CAMOS_771, TESTS_0001, TESTS_0002, TESTS_0003

==Register Samples for Scanning==
*Although samples can be registered immediately prior to a scan, it is much more efficient to register all your samples beforehand.
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Samples|'''µCT Samples''']] for instructional details.

==Log Sheets==
*Log sheets are used to record important information about scans that are performed, such as sample and measurement numbers ect.
*Log sheets are to remain in the lab. If you would like a copy of your log sheets, please make a photocopy or print two copies to record the scan information.
*Use the PDF file to print blank log sheets. Use the Excel file to make your own custom log sheet.

#Bone Lab for General Patients
#*[[Media:XCT_II_Log_(Studies).pdf|'''XCT II Log Sheet for Studies''']]
#*[[Media:XCT_II_Log_(Miscellaneous).pdf|'''XCT II Log Sheet for Miscellaneous''']]
#MicroCT Lab for General Non-Patients
#*[[Media:UCT_log_sheet_general.pdf|'''MicroCT Log Sheet for Studies (PDF)''']]
#*[[Media:UCT_log_sheet_general.xlsx|'''MicroCT Log Sheet for Studies (Excel)''']]

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==Patient Casts and Sample Holders==
===Patient Casts for XtremeCTs===

===Sample Holders and Scan SOP for microCTs===
====Ex Vivo Sample Holders====
*Ex vivo and inanimate samples are scanned in sample holder tubes. These tubes come in a variety of diameters. It is extremely important that the tube diameter corresponds to, or is smaller than, the field of view (FOV) set in your scanning control file.

*Biological tissues should be hydrated and wrapped in plastic wrap to prevent drying of the sample. Your sample should then be secured in the sample holder using foam to prevent it from shifting around during scanning, which would lead to poor image quality.

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=====Chemical Resistivity of Sample Holders=====
*White tube sample holders are made of PMMA (poly-methyl-methacrylate).
*Yellow tube samples holders are made of PEI (poly-ether-imide).
*Use the yellow tubes if you will need to disinfect the sample holder after scanning.

{| class="wikitable"
!colspan="3"|Thermal and chemical compatibility of sample holders
|-
! scope="col"| Properties
! scope="col"| White Tubes (PMMA)
! scope="col"| Yellow Tubes (PEI)
|-
! scope="row"| Max. Temperature
| +85°C
| +170°C
|-
! scope="row"| Sterilization Steam Autoclave
|non resistant
|resistant (138°C for 20 Min. at 1 bar)
|-
! scope="row"| Water
|resistant
|resistant
|-
! scope="row"| Inorganic Acids
|limited resistance
|resistant
|-
! scope="row"| Inorganic Bases
|non resistant
|limited resistance
|-
! scope="row"| Aldehydes (Formaldehyde)
|limited resistance only in diluted form
|resistant
|-
! scope="row"| Alcohols
|limited resistance
|resistant
|-
! scope="row"| Bleach
|non resistant
|resistant
|}

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=====Mounting of Sample Holders=====
[[File:Uct35_holder.jpg|thumb|right|100px|µCT35 setup]]
*The spindle (metal bit) of the sample holder has a slot, which must be aligned in the scanner or adapter plate.
*The sample holder sits vertically in the µCT35 while horizontally in the VivaCT80 and VivaCT40.
*For the vivaCT40, attach the adapter plate for the tube sample holders to one of the animal bed. The tube sample holders are held horizontally in the vivaCT 40.
:[[File:Vivact40_holder.jpg|thumb|none|700px|VivaCT40 setup]]

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=====Ex vivo rodent scanning SOP=====
*Refer to [[Media:Ex_vivo_scan_sop.pdf|'''Ex Vivo Rodent Scanning''']] for its scan SOP.
*Refer to [[Media:Ex_vivo_scan_sop.docx|'''Ex Vivo Rodent Scanning in docx''']] for its Word version.

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====In Vivo Sample Fixtures and Anesthetic System====
*[[Media:VivaCT40_Anaesthetic_System.pdf |'''Anaesthetic System''']] : You must receive training to use the anaesthetic system.
*[[Media:VivaCT40_Mouse_and_Rat_Tibia_Fixture.pdf |'''Mouse/Rat Tibia Fixture''']]
*[[Media:VivaCT40_Mouse_Lower_Body_Fixture.pdf|'''Mouse Lower Body Fixture''']]
*[[Media:VivaCT40_Mouse_Whole_Body_Tube.pdf|'''Mouse Whole Body Tube''']]

=====In vivo rodent scanning SOP=====
*Refer to [[Media:In_vivo_scan_sop.pdf|'''In vivo rodent scanning''']] for its scan SOP.
*Refer to [[Media:In_vivo_scan_sop.docx|'''In vivo rodent scanning in docx''']] for its Word version.

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====Align whole body device in FOV====

It's important to have your whole sample in the field of view for accurate density measurements.
* Refer to [[Media:wholebody.pdf |'''Align the device''']] for detailed instructions.

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==Scan Parameters (Controlfiles)==

:{| class="wikitable" style="text-align:center;"
|-
! scope="row"| Manufacturer
| colspan="5"|[http://www.scanco.ch '''Scanco Medical AG''']
| [https://www.zeiss.com/microscopy/int/products/x-ray-microscopy.html '''Carl Zeiss X-ray Microscopy''']
|-
! scope="col" rowspan="2"| Model
! scope="col"| XtremeCT II || XtremeCT I || VivaCT80 || VivaCT40 || µCT35 || Xradia 520 Versa
|-
|[[File:XtremeCT.jpg|150px]]
|[[File:XtremeCT.jpg|150px]]
|[[File:VivaCT80.jpg|120px]]
|[[File:VivaCT40.jpg|135px]]
|[[File:UCT35.JPG|150px]]
|[[File:Xradia-520-versa-small.jpg|160px]]
|-
! scope="row"| Application
|colspan="2"| Clinical studies for human extremities in vivo
Horizontal static patient setup
|colspan="2"| Preclinical in vivo animal studies
Horizontal static animal setup
|colspan="2"| High resolution ex vivo specimen scans
Vertical rotational sample setup
|-
! scope="row"| E (KVp)
| 68 || 60
|colspan="3"| 45, 55, 70
| 30 ~ 160
|-
! scope="row"| Power (W)
| 100 || 54
|colspan="3"| 4, 8
|4 ~ 10
|-
! scope="row"| Filter
| Fixed 0.2mm Cu + 1mm Al
(Equivalent 6.7mm Al)
| Fixed 0.1mm Cu + 0.6mm Al
| Default 0.5mm Al,
Air, 0.1mm Al, 0. mm Cu
| Fixed 0.5mm Al
| Fixed 0.5mm Al
| Air, LE1~LE6, HE1~HE6,
customizable filter
|-
! scope="row"| FOV (⌀ * L) (mm^2)
| 140 ⌀ * 200 L
| 126 ⌀ * 150 L
| 31.9 ~ 80 ⌀ * 145 L
| 21.5 ~ 38.9 ⌀ * 148 L
| 7.2 ~ 38 ⌀ * 140 L
(75 L standard)
| 90 ⌀ * 100 L
|-
! scope="row"| Image Matrix
| 4608*4608 ~ 512*512
| 3072*3072 ~ 512*512
| 4096*4096 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
| 2048*2048 ~ 512*512
|-
! scope="row"| Voxel Size (µm)
| Standard 60.7
(30.3 ~ 273.4)
| Standard 82.0
(41.0 ~ 246.0)
| 5 ~ 156
| 10.5 ~ 76
| 3.5 ~ 74
| 0.7 ~ 50
|-
! scope="row"| Sample Image
|[[File:XCT2_human_distal_femur.png|160px]]
human distal femur
|[[File:XCT1_human_distal_tibia.JPG|160px]]
human distal tibia
|[[File:VivaCT80_Rat_distal_femur.JPG|160px]]
rat distal femur
|[[File:Vivact40_in-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Uct35_ex-vivo_dist_femur.jpg|160px]]
mouse distal femur
|[[File:Xradia_mouse_distal_femur.png|160px]]
mouse distal femur
|}

Controlfiles are used to specify the parameters for the scans. Once your controlfile is setup, you should not modify it over the course of your project.

[[File:XCT2 ControlFile.JPG|right|600px]]

*'''Control File Name''': Specify a meaningful name so that others can reuse yours.

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===General Settings===
*'''Holder Type''': Choose the used holder type for XtremeCT II from Standard Casts, Knee Cast and Elbow Cast. No option for XtremeCT I scanner. For microCTs, Choose the used sample holder type with the correct diameter.

*'''Mode of operation''': Default is continuous operation for all scanners. Gated operation mode is available for VivaCT80 and VivaCT40 scanners.

*'''Evaluation Script''': This sets the default evaluation script used for the analysis. You can manually select a different script from the evaluation program.

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===X-ray Settings===
*'''Tube Energy (KVp)''': Fixed energy for XtremeCTs while having 3 options for each of microCTs: Use the 70 KVp for most samples, use the 55 or 45 KVp for low density objects (e.g., soft tissue) or specimens with a diameter less than 20 mm. Lower energies provide better contrast while higher energies provide better signal to noise (SNR).

*'''Tube Current (µA)''': Fixed current for XtremeCTs while having 2 options for each of energy settings of each microCTs: Use the higher current except when the voxel size is set for the best resolution of the scanner. The higher current will yield better SNR but a larger spot size.

:{| class="wikitable" style="text-align:center;"
|-
! scope="col"|
! scope="col"| XtremeCT II
! scope="col"| XtremeCT I
! colspan="3"| vivaCT80，vivaCT40， µCT35
|-
! scope="row"| E (KVp)
| 68
| 60
| 70
| 55
| 45
|-
! scope="row"| I (µA)
| 1470
| 900
| 114, 57
| 145, 72
| 177, 88
|-
! scope="row"| Power (W)
| 100
| 54
|colspan="3"| 8, 4
|}

*'''Filter''': Fixed filter settings for all scanners except VivaCT 80 has 4 filter options.

*'''Calibration''': This sets the mu scaling factor, density and beam hardening correction used for the reconstruction. For standard patient scans use 200 mg HA/cm3. For ex vivo bone scans, use 1200 mg HA/cm3, for soft tissue use the plexi scaling, and for non-biological tissues use the aluminum scaling.

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===Scout-View Settings===
Normally you will want to enable this and here you can specify the default start and end position, and scout-view angle, which you may override for each scan.

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===CT Scan Settings===

*'''Resolution''': This setting includes the reconstruction matrix size (2048x2048, 1536x1536, 1024x1024, or 512x512) and the number of projections per 180°. The lower the resolution setting, the better the SNR and larger the voxel size.

*'''FOV / Diameter''': This field of view must fully contain the sample holder for accurate density measurements. Fixed FOV for XtremeCTs while having 5 options for each of microCTs: If you choose a smaller FOV than the sample holder, the scan may be aborted to prevent damage to the scanner. For the best resolution, you should choose the smallest holder that contains your sample.

*'''Voxel Size''': The nominal isotropic voxel size is determined by the FOV and the reconstruction matrix.

*'''Number of Slices''': You can specify a specific number of slices or image stacks to acquire (1x110 = 1 image stacks of 110 slices). The scan time increases with each image stack, therefore pay attention to the stack boundaries (e.g., 111 slices will take 2x longer to scan than 110 slices).

*'''Rel Position of First Slice''': This option enables you to offset the scan region from the reference line. This is useful for scanning a region a specific distance from the growth plate or centering the scan region around the reference line. If you disable the scout view, then the position is relative to the absolute 0 position of the scanner (top of the sample holder for the µCT35 and towards the back of the scanner for the vivaCT40).

*'''Integration Time''': The higher the integration time, the better the SNR and longer the scan time. Use 100 ms for patient scans and higher values for ex vivo scans of better image quality. To get the highest integration time, uncheck the "Continuous ROT" button. For standard microCT measurements, use ~400 ms for the µCT35 and ~200 ms for the vivaCT40. The maximum integration time is scanner-specific and limited to prevent saturation of its detector.

*'''Average Data''': This is often referred to as frame averaging and is used to improve a scan's SNR. Multiply the average data value by the integration time to calculate the effective integration time. Only use this if the integration time is maxed out.

*'''Measurement Time''': This is the estimated scan time without the time performing the scout view or warm-up of the scanner.

*'''CTDIvol''': Computed Tomography Dose Index (CTDI) is a standardized measure of radiation dose output of a CT scanner for scanner settings' comparison purposes only, and it represents the average absorbed dose along the longitudinal axis from a series of contiguous CT exposures. Volumetric CTDI is the ratio of the weighted-CTDI to the level of overlap between slices (pitch). CTDIvol has no consideration of real scan length and does not represent actual dose administered to the patient.
:[[File:CTDI.JPG|600px]]

*'''DLP''': Dose Length Product DLP = CTDIvol * Scan Length in unit of mGy-cm.

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====XtremeCT II Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 4608
| 2304
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 3000
| 900
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 140 mm
| 30.3
| 60.7
| 91.1
| 136.7
| 273.4
|-
! colspan="2"| Slices/Stack
| 338
| 168
| 112
| 74
| 37
|-
! colspan="2"| Stack Thickness (mm)
| 10.24
| 10.20
| 10.20
| 10.12
| 10.12
|-
! colspan="2"| Time/Stack (min, at 43 ms Integration Time)
| 8.1
| 2.0
| 2.0
| 1.4
| 0.7
|-
! colspan="2"| Time Current Product (mAs)
| 238
| 71
| 59
| 40
| 20
|-
! colspan="2"| CTDIvol (mGy)
| 37.4
| 11.2
| 9.3
| 6.4
| 3.2
|-
! colspan="2"| DLP (mGycm)
| 38.3
| 11.4
| 9.5
| 6.4
| 3.2
|}

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====XtremeCT I Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Custom
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
|-
! colspan="2"| Image Matrix
| 3072
| 1536
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 750
| 500
| 250
|-
! scope="row"| Voxel Size (µm)
! scope="row"| FOV/Diameter 126 mm
| 41
| 82
| 123
| 246
|-
! colspan="2"| Slices/Stack
| 221
| 110
| 73
| 36
|-
! colspan="2"| Stack Thickness (mm)
| 9.06
| 9.02
| 8.98
| 8.86
|-
! colspan="2"| Time/Stack (min, at 100 ms Integration Time)
| 3.7
| 2.8
| 1.9
| 1.0
|-
! colspan="2"| Time Current Product (mAs)
| 114
| 86
| 57
| 29
|-
! colspan="2"| CTDIvol (mGy)
| 7.3
| 5.5
| 3.6
| 1.9
|}

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====VivaCT80 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| Native
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 3072
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1500
| 1000
| 500
| 250
| 125
|-
! rowspan="6"| Voxel Size (µm)
! scope="row"| FOV/Diameter 31.9 mm
| 10.4
| 15.6
| 31.9
| 31.2
| 62.4
|-
! scope="row"| FOV/Diameter 35.9 mm
| 11.6
| 17.5
| 35
| 35
| 70.1
|-
! scope="row"| FOV/Diameter 39.9 mm
| 13
| 19.5
| 39
| 39
| 78
|-
! scope="row"| FOV/Diameter 49.8 mm
| 16.1
| 24.2
| 48.5
| 48.5
| 97.1
|-
! scope="row"| FOV/Diameter 63.9 mm
| 20.8
| 31.2
| 62.4
| 62.4
| 124.8
|-
! scope="row"| FOV/Diameter 79.9 mm
| 26
| 39
| 78
| 78
| 156
|-
! colspan="2"| Slices/Stack
| 333 ~ 328
| 222 ~ 219
| 111 ~ 109
| 111 ~ 109
| 55 ~ 54
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 14.9
| 10.0
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 73
| 48
| 24
| 12
| 6
|}

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====VivaCT40 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 21.5 mm
| 10.5
| 21
| 21
| 42
|-
! scope="row"| FOV/Diameter 25.6 mm
| 12.5
| 25
| 25
| 50
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 35.8 mm
| 17.5
| 35
| 35
| 70
|-
! scope="row"| FOV/Diameter 38.9 mm
| 19
| 38
| 38
| 76
|-
! colspan="2"| Slices/Stack
| 213
| 106
| 106
| 53
|-
! colspan="2"| Time/Stack (min, at 200 ms Integration Time)
| 9.9
| 5.0
| 2.5
| 1.3
|-
! colspan="2"| Time Current Product (mAs)
| 61
| 31
| 15
| 8
|}

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====µCT35 Scan Settings====

:{| class="wikitable" style="text-align:center;"
|-
! colspan="2"| Resolution Choice
! scope="col"| High
! scope="col"| Medium
! scope="col"| Standard
! scope="col"| Custom
|-
! colspan="2"| Image Matrix
| 2048
| 1024
| 1024
| 512
|-
! colspan="2"| Projection/180°
| 1000
| 500
| 250
| 125
|-
! rowspan="5"| Voxel Size (µm)
! scope="row"| FOV/Diameter 7.2 mm
| 3.5
| 7
| 7
| 14
|-
! scope="row"| FOV/Diameter 12.3 mm
| 6
| 12
| 12
| 24
|-
! scope="row"| FOV/Diameter 20.5 mm
| 10
| 20
| 20
| 40
|-
! scope="row"| FOV/Diameter 30.7 mm
| 15
| 30
| 30
| 60
|-
! scope="row"| FOV/Diameter 37.9 mm
| 18.5
| 37
| 37
| 74
|-
! colspan="2"| Slices/Stack
| 232 ~ 235
| 116 ~ 117
| 116 ~ 117
| 58
|-
! colspan="2"| Time/Stack (min, at 400 ms Integration Time)
| 23.9
| 12.3
| 6.5
| 3.5
|-
! colspan="2"| Time Current Product (mAs)
| 119
| 60
| 30
| 15
|}

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===Advanced Settings===
*'''Number of Det-lines (for Scout-View)''': Defines how many lines on the detector shall be used during the Scout-View. Using all available lines provides faster Scout-Views but some faint horizontal lines might be seen between the stacks. Limit the number of lines to a small number to obtain Scout-Views without these artifacts but the time of the Scout-View will increase.

*'''Number of Det-lines (for CT-scan)''': Defines how many lines on the detector should be used. This number influences the number of slices within a stack. Limit the number of detection lines if you see residual cone beam artifacts.

*'''FOV/Scan Diameter''': Chose the diameter of the FOV. This action is cropping the area of the detector.

*'''Software binning''': factor of the pixels on the detector.

*'''Hardware binning''':

*'''Samples''': number of (possibly binned) pixels on the detector that are used for each slice (note: this number is given for the whole FOV).
*'''Proj/180°''': number of projections taken per 180° turn of the sample.

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===Reconstruction===

*After each image stack is acquired, it is automatically submitted to the queue (sys$slow) for reconstruction. The reconstruction for each image stack is split into four jobs to make efficient use of processors.
*The reconstruction time depends on the resolution setting, with low resolution scans reconstructing faster than high resolution scans. Normally scans are reconstructed within a day or two.
*It is possible to resubmit a scan for reconstruction (refer to [[Scanco_Administration#Reconstruction | '''Scanco Administration's Reconstruction''']]) for details. This may be necessary or desirable for several reasons:
#The sample did not reconstruct properly (e.g., due to a power failure)
#To reconstruct the object at an angle (e.g., so that the anterior surface of a bone is always in the same direction).
#A new beam hardening correction was applied to the sample
#The scaling was changed for the sample to change the brightness

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==Perform a Scan==
===Perform a Single Scan===
*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] for instructional details.

===Perform Batch Scans===
*Batch scan mode is only available on microCT scanners.
*Batch scans can be setup for different regions of interest (ROI) within a sample or for different samples contained within a sample holder.

#'''Setup the First Scan'''
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Tomography|'''µCT Tomography''']] to use the "Other..." button to find your sample number, choose a controlfile, perform a scout view (a mouse's whole body in this example), use the reference line to setup the first scan region (mouse skull in this example).
#*To add a batch scan press the "Batch Measurement" button.
#:[[File:Batch_scan_01.preview.jpg|600px]]
#*An information window is displayed with the scan measurement number. Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']] then press "OK" to close the window. An entry is also added to the measurement history for the sample.
#:[[File:Batch_scan_02.preview.jpg|600px]]
#'''Setup the Next Scan'''
#*Using the "Other..." button, find your next sample number, choose a new control file (if desired).
#*If the next region of interest or sample is not in view of the current scout view, adjust the parameters of the scout view and obtain a new one.
#*Use the reference line to set a new scan region (upper limbs in this example).
#*To add a batch scan press the "Batch Measurement" button.
#*As the first scan, a measurement number is assigned for this new scan. Record the measurement number on your [[Scanco_User_Instructions#Log_Sheets|'''log sheet''']].
#:[[File:Batch_scan_03.preview.jpg|600px]]
#*Repeat this process until you have added all your scans.
#'''Start the Batch Scans'''
#:There are two ways to start a batch scan:
##Click the "Start Batch Scans" button: the program will automatically close so that control of the scanner can be allotted to the queue.
##Exit the scanning program.
#:[[File:Batch_scan_04.preview.jpg|600px]]
#'''Check the Queue'''
#*Batch jobs will be submitted to the SCEVA2_BATCH queue for µCT35 or SC5019_BATCH queue for vivaCT40.
#*Initially the jobs will show up as temporary (TMP) jobs:
#:[[File:Batch_scan_05.preview.jpg]]
#*After about 30 seconds, the sample number will show up in entrie names:
#:[[File:Batch_scan_06.preview.jpg]]
#'''Request an Email Notification'''
#*There is a script in the commands (com) directory that will put an entry into the batch queue to send an email. Run the script and input parameters (queue and email) as prompted.
#:[[File:Batch_scan_07.preview.jpg]]
#'''Cancel a Batch Scan'''
#*For errors made during batch scan setup, to cancel a scan in progress, or to cancel a pending scan.
#:[[File:Batch_scan_08.preview.jpg]]
#*If you cancel all the scans and the scanner door does not unlock automatically (µCT 35 only), then start the measurement program and the scanner will unload, unlocking the door.

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==Action on Image Artifacts==
===Rescan for===
*'''Motion Artifacts'''
*'''Sample Out of the Field of View'''

===Contact Scanco Medical for===
*'''Ring Artifacts''' (Bad Detector)
:*Ring artifacts are caused by a faulty detector pixel and show up in the reconstructed image as a full or partial white circle.
:*When noticed, please notify lab technicians who will contact Scanco Medical to perform a "Pixel Correction", which will correct this artifact for future scans and can be used to update previous scans.
:*You should not rescan the sample if there is a ring artifact.
<div><ul>
<li style="display: inline-block;"> [[File:Ring_artifact.jpg|thumb|none|350px|Image with Ring Artifact]] </li>
<li style="display: inline-block;"> [[File:Ring_artifact_corrected.jpg|thumb|none|350px|Same Image after with Detector Correction]]</li>
</ul></div>

*'''Bad Centre Calibration Values'''
*'''Defective Shutter Artifact'''

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=Evaluation=
==Evaluate a Scan==
*To evaluate a scan, refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.

===Open default ISQ===
You can load a defual ISQ usig uct_evaluation program:

<pre>
$ def uct_default_isq DISK3:[MICROCT.PROJECTS.VALIDATION.MODELS]C0000123.ISQ ! or
$ def uct_default_isq DISK2:[MICROCT.DATA.00001234.00005678]C0003456.ISQ
$ uct_evaluation
</pre>

Hit <code>cancel</code> when asked files to load, and the file you just set as default will be loaded.

*Use the whole pathname for ISQ.
*If you don't import your data into the system, you cannot store your evaluation results in the measurement database. You will have to use the LOG file to access your results.
*Only start a 3D evaluation if and only if the sample (patient) and measurement index are correct in the ISQ full path! Also, no results will be stored in the database unless the ISQ header info (samp/meas) is correct.
*Many of the UCT_xxx.COM scripts use the whole filename to extract the sample and measurement numbers, so it is possible that some evaluations will not run. UCT_xxx_BATCH_V4.COM is an example of an evaluation that will not run, but UCT_CUTOUT.COM will run (doesn't need any sample/meas info).

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==Draw Contours==
*Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
*Contouring is the first step in the analysis process, which allows you to segment the desired bone from surrounding tissues.

===Contouring Tools Reference Sheet===
*[[Media:Contouring-tools.pdf |'''Contouring Tools Reference Sheet''']]
*Contours must always be drawn COUNTER-CLOCKWISE!!!

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===Contour and Run the Standard Patient Evaluation===
The following instructions are for contouring standard patient radius and tibias.

#Open the Evaluation Program and select your sample.
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.
#Zoom into the desired bone (Radius or Tibia)
#*Using the zoom menu from the top panel, zoom into the Radius or Tibia.
#*Usually 3x zoom is appropriate.
#Draw contours roughly around the bone.
#*Select the first contouring tool (top left button) and draw COUNTER-CLOCKWISE.
#Automatically generate contours for all slices in the scan.
#*Double click the image to bring up the contouring window.
#*Double click again and the program will attempt to snap the contour to the bone. Double click again if needed.
#*Select Forwards, and then Iterate Forwards to have the evaluation program automatically segment the bone.
#Modify any contours as needed.
#*Select the second contouring tool (2nd button from top) to fix any "wrong" contours.
#*Draw COUNTER-CLOCKWISE!!
#*If many contours cannot be automatically generated correctly i.e. cortical bone is porous and evaluation program misses a lot of bone, it may be better to use the Range/Morph function rather than fixing each individual slice.
##This is done by first clearing all the breakpoints (Clear all BP in contouring window). The boxes will now become red.
##Manually fix the slice that does not have the correct contour automatically drawn, skip a few slices and manually fix that slice as well. The slices that you have fixed will turn green, indicating that it is a breakpoint (BP).
##Now you can morph between the two breakpoints (BP, green boxes) you have just created. Select the BP with the higher slice number, select range (first column on left) from the contouring window, followed by morph (second column from left).
#Save Contour (.GOBJ): Make sure you save your work!
#Run the 3D Standard Evaluation for your specific project (and timepoint).
#*Select 3D evaluation under Tasks to bring up the window. You'll then need to Select... the evaluation specific for your project.
#*There are a variety of evaluations to choose from, you can search for your project's evaluation script by typing in the name of your project in the filter window.
#Check the queue to ensure that the evaluation is running properly.
#*Type <code>$ show que</code> in a terminal window will allow you to see all running processes.

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===Correct Trabecular Contours and Run the Cortical Evaluation===
Once the standard evaluation has been completed, an auto-segmentation process is completed to segment the cortical from the trabecular bone. However, the auto-segmentation is not always accurate, and hence the contour (TRAB.GOBJ) will need to be checked.

#Load TRAB.GOBJ by selecting File, then load GOBJ from the top panel.
#*You will now see a list of all GOBJ files pertaining to your sample. You'll need to load the TRAB.GOBJ.
#*When the TRAB.GOBJ has loaded, you will see that the loaded contour is between the cortical and trabecular bone.
#Correct contours as needed
#*Can manually adjust the slices or use the Range/Morph function.
#*Remember to draw COUNTER-CLOCKWISE!
#Run the 3D cortical evaluation for your specific project (and timepoint, if relevant).
#*Select 3D evaluation under Tasks to select the appropriate evaluation script.

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==Evaluation Scripts==
===Scanco Standard Evaluation Scripts===
The following are descriptions of some of the standard evaluation scripts provided by Scanco Medical.

*'''3D Segmentation of VOI, 1 solid object'''
:Produces a 3D segmented (binary) object with values 0 (background, hidden) and 127 (solid). Input Gaussian filtering and threshold parameters. Draw contour to isolate the object of interest (optional).

*'''3D Seg. of 2 VOIs: solid dense in transparent low dens obj'''
:Produces a 3D segmented object with values -1 (transparent), 0 (background, hidden), and 127 (solid). Input two sets of Gaussian filtering and threshold parameters (input the second set by pressing the red 2 button). The preview shows the solid object in white and the transparent object in red. Draw one contour to isolate the object of interest (optional). This script is useful for showing soft tissue and bone.

*'''Bone Trab. Morphometry (3D Seg, 3D Calc, Print Sheet)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour to isolate the trabecular bone. Performs model-independent (direct) measurements on the trabecular region. Outputs: BV, TV, BV/TV, TbBMD, TbTMD, BS, SMI, DA, ConnD, TbTh, TbThSD, TbSp, TbSpSD, TbN, and Tb1/NSD.

*'''BV/Density only Bone Eval. (3D Seg, BV and Dens Calc, Print)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour to isolate the region of interest. Outputs: BV, TV, BV/TV, BMD, and TMD.

*'''Bone Midshaft Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour on the outer surface of the bone. Outputs: BV, TV, BV/TV, BMD, TMD, and moment of inertia parameters.

*'''Bone Midshaft more than e.g. 50 slices Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs. Draw contour on the outer surface of the bone. If you wish to exclude the medullary area from the analysis, then draw a counterclockwise contour on the outer surface of the bone and a clockwise contour on the inner surface of the bone. Performs direct measurements in addition to the standard midshaft analysis. Outputs: BV, TV, BV/TV, BMD, TMD, moment of inertia parameters, Th, and Sp.

*'''Convert to TIFF'''
:Converts the grayscale data to TIFF slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Convert to DICOM'''
:Converts the grayscale data to DICOM slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Reformat to Axial Cuts'''
:Flips the dataset from the XY plane to the XZ or YZ planes (specify in the advanced options for the script). This is useful if you want to contour your sample in a different plane. The flipped sample is imported as a new measurement under the same sample number as the original data.

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===Understanding Evaluation Scripts===
Following are some example evaluation scripts full of comments to promote understanding:
*[[Media:IPLV6_VOI.pdf|IPLV6_VOI script]]
*[[Media:IPLV6_MIDSHAFT.pdf|IPLV6_MIDSHAFT script]]
*[[Media:IPLV6_TRABECULAR_BONE.pdf|IPLV6_TRABECULAR_BONE script]]

===Setup Customized Evaluation Scripts===
To setup an evaluation script customized to your project, in the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']]:
*Choose "Scripts" then "Import from" then "TEMPLATES", pick a Scanco Standard Evaluation Scripts and Save.
*Choose "Scripts" then "Modify". Choose the script that was just imported and click "OK", Change the name of the script.
*Modify the default segmentation and other parameters for the script. When finished making changes press "Save" then "OK".

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==Image Processing Language (IPL) Scripting==
The following documentations related to IPL scripting, as it applies to image analysis was compiled by Jan Owoc in July 2013 based on numerous sources including own experience.

===Your First IPL Script===
*'''Prerequisite''': you are familiar with navigating the VMS system.
*'''"$" or "ipl>"''': the DCL and IPL prompts respectively, and you should only type the text after the prompt.
*If you FTP the file to the OpenVMS system, ensure you use "binary" to transfer the file.
You can run these commands on almost any greyscale AIM file. Example file here: MJ7101.AIM

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====Interactive IPL====
*Command <code>$ ipl</code> starts IPL interactively, that is you see the result of each command as you run it.
*While it is useful for testing, running large scripts interactively may interfere with others using the computer.
 
*'''Reading an AIM file'''
:Before you can run any analysis on the AIM file, you need to read it into IPL and assign it a file handle. This is done using the command <pre>ipl> read in MJ7101.AIM</pre>
:A fraction of a second later, the file should have been read into memory and assigned the internal name "in". If we want to do some basic density calculations on it, we can use the command<pre>ipl> vox_ in 0</pre>
:*IPL, much like DCL, will automatically complete the command if it is given enough characters.
:The "vox_" was expanded to the command "vox_scanco_param" (calculates voxel-counting parameters) and told you that the mean density of the cube is 114 mg HA/cm3 and a standard deviation of 283 mg HA/cm3.
:The argument "in" is the internal name of the image.
:The argument "0" is the region. The command vox_scanco_param supports several numbered regions if, for example, you wanted to separately compute the density for the trabecular region and the cortical region.
 
*'''Segmenting an AIM file'''
:Some parameters, like average density, are computed from the [[Scanco_User_Instructions#Grayscale_Images|'''Greyscale Image''']]. Other parameters, like the trabecular number, require an image that has been segmented to [[Scanco_User_Instructions#Binary_Images|'''Binary Images''']], that is converted into "bone" and "not bone".
:There are many ways to separate bone from non-bone, and parameters that work well for one dataset will not generally work for images of different samples, or acquired at different resolutions.
:One of the simplest segmentation methods "seg_gauss" is to apply Gaussian smoothing to the sample, to eliminate the noise present in the image, followed by a semi-arbitrary threshold that preserves the trabecular structure.
<pre>
ipl> seg_gauss in seg

-sigma [1.000000] >
-support [2] >
-lower_in_perm_aut_al [300.000000] >
-upper_in_perm_aut_al [100000.000000] >
-value_in_range [127] >
-unit [0] > 2
</pre>
:seg_gauss expects 8 parameters, and we have provided only 2. It will now prompt us for the remaining 6 one-by-one.
:Leave everything at the defaults (simply hit "Enter") except the unit, which we will change to "2".
:For young human trabecular bone from the distal tibia scanned at 20 um in the uCT 35, but then downscaled to 80 um, the above parameters give a reasonable representation of the trabecular structure. With other bones at other resolution, you may need to change the sigma, the support, and the lower threshold.
:The unit of "2" simply means that we are working in units of mg HA/cm3.
:Now that the cube is segmented, we can run the same voxel-counting command as above and obtain more information. <pre>ipl> vox_ seg 0</pre>
:We now know that our combination of smoothing and threshold resulted in an object volume of 103 mm3 (i.e. volume of bone) and a bone volume ratio of 22.88%.
 
*'''Writing out a file'''
:we can write the segmented file out for future use. Accept the defaults for the remaining arguments. <pre>ipl> write seg MJ7101_SEG.AIM</pre>
:Now you can quit IPL and verify that the segmented file has been written out. <pre>ipl> quit</pre>

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====Batch IPL====
*Command <code>$ ipl_batch</code> starts IPL inside a script that would be submitted to a queue.
While the following code is likely to work, it is not very readable:
<pre>
$ IPL_BATCH
read in MJ7101.AIM
vox_ in
seg_gauss in seg 1 2 300 100000 127 2
vox_ seg
write seg MJ7101_SEG.AIM
..
$ EXIT
</pre>
*Instead, it is recommended that you copy and paste the "pretty" output of the command after you have run it once interactively.
*Values that are likely to change should be variables, defined at the top of the script.
*To substitute a variable from DCL into IPL, use a double-quote character before the variable name, as shown in the example below.
Copy and paste the below into a text editor.
<pre>
$ modelname :== MJ7101.AIM
$ threshold == 300
$ outputfile :== MJ7101_SEG.AIM
$
$ IPL_BATCH

/read
-name in
-filename "modelname

/vox_scanco_param
-input in

/seg_gauss
-input in
-output seg
-sigma 1.000000
-support 2
-lower_in_perm_aut_al "threshold
-value_in_range 127
-unit 2

/vox_scanco_param
-input seg

/write
-name seg
-filename "outputfile

..
$ EXIT
</pre>
Now, it is clear what the full names of the commands are, and what the parameters mean.
*If a parameter isn't important and can be left at the default (for example the region number during vox_scanco_param), you can leave it out of the file.
Save the file as MYSCRIPT.COM and run it using <code>@MYSCRIPT.COM</code>.

 
*'''Submitting to the queue'''
:As mentioned in the introduction, running IPL interactively on larger models negatively impacts other users of the system. Copying the commands to a file and running it from the command line has the same effect.
:*The correct way to run larger scripts is to submit the job to the queue. <pre>SUBMIT/QUE=SYS$FAST MYSCRIPT.COM</pre>

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===IPL Reference===
*[[Media:SCANCO_-_Software_-_IPL_instruction_manual_0.pdf|'''Official Scanco IPL Documentation''']]
*[[Media:scanco-software-ipl-instruction-manual.pdf|'''Scanco IPL Manual]]

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====Standard Read Write etc. Functions====
*'''/read''': Reads a file into ipl and gives the file an internal name
*'''/aim_read''':
*'''/read_versatile''':
*'''/write_v020''': Writes an aim file to the directory in which ipl is open (or specified directory if in a script)
*'''/write_new''':
*'''/write_part''':
*'''/copy''': Copies an internal file (a file that is already in the ipl system) and allows the copy to be given a new name.
*'''/delete''': Deletes an internal file (a file that is already in the ipl system)
*'''/rename''': Changes the name of the file (input is the old name and output the new name)
*'''/list''':
*'''/options''':
*'''/release_history''':
*'''/commands_write_log''':

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====Segmentation Functions====
*'''/gauss_lp''': Applies a low pass gaussian filter with specified sigma and support values
*'''/fft_laplace_hamming''':
*'''/median_filter''': Applies a low pass median filter to reduce unwanted noise in an image
*'''/seg_gauss''': Segments aim files using the input sigma of gauss and the filter support for gauss. A threshold can also be applied using this function.
*'''/threshold''': Removes data outside of the specified range
*'''/absolute_threshold''':
*'''/adaptive_threshold''':
*'''/adaptive_iter_threshold''':
*'''/matching_threshold''':

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====Gobj and Masking Functions====
*'''/gobj_maskaimpeel_ow''': Cuts an aim file with a gobj so that only the portion of the aim within the gobj remains. Peel_iter value used to specify the number of pixels within the gobj the function will need to cut.
*'''/gobj_to_aim''': Reads a gobj file from the directory and makes an aim file (the aim file is in ipl, to output it to the directory use write).
*'''/togobj_from_aim''': Takes an aim file and writes a gobj file (the gobj is output to directory).
*'''/gobj_circumf_area''':
*'''/gobj_join''':
*'''/gobj_join_consec''':
*'''/gobj_scale''':
*'''/gobj_isotrop''':
*'''/cortex_maskoff''':
*'''/peel3d''':

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====Voxel-Counting, Density and Triangulation Functions====
*'''/db_scanco_activate''':
*'''/db_clear_eval''':
*'''/db_calib_unit_fill''':
*'''/db_set_mean_accur''':
*'''/voxgobj_scanco_param''': Inputs an aim file and a gobj and provides information (including total volume, object volume and the mean value of the points) on the region within the gobj.
*'''/vox_scanco_param''': Inputs an aim and provides information including total volume, object volume and the mean value of the points.
*'''/tri_da_metric_db''':
*'''/tri_direc_distr''':
*'''/connectivity''': Receives a component labelled aim object and calculates the connectivity of the labelled components.
*'''/conn_nocl''':
*'''/conn_bgcl''':
*'''/fractal_dimension''':

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====Distance Transformation (Sphere Filling) Functions====
*'''/dt_object_param''':
*'''/dt_ow_object_param''':
*'''/dt_background_param''':
*'''/dt_mat_param''':
*'''/dt_cortex_obj_param''':
*'''/dt_value_output''':
*'''/dt_mat_output''':

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====Statistical Functions====
*'''/examine''': Receives an AIM object and outputs specified information based on the item input.
*'''/histo''':
*'''/moment2d_of_inertia''':
*'''/moment3d_of_inertia''':
*'''/zmeanmax''':

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====Voxelsize-Scaling Functions====
*'''/isotrop''':
*'''/scale_elsize''':
*'''/ipscale_elsize''':
*'''/noipscale_elsize''':
*'''/scale_ow_elsize_noip''':

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====Component Labeling Functions====
*'''/cl_ow_rank_extract''': Receives AIM file and over writes it with an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl_rank_extract''': Receives AIM file and outputs an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl26_rank_extract''':
*'''/cl_image''':
*'''/cl_extract''':
*'''/cl_slicewise_extractow''':
*'''/cl_nr_extract''':

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====Add, Concat, Cut etc. Functions====
*'''/add_aims''': Adds the values of two AIM images in a 3D space.
*'''/add_constant_ow''':
*'''/border_change''':
*'''/bounding_box_cut''': Cuts extra space out of an aim file so that only the region with the data remains. A border can be added to the image using the border input.
*'''/concat''': Takes two aim files and combines them. The data from both aims or just the common region can be kept. To add the images add_not_overlay is set to true (for example if image 1 has a value of 41 and image 2 has a value of 82, the combined value will be 123).
*'''/concat_adapt''':
*'''/divide_volumes''':
*'''/fill_min_max_ow''':
*'''/header_geo_set''':
*'''/header_log_set''':
*'''/header_calib_ov''':
*'''/invert_ow''':
*'''/mult_constant_ow''':
*'''/multiply_volumes''':
*'''/sqr_to_float''':
*'''/sqrt_to_float''':
*'''/offset_add''':
*'''/offset_set''':
*'''/clear_offset''':
*'''/fill_offset_mirror''':
*'''/fill_offset_duplicate''':
*'''/set_value''': Sets the values of the object and background of an aim file to chosen values
*'''/sub_get''': Extract a portion of an image 
**-pos corresponds to x,y,z origin -1 -1 -1 maintains the original coordinates 
**-dim corresponds to x,y,z dimensions -1 -1 -1 maintains the original dimensions (within maximum range) 
**indexing starts at 0 instead of 1
*'''/sub_pick''':
*'''/subtract_aims''': Subtracts one aim from another and outputs the remaining region.
*'''/sup_divide''':
*'''/transparent_concat''':

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====Erosion Dilation Open Close Functions====
*'''/erosion''':
*'''/dilation''':
*'''/open''':
*'''/close''':
*'''/erosion_dilat_variable''':

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====Import Export Conversion Norming Functions====
*'''/import_freeformat''':
*'''/dicom_to_aim''':
*'''/todicom_from_aim''':
*'''/dicom_list_series''':
*'''/isq_to_aim''':
*'''/isq_gobjfit_to_aim''':
*'''/toisq_from_aim''': Writes an isq file to the directory ipl is open in (or specified directory) from an aim file. The isq name should be 8 characters long.
*'''/mesh''':
*'''/msq_from_aim''':
*'''/rsq_to_aim''':
*'''/stl_tri''':
*'''/convert_to_type''':
*'''/convert_unsigned''':
*'''/norm_max''':

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====Functions for Root Canal Evaluations====
*'''/separ_roots''':
*'''/calc_ctr_mass_list''':
*'''/calc_ctr_mass_diff''':
*'''/treated_surf''':
*'''/match_cut''':
*'''/match_cut_adapt''':

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====Miscellaneous Functions====
*'''/align_z''':
*'''/dcl''':
*'''/flip_aim''':
*'''/growback_to_orig''':
*'''/turn3d''':
*'''/turn2d''':
*'''/upat_filldb''': Fill special Upat DB for patient (radius/tibia) evaluation
*'''/xray''':

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====Obsolete, Experimental and Duplicate Functions====
*'''/curv_tri''':
*'''/cut2D_shape_ow''':
*'''/join_uncompress''':
*'''/mil_param''':
*'''/milv1_param''':
*'''/gauss_seg''': duplicate of /seg_gauss
*'''/from_aim_to_isq''': The function toisq_from_aim will also convert an aim to an isq
*'''/local_threshold''':
*'''/edge_canny''':
*'''/sobel_grad''':
*'''/hysteresis_thresholg''':

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====Functions only available in iplfe====
*'''/register''': Registers two aim files and output a transformation matrix of the transformation to moving input 2 into the space of input 1. Gobjs can be input (registration is more successful with gobjs). Orientation search can be done with masscenter, and/or moment of inertia (MoI), or degree intervals.
*'''/transform''': Transforms an aim file using a transformation matrix (a text file of the matrix can be input). Interpolation options are nearest neighbor, linear, and cubic interpolation. The inverse of the transform provided can be done by setting Tmat_invert to true.
*'''/fe_solveD''': A number of finite element functions are available in iplfe, not all are listed here

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=Results=

==Images and Animations==
Refer to [[Scanco_User_Instructions#.C2.B5CT_Ray|'''µCT Ray''']] for detailed instructions.

===[[#Change_the_View|Change View]]===
===[[#Change_the_Colours|Change Object Colors]]===
===[[#Cutplane_and_Subdim|Show a Section-View of an Object]]===

===Save a Screetshot Image===
#Open XV from a dec terminal on a workstation by typing <code>$ xv</code>.
#Open and frame the image, program etc. that you would like to save an image of.
#In XV, click GRAB. You can either autograb the entire screen after a delay or manually grab a desired area.
#After grabbing the desired section, click Save in XV.

===[[#Save_the_Image|Save Image]]===
===[[#Save_for_Animation|Save Frames for an Animation]]===

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===Convert AIM to TIF series===

Use the utility SEQ_TO_IMAGE located in the UT directory. A symbol has been set up to run this called TIF.

<pre>
$ mcr ut:seq_to_image
Program: seq_to_image V1.1b
Input-File []: WISDOM_L_R05.AIM
File Format [TIF]:
Default TIF Names: WISDOM_L_R05_xxxx.TIF

Output-File [WISDOM_L_R05]:
!> Reading AimVersion020
Start Slice [0]:
End Slice [179]: 5
Number of images thereof (count) [6]:
Scale Factor (Integer) [1]:
global_pos (1=true, 0=false) [0]:
Max value to norm to 255 [32767]:
Slice: 0
Slice: 1
Slice: 2
Slice: 3
Slice: 4
Slice: 5
$ dir wisdom*

Directory DISK1:[MICROCT.SCRATCH]

WISDOM_L_R05.AIM;1 WISDOM_L_R05_0000.TIF;1 WISDOM_L_R05_0001.TIF;1
WISDOM_L_R05_0002.TIF;1 WISDOM_L_R05_0003.TIF;1
WISDOM_L_R05_0004.TIF;1 WISDOM_L_R05_0005.TIF;1

Total of 7 files.
$
</pre>

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===Generate TIF (or others) from 3D rendered volume===

This replaces uct_movie that operated on the alpha systems. UCT_3D can be called in batch mode.

A pdf describing this tool is located here: [[Media:UCT_RAY V4.0-1.pdf]]

To interactively declare the desired settings:
<pre>
$ uct_3d_batch
?CT RAY_BATCH V4.0-1

UCT_R: Application initialized
Filename []:
Print-Filename [SYS$SCRATCH:TEMP_3D.PS]:
Ambient (0.0..1.0) [0.200]:
Shadows (0/1) [1]:
Size (1..1024) [1024]:
Elevation (-90..90) [30]:
Rotation (-180..180) [35]:
Copies (0..9) [1]:

</pre>

To apply a saved set of settings, a setup-file can be created by running uct_3d in interactive mode. Select "Presets" from the toolbar and save the settings you desire (e.g. elevation 90, rotation 0).

<pre>
$ uct_3d_batch setup-file [data-file printfile]

Examples:

$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.ps
$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.tif

</pre>

To automatically generate tifs for many files, a script was created to replace PRINT_3D.COM
The script is currently stored in the xtremect2 com directory.

<pre>
@COM:PRINT_REG_TIF.COM

Generates a 3D image from a segmented file.

The outputs include:
- two 3D renderings (TIF)

Use full pathnames for the segmented AIM.

P1 - Segmented AIM

Usage:
@COM:PRINT_REG_TIF.COM DISK2:[MICROCT.DATA.00000379.00001376]C0001234_SEG.AIM
</pre>

This script can be modified to use a custom preset file.

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===Make an Animation===

To calculate an Animation, two (separate) tools of the 3D program are used: the set-up of start and end point of the Animation, and the 'Auto-Print' tool that automatically creates the TIF files for every rendered image.

This is a 'step by step' guide to create an animation using TIFF files:
:* Open your sample in the 3D program.
:* Now, open 'options','Animation'
:* Render your Image the way you want your animation to start. e.g. observer rotation -179 degrees. You may interrupt if you want. If you are satisfied with all the settings (rotation, elevation, transparency, colors etc.) the Click on 'Get Settings A'
:* Then, adjust all the settings for the endpoint of your animation (with the mouse or the sliders) e.g. observer rotation +179, and start the rendering. If satisfied, click 'Get settings B'

Note: To test, put # of views to 5 or 10... You can also interrupt the build-ups for faster viewing.
:* Click the START button again, wait till the build-up of the 3D image is finished.
:* DO NOT HIT 'START CALCULATION' YET!
:* First, you also need to set-up the 'Auto-Print' mode:
:* Go to the 'Print' menu (file --> print), choose print to TIF and to File and enter THE BEGINNING OF A FILENAME, e.g. sys$scratch:test_ (the program will append 0000.TIF, 0001.TIF etc afterwards) Or enter (possibly with middle-mouse-click): "DK0:[MICROCT.DATA.00001234.00003456]ANIMATION_" to have the result go to the measurement directory.
:* Click on the 'Auto-Print' box. Then 'ok'
:* Adjust the number of views (e.g. 200), then click on 'Start Calculation', and it will render. This may well take a long time.
:* Take those TIFF files to your PC, and combine the sequences in the program that you are using to convert the TIFF files to AVI or MOV files (like Windows Movie Maker 2, or Quick Time Pro, or Adobe Premiere etc.)

Notes/Hints:
:* The order in the above list can also be reversed: You can first set up the 'Auto-Print', and then go into the 'Animation' menu, choose start and end settings, and hit 'Start Calculation'
:* The positions A and B can be any: e.g. with subdim, you can first take everything (A), then slide it back to nothing (B).
:* You can even slowly change the color of an object. Or slowly hiding objects: choose 'transparent' for object, but change from 0.0 (A) to 1.0 (B)
:* If you want to create a movie with different sections, e.g. first rotate around, then slowly make bone transparent, then cut in: Do this in multiple sections with the 3D program, e.g. first create Auto-Print files 'rotation_0000 to rotation_0200', then 'transp_0000 to transp_0050', and then 'cut_0000 to cut_0100'. Make sure ALL the settings from the last view of the previous section match those of the first view of the next section so you get smoot transitions.
:* The 'Auto-Print' box is also usable without the 'Animation' Menu: Activate it, Like above, with sys$scratch:test_ only the beginning of filename. 'ok' Then, whenever a 3D image is completely built-up (so when you are happy with a view and you do not interrupt the build-up), automatically a TIF file is generated, numbered sequentially.

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===Combine two volumes to create transparent image===

First create your two start "seg.aim" images
Start by running either the normal eval, or $ voi to get one _seg.aim file of one region

Rename it to a better name in the session manager, e.g. c0001234_all.aim

Then either by choosing different contours, or a different threshold, start the $ voi or the normal evaluation again, which will create another _seg.aim file.

Load them in the 3D viewer ('all files') to check that they look like expected.

Now we will go into IPL and concatenate those two volumes.

<pre>
$ ipl
/read all xx_all.aim
/read trab xx_seg.aim
/transparent
-input_solid trab
-input_transp all
-output out
</pre>

Note: the solid volume is OVERWRITING the transparent input volume, so usually, it
is the smaller (inner) of the two.

<pre>
/write out xxx_transp.aim
/quit
</pre>

Then load the _transp.aim file in 3D, go to 3D program FAQ to see how to change transparency levels in the Display options there.

See IPL FAQ or 3D program FAQ if you need help with these parts.

Step by Step Example: Showing your chosen trab VOI within whole bone
:* $ voi, enter threshold in ipl_voi.com, start 3d eval WITHOUT contours
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_all.aim
:* Start up normal eval program, draw trabecular contours, check threshold in ipl_fixed_batch_v4.com, start 3D eval.
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished

Step by Step Example: Showing high-dense volume surronded by lower density volume

:* Start normal 3D eval with HIGH threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_high.aim
:* If wished: read out 3d result database with $ uct_list
:* Start normal 3D eval with LOW threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished

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==Image Tours==
===XtremeCT Image Tours===

===MicroCT Image Tours===
*Refer to [[Media:Tours_image_gallery.pdf|'''MicroCT Image Gallery''']] with its [[Media:Tours_image_notes.pdf|'''Image Notes''']].
*Refer to [https://youtu.be/tT3dz4VrwfE '''MicroCT Image Tour YouTube Video''']
*Hover over a thumbnail and click on its overlaid description to see the animated GIF or a larger version of the image.

<gallery mode="packed-hover" heights=220px caption="Micro-CT Scans">
Image:MOUSE_SKELETON_PIC01.jpg|[[Media:MOUSE_SKELETON_360.gif|Mouse (38µm)]]
Image:Segmented_Mouse_Femur.jpg|[[Media:Segmented_Mouse_Femur.jpg|Mouse Femur showing Cortical and Trabecular Bone (10µm)]]
Image:LIZARD_WHOLE_VIEW_P1_0044.jpg|[[Media:LIZARD_SKELETON_360.gif|Lizard (88µm)]]
Image:LIZARD_SKULL.jpg|[[Media:LIZARD_SKULL.jpg|Lizard Skull showing Thickness Distribution (25µm)]]
Image:DUCK_BEAK_PIC01.jpg|[[Media:DUCK_BEAK_360.gif|Duck Beak (60µm) Courtesy of Dr. A. Iwaniuk]]
Image:Human_Tooth.jpg|[[Media:Human_Tooth.jpg|Human Tooth (30µm) Courtesy of Dr. C. Stewart]]
Image:PINECONE_TH_PIC05.jpg|[[Media:PINECONE_360.gif|Pinecone showing Thickness Distribution (69µm)]]
Image:SHELL01_SEG_PIC01.jpg|[[Media:SEASHELL_360.gif|Seashell (50µm)]]
Image:TURTLE_SKULL.jpg|[[Media:TURTLE_SKULL_360.gif|Turtle Skull (60µm)]]
Image:SAND_DOLLAR.jpg|[[Media:SAND_DOLLAR.jpg|Sand Dollar (37µm)]]
Image:MOUSE_L1-L6.jpg|[[Media:MOUSE_SPINE_SEG_360.gif|Mouse Spine showing Cortical and Trabecular Bone (10µm)]]
Image:MOLAR.jpg|[[Media:MOLAR.gif|Human Tooth (60µm) Courtesy of Dr. C. Stewart]]
</gallery>

<gallery mode="packed-hover" heights=220px caption="Contrast-Enhanced Micro-CT Scans">
Image:Contrast_mouse_head_XZ_thumb.jpg|[[Media:Contrast mouse head XZ.jpg|Mouse Head (60µm, XZ plane)]]
Image:Contrast_mouse_head_XY_thumb.jpg|[[Media:Contrast mouse head XY.jpg|Mouse Head (60µm, XY plane)]]
Image:Contrast_mouse_head_YZ_thumb.jpg|[[Media:Contrast mouse head YZ.jpg|Mouse Head (60µm, YZ plane)]]
</gallery>

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==Extract Results==
===Automatic Results===
Results are generally automatically extracted after each analysis to the UCT_RESULTS directory. 
The results files have the form of:
*UCT_LIST_*''PROJECT''*.TXT for XtremeCTs: e.g. result file UCT_LIST_KYLA.TXT for the following project.
*UCT_LIST_3DLOG_*''PROJECT''*.TXT for microCTs: e.g. result file UCT_LIST_3DLOG_KYLA.TXT for the following project.
*where ''PROJECT'' is specified in the evaluation tool script setup.
[[File:Script_modify_basic_project.jpg|500px]]

Open the result file and copy and paste it into Excel, e.g.
<pre>
$ dir uct_results:*kyla*
$ eve uct_results:UCT_LIST_3DLOG_KYLA.TXT
</pre>

Or transfer the file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].
*microct/vivact account UCT_RESULTS location: ADISK1:[MICROCT.RESULTS]
*invivo/invitro account UCT_RESULTS location: ADISK1:[BONELAB.RESULTS]

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===Extract Results from XtremeCT Database using UPAT_LIST===
*Run <code>$ UPAT_LIST</code> to take in a range of samples and extract the standard patient results, which may include scans from other projects.

*Run <code>$ @com:EXTRACT_UPAT_LIST</code> to take in a list of sample numbers and extract the standard patient results with follow-ups and append them to a result file.
<pre>
$@COM:EXTRACT_UPAT_LIST P1 P2 P3 P4 P5

P1 = Sample List
P2 = Site (RR, RL, TR, TL, R*, T*, *)
P3 = Number of Follow-Ups (max 19)
P4 = Results Output File
P5 = Eval type (4=XT1, 5=Trab, 6=Cort)
</pre>

An example to extract all sites:
<pre>
$ @com:EXTRACT_UPAT_LIST mysamples.txt * 19 myresults.txt
</pre>

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===Extracts Results from microCT Database using UCT_LIST===
*Run <code>$ UCT_LIST</code> to take in a range of samples and extract the results, by specifying the first and last measurement numbers for the range they want to extract
*This may include scans results from other projects, but you can delete unrelated results that are extracted afterwards.
*The program will output a tab-delimited text file, which can be read into Excel or other analysis programs.
<pre>
$ uct_list

UCT_LIST.EXE Version V5.22
Template-File [UCT_3D_LIST_SHEET]: !Press Enter to use the default results sheet.
Output-File [SYS$SCRATCH:UCT_EVAL.TXT]: !Enter a filename, e.g., BUIE_RESULTS.TXT.
Density units (0 default) [0]: !Press Enter.
From Meas. # [0]: !Enter the first measurement number, e.g., 100.
To Meas. # [0]: !Enter the last measurement number, e.g., 101.

Processing measurement 100
Processing measurement 101
</pre>
*An example output file: [[Media:Buie_results.xlsx|Buie_results.txt]]
*Or Run <code>$ @com:extract_results.com</code>

*References of results template:
:*Formatted [[Media:Results_template_uct_list.xlsx|Excel template 1]] for results extracted with uct_list.
:*Formatted [[Media:Results_template_extract_results.xlsx|Excel template 2]] for results extracted with extract_results.com.
:*In vivo spreadsheet template for UCT data: [[Media:In vivo results template.xls| In vivo results template.xls]]
:*In vitro spreadsheet template for UCT data: [[Media:In vitro results template.xls| In vitro results template.xls]]

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===Understand Morphological Parameters===
*Refer to [[Media:Reference_Document_-_Parameters_from_upat_list.doc|'''Explanation of UPAT_LIST Output''']] to understand the result file.
*Refer to [[Media:Reference_Document_-_Parameters_from_uct_list.doc|'''Explanation of UCT_LIST Output''']] to understand the result file.

All values are determined on a slice-by-slice basis, then averaged over all the slices to calculate morphological results:

:*BV/TV -> Sum all raw data withing the GOBJ and divide by 1200 mg/cc HA
:*Tb.N -> As per standard method
:*Tb.Th and Tb.Sp -> Derived from BV/TV and Tb.N above (semi-derived method)
:*D100 -> Average density of entire cross section
:*DTrab -> Average density of trabecular region
:*Ct.Th -> Cortical area (from seg) divided by circumference (from GOBJ)
:*GOBJ circumference can be determined with /gobj_circum.

<pre>
BV/TV -> VOX-BV/TV
BS/BV -> TRI-BS/BV
Tb.Th -> DT-Tb.Th
Tb.Sp -> DT-Tb.Sp
Tb.N -> DT-Tb.N
ConnD -> Conn-Dens
SMI -> TRI-SMI
DA -> TRI-DA
</pre>

Usually I'd use the names on the left for the plots, but these correspond to the names on the right of the arrow in the Scanco output files.

Note, if you use the TRI-Tb.Th rather than the DT-Tb.Th*, then you are using the derived (plate-model) morphological parameters. These are less accurate than the direct parameters. They are calculated by triangulating the surface (marching cubes) to get BS, and then calculate thickness
Th = 2 * BV / BS, etc...

'''Mean Values'''
<pre>
mean 1: mean of bone AND marrow --> 'apparent density'
mean 2: mean of what was considered bone only (i.e. what was segmented)
'bone tissue density'
</pre>

Note, there are five possible categories for the mean Mu. They are assigned by setting <code>-region_number</code> in the <code>/voxgobj_scanco_param</code> function. The region number is zero-based, so setting it to 0 corresponds to mean1, 1 corresponds to mean2, etc. So, although mean1 and mean2 are typically apparent and tissue density, respectively, this can be adjusted in the IPL script by setting the region_number. Mean3 might be useful for storing cortical bone density, for example.

<pre>
/voxgobj_scanco_param Voxel or Mu Scanco Parameters
-input Gray scale or Segmented AIM object
-gobj_filename GOBJ: input or Automatic
-peel_iter Peel Iterations or Automatic
-region_number Region number for Mu only

! -region_number 0 ! mean1
! -region_number 1 ! mean2
! -region_number 2 ! mean3
! -region_number 3 ! mean4
! -region_number 4 ! mean5
</pre>

What you should also know: because of partial voluming effects, for Mean2, we are DISCARDING the 2 surface voxels of EVERY trabeculae - thus, to get meaningful Mean2, you have to do your scan with the chosen resolution high enough, such that the mean trabeculae is depicted by at the very least 5 pixels, better actually more than 6 pixels thickness. (You can do this check at the end in the XLS sheet: divide DT-Tb.Th* by el-size-mm.x, and you need to get numbers bigger than 6 or 7 or 10 or so.

For parameters such as ConnD where no GOBJ is taken as input, the TV is determined from the processing log stored in an AIM that has previously had a GOBJ applied (stored as the relative region of interest; ROI). So, it is important to apply a GOBJ prior to ConnD measurements to ensure the TV is correctly determined (and not taken as the whole AIM).

'''Trabecular Number (TbN)'''
The epsilon values can be set to account for differences in scanner resolution, and hence 'surface roughness' for individual pixel suppression.

For microct, for good resolution: if there is a pixel 'sticking out' from a flat surface we do not assign that pixel with a thickness value of 1, but we let it 'get eaten' by the bigger sphere that sits in the center of the trabeculae. So this is nice for 'noise' (0.9/1.5).

For XT resolution, where also many 'good' features are just one or two pixels wide, I liked a lower epsilon value better (0.9/0.5).

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==Generate Report==
===Generate Standard Patient Report===
The standard patient reports are extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.
*The number of follow-ups specified will determine if a baseline or follow-up report is generated.

<pre>
$ upat_list

Mode (1 = list, 2 = print, 3 = show) [1]: 2
Patient # (1-3162) [1]: !input the patient's sample number
Site (found RR) [RR]: !RR or RL or TR or TL
Maximum # of follow-ups (0-19) [19]: !0 for baseline report, press return for follow-ups
Template file [default]: !press return to use the default template
Output filename [SYS$SCRATCH:UPAT...]: !default output file (with sample number and the site) goes to sys$scratch
# copies [1]: !the number of printouts, 0 if no printout is desired
</pre>

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===Generate CaMos Patient Report===
The [http://www.camos.org '''CaMos'''] patient report is extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.
*To ensure the report is generated using the appropriate normative results, the patient's sample remarks should be in the form "F-RHRF" where the first character indicates the sex of the individual, otherwise the patient is assumed to be male.
<pre>
$ upat_list

Mode (1 = list, 2 = print, 3 = show) [1]: 2
Patient # (1-3162) [1]: !input the patient's sample number
Site (found RR) [RR]: !RR or RL or TR or TL
Maximum # of follow-ups (0-19) [19]: !0 - 1st scan, 1 - 2nd scan, 2 - 3rd scan...press return for latest scan report
Template file [default]: COM:UPAT_EVAL_CAMOS.PS
Output filename [SYS$SCRATCH:UPAT...]: !default output file (with sample number and the site) goes to sys$scratch
# copies [1]: !the number of printouts, 0 if no printout is desired
</pre>

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===Print out report sheets===

The postscript report sheets can be generated and printed on the command line. For the XtremeCT system, use <code>UPAT_PRINT_LIST.EXE</code> which can be run (using the symbol):
<pre>
$ UPAT_LIST
</pre>

Look in the UU: directory to see options for the template files (UPAT*.TXT) and the postscript output files (*.PS).
:* UU:UPAT_EVAL_FUP05_SCUSA.PS
:* UU:UPAT_EVAL_BASELINE_SCUSA.PS

For other options, see the upat_list help:
<pre>
$ UPAT_LIST -h
</pre>

One particular option that may be useful, is to turn off slice matching:
<pre>
$ UPAT_LIST -nomatch
</pre>

Here is an example of producing a report for the third measurement of TL for a patient, where we want only the most recent results in the report, without slice matching:
<pre>
$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=UU:UPAT_EVAL_BASELINE_SCUSA.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_0fu.ps

$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=DISK1:[MICROCT.COMMANDS]UPAT_EVAL_CAMOS.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_camos.ps
</pre>
The first command line generates a normal Scanco report, and the second command line generates a CAMOS report.

For reports from non-patient measurements (i.e., the vivaCT system or non-patient scans on the XtremeCT), the template files are different (UCT*.TXT) and the postscript outputs are different (UCT*.PS). To print a result sheet use:
<pre>
$ RUN UM:UCT_RAY_BATCH.EXE
</pre>

If you want to create a postscript file, but not send it to the printer, set the number of copies to zero (interactive). Then, find the postscript file from the <code>SYS$SCRATCH</code> directory and transfer it to your PC. You must transfer the postscript file in ASCII mode. The files are typically called TEMP_3D.PS or UPAT_PAT_62_RR.PS. A program such as Adobe Photoshop can convert the postscript file to a different format.

See also our custom scripts:
<pre>
$ @COM:PRINT_2D.COM
$ @COM:PRINT_3D.COM
</pre>

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===Convert PS to PDF report===
The report can be converted to PDF using <code>$ @SCOM:PS_TO_PDF</code> by:

#Follow the instructions above for creating a report, using "2" to print and "0" for the number of copies. (Use the default template file and output filename.)
#Locate the file on the sys$scratch by <code>$ cd sys$scratch</code> and <code>$ dir</code>
#*The file should read "UPAT_PAT_[sample #]_[site].PS;1" (e.g. UPAT_PAT_0010_RL.PS;1)
#*You can view this file on the monitor by typing <code>$ gs UPAT_PAT_0010_RL.PS;1</code>
#Convert the postscript to PDF by typing in the command followed by the .PS file to convert <pre>$ @SCOM:PS_TO_PDF UPAT_PAT_0010_RL.PS;1</pre>
#The PDF file can then be located again in the sys$scratch directory.

You can transfer the result file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].

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=Data Management=
==Trainee’s Data Responsibility==
#Perform '''Contouring and Data Analysis''' on Data Disk ideally 1-2 months after scanning.
#After finished onsite analysis, [[Scanco_User_Instructions#Move_data_from_Data_Disk_to_Project_Disk|'''use Scripts''']] to '''Copy and Rename''' image data (no RSQ, no ISQ, only AIM, SEG.AIM, GOBJ, COM, LOG, PDF, PS ect) to your specific project folder on Project Disk.
#After finished copying all your image data to Project Disk, '''Notify''' lab personal to delete your data on Data Disk by providing a [[Media:Data_Scans_to_delete_template.xlsx|'''Data Scans to Delete Template''']].
#'''Notify''' lab personal to backup your project folder on Project Disk to Winston server on a monthly basis.
#*Only the two most recent backups (A or B version) are kept for each project on Winston:
#:Backup version "_A" for odd months (Jan, Mar, May, Jul, Sep, Nov), e.g. YZHU_A_OTHER_2017-01-12.SAV
#:Backup version "_B" for even months (Feb, Apr, Jun, Aug, Oct, Dec), e.g. YZHU_B_OTHER_2020-04-08.SAV
#When a project is finished, '''Notify''' lab personal to archive your project to HOG server.
#When a trainee is about leaving, '''Notify''' Steve and lab personal to determine either to backup or to archive your project.

[[File:BoneLabDataManagement.JPG|800px]]

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==Move data from Data Disk to Project Disk==
This is generally done after onsite analysis (i.e. autocontour, cortical porosity, FE etc.) is done. Examples of this can be found in DISK3:[MICROCT.PROJECTS.GRACE.COM] 
1. Go to the specific project's .COM directory, for example:
<pre>
$ cd DISK3:[MICROCT.PROJECTS.GRACE.COM]
</pre>
2. Create a script that will move all IMA (i.e. .AIM, .GOBJ, _SEG.AIM, _CORTEX.AIM, _LHTH_DTN.AIM) to the .MODELS directory for the project. You will use the rename_to_models.com script to generate this script. To move Grace data for example, with a measurement range of 2684 to 2685, you would use:
$ @com:rename_to_models.com meas#1:meas#2 DESTINATION DIR
$ @com:rename_to_models.com 2684:2685 DISK3:[MICROCT.PROJECTS.GRACE.MODELS]

3.This will create a file named RENAME_ALL.COM to the project's COM directory. You will now have to open the RENAME_ALL.COM file and add site + other details into the script. Following the same example as above, it should look like this:
$ eve RENAME_ALL.COM ! to open the file using a text editor
$ COPY DISK2:[MICROCT.DATA.00000700.00002684]C0002040.AIM -
DISK3:[MICROCT.PROJECTS.GRACE.MODELS]GRACE_020_00MTH_RR.AIM
$! DELETE/CONFIRM DISK2:[MICROCT.DATA.00000700.00002684]C0002040.AIM;1
$ COPY DISK2:[MICROCT.DATA.00000700.00002685]C0002041.AIM -
DISK3:[MICROCT.PROJECTS.GRACE.MODELS]GRACE_020_00MTH_RL.AIM
$! DELETE/CONFIRM DISK2:[MICROCT.DATA.00000700.00002685]C0002041.AIM;1
4. You also need to copy the rest of the standard patient image files (i.e. .AIM, .GOBJ, _SEG.AIM, _CORTEX.AIM, _LHTH_DTN.AIM) which is easily done by copying the above lines and replacing .AIM with the respective files.

[[Image:Bones2.jpg|20px]] Warning: Always use the same account consistently to create all files and subfolders within their Project folder, otherwise you way miss data when doing Project Backup or Archive!

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=Import and Export=
==Import Foreign Data to Scanco System==
Only RSQ and ISQ files can be imported into the database, however it is possible to convert other types of data into ISQ files (i.e., stacks of BMPs into ISQ).

PART 1:

After transfering your data to the VMS system (use the data disk <code>disk2</code>, NOT the user disk <code>disk1</code>), use the IPL commands <code>/import_freeformat</code> or <code>/read_aim function</code> to import your data for conversion to an ISQ.

For AIM files, navigate to the location of the AIM file. Then open IPL by:

<pre>$ IPL</pre>

In IPL, read in the .AIM file:

<pre>ipl> read in [.AIM file]</pre>

IPL will do the following:

<pre>ipl> read in STUDYID_001_RL.AIM

/read
-name in
-filename STUDYID_001_RL.AIM
!> Reading AimVersion020

!% /read completed: CPU: 00:01.03 ELAP: 00:01.55 </pre>

For DICOM files, start IPL and run the <code>/dicom</code> function to import. For DICOM, if your object is a single 3D file (-multifile false) or many many individual slice files (-multifile true, and give beginning of filenames, and –extension).

There may be requests by IPL to convert your data to <code>signed short</code> or <code>signed char</code> from other data types. Obey these requests and do it by running the <code>/convert_unsigned</code> function.

Then, write the ISQ file using either the "toisq" or "from_aim" commands:
<pre>ipl> toisq
-aim_name [in] >[leave blank as you defined “in” as .AIM file.]
-isq_filename [default_file_name] > C0001234.ISQ [Create a 1 letter and 7 digit file name]
-square_flag [true] > false
-original_position [true] > false

ipl>toisq_from_aim
-aim_name in
-isq_filename C0001234.ISQ
-square_flag false
-original_position false

!% Dimensions of ISQ file: dim.x dim.y dim.z 558 638 168
Write_ctdata_headerext_new: no mhext found. Init mhext.
Extended header successfully added of type 8

!% Writing ISQ slice 167 (Done: 168/168)

!% /toisq_from_aim completed: CPU: 00:05.12 ELAP: 00:10.47 </pre>

Type ipl>help toisq [or ipl>help from_aim] to see details of the command.

This writes the ISQ file. Make note of the ISQ file name.

Remember, the ISQ name must be 8 characters long (1 character followed by seven digits)!!! The letters and numbers can be chosen freely.

Exit IPL:

<pre>ipl>quit</pre>

PART 2:

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

The measurement can be verified by looking at the Header Information. (File, Header)

If you only needed to view the ISQ, delete the file when finished by:

<pre>$ dir/sincet
$del [.ISQ file]</pre>

PART 3:

To use the ISQ further (e.g. for evaluations, contouring, etc.) create a sample in the database and write down the sample and measurement number. Then, run:

<pre>$ run um:uct_import ! will import both RSQ and ISQ (modify patient index, etc)</pre>

and give the new ISQ file, the new sample-number and check that the feedback is correct (i.e., that the name from the database is matching the name from the ISQ file header). If the Patient Name in the ISQ header doesn't match the measurement database Patient Name (very likely), then upon importing the RSQ/ISQ the headers will be updated to the new Patient Name.

Operator and controlfile can be left 0 if you want. However, controlfile should be set appropriately if the data being imported is for the XtremeCT patient database.

If you are also importing the RSQ, put it in the same directory as the ISQ.

Then it changes the sample and measurement number in the ISQ file, makes the correct directory on <code>DK0</code>, and gives you the line on the screen of how to rename the file to the correct, new directory. Take this line and use it on the command line. Done!

You can now use the normal <code>uct_evaluation</code> program with this file. If the control file was set properly, then the evaluation will be done correctly (i.e., for XtremeCT patient measurements).

Note: Any AIMs created from the original ISQ should be recreated. So, it is important that you re-evaluate your newly imported ISQ. It is OK to move the GOBJ from the old directory to the same directly as the newly imported ISQ (it does not have a 'registry' in the database).

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==Import MRI/DICOM to Scanco System==
#Load MR data in Osirix
#Export from Osirix
#*Click export button in top left in osirix.
#*Select "flat" and "decompress all DICOM files"
#Copy files to correct folder in scanco system
#*Use Fillezilla or FTP (make sure it's set to binary mode)
#Use IPL to convert dicom to aim or isq

<pre>
/dicom_to_aim
-aim_name in
-dicom_filename IM-0001-0001.DCM ! Note - choose the first filename of the series
-multifiles true

/convert_unsigned
-input in
-shift_flag false
-divide_by_2 true

/write_v020
-name in
-filename PREOA_023_L_MR.aim
-compress_type bin
-version_020 true

/toisq_from_aim
-aim_name in
-isq_filename MROA023L.isq
-square_flag true
-original_position true''

</pre>

5. Delete dicoms

<pre>
/del *.dcm;1
</pre>

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==Import Xradia *.bin to Scanco System==
Xradia scanner exports a *.bin image that is:

- 16-bit unsigned ! This is "short" (8-bit is char - we don't want this for a grey-scale image)
- 2 bytes per voxel
- little endian notation

To upload this binary image to Scanco database, the steps are as follows:

#Ftp the *.bin to Scanco system using binary transfer (not ascii)
#Convert it to an AIM or ISQ in IPL

$ipl

/import_freeformat
-internal_name in
-file_name BMLPL_006.BIN
-sample_name BMLPL_006
-data_offset 0
-data_dim 1000 1024 1016 !dimensions from header file
-data_el_size 0.013 0.013 0.013 !voxel size from header file
-bytes_per_voxel 2
-data_endian little_endian
-data_type integer
-signed_type unsigned !correct
-multifiles false

/convert_unsigned
-input in
-shift_flag true !shift_flag = TRUE will produce an ISQ/AIM with negative values which may not be visualized properly using uct_evaluation, but keeps the original image resolution.
-divide_by_2 false !divide_by_2 = TRUE will down grade image resolution, but all positive values in an ISQ/AIM will be visualized properly using uct_evaluation.

/write_v020
-name in
-filename test.aim
-compress_type bin
-version_020 true

/from_aim_to_isq
-aim_name in
-isq_filename bmlpl006.isq !ISQ name requires 8 characters
-square_flag true
-original_position true

quit

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

Alternatively the image can be converted to a 16-bit signed in ImageJ (and cropped) before importing to ipl. It then becomes:

- 16-bit signed
- 2 bytes per voxel
- big endian notation

It can then be imported into ipl without the need to run <code>/convert_unsigned</code>.

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

==Get Your Files==
===MAC/Linux Options===
====Fetch====
#Download and install [http://fetchsoftworks.com/fetch/|'''Fetch''']
#*This program is free for university staff and students.
#Fill out [http://fetchsoftworks.com/fetch/free|'''a form'''].

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====FTP from Terminal====
#Open a terminal
#*MAC: open the "Applications" folder, choose "Utilities", then "Terminal".
#Navigate to where you want to transfer the files to.
#Connect to the micro-CT ftp server using the ftp command in the terminal:
#*Login with the micro-CT user account and password.
#Navigate to the directory of interest on the micro-CT system.
#*Logicals such as "ur" can be used as short cuts. Whole directory names must be used.
#Set a filename mapping convention to remove OpenVMS version numbers.
#*The command <code>ftp> nmap $1;$2 $1</code> sets anything before the version number to parameter $1 and anything after the version number to $2. The file output will be set to $1, therefore the version number will not be kept.
#Set the file transfer mode.
#*[[File:Important.JPG|20px]] If you transfer an .AIM file in ascii mode, you will receive a "mesh generation" errors and "material ID out of range" message.
#Transfer your files.
#*Option: Turn off prompt so does not ask you whether or not to transfer each file.
#*If you do not turn off the prompt prior to transferring the files, press "a" (for all) to transfer all files at once.
#Exit FTP.

<pre>
$ FTP 136.159.74.231 !Connect to an FTP Server. Need to input user name and password.
$ FTP emily.ucalgary.ca !Connect to an FTP Server. Need to input user name and password.
$ FTP microct@emily.ucalgary.ca !Connect to an FTP Server. Need to input password.

FTP> cd ur !Navigate to the directory containing the target files.
FTP> cd sys$scratch !Navigate to the directory containing the target files.

FTP> nmap $1;$2 $1 !Set a filename mapping convention to remove OpenVMS version numbers.

FTP> bin !Set transfer mode to binary (.aim, .gobj, .isq, and most image file types).
FTP> ascii !Set transfer mode to ascii (.txt, .log, .com, .ps, .pdf and all other files in general).

FTP> put test.aim !Put the file
FTP> get test.aim !Get the file

FTP> prompt !Interactive mode off before transferring multiple files without having to be prompted.
FTP> mput *.aim !Put all files with the .aim extension on the FTP server (mput = multiple put).
FTP> mget *.aim !Get all files with the .aim extension from the FTP server (mget = multiple get).
FTP> mget *.aim; !Transfer the latest version of all aim files in a directory.

FTP> quit !Disconnect from the FTP Server.
</pre>

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Windows Options===
====Scanco Medical µCT FTP====
#Downlod '''Scanco Medical MicroCT FTP 3.4''' from BoydDrive:\\04 - Resources\04 - Software\Scanco Medical MicroCT FTP 3.4\
#Install the software using the default parameters.
#Click on FTP Connection and input the host to connect to, the username, password.
#Give this profile a name.
#:[[File:Microct_FTP_pic01.jpg|600px]]
#Click on the options tab to set the locations to connect to (e.g., project disk, scratch) and the location on your computer to transfer files to.
#:[[File:Microct_FTP_pic02.jpg|600px]]
#Go back to FTP Connection and press the Connect button.
#*If you are connecting from off campus to the XtremeCT you will need to use the VPN to gain access through the firewall.
#Use the left tree to navigate folders.
#*Use the file filter to search for specific file types or file names (bottom left).
#Select files to download and press the Download Selected Files button (bottom right).
#:[[File:Microct_FTP_pic03.jpg|600px]]
#Press the Exit button to disconnect.

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====Filezilla====
#Download '''Filezilla 2.2.32''' from BoydDrive:\\04 - Resources\04 - Software\Filezilla 2.2.32\
#*This version of Filezilla will remove the OpenVMS version number from files, the new version will not!
#*The left side of the program shows your computer, the right side will show the micro-CT system once you have connected.
#:[[File:Filezilla_pic01.jpg|500px]]
#On the top menu, choose "File", then "Site Manager".
#Create a "New Site" for all the directories that you frequently access.
#*Give the site a meaningful name.
#*For the host, you may connect to "emily.ucalgary.ca" or "sceval.ucalgary.ca".
#*For the logon type choose "Normal" and input the micro-CT user name and password.
#:[[File:Filezilla_pic02.jpg|400px]]
#Click on the "Advanced..." button to set the default remote directory (i.e., on the micro-CT system).
#Set the default local directory if there is a specific location you plan to always transfer files to.
#Setup any additional sites you want then press "Save and Exit".
#:[[File:Filezilla_pic03.jpg|300px]]
#To connect to a session, hold the left mouse button down over the arrow next to the site manager button (computer icon under "File") to bring up your list of sites. Highlight the site of interest then release the mouse button to connect.
#Once connected, you can drag and drop files from the remote site to your local computer.

;*Common FTP locations
{| class="wikitable"
|-
! scope="col"| Account
! scope="col"| Location
! scope="col"| Path
|-
| microct / vivact || Data Disk ||DISK2:[MICROCT.DATA]
|-
| microct / vivact || Projects Disk ||DISK3:[MICROCT.PROJECTS]
|-
| microct / vivact || Scratch Disk ||ADISK1:[MICROCT.SCRATCH]
|-
| invivo / invitro || Data Disk ||DISK4:[BONELAB.DATA]
|-
| invivo / invitro || Projects Disk ||DISK5:[BONELAB.PROJECTS]
|-
| invivo / invitro || Scratch Disk ||ADISK1:[BONELAB.SCRATCH]
|}

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=Remote Access=

== VPN Setup ==

Access to the OpenVMS workstations from campus does not require VPN setup; however, to access from off the campus requires establishing a VPN connection prior to connecting.

*The VPN server is: gpvpn2.ucalgary.ca

*The client needed for VPN connection is '''FortiClient SSL''' which is available through [https://ucalgary.service-now.com/it| UofC IT Service Request] "Order Something".

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== Setup for MAC/Linux ==

=== Terminal and XQuartz ===
You need following to access the MicroCT system remotely.
#'''Terminal''': an SSH client
#*Preinstalled in MAC/Linux.
#'''XQuartz''': an X server for X11 forwarding
#*X11 was previously distributed with Mac OSX but has since stopped.
#*Check if preinstalled in MAC: open the "Applications" folder, choose "Utilities", there should be a file called "XQuartz". No need to open.
#*If not preinstalled, download the most recent [https://www.xquartz.org/ '''XQuartz.dmg'''].
#*Once downloaded, double click the .dmg file to follow the instructions and install.
 
;SSH from terminal
#Open a terminal.
#*MAC: Open the "Applications" folder, choose "Utilities", then "Terminal".
#Type <pre>$ ssh xtremect2@emily.ucalgary.ca -Y</pre>
#*The -Y flag activates X11 forwarding.
#Or type <pre>$ ssh -Y -p22 -c 3des-cbc -o KexAlgorithms=+diffie-hellman-group1-sha1 -o HostKeyAlgorithms=+ssh-dss xt2recalib@emily.ucalgary.ca </pre>
#*Type <pre>$ alias xt2recalib='<ssh command above>'</pre> allows you to only type <pre>"$ xt2recalib"</pre> in the terminal from here on out to access the MicroCT system.
#You're good to go!

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== Setup for Windows ==
=== MobaXterm ===

There is only one program required to access MicroCT remotely: MobaXterm. It will act as both an SSH client and as an X server.

*Download [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Home Edition (Portable Edition)]
 
;Configure MobaXterm
*Run the .exe file after downloading MobaXterm.
:[[File:MobaXterm_init.PNG|500px]]

*Click on "Sessions" -> "User Sessions" and choose "SSH" in the top left of the "Session settings" window.
*Input your host info into the "Remote host" dialogue box such as "emily.ucalgary.ca", check on "Specify username" and input your username such as "xt2recalib" and ensure "X-11 Forwarding" is checked in "Advanced SSH Settings" tab, and click OK.
:[[File:MobaXterm_SSH.PNG|500px]]
 
;Start the session
*Launch the MobaXterm client and under "Sessions" -> "User session" you should have something titled "xt2recalib@emily.ucalgary.ca".
*Double click that session and you're good to go!
:[[File:MobaXterm_Session.PNG|500px]]

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

=== PuTTY and Xming ===
There are two programs required:
#'''PuTTY''': an SSH client
#*Download [http://www.chiark.greenend.org.uk/~sgtatham/putty/ '''PuTTY'''] or from BoydDrive:\\04 - Resources\04 - Software\PuTTY.
#'''Xming''': an X server
#*Download [https://sourceforge.net/projects/xming/files/latest/download?source=files '''Xming 6.9.0.31''']
#*Download [https://sourceforge.net/projects/xming/files/Xming-fonts/7.5.0.93/Xming-fonts-7-5-0-93-setup.exe/download '''Xming Fonts''']
 
;Configure PuTTY
*Under categories, expand the "Connection" and "SSH" trees. Click on "X11" and check the "Enable X11forwarding" box.
:[[File:Putty1.png|400px]]
*Under categories, now choose "Sessions".
*Under host name, put in "emily.ucalgary.ca". Choose "SSH" for the connection type.
*Under Saved Sessions, give the session a name (e.g., Emily). Click the "Save" button.
:[[File:Putty2.png|400px]]
 
;Start the Session
*Launch the Xming program, nothing should open except the Xming icon on the task bar.
*Open PuTTY. Double-click on the saved session, which will open a DEC terminal.
*Any program that you run remotely will be displayed by Xming.

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

==Remote Access FAQ==
=== MAC Open SSH Authentication Issue ===
You might get an error similar to the following especially after a recent OS update:
Unsupported KEX algorithm "+diffie-hellman-group1-sha1"
command-line line 0: Bad SSH2 KexAlgorithms '+diffie-hellman-group1-sha1
This is not Apple’s fault, it’s OpenSSH version 7. SHA1 is weak, so support for it has been removed. Which is fine, but VMS clients are probably using RSA/SHA1. So until they’re all updated (i.e. never!) we need to re-enable SHA1.

Open a terminal windows and execute the following:
sudo nano /etc/ssh/ssh_config
ENTER YOUR PASSWORD

Locate the line ‘# MACs hmac-md5,hmac-sha1,umac-64@openssh.com,hmac-ripemd160′ and remove the Hash/Pound sight from the beginning.

Locate the line ‘# Ciphers aes128-ctr,aes192-ctr,aes256-ctr,aes128-cbc,3des-cbc’ and remove the Hash/Pound sight from the beginning.

Then paste the following on the end;

HostkeyAlgorithms ssh-dss,ssh-rsa
KexAlgorithms +diffie-hellman-group1-sha1
There’s no reason to reboot, it should work straight away.
 

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=== SSH Speed Issues ===
 
If you notice that the remote display is quite slow, you may prefer to enter the 'manual' X display redirection after connecting with ssh. 
 
The steps to enter the 'manual' X display redirection are outlined in one of Scanco's FAQs found [http://www.scanco.ch/en/support/customer-login/faq-customers/faq-customers-general.html here]. 
Click the "Remote Graphical Access from your PC to the MicroCT" tab (5th tab) and scroll down to "SSH Speed Issue" for more information.

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=== MobaXterm Backspace Issue ===
If the Backspace/Delete key doesn't work on your MobaXterm

#Right-click on a session name on the left column and click "Edit session"
#:[[File:MobaXterm1.png|500px]]
#: 
#Under "SSH" page "Terminal settings" tab, toggle off "Backspace sends ^H" and "Save"
#:[[File:MobaXterm2.JPG|500px]]

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Main Page

2021-05-06T02:30:01Z

Yingzhu:

__NOTOC__
<center>Bone Imaging Laboratory Wiki

<table width="100%" border="0">
<tr>
<td width="15%" align="center" valign="middle" bgcolor="#ccff66">
<div align="center"> Wiki Concept</div>

 The idea of the 'Wiki' site is that any authorized user, in this case a member of the lab, can see and edit any of the pages on this site, as well as create new pages as required. 

 

<div align="center"> The Purpose</div>

It's to facilitate information exchange within the lab and keep up-to-date How To and User Manuals for lab's technical procedures and FAQ.

</td>

<td bgcolor="#ccff66"> [[File:BonelabScanners.JPG|center|750px]]</td>

<td width="25%" align="left" valign="middle" bgcolor="#ccff66">
<div align="center"> Read me</div>


#Use '''Ctr+F''' to search within any page.
#Never include login credentials especially password anywhere.
#It's all users' responsibility to keep the info precise, updated, abundant, and useful, through editing/addition/deletion as needed by clicking [edit] on the top-right corner of a page or item. This includes combining same/similar topics besides an item whenever appropriate.
#Add a redirect line after each new item for consistency:
#:[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]
#Click '''Help''' on navigation list on the left penal for detailed editing instructions.
#Contact Ying if you are not sure where to put a new item or could not find an item.

</td>

</tr>
</table>

</center>

{| border="0" align="center" width="98%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|

==[[Scanco User Instructions]]==
[[Scanco_User_Instructions#OpenVMS_Basics| '''OpenVMS Basics''']]
*[[Scanco_User_Instructions#OpenVMS_Beginner.27s_Reference| Beginner's Reference]]
*[[Scanco_User_Instructions#Session_Manager| Session Manager]]
*[[Scanco_User_Instructions#DEC_Terminal_and_Digital_Command_Language_.28DCL.29| DEC Terminal and DCL]]
*[[Scanco_User_Instructions#DCL_Programming_Guide| DCL Programming Guide]]
*[[Scanco_User_Instructions#List_of_basic_commands| List of basic commands]]

[[Scanco_User_Instructions#Micro-Computed_Tomography_.28.C2.B5CT.29_Basics| '''Micro-CT Basics''']]
*[[Scanco_User_Instructions#User_Tutorials| User Tutorials]]
*[[Scanco_User_Instructions#Micro-CT_Image_Basics| µCT Image Basics]]
*[[Scanco_User_Instructions#Image_Data| Image Data]]
*[[Scanco_User_Instructions#Scanco_Medical_Micro-CT_Software| Scanco Medical µCT Software]]

[[Scanco_User_Instructions#Scanning| '''Scanning''']]
*[[Scanco_User_Instructions#Sample_Name_Convention| Sample Name Convention]]
*[[Scanco_User_Instructions#Register_Samples_for_Scanning| Register Samples for Scanning]]
*[[Scanco_User_Instructions#Log_Sheets| Log Sheets]]
*[[Scanco_User_Instructions#Patient_Casts_and_Sample_Holders| Patient Casts and Sample Holders]]
*[[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29| Scan Parameters (Controlfiles)]]
*[[Scanco_User_Instructions#Perform_a_Scan| Perform a Scan]]
*[[Scanco_User_Instructions#Action_on_Image_Artifacts| Action on Image Artifacts]]

[[Scanco_User_Instructions#Evaluation| '''Evaluation''']]
*[[Scanco_User_Instructions#Evaluate_a_Scan| Evaluate a Scan]]
*[[Scanco_User_Instructions#Draw_Contours| Draw Contours]]
*[[Scanco_User_Instructions#Evaluation_Scripts| Evaluation Scripts]]
*[[Scanco_User_Instructions#Image_Processing_Language_.28IPL.29_Scripting| IPL Scripting]]

[[Scanco_User_Instructions#Results| '''Results''']]
*[[Scanco_User_Instructions#Images_and_Animations| Images and Animations]]
*[[Scanco_User_Instructions#Image_Tours| Image Tours]]
*[[Scanco_User_Instructions#Extract_Results| Extract Results]]
*[[Scanco_User_Instructions#Generate_Report| Generate Report]]

[[Scanco_User_Instructions#Data_Management| '''Data Management''']]
*[[Scanco_User_Instructions#Trainee.E2.80.99s_Data_Responsibility| Trainee’s Data Responsibility]]
*[[Scanco_User_Instructions#Move_data_from_Data_Disk_to_Project_Disk| Move data from Data Disk to Project Disk]]

[[Scanco_User_Instructions#Import_and_Export| '''Import and Export''']]
*[[Scanco_User_Instructions#Import_Foreign_Data_to_Scanco_System| Import Foreign Data]]
*[[Scanco_User_Instructions#Import_MRI_to_Scanco_System| Import MRI Images]]
*[[Scanco_User_Instructions#Import_Xradia_.2A.bin_to_Scanco_System|Import Xradia *.bin]]
*[[Scanco_User_Instructions#Get_Your_Files| Get Your Files]]

[[Scanco_User_Instructions#Remote_Access| '''Remote Access''']]
*[[Scanco_User_Instructions#VPN_Setup| VPN Setup]]
*[[Scanco_User_Instructions#Setup_for_MAC.2FLinux| Setup for MAC/Linux]]
*[[Scanco_User_Instructions#Setup_for_Windows| Setup for Windows]]
*[[Scanco_User_Instructions#Remote_Access_FAQ| Remote Access FAQ]]

|bgcolor="#CCCCCC"|
|valign="top"|

==[[Scanco Administration]]==
[[Scanco_Administration#OpenVMS| '''OpenVMS''']]
*[[Scanco_Administration#OpenVMS_References| OpenVMS References]]
*[[Scanco_Administration#Unix_related| Unix related]]
*[[Scanco_Administration#Graphical_Applications| Graphical Applications]]
*[[Scanco_Administration#File_Operations| File Operations]]
*[[Scanco_Administration#Administrative_Commands| Administrative Commands]]

[[Scanco_Administration#Calibration_and_QC | '''Calibration and QC''']]
*[[Scanco_Administration#System_Updates| System Updates]]
*[[Scanco_Administration#Calibration_and_Conversion| Calibration and Conversion]]
*[[Scanco_Administration#Quality_Control_.28QC.29| Quality Control (QC)]]

[[Scanco_Administration#Scanning| '''Scanning''']]
*[[Scanco_Administration#Scanner_User_Manual| Scanner User Manual]]
*[[Scanco_Administration#Scanco.27s_FAQ| Scanco's FAQ]]
*[[Scanco_Administration#Scan| Scan]]
*[[Scanco_Administration#Reconstruction| Reconstruction]]
*[[Scanco_Administration#Manipulate_RSQ| Manipulate RSQ]]
*[[Scanco_Administration#Manipulate_ISQ| Manipulate ISQ]]
*[[Scanco_Administration#Image_Artifacts| Image Artifacts]]

[[Scanco_Administration#Evaluation| '''Evaluation''']]
*[[Scanco_Administration#Analysis_Topics| Analysis Topics]]
*[[Scanco_Administration#UCT_EVALUATION| UCT_EVALUATION]]
*[[Scanco_Administration#Evaluation_FAQ| Evaluation FAQ]]
*[[Scanco_Administration#IPL_FAQ| IPL FAQ]]

[[Scanco_Administration#Results| '''Results''']]
*[[Scanco_Administration#Extract_Results| Extract Results]]
*[[Scanco_Administration#Database| Database]]
*[[Scanco_Administration#Other_FAQ| Other FAQ]]

[[Scanco_Administration#Data_Management | '''Data Management''']]
*[[Scanco_Administration#Lab.E2.80.99s_Data_Responsibility| Lab’s Data Responsibility]]
*[[Scanco_Administration#HP_Server_and_Disk_Array| HP Server and Disk Array]]
*[[Scanco_Administration#Tape| Tape]]
*[[Scanco_Administration#USB_Drive| USB_Drive]]
*[[Scanco_Administration#CDROM| CDROM]]
*[[Scanco_Administration#Saveset_and_Zip_files| Saveset and Zip files]]
*[[Scanco_Administration#Backup_and_Archive| Backup and Archive]]

[[Scanco_Administration#Process.2C_Printer_and_System| '''Process, Printer and System''']]
*[[Scanco_Administration#Processes_and_Jobs| Processes and Jobs]]
*[[Scanco_Administration#Printer| Printer]]
*[[Scanco_Administration#System| System]]

[[Scanco_Administration#Remote_Access|'''Remote Access''']]
*[[Scanco_Administration#For_Scanco_support| For Scanco support]]
*[[Scanco_Administration#Access_VMS_filesystem| Access VMS filesystem]]
*[[Scanco_Administration#Setup_remote_access_FAQ| Setup remote access FAQ]]
*[[Scanco_Administration#Physical_connections| Physical connections]]

[[Scanco_Administration#Dose| '''Dose''']]
*[[Scanco_Administration#Dose_Calculations| Dose Calculations]]
*[[Scanco_Administration#Optimize_Scan_for_Low_Dose| Optimize Scan for Low Dose]]

|bgcolor="#CCCCCC"|
|valign="top"|

==[[Xradia Instructions]]==
*[[Xradia_Instructions#User_Tutorials| User Tutorials]]
*[[Xradia_Instructions#Scanning| Scanning]]
*[[Xradia_Instructions#Reconstruction| Reconstruction]]
*[[Xradia_Instructions#Special_Topics| Special Topics]]
*[[Xradia_Instructions#Image_Tours| Image Tours]]

==[[Books and References]]==
[[Books_and_References#Imaging|'''Imaging''']]
*[[Books_and_References#Essential_Physics_of_Medical_Imaging| Essential Physics of Medical Imaging]]

[[Books_and_References#Bone|'''Bone''']]
*[[Books_and_References#Books_on_Bone| Books on Bone]]
*[[Books_and_References#Bone_Morphometry_and_Densitometry| Bone Morphometry and Densitometry]]

[[Books_and_References#Student_Reports|'''Student Reports''']]

==[[Image Registration]]==
[[Image_Registration#Scanco_Image_Registration|'''Scanco Image Registration''']]
*[[Image_Registration#Image_Transformation|Image Transformation]]
*[[Image_Registration#Image_Registration|Image Registration]]
*[[Image_Registration#Register_MRI_to_HR-pQCT|Register MRI to HR-pQCT]]

[[Image_Registration#Similarity_Registration|'''SimilarityRegistration''']]
*[[Image_Registration#Understand_rotation_parameters| Understand rotation parameters]]
*[[Image_Registration#Set_optimizer_scales| Set optimizer scales]]

[[Image_Registration#SkiRegistration|'''skiRegistration''']]
*[[Image_Registration#ITK_Rigid_registration_for_HR-pQCT| ITK Rigid registration for HR-pQCT]]

==[[Finite Element Modelling]]==
*[[Finite_Element_Modelling#Scanco_Finite_Element_Modelling| Scanco Finite Element Modelling]]
*[[Finite_Element_Modelling#FAIM_Finite_Element_Solver| FAIM Finite Element Solver]]
*[[Finite_Element_Modelling#FE_Tutorial| FE Tutorial]]
*[[Finite_Element_Modelling#Prepare_AIMs_for_FE_Analysis| Prepare AIMs for FE Analysis]]

==[[Software Plugins and Codes]]==
----
*[[Software_Plugins_and_Codes#ImageJ| '''ImageJ''']]
*[[Software_Plugins_and_Codes#Amira| '''Amira''']]
*[[Software_Plugins_and_Codes#R|'''R''']]
*[[Software_Plugins_and_Codes#ParaView| '''ParaView''']]

==Languages and Toolkits==
*[[C++|'''C++''']]
*[[VTK|'''VTK''']]
*[[ITK|'''ITK''']]

==Miscellaneous==
*[[Software_Development_Platforms| '''Software Development Platforms''']]
*[[Archive|'''Archive''']]

|}

----
<table align="left" width="85%">
<tr>
<td align="left" valign="middle" >
To: [https://www.ucalgary.ca/labs/bonelab/team/steven-boyd '''Steve Boyd's homepage''']
</td>
<td align="left" valign="middle"> To: [https://www.ucalgary.ca/labs/bonelab/home '''Bone Imaging Lab homepage''']</td>
</tr></table>

Scanco Administration

2021-04-20T17:28:42Z

Yingzhu: /* Delete a directory */

=OpenVMS=

==OpenVMS References==
*[[Media:OpenVMS Users Manual.PDF| OpenVMS User Manual]]
*[[Media:Vmsfaq.pdf| OpenVMS FAQ]]

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

==Unix related==
*[[Media:Vms-unix-commands.pdf| OpenVMS Commands with UNIX equivalents]]

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===Unix filenames on VMS with multiple '.'===

The directory names would have been cvs-1.11.21.dir on Linux. However VMS doesn't allow more than 1 . in the name. If you enter

<pre>$ set process/parse=extended</pre>

in a terminal you'll be able to access these files. You could consider renaming them i.e. cvs-1_11_21.dir.

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Unix command line basics===
====Twelve Essential Commands====

These are the commands which you have to know in order to be basically functional with a shell (command line).

{|
|-valign="top"
|width="80pt"| <tt>ls</tt>
| List directory contents.

<tt>ls -l</tt> long listing with dates and permissions

<tt>ls -a</tt> list all, including hidden files (hidden files start with a period)

|-valign="top"
| <tt>cd</tt>
| Change directory.

<tt>cd -</tt> change to previous directory

<tt>cd ~</tt> change to home directory

<tt>cd ..</tt> change to parent directory

|-valign="top"
| <tt>pwd</tt>
| Print current (working) directory.
|-valign="top"
| <tt>cp</tt>
| Copy file(s).

<tt>cp -r somedir somedest</tt> Copy recursively (directory and all contents)

|-valign="top"
| <tt>mv</tt>
| Move (or rename) a file (or directory)
|-valign="top"
| <tt>rm</tt>
| Delete (remove) a file.

<tt>rm -r somedir</tt> Delete recursively (directory and all contents)

<tt>rm -ri somedir</tt> Delete recursively, but prompt before each removal

<tt>rm -rf somedir</tt> Delete recursively, never prompt

|-valign="top"
| <tt>mkdir</tt>
| Create directory.
|-valign="top"
| <tt>rmdir</tt>
| Remove (empty) directory.
|-valign="top"
| <tt>cat</tt>
| Print file contents (to console).
|-valign="top"
| <tt>less</tt>
| Scroll through file contents, one page at a time. SPACEBAR to advance a page, B to go back a page, Q to quit, /pattern to search for pattern
|-valign="top"
| <tt>man</tt>
| Get help on <tt>command</tt>. (eg. <tt>man ls</tt> for help on <tt>ls</tt>). You move around in man as you do with less: SPACEBAR is forward a page, and so on.
|-valign="top"
| <tt>exit</tt>
| Close shell (i.e. the terminal). If this is your login shell, you will log out.
|}

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====File names with spaces====

Spaces on the command line separate arguments. Therefore file names containing spaces require special treatment to avoid being interpreted as two separate files. There are a couple of methods. You can use quotes:

cp "file name with spaces" file_name_without_spaces

You can also use the backslash, which indicates that any special significance is to be removed from the following character. Thus a space, instead of being the delimiter for arguments on a command line, is to be interpreted as a regular character.

cp file\ name\ with\ spaces file_name_without_spaces

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====Copying and pasting====

Copying and pasting in a terminal is generally done with the middle mouse button. Just mark the text you want to copy with the mouse, holding down the left mouse button in the usual way. Then move the cursor (which is different than the mouse pointer - move the cursor with arrow keys typically) to where you want to insert and click the middle mouse button (on a wheel mouse the middle button is the wheel).

Tip: You can double-click to mark a whole work, or triple-click to mark a whole line. Remember - you haven't only marked it, you've put it in the clipboard.

Note: This applies to X11, for example on Linux. If using OS-X, just use Option-C and Option-V as usual.

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====Recalling previous commands====

You can scroll though your previous commands (command history) by using the UP and DOWN arrow keys.

A more advanced trick is to use CTRL-R, which is particularly useful when you want to recall a command you used some time ago. Hit CTRL-R and then start typing some fragment of the command you're searching for. The prompt will automatically update to show you the most recent match to the fragment you've typed so far. If you want the matching command previous to the one shown, hit CTRL-R again. Once you've got the previous command you're looking for, hit ENTER to run it again, or start editing it.

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====Be lazy: use TAB to minimize typing====

Some commands and especially some file names can be pretty long. Don't want to type it all? Type the first few letters, then hit TAB. The shell will fill in the rest, as far as there is a unique completion (either command or filename). If there is not a unique completion to the end, you might have to type another character or two and then hit TAB again.

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====Keyboard Shortcuts====

Here are some common command line keyboard shortcuts. Some of these are bash-specific shortcuts, so not all of them will work on all systems.

Note: If you're using OS-X, a number of the editing shortcuts below work in ALL programs in OS-X. (With the sad exception of Microsoft Office, which overrides the system-wide key bindings.)

{|
|+ Table 1. Common editing key bindings
|-
|width="80pt"| <tt>CTRL-A</tt> || Move to the end of the line.
|-
| <tt>CTRL-E</tt> || Move to the beginning of the line.
|-
| <tt>CTRL-F</tt> || Move forward one character.
|-
| <tt>CTRL-B</tt> || Move backward one character.
|-
| <tt>ALT-F</tt> || Move forward one word.
|-
| <tt>ALT-B</tt> || Move backward one word.
|-
| <tt>CTRL-D</tt> || Delete one character forward.
|-
| <tt>CTRL-H</tt> || Delete one character backward.
|-
| <tt>ALT-D</tt> || Delete one word forward.
|-
| <tt>CTRL-W</tt> || Delete one word backwards.
|-
| <tt>CTRL-K</tt> || Delete (Kill) everything from the cursor forwards (to the end of the line).
|-
| <tt>CTRL-U</tt> || Delete everything from the cursor backwards (to the beginning of the line).
|-
| <tt>CTRL-T</tt> || Transpose two characters.
|-
| <tt>ALT-T</tt> || Transpose two words.
|-
| <tt>ESC .</tt> || Insert the last argument (word) from the previous command.
|-
| <tt>CTRL-X-X</tt> || Move between end of line and current cursor position
|}

{|
|+ Table 2. Common control key bindings
|width="80pt"| <tt>CTRL-C</tt> || Terminate the current program, or sometimes cancel some operation.
|-
| <tt>CTRL-\</tt> || Seriously kill the current program! Use only after <tt>CTRL-C</tt> has failed.
|-
| <tt>CTRL-D</tt> || End-of-file. This is often used to signal the end of input, or to exit a program.
|-
| <tt>CTRL-G</tt> || Cancel the current operation. An occasionally useful command to get yourself out of things.
|-
| <tt>CTRL-L</tt> || Redraw the console. Mostly useful if some program running in the background spews a lot of stuff onto your terminal.
|-
| <tt>CTRL-Q</tt> || The only time you need this is if you accidently hit <tt>CTRL-S</tt>. In that case the console is locked until you hit CTRL-Q to unlock it. Apparently once a long long time ago this was actually a useful feature.
|-
| <tt>CTRL-R</tt> || Recall command containing characters. After hitting <tt>CTRL-R</tt>, type the fragment you want to search for. If it returns a command which isn't the one one want, hit <tt>CTRL-R</tt> again to cycle through matches.
|-
| <tt>CTRL-Z</tt> || Suspend the current program and put it in the background. This is very useful once you figure out how it works. Refer to the section on putting jobs in the background.
|}

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====Using scp to copy files between computers====

scp is a secure copy command that works bewteen computers. Typically any computer that supports ssh also supports scp. You must have an actual user account on the target computer, so for example you typically won't be able to scp to mike.kin .

scp works just like the cp command, with a few extra decorations:

scp eric@mighty-mac.kin.ucalgary.ca:Documents/important_file.txt .

In this example the file I want to copy is on the computer mighty-mac.kin.ucalgary.ca, and I used eric@ to specify my user name. You can leave off the user name if it is the same on both computers. The period as the destination is just standard Unix short-hand for the current directory. You can use the -r flag to copy whole directories. For example:

scp -r calculations mighty-mac.kin.ucalgary.ca:Documents/Projects

In this example calculations is a directory containing many files, and possibly subdirectories. This example copies files to mighty-mac instead of from it.

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====Running long calculations====

Here are some useful tips for running long jobs.

=====Getting the prompt back after starting a job=====

Use & at the end of the command. This puts the job in the background. For example:

./myjob someargs &

To see all your background jobs (the ones started in the current shell), enter:

jobs

To bring one of these to the foreground, use:

fg %n

where <tt>n</tt> is the job number (yes it needs a <tt>%</tt> in front of it). To move it to the background again, hit CTRL-Z. This however doesn't just move the job to the background, it suspends it. To get it running again, use

bg %n

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=====Keeping a job running after you log out=====

Use nohup. For example, suppose you want to run <tt>./myjob 20</tt>. In this case, you could use:

nohup nice ./myjob 20 &> output &

There are several things to note here:

* The <tt>&</tt> at the end of the command line is there so you get the command prompt back immediately (see the previous section).
* We have redirected the output to a file out_file with <tt>&> output</tt>. If you don't do this, any output to STDIN (normally the console) will automatically go into a file called <tt>nohup.out</tt>.
* We've niced the job to reduce it's execution priority. This is courteous if you're a multiuser system.

If you want to see what's in nohup.out (or whatever you called it) at any time, you can do the usual

cat nohup.out

Here's another potentially more useful command:

tail -f nohup.out

tail shows you the last few lines of the files. In addition, the -f flag ("follow") means that as lines get added to the file, they are displayed on the screen. This looks just like when you run the program without nohup, except when you hit CTRL-C, the program keeps on running in the background.

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=====Finding out if any of your jobs are still running=====

This command will show all jobs that belong to user "eric":

ps -u eric

Another useful command is "top", which will show interactively which processes are using the most processor cycles.

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=====Terminating a job prematurely=====

If you decide that you want to kill the job before it completes, this is the command:

kill PID

where PID is the actual PID (a number) of the process. You find the PID with 'top' or 'ps -u eric' (replace eric by your user ID of course).

Occasionally a process will decline to terminate when you request it to. This is the more brutal, never-fails method to kill a job immediately:

kill -s KILL PID

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=====Suspending a long-running job and restarting it later=====

First find the PID (process ID) with top or with ps. For example, I might list all jobs belonging to me with:

ps -u eric

To stop the job, send it a STOP signal:

kill -s STOP PID

(replace PID with the actual PID number). It is now no longer running, but it still occupies memory (although the memory it uses will probably be swapped out to disk). When you want to resume execution, give it a CONT signal:

kill -s CONT PID

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==Graphical Applications==

===Calendar - Fix corruption===

Sometimes the calendar file can be corrupted, which is annoying every time you log onto the system.

When we login to a server through a workstation, there is a "File is not a Calendar Datafile." information message pops up.

This means that the calendar database got corrupted during an improper interruption such as a system crash due to a power outage.

To fix this, you will need to login to the Server through the Workstation

Once logged in:
cd xdefaults
dir *calendar*.dat /date

Delete the calendar file for the workstation, such as the following James workstation:
del decw$calendar_sc3401.dat

Once logged out and logged in again, you will be asked if you want to create a new calendar file.
Say "yes" there and a new calendar will open.

In the calendar window menu "options" -> "general" set the "start iconized" -> apply and "ok", then "options" -> "save settings".

So next time you log in, the calendar window will be minimized in the right lower corner.

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===Session Manager - Create a customized button===
The session manager part to enable the double-click on the AIM file:
Session Manager, 'Options', 'Menu', enter new item
SAP
with command:
<pre>
@decw$user_defaults:sap$vue
</pre>
Then move that menu point into 'Applications' menu.
Also:
'Options', 'File types', Create 'AIM' file type.
Move 'rename', 'copy', 'purge' etc. into menu, Select 'SAP', click on
'Change double click', and also move SAP into menu.

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===EVE Editor===

====Launch EVE editor====

On the command line
$ edit/display=decwindows/tpu fname.txt

Or to set it up permanently, edit <code>DISK1:[MICROCT]MICROCT_SETUP_USER.COM</code> to include

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====Configure EVE editor====

The following file, called <code>tpu.dat</code>, should be installed in <code>disk1:[microct.xdefaults]:</code>
<pre>
#
# DECTPU V3.1 1993-04-22 15:50 defaults
# CHANGED B.KOLLER 21-JUN-90
#
# Copyright (c) 1993 Digital Equipment Corporation. All rights reserved.
#
#
# The following are all the resource names that DECTPU supports.
#
Tpu.Tpu$MainWindow.Title: DECTPU Copyright © Digital Equipment Corporation 1992. All Rights Reserved.
Tpu.Tpu$MainWindow.ApplicationTitle: DECTPU
Tpu.Tpu$MainWindow.IconName: DECTPU
Tpu.Tpu$MainWindow.X: 610
Tpu.Tpu$MainWindow.Y: 0
#
# The following resource names are commented out so that users can specify
# *rows and *columns and have DECTPU obey those directives. If DECTPU finds
# finds no resource names governing the number of rows and columns it should
# have, it uses 24 rows and 80 columns.
#
#
Tpu.Tpu$MainWindow.Columns: 80
Tpu.Tpu$MainWindow.Rows: 56
*EVE_MENU_BAR*background: #ADADADADADAD
Tpu*XmScrollBar*background: #ADADADADADAD
Tpu*XmDialogShell*background: #ADADADADADAD
Tpu*XmMenuShell*background: #ADADADADADAD
*background: white
Tpu*condensedFont: OFF
Tpu*fontSetSelection: 0

# 0 = big font
# 1 = little font
# 2 = GS font (German Standard)
# 3 = Fine font (used only for non-latin 1 fonts?)
</pre>

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====EVE editor Commands====

* mark -> ctrl-space
* delete -> remove (delete)
* insert -> insert here (insert)
* learn -> ctrl-k (ctrl-r to stop)
* The right 'alt' key on the PC accesses the menu for EVE.

{| class="wikitable"
| copy
| <code><PF1><Remove></code> on VMS
|-
| paste
| <code><Insert Here></code> on VMS or <code> <ctrl><insert></code> on PC
|-
| cut
| <code><Remove> </code> on VMS or <code><delete> </code> on PC
|-
| learn
| <code><CTRL><K></code>
|-
| stop
| <code><CTRL><R> </code> (then give a key sequence such as <code><CTRL><Q></code>)
|-
| repeat
| <code><PF1><#><(CTRL-Q)> </code> (the <code>CTRL-Q </code> depends on the given key sequence).
|-
| find next
| <code><PF3></code>
|-
| enter search string
| <code><PF1><PF3></code>
|-
| replace string
| <code><PF1><S></code>
|-
| margins
| Mouse click bottom of window type: <code>set right 999</code>
|-
| kill line
| <code><PF4></code>
|-
| kill word
| - (minus key on number pad)
|-
| advance next line
| <code>0</code> (zero on number pad)
|-
| select text
| <code><CTRL><SPACE></code>
|}

*To avoid having the EVE editor automatically create multiple lines from a long input sequence set the margins [FORMAT - SET MARGINS] to some high number eg. 500.

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====Use Commands Remotely with XWin32====

Default key settings:

{| class="wikitable"
| remove (cut) and append to previous paste buffer
| <code>9</code> (nine on number pad)
|-
| paste
| <code><insert></code>
|-
| learn
| <code><CTRL><K></code>
|-
| stop
| <code><CTRL><R></code> (then give a key sequence such as <code><CTRL><Q></code>)
|-
| repeat
| <code><CTRL>-Q</code> or given key sequence
|-
| kill word
| - (minus key on number pad)
|-
| advance next line
| <code>0</code> (zero on number pad)
|-
| go to end of line
| <code>2</code> (two on number pad) or <code><CTRL><E></code>
|-
| go to start of line
| <code><backspace> or <CTRL><H></code>
|-
| go to start of word
| <code>1</code> (one on number pad)
|-
| delete line to left of cursor
| <code><CTRL></code>
|-
| turn on/off select text
| <code><CTRL><SPACE> or .</code> (on number pad)
|-
| select all text
| <code><CTRL><O></code>
|-
| turn on/off overstrike
| <code><CTRL><A></code>
|-
| save and exit
| <code><CTRL><Z></code>
|-
| enter command
| <code><CTRL></code>
|}

You may find it useful to define keys. For example, define keys to cut, copy and paste:

*To Cut <code><CTRL><X></code>:
:<code><CTRL></code> (enter command)
:Command: <code>define key=Ctrl/x cut</code>

*To Copy <code><CTRL><C></code>:
:<code><CTRL></code> (enter command)
:Command: <code>define key=Ctrl/c copy</code>

*To Paste <code><CTRL><V></code>:
:<code><CTRL></code> (enter command)
:Command: <code>define key=Ctrl/v paste</code>

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====Use terminal based editor (EVE)====
<pre>
$ edit file.txt
</pre>
If you are using this from a remote terminal, you will need to initiate a vt100 terminal.
<pre>
$ set term /vt100
</pre>
Some useful commands:
:* ctrl-z -> exit with save
:* ctrl-y -> kill without saving
:* do-key, then type 'quit' or 'exit' (what is the do key on a remote terminal?)
:* PF2 -> shows special keypad functions
:* GoldKey -> PF1

====Use EVE editor Remotely====
For remote sessions, once used $ EVE to start the text editor, press Ctrl-B to bring up a command line at the bottom of the screen.

*Command: @eveconfig

This will set backspace to delete normally.
*Ctrl-X cut
*Ctrl-C copy
*Ctrl-V paste
*Ctrl-S save file
*Ctrl-L learn command
*Ctrl-F find next
*Ctrl-Q quit
*Ctrl-O open
*Ctrl-space to select

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===Scout Views===
====View scout views in two locations====
Go to scout view directory
<pre>
XtremeCT side:
$ cd DISK1:[MICROCT.DATA.SCOUTS]

VivaCT side:
$ cd ADISK1:[VIVACT.DATA.SCOUTS]</pre>

Use the program ximage
<pre>$ x asdf.SCV</pre>

For XtremeCT users, 2 sets of scout views are saved. Scout views can be viewed from the main scouts directory (above) and in the data directory under specific patient and measurement numbers. For example using patient #: 2795 and meas#:9933:
$ cd DISK2:[MICROCT.DATA.00002795.00009933]
$ x C00008848.SCV

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====Reuse old scout views====
Reference SCV files are not overwritten. When you Save a new reference within the scout view Dialog, it writes a new version that is read by the measurement program.

If you want to return to an old scout view reference, you will have to manipulate files manually.

Typically all the scouts are accessible here:
DISK1:[MICROCT.DATA.SCOUTS]0000PPPPSS.SCV

PPPP being the patient number, and SS the Site Code number [i.e. 20,21,38,39 = RL, RR, TL, TR].

Assuming you have only version;1 and ;2 what you can do is to rename/delete version;2, so that it is not read anymore by the measurement program.
Or copy version;1 as version;3, but this is rather messy.

Note: Do not look in the measurement directories. There are copies of the SCV files, but those are not the one called by the measurement program.

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==File Operations==

===Copy and Move===
====Copy files between accounts/users====

As user <code>system</code> you can copy files between accounts (e.g., microct and devel). There is no need to set user/priv=bypass as this is set by default as user system.

If you want to copy between two users (i.e. normal users, not calibration or system), then you can only write on the user directories for which you are logged in. So, if you want
to copy files from account xtremect2 to microct, you need to log into microct account and copy the file from xtremect2 to microct

If you want to use the backup command for copying multiple subdirectories with
the three dots (e.g., <code>disk2:[microct.data.00000034...]</code>) then you HAVE to put an <code>/owner=devel</code> at the end:

<pre>
$ backup/log disk2:[microct.data.00000034...] -
disk2:[devel.data.00000034...]/own=devel
</pre>

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====Move a directory on the same device====

You can simply use the rename command to move a directory on the same device, but you need to set DELETE protection for the file owner for this to work
$ set prot=o:rwed <dir>.dir
$ ren <dir>.dir new:[parent.directory]
$ set prot=o:rwe new:[parent.directory]<dir>.dir

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====Move a whole directory structure with BACKUP command====

Sometimes we want to move entire directories. For example, moving a measurement directory from DISK2 to DISK6, or moving a project to another disk.

Here is how to move a project:
$ BACKUP DISK2:[MICROCT.PROJECTS...] DISK3:[MICROCT.PROJECTS...]/VERIFY

Note the use of <code>...</code> in both places.

If you move a data measurement, you could do it as follows:
$ BACKUP DISK2:[XTREMECT2.DATA...] DISK6:[XTREMECT2.DATA...]/LOG/VERIFY

In both cases, you can add a <code>/DELETE</code> command to so that it deletes after the move is completed and verified.
$ BACKUP/VERIFY/DELETE DISK2:[XTREMECT2.DATA...] DISK6:[XTREMECT2.DATA...]/LOG/VERIFY

Alternatively, you can simply check that the move was successful, and then delete the original files:
$ delete disk2:[microctt.projects...]*.*;*
$ dl disk2:[microctt.projects...]*.dir ! A for all; do until sub-dirs are gone

Note that I've misspelled "microctt" on purpose as these commands are VERY dangerous. You could wipe out a lot of data by accident. Be careful!

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====Fix corrupted VMS files when moved to or from a PC====

We start by getting good file format/attributes from a good aim/isq/gobj, etc.

$ ana/rms/fdl/out=correct.fdl good.aim

Then we edit the file correct.fdl, leaving only 5 lines:
RECORD
BLOCK_SPAN yes
CARRIAGE_CONTROL none
FORMAT fixed
SIZE 512

Now we have to set the file attributes of the affected aim (isq, gobi) file:

$ set file/attr=lrl=514 bad.aim ! Yes, 514
$ set file/attr=lrl=514 *.AIM ! do a bunch at a time

Finally we create a fixed file

$ convert/fdl=correct.fdl/trunc bad.aim converted.aim

This process discards the superfluous 2 bytes, usually caused by transferring to/from a PC.

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===Delete===

====Delete older versions of files====
Use the PURGE command.[[Image:Bones2.jpg|20px]] Warning: Extreme caution!
<pre>
$ PURGE !Removes older versions of all files in the directory! CAREFUL!!!!
$ PURGE myfile.aim !Removes older versions of myfile.aim.
$ PURGE /KEEP=3 !Removes all but the three most recent versions of all files.
$ HELP PURGE !More information on the PURGE command.
</pre>

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====Undelete Files====

The Disk/File Utility (DFU) will allow you to restore files that have been deleted, however, you will only be able to do so if the disk space hasn't been overwritten. This means that unless all scanning and access to the disk is stopped, you likely only have a couple of hours at most to undelete the files. 
 
Login as the system user and start the disk file utility program, DFU. 
<pre>
$ dfu
DFU> undelete diskX: /file=myfile OR undelete filepath/filename
</pre>
 
For example, suppose we want to restore an RSQ (C0001234.RSQ) that was deleted from the BH data disk (disk2): 
<pre>
DFU> undelete disk2:/file=C0001234.RSQ
</pre>
If the file can be undeleted successfully (i.e., without corruption), then you will be asked if you wish to restore the file. Type "y" or "n". 
When done restoring desired files, to get out of dfu:
<pre>
DFU> exit
$ logout
</pre>
 
*The undelete function will lock access to the disk while it searches for a file and until you respond "y" or "n" to restoring it. This means that all programs and commands trying to access the disk (i.e., by other people using the system) will appear to freeze momentarily until the disk is unlocked.
*If you search for a specific file, the lock period will be very short (maybe 15-30 seconds). If you search for files in general (e.g., *.RSQ), the lock period will be longer (maybe 5 to 10 minutes).
*You cannot search specific locations for files (i.e., a folder on a disk).
*Files are restored to their original location on disk.
*More information on DFU can be found here: http://digiater.nl/dfu.html

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====Delete a directory/file====
Use the DL command (this calls the script $ @SCOM:DL.COM), but first remove all files from the directory.
[[Image:Bones2.jpg|20px]] Warning: Extreme caution!
<pre>
$ DEL [.subdir...]*.*;* !Deletes all files in subdir. CAREFUL!!!
$ DL subdir.dir; !Deletes subdir.dir with confirmation.
$ DL disk:[dir.subdir...]*.dir !* for all; do until subdirs are gone.
</pre>

Use the DELETE command, but first remove all files from the directory and set file protections to enable deletion of the directory.
<pre>
$ SET FILE/PROT=O:RWED [.subdir...]*.*;* !Changes protections so you can delete the files. O is short for OWNER and RWED refers to Read, Write, Edit, Delete.
$ DEL [.subdir...]*.*;* !Deletes all files in subdir. CAREFUL!!!
$ SET FILE/PROTECTION=O:RWED subdir.dir !Changes protections so you can delete the subdirectory subdir.dir.
$ DEL subdir.dir; !Deletes the subdirectory.
</pre>

If the file cannot be deleted to due a permission error
<pre>
$ purge 12_RAD_FX.AIM
%PURGE-W-FILNOTPUR, error deleting DISK4:[BONELAB.PROJECTS.MULTILOAD.CAMOS]12_RAD_FX.AIM;1
-RMS-E-FLK, file currently locked by another user
</pre>
Do the following:
<pre>
$ set ho 0 ! log in as calibration
$ spb
$ del DISK4:[BONELAB.PROJECTS.MULTILOAD.CAMOS]12_RAD_FX.AIM;1
$ logout
</pre>

If that still doesn't work, then maybe you need to kill a process first:
<pre>
$ show device disk4 /file ! shows all the files currently involved in a process
$ set ho 0 ! log in as 'system'
$ stop /id=2081F1EC
$ del DISK4:[BONELAB.PROJECTS.MULTILOAD.CAMOS]12_RAD_FX.AIM;1
$ logout
</pre>

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===Authorizations===

====Can not access a Projects directory====
In principal, all Scanco user accounts (even including the calibration ones) should have read and write access to the Projects directories. While it (denied reading or writing access to a Project folder) did happen for a reason (used different accounts to create a file or a subfolder within a Projects folder), you could let lab administrator know and carefully run the following command to overwrite the authority, or switch to microct or xtremct2 account to perform as a walkaround.

<pre>
$ set file/prot=(g:rwe,o:rwe) disk4:[bonelab.projects.danielle...]*.*;*
</pre>

To avoid this happening again, make use always using the same account consistently to create all files and subfolders within their Project folder.

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==Administrative Commands==

===Query commands===
====Check licenses on VMS system====

This can be used to see what educational licenses (and other licenses) are currently on the system:

<pre>
$ SHOW LICENSE
</pre>

To apply for an educational license go to http://www.openvmsedu.com

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====Check MAC address of VMS system====
You can check them using the command
$ mcr lancp sh dev/char
For example, the result on percy.kin.ucalgary.ca gives

Device Characteristics EIA0:
Value Characteristic
----- --------------
1500 Device buffer size
Normal Controller mode
External Internal loopback mode
00-02-A5-20-29-99 Hardware LAN address
Multicast address list
CSMA/CD Communication medium
FF-FF-FF-FF-FF-FF Current LAN address
128 Minimum receive buffers
256 Maximum receive buffers
Yes Full duplex enable
Yes Full duplex operational
TwistedPair Line media type
100 Line speed (mbps)
Disabled/No Failset Logical LAN state
0 Failover priority

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===Update commands===

====Change hosts====
<pre>
$ mcr latcp show service * ! and if it shows you SCTHIN:
$ set host scthin ! or
$ set host scthin/lat
</pre>

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====Update OpenVMS Licenses====
This needs to be done on all the Calgary workstations, XtremeCT, vivaCT40/uCT35, and uCT100. 
Request licenses from HP:
*School Identification (for U of C): 855803-9502
*License type: OpenVMS VAX/Alpha (uCT100: OpenVMW Integrity) Layered Products? (Or try others)
*Member of DSPP or AlicanceONE: No
*Do you use a VAX or Alpha Emulator: No

On every workstation, you need to check which licenses are loaded and update those with a termination date.
<pre>
$ show license

Active licenses on node SCEVA3:

------- Product ID -------- ---- Rating ----- -- Version --
Product Producer Units PCL Activ Version Release Termination
C DEC 0 0 100 0.0 (none) 1-OCT-2012
CMS DEC 0 0 100 0.0 (none) 1-OCT-2012
CXX-V DEC 0 0 100 0.0 (none) 1-OCT-2012
FORTRAN DEC 0 0 100 0.0 (none) 1-OCT-2012
LSE DEC 0 0 100 0.0 (none) 1-OCT-2012
MMS DEC 0 0 100 0.0 (none) 1-OCT-2012
VMSCLUSTER DEC 0 0 100 0.0 (none) 1-OCT-2012
OPENVMS-I64-FOE HP 4 1 0 0.0 (none) (none)
</pre>

*HP will provide you with a script file ([[media:Openvms_license_update_hp.docx |'''Example script from HP''' ]]) containing a large number of licenses.
*Modify the script to contain only the relevant licenses and load the licenses ([[Media:Openvms_license_update.docx |'''Example modified script''']]).
*Login as user: system
*Re-check the licenses on the workstation to ensure that the termination date has been updated.
*The date after expiry, if cannot log in, then there is a problem with the VMS Cluster license, which was installed by Scanco. Contact Mark Blanchard (mblanchard@scanco.ch) about this problem.

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====Understanding how to set default parameters with OpenVMS====

Here is how the files all hang together...

LOGIN.COM is called automatically during login and calls
::MICROCT_SETUP.COM, which sets the scanner ID, data device, etc. This file calls
::::MICROCT_SETUP_COMMON.COM to create general settings. This file is located in DISK0:[MICROCT_COMMON] and calls
::::::MICROCT_FE.COM, if present, to setup the environment for Bert's FE program
::::::MICROCT_SETUP_SITE_SPECIFIC.COM to create local settings for all accounts (e.g. ICALC)
::::::MICROCT_SETUP_COMMON_*.COM, if present, typically to create application-specific settings for all accounts
::::::MICROCT_SETUP_GROUP_*.COM, if present, to create local settings for specific groups (e.g. group 3401)
::MICROCT_SETUP_USER.COM to create user-specific settings.

Note that the $UM designation is the MAIN directory, and the location of the binary files. To see a list:

$ dir DISK0:[MICROCT_COMMON.MAIN]

This is where you'll find IPL_SCANCO_FE.EXE, IPL_SCANCO_M.EXE, etc.

Lots of stuff here:

Directory DISK0:[MICROCT_COMMON]

3309.DIR;1 DATABASE.DIR;1 DEMO.DIR;1 EVAL.DIR;1
MAIN.DIR;1 TEMPLATES.DIR;1 TIPS.DIR;1 UIL.DIR;1
UTIL.DIR;1 WWW.DIR;1

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====Edit Symbol====

=====Edit SCANCO_SUBMIT_COMMAND=====

*Check the current setting:
<pre>
$ show sym *submit*
</pre>

In directory <code>DISK2:[MICROCT]MICROCT_SETUP_USER.COM</code> add the following line:
<pre>
$ SCANCO_SUBMIT_COMMAND :== SUBMIT/NOPRINT/QUE=SYS$SLOW /NOTIFY/LOG=SYS$SCRATCH:
</pre>
Then end session and log in again. Definition of the symbol in the
<code>MICRO_SETUP_USER.COM</code> supersedes the standard setting.

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=====Edit AIX=====

[[Image:Bones2.jpg|20px]] Warning: Extreme caution! Explicit permission for this change or similar changes must be obtained from Dr. Steven Boyd.

Log in as user calibration (Xtremect: calibration; VivaCT40: calib5019; uCT35: calib2339), the password is the same as for the system user.
Set priviledges to bypass.
$ set proc/priv=bypass
Or
$ spb
Change to the MICROCT_COMMANDS directory.
$ cdc
$ sea *.com aix
$ eve microct_setup_common.com
Edit the file which is called <code>MICROCT_SETUP_COMMON.COM</code>

''Another example'': To make the backspace/insert keys work properly, edit the <code>login.com</code> and insert the line
<pre>
$ set terminal/insert
</pre>
Anywhere suitable.

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====Setup Time====
=====Change system date and time=====
The OpenVMS system should adjust for daylight savings, however, this is currently incorrect for the alpha systems. The alpha systems will need to be manually moved forward in March and moved back in April. To do this, you will need to login as system
<pre>
$ set host 0
user: system
password:
$ show time
$ set time=dd-mmm-yyyy:hh:mm:ss/cluster !/cluster to change the time on all computers at once
$ set time=01-APR-2012:18:00/cluster !Example: Set the system to April 1, 2012, 6 pm.
</pre>

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=====Set time zone=====
As user system:

$ @sys$startup:utc$time_setup
Choose "CANADA" from the menu.
Choose "MOUNTAIN" from the menu.

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=====Disable Distributed Time Synchronization Service (DTSS)=====
DTSS will automatically adjust the clocks for daylight savings (i.e., 2am to 1am on the 2nd Sunday in March, 2am to 3am on the 1st Sunday in November). As user system:

$ mcr ncl disable dtss
$ mcr ncl delete dtss
$ eve sys$startup:sylogicals.com

Add line to disable DTSS
$ DEFINE/SYSTEM/EXEC NET$DISABLE_DTSS TRUE
Save and exit.
Now re-set the time zone.

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=====Configure Network Time Protocol (NTP) server to synchronize clocks=====
*NTP must be configured for each node (computer). Login as user system.
NTP can only synchronize the system clock if the error is less than 1000 seconds.

Synchronize the system clock to UofC's NTP server (ensures time is correct to within 1000s):

$ mcr sys$system:tcpip$ntpdate ntp.cpsc.ucalgary.ca

Enable NTP:

$ cd sys$startup
$ @tcpip$config
3 - Server components
12 - NTP
1 – Enable service on this node
E – Exit menu
E – Exit configuration procedure
N – don’t start service

Create the NTP configuration file:

$ sys$sysroot:[tcpip$ntp]
$ copy/log tcpip$ntp.template tcpip$ntp.conf
$ eve tcpip$ntp.conf

Comment out existing peer and server entries (# for comments).
Add entries for local servers.
server ntp.cpsc.ucalgary.ca
server ntp1.cpsc.ucalgary.ca
Save and exit.

Start NTP:

$ @sys$startup:tcpip$ntp_startup

Check the log:

$ type/cont/int=1 sys$sysroot:[tcpip$ntp]tcpip$ntp_run.log

Sample log file:

$ Set NoOn
$ VERIFY = F$VERIFY(F$TRNLNM("SYLOGIN_VERIFY"))
11 Apr 09:22:34 ntp[547708872]: ntpd version = 4.1.0
11 Apr 09:22:34 ntp[547708872]: precision = 976 usec
11 Apr 09:22:34 ntp[547708872]: drift file 'SYS$SPECIFIC:[TCPIP$NTP]TCPIP$NTP.DRIFT' does not exist: no such file or directory
11 Apr 09:22:34 ntp[547708872]: will attempt to create drift file

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====Setup Email====
=====Setup email server=====
The SMTP protocol is not enabled by default. If you use <code>tcpip$config</code> you can switch on the mail server under Client Components. As system:

$ set host 0
user: system
password:
$ @SYS$MANAGER:TCPIP$CONFIG
Or
$ @tcpip$config
-> 2 (client components)
-> 6 (SMTP)
-> 2 (Enable & Start services)

*Select option 2 (client components) from the menu.
*Select option 6 (SMTP) from the next menu to enable and start it.

Since your smtp server is not registered anywhere, it can be that emails sent from this server will be filtered out as spam on the way to your mailbox. In that case you would need a so called MX record for your mail server. Contact UofC IT to resolve this issue.

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=====Send an email=====
Example: Send an email without an attachment.
$ mail sys$scratch:email_message.txt/subject="email subject" "hbuie@ucalgary.ca,mkan@ucalgary.ca"

Example: Send an email with an attachment.
$ MIME :== $MIME.EXE
$ MIME MIME> NEW /NOEDIT sys$scratch:file.txt
MIME> ADD /TEXT thisattached.txt
MIME> ADD /BINARY thatattached.zip
MIME> ADD /MESSAGE this_is_written.txt
MIME> SAVE
MIME> EXIT
$ MAIL /SUBJECT="MIME-encoded Message" - sys$scratch:file.txt "hbuie@ucalgary.ca,mkan@ucalgary.ca"
$
*MIME> ADD /TEXT *.txt does not work

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===Action commands===
====Send a message to terminals====
<pre>
$ reply /all "Merry Christmas to Bone Imaging Lab!"

Reply received on SCEVA2 from user XTREMECT2 at _SCEVA2$FTA8473: 09:21:58
Merry Christmas to Bone Imaging Lab!

4 terminals have been notified on SCEVA2.
$
1 terminal has been notified on SCSRV2.
$
1 terminal has been notified on SC3309.
$
3 terminals have been notified on SCEVA1.
$
</pre>

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====<code>mcr</code> vs <code>run</code> command====

The command <code>mcr</code> is the same as <code>run</code>, but only with mcr you can hand over 'in-line' parameters to an .exe file:

<pre>$ run ut:ctheader.exe c000124.isq</pre>
does not work, but you have to say
<pre>$ mcr ut:ctheader.exe c000124.isq</pre>

But funnily if you define a symbol in <code>microct_setup_user.com</code> (or <code>login.com</code>),

<pre>$ ctheader :== $ut:ctheader.exe</pre>

with just neither run nor mcr, but the 'funny' $ sign, then you can also hand over the ISQ name in-line.

Small detail with big effect...

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====File Do All (fda) - apply a command to a set of files====

<code>$ fda ctheader dk0:[microct.data.0001234...]*.isq </code>

to see the header of all isq files of sample 1234 (the three dots ... means all subdirectories)

Or:

<code>$ fda aix dk0:[microct.data.0001234.00005678]*.aim</code>

to see the processing log of all aim files of scan 5678

Wildcard "*" means multiple characters, "%" is for ONE character:

<code>$ fda aix dk0:[microct.data...]C%%%%%%%.aim</code>

(yes, 7 %'s)

to show the aim header of the gray-scale c0000135.aim (etc) files only, and NOT from the _seg.aims also.

[[Image:Bones2.jpg|20px]] Warning: CAUTION! Always test the wildcard expression first with

<code>$ dir dk0:[xxx...]*.aim </code>

The 'file do all' fda command can even be combined with a pipe, or an /output qualifier:

<code>$ pipe fda aix dk0:[microct...]*.aim | search sys$pipe "Slope" </code>

will show you all "Slopes" in a row. (but you may not see which slope belongs to which aim file anymore...)

or:

<code>$ fda/output=sys$scratch:all_headers.log aix dk0:[microct...]*.aim</code>

will write all the output into the .log file - which you can then either edit, or
<code>$ search sys$scratch:all_headers.log "String"</code>

or whatever you want.

Another example with output:

<pre>$ pipe fda type *.log | search sys$pipe "BV/TV" /output=BVTV.txt</pre>

"fda" is our self-written script, so you may have to try-n-error a bit...

<code>$ fda command file_wildcard [Optional: further parameters]</code>

If the command consists of multiple words with spaces inbetween (e.g. mcr ut:xxx.exe), then enclose the command in double-quotes

<code>$ fda "mcr ut:uct_ext_header_display" dk0:[microct...]*.isq 8</code>

Grab more than one line using pipe and search command:

<code>$ pipe fda aix *.aim | search sys$pipe "dim", "pos", "name"</code>

*The further parameters may not contain wildcards - so unfortunately, the fda can NOT be used to 'adaptively' rename a whole bunch of files.

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====Make commands available to all users with symbols or paths====

DCL$PATH is one way to do that, WE don't use it...
<pre>
$ def dcl$path disk1:[microct.main],disk1:[microct.util]
</pre>
then, if you type
<code>
$ uct_t
</code>
it will first try to

<code>
$ @uct_t.com
</code>
and then
<code>
$ r uct_t.exe
</code>

however, we usually define it by giving full path:

<pre>
$ progx :== $disk1:[microct.main]progx.exe
$ com_proc_x :== @disk1:[microct.main]procedure.com
</pre>

then, you can just type the shortcut ('symbol' in VMS language)

We use the 'cd' to set the default path, you may also use this in your command procedure:

<code>proc.com</code>:

<pre>
$ cd 'p1'
$ dir *.*/size

$ define COM disk1:[microct.commands]
$ p :== @COM:PROC.COM
</pre>

these both go into <code>login.com</code>, but see the Wiki entry above to confirm exactly where...

then, you can just type:

<pre>
$ p disk4:[microct.data.0000007.000009]*.ISQ
</pre>

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=Calibration and QC=

==System Updates==
{| class="wikitable"
|-
! scope="row"| XtremeCT II
|
*22-OCT-2020: Recalibration
*01-OCT-2020: Recalibration
*31-JUL-2020: Pixel Correction
*21-Feb-2019: New X-ray source, recalibration
*28-Apr-2016: Recalibration
*04-Nov-2014: Recalibration
*21-May-2014: New Daily QC Phantom (Scanco concluded minimal differences from previous)
|-
! scope="row"| XtremeCT I
|
|-
! scope="row"| vivaCT80
|
*20-OCT-2020: Filter changer replaced, Recalibration
|-
! scope="row"| vivaCT40
|
*20-OCT-2020: New x-ray source, Recalibration
*09-NOV-2010: Recalibration (70KV energy only)
*01-NOV-2010: New x-ray source, Pixel Correction, Recalibration
|-
! scope="row"| µCT35
|
*20-OCT-2020: New x-ray source, Recalibration
*15-JUN-2011: Recalibration
*21-MAR-2011: Recalibration
*10-FEB-2011: Recalibration
*26-NOV-2010: Pixel Correction
*29-OCT-2010: Recalibration
|}

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==Calibration and Conversion==
===Attenuation measured by µCT===
A micro-CT 3D image of an object is basically a 3D map of local x-ray absorption in the object. The reconstruction from multiple angular views provides information on how much x-ray absorption is happening within each cubic voxel element of the scanned volume.

It is important to understand what is meant by “density” in a µCT image. The reconstructed grey-scale intensity of each image voxel does not relate directly to mass density alone, thus do not expect it to correspond with measurements of weight per volume, e.g. g.cm-3. The primary entity that is measured is x-ray absorption, defined as the x-ray linear attenuation coefficient in units of
1/distance, specifically, 1/cm. This is determined both by mass density and x-ray mass attenuation coefficient which is determined by the elemental composition of the material. The x-ray linear attenuation coefficients of typical material is shown blow.

[[File:Mu_comparison.JPG|thumb|center|600px|X-ray linear attenuation coefficient µ of typical material (image curtesy of Dr. Ying Zhu)]]

The images we obtain from the scanner are in a special scanner manufacturer format called AIM files. Each voxel in these images contains a scaled linear attenuation value (mu-value) to save disk space.

{| class="wikitable"
|-
! scope="col"| Symbol
! scope="col"| Name
! scope="col"| Unit
! scope="col"| Value Range
! scope='col'| Meaning or Comments
|-
! scope="row"| µ
| x-ray linear attenuation coefficient
| 1/cm
| µ > 0
| A constant that describes the fraction of attenuated incident photons in a monoenergetic beam per unit thickness of a material
|-
! scope="row"| mu_value
| linear attenuation in Scanco images
| 1/cm
| -8～8 typically
| mu value represented in Scanco images
|-
! scope="row"| pixel_Scanco
| pixel intensity value in Scanco images
| -
| −32768～32767
| Original format of Scanco images in 16-bit signed
|-
! scope="row"| pixel_uint
| pixel intensity value in converted Scanco images
| -
| 0～65535
| Converted format of Scanco images in 16-bit unsigned, using the same slope (unscaled) but an updated intercept
|}

<pre>
pixel_Scanco = mu-value * scaling_factor
</pre>

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===Calibration by BMD===
When we know that the x-ray absorption of a material is dominated by one specific material, then we can relate the measured x-ray linear attenuation coefficient (mu_value) to the mass density of that material. The calibration of [[Scanco_User_Instructions#Descriptive_Statistics_.28Mean.2C_Median.2C_SD.29_of_Calibrated_Voxel_Values| '''Bone Mineral Density (BMD)''']] is an example of this. We assume that the x-ray attenuation within mineralized tissues such as bone, dentine and enamel is dominated by, and can be approximated as, the x-ray attenuation of the mineral compound calcium hydroxyapatite (CaHA) which has the formula Ca5(PO4)3(OH).

Then we obtain “phantoms” with two or more known mass concentrations of CaHA. By linking these mass concentrations of CaHA with measured mu_value in the micro-CT images, we can establish calibration linking the two quantities, allowing us to infer from the micro-CT measured linear attenuation coefficient (mu_value) in a mineralized tissue, to the density of CaHA in mg.cm-3.

*The assumption of linear correlation between the two quantities is based on a well-applied beam hardening correction and the phantoms' diameter matching with the size of bone within the sample.

*This calibration system could be used to calibrate measurement of other substances apart from CaHA and bone, where x-ray absorption is known to be dominated by a certain substance and phantoms can be prepared with known concentrations of that substance.

{| class="wikitable"
|-
! scope="col"| Symbol
! scope="col"| Name
! scope="col"| Unit
! scope="col"| Value Range
! scope='col'| Meaning or Comments
|-
! scope="row"| BMD
| Bone Mineral Density
| mg HA/ccm
| 0～3000
| Volumetric density of calcium hydroxyapatite (CaHA) in a biological tissue in terms of mg/cm^3
|-
! scope="row"| BMD_value
| Bone Mineral Density in Scanco images
| mg HA/ccm
| -1500～3000 typically
| BMD value in Scanco images
|}

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===Conversion between Attenuation and Bone Density===
<pre>
BMD_value = mu-value * slope + intercept

mu-value = (BMD_value – intercept) / slope

pixel_Scanco = scaling_factor * (BMD_value – intercept) / slope

</pre>

For example, to convert mu_value of 1.7923 (1/cm) to BMD (mg HA/ccm):
<pre>
BMD_value = 1.7923 * 3.67162994e+02 + -2.06399002e+02 = 451.667 (mg HA/ccm)
</pre>

For example, to convert the lower threshold of 125 mg HA/ccm that is in the IPL script to pixel intensity in Scanco images:
<pre>
pixel_Scanco = 4096 * (125 - -2.06399002e+02) / 3.67162994e+02 = 3697
</pre>

*You could get the scaling_factor, intercept and slope values from the AIM header of your scan by using aix -l command:
[[File:Aix.JPG|400px]]

*Reference: [[Media:Jbmr.141.pdf|Bouxsein ML, Boyd SK, Christiansen BA, Guldberg RE, Jepsen KJ, Müller R, Guidelines for assessment of bone microstructure in rodents using micro-computed tomography. J Bone Miner Res. 25(7): 1468-86. 2010.]]

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===Convert CT numbers to mg HA/ccm / Houndsfield units (HU)===

The two byte numbers (short) can be converted to mu values by first dividing by mu_scaling which is probably 4096 (uCT35, vivaCT40) or 8192 (XtremeCT).

Houndsfield units (HU)

Here is the conversion formula from mu (lin.att. in 1/cm, our original, 'physical' image numbers) to HU:

<pre>HU(pixel) = -1000 + mu(pixel) * 1000/mu(water)</pre>

so the mu(water) is the 'constant' that is needed for this conversion of any pixel value mu(pixel) to HU of that pixel.

divide the 2-byte numbers in our dicom/aim/isq files by 4096 to get mu. (4096 --> 'mu_scaling' in our headers). E.g. you see
gray-scale number 8192 in our files --> mu = 2 [1/cm].

A reasonable result for the uCT35 is:

<pre>HU = (CT / 4096) * 1718.19 - 1000</pre>

and that means 1000/mu(water) = 1718.19 --> mu(water) = 0.58299 which is a reasonable number.

mg HA/ccm

<pre>
mg HA/ccm = (AIM/mu_scaling) * slope + intercept
mg HA/ccm = (AIM/4096) * 295.494 - 189.695 ! vivaCT40
mg HA/ccm = (AIM/4096) * 256.51 - 172.99 ! uCT35
mg HA/ccm = (AIM/8192) * 1402.549 - 340.953 ! XtremeCT
</pre>

These numbers are available in the AIM header, or the ISQ header (<code>$ run ut:ctheader</code>).

To look up slope, intercept and mu_scaling, check either the AIM header
<pre>$ aix C1234567.AIM</pre>
or
<pre>$ run ut:uct_update_calibration</pre>
and look at a record, and you'll find slope and intercept and mu-water.

<pre>
vivaCT40
!----------------------------------------------------------------------
Mu_Scaling 4096
Calibration Data 55 kVp, 200mg HA wedge, 4096 scaling
Calib. default unit type 2 (Density)
Density: unit mg HA/ccm
Density: slope 2.95493988e+02
Density: intercept -1.89695007e+02
HU: mu water 0.58200
!----------------------------------------------------------------------
</pre>
<pre>
XtremeCT
!-------------------------------------------------------------------------------
Mu_Scaling 8192
Calibration Data 60kVp, BH: 200 mg HA/ccm, Scaling 8192
Calib. default unit type 2 (Density)
Density: unit mg HA/ccm
Density: slope 1.40254895e+03
Density: intercept -3.40953003e+02
HU: mu water 0.23900
!-------------------------------------------------------------------------------
</pre>

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===Calibration FAQ===
====Change brightness scaling====
*Refer to [[Media:Mu-scaling.pdf|'''Change the brightness scaling''']].

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====Update a scan after pixel correction====
Contact Lab personnel with system-level priviledges to perform
<pre>
$ set host 0
! Username: calib2339 (µCT35)
! Username: calib5019 (vivaCT40)
$ spb ! set priviledge bypass to write in other user accounts
$ run ut:pixel_corr_apply

PIXEL_CORR_APPLY Version 1.5
Scanner ID from UCTD:UCT_SCANNER_2339.DAT : 2339 !2339 for µCT 35, 5019 for vivaCT 40
Is this Scanner ID correct ? [?]: y
Give RSQ-Filename (leave empty to exit) []: DISK4:[BONELAB.DATA.00005283.00011668]C0005128.RSQ
...
...
Copy .RSQ to _CORRECTED.RSQ befor correction ? [?]: y

$ logout
</pre>

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====Update calibration in ISQ====
If DICOM files are converted to ISQ with IPL and then used for patient evaluation, the calibration data in the ISQ header needs to be present and correct. If this information is missing, utilizing upat_list to extract the values will say 'Error: Density calibration not valid'. In order to add calibration data to an ISQ file, do the following as user calibration:
<pre>
$set proc/priv=bypass ! gain read/write access to the files
$mcr ut:uct_ext_header_add_calib ! provide ISQ file name and header type (I chose [2])
</pre>

If you need to adjust the calibration of a file, without changing the system calibration data, copy the calibration database into a different directory, e.g. sys$scratch. Then, add a new calibration record to this temporary calibration database. This way your new, temporary values will not show up in the scan program.

$ copy uctd:uct_calibration_3401.dat sys$scratch:

Define the following logical in a terminal MAKE SURE TO DO THIS!!!!

$ def UCT_CALIBRATION_DATABASE sys$scratch:uct_calibration_3401.dat

Run uct_update_calibration and click trough the current calibration record (always enter).

$ r ut:UCT_UPDATE_CALIBRATION.EXE
select current calibration record
enter...

$ r ut:UCT_UPDATE_CALIBRATION.EXE

Then select the last number (New Record), copy all values from above, change slope and intercept.

Then use

$ mcr ut:uct_ext_header_add_calib

for ISQ and RSQ.

At the end, close the terminal!

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==Quality Control (QC)==
===Scope===
*Only Authorized XCT and µCT Operators are permitted to perform QC scans, including both scan acquisition and analysis.
*Authorization is a formal process. If you are not sure whether you have or should have authorization, speak to Dr. Boyd or Dr. Hallgrimsson or the MoJo Operations Manager.
*Authorized XCT and µCT Operators are responsible for ensuring a QC schedule is maintained.
*Only the manufacturer can calibrate the scanner! QC only checks the calibration.

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===Overview===
*Micro-CT systems cannot directly measure the density of a material, however, the density is linearly correlated to the x-ray absorption (assuming a proper beam-hardening correction is applied), which can be measured by micro-CT. Density is therefore determined by measuring a reference material of known density (i.e., a phantom) to define a conversion function to relate x-ray absorption to density. Quality control of density and structural measurements for the micro-CT systems is achieved through weekly checks of phantom values to their reference values and recalibrating the system (i.e., defining a new conversion function) as necessary.

*Performing QC is essential to the:
# Safety of our study participants and lab members
# Validity of our research data

[[File:QC_phantom.jpg|thumb|center|600px|Scanco Medical quality control phantom (a) and its CT scans of the density QC1 (b) and the structural QC2 (c)]]

*Reference: Koller B, Laib A (2007) Calibration of micro-CT data for quantifying bone mineral and biomaterial density and microarchitecture. In: Advanced bioimaging technologies in assessment of the quality of bone and scaffold materials: techniques and applications. Springer, pp 79-84.

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===Density QC1===
QC1 measures the density of 5 different rods of known hydroxyapatite (HA) densities within the QC phantom: approximately 0, 100, 200, 400, and 800 mg HA/cm3. This tests 3 things:

# That the scanner’s last calibration is still valid. This is done by comparing daily QC values to an acceptable range.
# The presence of drifts and shifts in the calibration. This is done by plotting daily QC results over time and using Shewart’s Controls to mathematically look for drifts and shifts. (Shewart’s Controls replaces visual assessment.)
# The correct functioning of scanner hardware and electrical components. This is done by visual inspection for image artifacts.

*QC1 is checked daily or 3 times a week on XtremeCT scanners whenever used and weekly on microCT scanners.

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===Structural QC2===
QC2 measures the volume of 3 fine aluminum rods within the QC phantom (Al rod volume measurement). This tests for:

# Alignment of the gantry (or stability of architectural parameters)
# The correct functioning of scanner hardware and electrical components. This is done by visual inspection for image artifacts.

*QC2 is checked weekly on both XtremeCT and microCT scanners.

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===QC Scan Instructions===
*XtremeCT QC Scan Instructions: Boyd Drive:\02 - Operations\01 - Scanner QC, Specifications, & Maintenance\QC Workflows\QC 001.2 - XCT Quality Control.docx
*[[Media:Calibration-instructions-for-uct35.pdf |µCT35 QC Instructions]] or [[Media:uCT35_Calibration.pdf|µCT35 QC another Instructions]]
*[[Media:Calibration-instructions-for-vivact40.pdf |VivaCT40 QC Instructions]] or [[Media:VivaCT40_Calibration.pdf| VivaCT40 QC another Instructions]]

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===Print out QC reports===
After running a QC1 or QC2 analysis, the results are output to:
*DISK4:[BONELAB.PROJECTS.QC] for XtremeCT QC results
*DISK3:[MICROCT.PROJECTS.CALIBRATION] for microCT QC results performed by BH lab
:*login with microct account
*DISK5:[BONELAB.PROJECTS.CALIBRATION] for microCT QC results performed by Bone Imaging lab
:*RESULTS_QC1_UCT35.TXT;2
:*RESULTS_QC1_VIVACT.TXT;4
:*RESULTS_QC2_UCT35.TXT;2
:*RESULTS_QC2_VIVACT.TXT;2

As usual as [[Scanco_User_Instructions#Print_out_report_sheets|'''print out report sheets''']], you use
$ upat_list
When it asks for a template, you can select for a graphical report
template = UU:UCT_EVAL_PHANTOM_SCANCO.PS
or for a text output
template = UU:UCT_3D_LIST.TXT

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===System Stability and Precision===
System Stability and Precision here is based on the QC measurement, QC1 for density variations and QC2 for structure variations.
{| class="wikitable"
|-
! scope="col"| System Stability and Precision
! scope="col"| XtremeCT
! scope="col"| vivaCT40
! scope="col"| µCT35
|-
! scope="row"| Long Term Precision
|
*QC1: ± 8mg HA/cm3
*QC2: ± 2.0%
|
*QC1: ± 0.4%
*QC2: ± 0.7%
(Ref term: 26-NOV-2010 to 8-APR-2011)
|
*QC1: ± 1.0%
*QC2: ± 1.6%
(Ref term: 26-NOV-2010 to 8-APR-2011)
|-
! scope="row"| Short Term Precision
|
*QC1: ± 8mg HA/cm3
*QC2: ± 2.0%
|
*QC1: ± 0.4%
*QC2: ± 0.9%
(Ref term: 4-MAR-2011 to 8-APR-2011)
|
*QC1: ± 1.0%
*QC2: ± 0.7%
(Ref term: 6-MAR-2011 to 8-APR-2011)
|}

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===QC FAQ===
====Determine calibration drift for microCT QC1====
The microCT QC1 analyses provide an estimate of the calibration drift by considering 'mean5' values. Use <code>$ uct_list</code> and make sure to use UU:UCT_3D_MEANS.TXT as the template. Then give the measurement numbers of the QC1 measurements (or all of them and remove what's not needed later).

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====Update QC1 contours====
If the QC contours don't line up on the phantom, then the contours need to be updated on the system. Normally this should not happen unless the phantom has become loose - if this is the case, re-fix it.

1. Login as user system. Do not use the <code>$ set host 0 </code> command since you will not be able to open windows for program. 
2. Run the login script for the user that does the QC scans so that Scanco logicals point to that scan database.
$ @adisk1:[microct]login.com on the XtremeCT cluster
$ @adisk1:[microct]login.com on the vivaCT cluster
$ @disk1:[microct]login.com on the µCT100 cluster

3. Run the evaluation program.
$ uct_evaluation
4. Load the most recent QC scan and locate the contours. File-->Load Gobj... Filter: <code>uctd:*.GOBJ</code>. Locate the contours for the phantom: <code> UCT_PHANTOM_KP_HA_XXXX_Y.GOBJ </code> where XXXX corresponds with the scanner ID (XtremeCT 3309, vivaCT 5019, µCT35 2339, µCT100 6002) and Y corresponds with the rod number (1-5 and results mean1 - mean5. 

5. Adjust the contours to centre on the rods.
Load a contour.
Move the contour on the first slice to be centred on the rod.
Copy the contour.
Delete the contours on slices 2 to the end.
Paste the contour on the last slice.
Morph between the two contours.
Save the contours. They should be saved to (A)DISK0:[000000.MICROCT_COMMON.DATABASE].
6. Perform a new QC scan as the standard (i.e., microct) user. Check that the contours line up for the evaluation. Evaluate and check the results.

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====Update Gobj for QC1 Analysis====
Refer to [[Media:Fix_QC1_gobj.pdf| '''Fix QC1 Gobj''' ]] for instructions.

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====Update XtremeCT QC1 calibration====
This procedure needs to be done for each beam hardening correction (e.g., QC1 with 200 mg HA/cm3, QC1 with 1200 mg HA/cm3) and for each scan energy.

1. Perform 3 back-to-back QC1 scans, which ensures the x-ray tube is very warm. 
2. Evaluate the last QC1 scan. 
3. After the evaluation is done, determine parameters for the new calibration
<pre>
$ uct_calib_phantom
UCT_CALIB_PHANTOM Version V1.0

Reading UCTD:UCT_CALIB_PHANTOM_KP_HA_3309.TXT
Phantom Type in file: 6
Phantom Number in file: 304
Voltage in file: 0
No of Materials in file: 1
With each, no of steps: 5
and mus: 1.000000
No. of Cylinders: 5
Measurement No. (0 to Stop) [0]: 11404

Mus: 0.2382 0.3163 0.3823 0.5358 0.8112
*****************************************************
Calibration: Slope Intercept: 1398.628 -339.819
Enter in Calibration Records if wished.
*****************************************************
Measurement No. (0 to Stop) [0]:
End of program
$
</pre>

4. Save the above screen output in a file called CALIB_3309_YYYY-MM-DD.TXT.

5. Now update the calibration. For most settings, you will use the default value by pressing return. You need to choose the correct calibration record, the one that corresponds with the energy and beam hardening correction used in the QC1 scans you did. Next, you need to update the slope, intercept, and mu water values to those determined in step 3 (copy and paste values to avoid typos). The new values should be similar to the old ones. Finally, if you have not made any mistakes, then save the record.
<pre>
$ run ut:uct_update_calibration
UCT_UPDATE_CALIBRATION V2.5

IDX Calib/Rec. Description
1 1/42 60kVp, BH: 200 mg HA/ccm, Scaling 8192
2 2/43 60kVp, BH: 1200 mg HA/ccm, Scaling 4096
3 3/0 New Record
Choose Calibration Record (IDX): [2]: 1
Valid Flag [1]:
Scanner-ID [3309]:
Energy [V] [59400]:
Intensity [µA] [0]:
Description [60kVp, BH: 200 mg HA/ccm, Scaling 8192]:

Antiring Enable [0]:

Beamhardening Enable [1]:
Beamhardening Coeff file [MICROCT_COMMON:[DATABASE]UCT_BH_COEFF_60KV_0200HA_3309.TXT;5]:
Beamhardening Checksum [0]:
CCD_CORR: Read to mem: 500 bytes to correct 1 pixels (588 bytes allocated)

Default unit type (1=µ, 2=mg, 3=HU, 4=Custom) [2]:
µ Enable [1]:
µ-scaling [8192]:

Density Enable [1]:
Density units [mg HA/ccm]:
Density Slope [1402.549]: 1398.628
Density Intercept [-340.953]: -339.819

HU Enable [1]:
µ of water [0.239]: 0.2382

CUSTOM Enable [0]:

HW Filter Code [0]:
HW Filter Description []:

Save Record ? [Y]: Y
End of program
$
</pre>

6. Save the above screen output in a file called CALIB_3309_YYYY-MM-DD_ENTERED.TXT. Send both text files to support@scanco.ch for them to archive.

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====Update microCT QC1 calibration====
Refer to [[Media:QC1_Calibration_Update.pdf|'''QC1 Calibration Update''']] for instructions for the VivaCT40 and uCT35.

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====Update a scan with new calibration or BHC====
If the QC1 range was out of range but it was not possible to update the system calibration before scanning, you can update the scan with the new density calibration (i.e., slope and intercept). It is also possible to change the beam hardening correction that is applied (e.g., from 200 mg HA/cm3 to 1200 mg HA/cm3).

{| class="wikitable"
|-
! scope="col"| Type of Update ||RSQ||ISQ||AIM
|-
|QC1 was out of range, need new slope and intercept
(e.g., after updating the system calibration)
|Yes||Yes||No, Create New
|-
|Change beam hardening correction type
(e.g., 200 mg HA/cm3 to 1200 mg HA/cm3)
|Yes||No, Reconstruct||No, Create New
|}

Use the UCT_EXT_HEADER_ADD_CALIB program to update an RSQ and, if appropriate, repeat for the ISQ.
*Use default values for all prompts except those commented after !.
<pre>
$ mcr ut:uct_ext_header_add_calib

UCT_EXT_HEADER_ADD_CALIB V 1.1
Raw-Data-File []: !give the name of the RSQ/ISQ with full path if not in that directory

Reading Raw Data ...
IDX Calib Description
1 1 45 kVp, 200mg HA wedge, 4096 scaling
2 2 55 kVp, 200mg HA wedge, 4096 scaling
3 3 70 kVp, 200mg HA wedge, 4096 scaling
4 4 General, non-bone-density-calibrated scan, scale 4096
5 5 45 kVp, BH: 1200 mg HA/ccm, Scaling 4096
6 6 55 kVp, BH: 1200 mg HA/ccm, Scaling 4096
7 7 70 kVp, BH: 1200 mg HA/ccm, Scaling 4096

Calibration Record No [0]: !specify the new calibration, e.g. 6

Calibration No. 6
Description 55 kVp, BH: 1200 mg HA/ccm, Scaling 4096
Scanner-ID 5019
Energy [V] 55000
Antiring Enable 0
Beamhardening Enable 1
Beamhardening Coeff file UCTD:UCT_BH_COEFF_55KV_1200HA_5019.TXT
Default unit type (1=µ, 2=mg, 3=HU, 4=Custom) 2
Same type already found. Setting old to invalid
SUCCESS: calib hext written
updating header...
SUCCESS: Header successfully updated.

Calib record indicates that BH-Corr is usually applied.
Info: There is a BH-Corr corr already in hext.
Add another BH-Corr from file again? (Y/N) [N]: Y
</pre>

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====Update a scan with new QC1 calibration====
Refer to [[Media:Update_Scan_with_new_QC1.pdf|'''Update Scan with new QC1''']] for instructions.

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====Fix: un-centered QC1 Gobj====
The contour for the QC1 scan is not centered on the on hydroxyapatite rod, which will result in erroneous low density values.

This can occur for a couple of reasons:
*The metal spindle has come loose on the phantom, in which case re-glue it and update the contours
*The slot on the phantom's spindle was not correctly aligned
*For the vivaCT 40, the sample bed was not pushed to the right before locking it in place
[[File:Phantom_not_pushed_right.jpg|600px]]

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====Fix: rods in QC2 images====
The QC2 scan has aluminum rods AND hydroxyapatite rods. This happens because the slot on the phantom's spindle was not correctly aligned and the phantom positioning is off slightly. Adjust the phantom and re-scan.

[[File:Phantom_spindle_not_in_right.jpg|600px]]

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=Scanning=

==Scanner User Manual==
For XtremeCTs:

* [[Media:Scanco - Manual_XtremeCTII_2.5.pdf |XtremeCT II User's Guide V2.5]]
* [[Media:XtremeCT User Guide XCT I.pdf |XtremeCT I User's Guide V6.4]]

For microCTs:
* [[Media:Manual_vivaCT_80.pdf |VivaCT80 User's Guide V1.5]]
* [[Media:scanco-manual-vivact40.pdf |VivaCT40 User's Guide V4.05]]
* [[Media:Scanco-manual-uct35.pdf |MicroCT35 User's Guide V4.05]]

==Scanco's FAQ==
Navigate to the manufacturer [http://www.scanco.ch/index.php?id=customer_login Scanco Medical FAQ].

* Username: users@scanco.ch
* Password: basser5dorf

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==Scan==
===Scan SOP===
====Image Quality====
*Refer to [[Media:Scanco-faq-image-quality.pdf|'''Image Quality: Resolution vs. Noise''']] by Scanco Medical.

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====Optimize Control File Settings====
*Refer to [[Media:ControlFileSettingsUserMeeting2014Final.pdf|'''Optimize Control File Settings''']] with regards to resolution, contrast and scan time.

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====Scan materials of different densities====
*Refer to [[Media:UM_HongKong_DifferentDensityMaterials.pdf|'''Scan materials of different densities''']].

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====Optimize Scan for Soft and Adipose Tissue Separability====
*Refer to [[Media:Scanco-faq-adipose-vs-soft-tissue.pdf|'''Scan Protocol Optimization for Soft and Adipose Tissue Separability''']].

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====Measure multiple samples in one scan====

This quite often happens when you want to scan 6 rat bones, for example, but using our six-gun sample holder you scan them in one go. But, you want to analyse them separately, so you have to import the ISQ multiple times as new MEASUREMENTS into each SAMPLE.

There are two options: manual and auto. Read this entire HowTo before proceeding. There is significant potential for mistakes!

<pre>
$ @com:import_manual.com

P1: Measurement Number to duplicate
P2: New Sample Number from Database
P3: New Start Letter of ISQ file
P4: Optional: Operator Number
P5: Optional: Controlfile Number
</pre>

So:

<pre>$ @com:import_manual.com 1234 342 D</pre>

will copy the ISQ from measurement 1234, import it into the database to sample 342, give some feedback lines with 'old' and the new samplename, CHECK IT, and at the end it gives the feedback line on the terminal which you take with the mouse and drop to rename the data over to the new location.

IMPORTANT: BE VERY SURE NOT TO MIX UP MEASUREMENT AND SAMPLE NUMBER !!!

This distiction needs to be VERY clear in your mind! Of course, you can duplicate one scan and give it to the same samplenumber again (e.g. to evaluate different parts of the same sample, and each has its database
entry).

Please build up some system so you see immediately that the right meas. goes to the right sample. E.g. all four bones in one scan have the same part in the name, distinct from other 4 bones. If there is any trace of a doubt later on that somebody MAY have messed up the samples in this duplication step, you'll most probably have to start from scratch again...

Of course, I'll have to make you aware that Scanco declines all responsibility - this program is NOT in the normal user-friendly, quite fool-proof Scanco controlbox, but it's up to you to use it carefully, and not on Friday night when you're sleepy and mistakenly mix up sample and meas. numbers...

The new startletter I built in so you always know which one was the 'original' measurement (which has an RSQ), and which are the duplicated ones.

Backup
And the organization of how you know which duplicated scan is which part is
completely up to you - as well as how you want to handle the backup - our
software allows you to back-up each duplicated scan (but this might be an
overkill, since it's the same ISQ always) so you may choose to delete the
duplicated ISQ by hand in the session manager (only keep the 'original' ISQ), and only backup the .gobj, .aim and _seg.aim etc. (but then you will need to know not to get scared if you retrieve a scan, and the ISQ is missing...) (Or you just 'move to trash' the duplicated scans to nicely delete them with the backup program if you want to remove them completely (but you still have the 3D results in the evaluation database))

Autosubmit

<pre>$ import_autosubmit.com</pre>

Please use the manual one for a while. Then, if you feel comfortable, use the autosubmit one (which also does the last command automatically, the renaming of the isq to the new location.) Because it goes into a batch que, you can quickly submit all duplications, and do not have to wait for the whole file-copying like in the manual one.

One thing you should check there:
$ show que sys$fast/full

This needs to be one single queue (/job_limit=1). In a clustered enviroment,
this might be a '/generic=' que that then gives the jobs to multiple queues in the cluster. This is NOT good. If this is the case, please edit the autosubmit script, and replace sys$fast in the following line at the end by ONE of the generic fast queues, e.g. SC4240_FAST or whatever the name is (preferrable the one computer where also the data disk DK0 is sitting:

<pre>
$!
$ SUBMIT/NOPRINT/QUE=SYS$FAST/DELETE/NOTIFY/LOG=SYS$SCRATCH: 'COMMANDFILE'
$!
</pre>

(Reason: if multiple uct_imports would run at exactly totally the very same time, both jobs might get the same new measurement number... bad...)

I also suggest to add the following line to your login.com

<pre>$ dupl*icate :== @com:import_autosubmit.com</pre>

then you can just start it with

<pre>$ dupl 1234 342 D</pre>

And I also recommend to put into login.com:

<pre>
$ check_dup :== search sys$scratch:import*.log """ name:""
</pre>

(yes, with all these double-quotes)

Then use it to check the feedback that the right scans were given to the right samples.

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===Scan FAQ===
====Unlock a locked controlfile====
If you accidentally locked a controlfile, it is possible to unlock it so that it can again be modified.

Login as the calibration user (Xtremect: calibration; VivaCT40: calib5019; uCT35: calib2339), the password is the same as for the system user, Set priviledges to bypass.
$ spb

Set the controlfile database to the microct, or other, user where the controlfile is locked.
*The file is usually located on (a)disk1:[username.database] and may be accessible using the uctd logical.
*The database file contains the scanner ID (e.g., 3309 for the XtremeCT, note there's no SC before 3309).
$ def uct_controlfiles_database adisk1:[microct.database]uct_controlfiles_3309.dat
$ run ut:uct_upd_controlfiles

Choose the controlfile.Use T and F to indicate true and false.
*YOU MUST SAY YES TO UPDATE CTRL-FILE! There is a bug so do this even if you make a mistake.

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====Warning: Selected operator is not an operator CODE: 24====
You must enter an operator name in the micro-CT control panel.
*You only need to enter the beginning part of your operator name (e.g., Bo for Bone Imaging Lab) or your operator number.
*You can also press "Edit..." and then press the "Find..." and press "OK" to show a list of all the operators that have been registered.

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====Warning: Error assigning IO-channel for UCT_ACQ_LINE, device already allocated to another user CODE: 2112====
Only one person can be given control of the scanner at any time. Most likely the scanning program is already open. Check the minimized icons on the desktop.

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====Error: ROT (M1) end switch detected, Motor stopped CODE: 3031====
We're not sure why motor errors occur occasionally. The solution is to exit the scanning program and turn off the scanner (the switch is on the side of the machine). Wait 30 seconds. Turn the scanner on again. Re-start the scanning program. Wait for the scanner to warm up (20 min).

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====Error: Acquisition error, Buffer overrun CODE: 1005====
This error occurs if the computer hooked up to the scanner is overloaded and does not accept the stream of CT data quickly enough. Check that no large calculations are running interactively (e.g., loading a large dataset into the 3D viewer while the scan is running). If you happen to be there at the very exact second when the buffer overrun happens, do the following:
<pre>
$ show user/node/full !check how many users/processes there are
$ monitor system/int=1 !check the process that is using the most cpu and page file quota
</pre>
Advise lab personal of the problem. If nobody is around, put the output of the above commands into a text document, stop the queues for the computer, and repeat the scan.
<pre>
$ stop/que/next sc5019_fast !for the vivaCT 40
$ stop/que/next sc5019_slow !for the vivaCT 40

$ stop/que/next sceva2_fast !for the µCT35
$ stop/que/next sceva2_slow !for the µCT35
</pre>
When finished, restart the queues that you stopped by <code>$ start/que queue_name </code>.

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====Error: Shutter fail safety test timeout CODE: 2101====
This happens if the scanning program has accidentally be left on overnight and the shutter fail safe test cannot be performed. Ensure that uct_tomography is closed at the end of the day and the scanner computer is logged out at the end of the day to avoid this error.

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====Error: Input error detected, Z protection detected CODE: 4001====
This means the big plate that you can see through the gantry has moved or been touched, activating one of the Z protection switches. This can happen during positioning a patient for a tibia scan if the person's leg isn't pushed into the scanner straight. The cast can potentially touch the plates and cause this error.

In the rare case where this error occurs spontaneously during or at the end of a scan, or during a precalibration, one of the switches may have become activated due to the position of the Z plate. To determine the position(s) this error is triggered, do the following:
<pre>
$ set host 0 Username: calibration Password:

$ sdl
$ spb
$ run um:ccd_2d
</pre>
The Scanco test programs will open. First click on the Reset Z button (upper left corner). Then move the Z slider all the way to the right and hit move. If the Z-protection error appears, record exactly which Z position triggers the error (should be a red number on the left hand side of the slider). When you are done with this test, hit Reset Z again, wait until the motor comes to a complete stop (max. 15 seconds), close the software and in the same terminal by <code>$ logout </code>.

Contact Scanco regarding this error and provide the details from running the ccd program. They will provide further instructions on how to proceed and fix the problem.

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====Fatal: CCD frame timeout, HOTLink reframing CODE: 1007====
Take a screenshot of the error message and email Scanco immediately. Message indicates that X-ray tube is arcing. Try and warm up the X-ray tube again, and notify Scanco if there is any abnormal activity and whether the tube was able to warm up.

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====Fatal: Invalid Scanner ID CODE: 24====
You have logged in with the incorrect user name. End the session and login with the correct user name (vivaCT 40: vivact or invivo; µCT 35: microct or invitro).

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====Fatal: Unable to create shared memory, global page table full CODE: 196====
The temporary fix is to reboot the system. But before you restart, if you have system access, do the following and save the output to a text to send to Scanco.
<pre>
$ set host 0
Username: system
Password:

$ search sys$system:agen$feedback.dat gblpages
$ write sys$output f$getsyi("contig_gblpages")
$ write sys$output f$getsyi("free_gblsects")
</pre>

==Reconstruction==

===Standard Reconstruction===
Scans are automatically submitted for reconstruction, so manual submission is usually only necessary if there was a problem during reconstruction (e.g., a power failure).

*To reconstruct all slices from the RSQ, first delete or rename the old ISQ.
*To reconstruct a selection of slices, a valid ISQ must exist. There is an offset of 1 slice when designating slice selection.
'''General Usage for Interactive Reconstruction''':
<pre>
$ uct_reconstruction P1 P2 P3

P1: RSQ Filename
P2: Slice number (A – all, start:finish)
P3: Log file of batch job
</pre>
'''General Usage for Non-interactive Reconstruction''':
$ submit/noprint/que=sys$slow um:uct_reconstruction.com/params=(DISK2:MICROCT.DATA.00000610.00002449]C000####.RSQ , a)
*Normally jobs are submitted to sys$slow queue instead of running them interactively.

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====Reconstruct a selection of slices====
Here are examples of how to reconstruct a single RSQ file: C0007655.RSQ, sample 4111 and measurement 9899. 
To reconstruct slices 101 to 201 and submit the job to the sys$slow queue:
<pre>
$ submit/noprint/que=sys$slow um:uct_reconstruction.com /log=sys$scratch:reco4111.log/para=(dk0:[microct.data.00004111.00009899]C0007655.rsq, 100:200, sys$scratch:reco4111.log)
</pre>
*The command must be all on one line (or use hyphen), and it wants the 3 parameters: filename, slices, and log.file name

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====Reconstruct all slices====
To reconstruct all slices, use “a” for all slices and submit the job to the sys$slow queue:
<pre>
$ delete C0007655.ISQ;*
$ submit/noprint/que=sys$slow um:uct_reconstruction.com/log=sys$scratch:reco4111.log/para=(dk0:[microct.data.00004111.00009899]C0007655.rsq, a, sys$scratch:reco4111.log)
</pre>
*The .log filename is up to you, as long as it's the same at both places.
*Give full pathname for RSQ file.

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====Reconstruct multiple files====
For multiple files, create a script and submit the job to the sys$slow queue. For example,
<pre>
$ cd sys$scratch
$ eve reco_all.com
</pre>
Or open editor (command 'Edit'), put the following lines in the file and save it as .e.g sys$scratch:reco_all.com:
<pre>
$ uct_reconstruction dk0:[microct.data.00004111.00009899]C0007655.rsq a
$ uct_reconstruction dk0:[microct.data.00004111.00009900]C0007656.rsq a
$ uct_reconstruction dk0:[microct.data.00004111.00009001]C0007657.rsq a
$ exit
</pre>
Save the script and exit the text editor, then submit the job (e.g. to sys$slow):
<pre>
$ submit/noprint/que=sys$slow/log=sys$scratch:reco4111.log sys$scratch:reco_all.com
All the files will be reconstructed as a single job, with one log file.
</pre>

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====Batch reconstruction on XtremeCT2====
The reconstruction software available for the XT2 supports the /batch syntax that replaces reco_all.com.
You can split a manual reconstruction into several jobs using

$ uct_reconstruction DK0:[XTREMECT2.DATA.00001234.00005678]D0123456.RSQ a/batch=16

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====Update to uct_reconstruction V6.2-5, March 2019====

As of March 2019, we should only use uct_reconstruction v6.2-5 on xtremect2.
For studies with baseline and follow-up scans overlapping this time, the old version (V6.2-2) can still be accessed using
<pre>
$ uct_old_recon
</pre>
Changing reconstruction versions can lead to small systematic differences in the result parameters of a trabecular bone analysis. The old version should only be accessed by those who absolutely need to use it. (Scanco recommends re-reconstructing all measurements of a study with version 6.2-5 instead).

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=== Rotated Reconstruction (about z-axis)===
#Use the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] to measure the angle for the rotated reconstruction.
#*To start the program type <code>$ uct_evaluation </code> in a DEC terminal, or use the graph button.
#*Load your sample and select the angle measurement button.
#*Drag the ends and the intersection of the green lines to measure the desired rotation angle.
#:[[File:Angle meas.preview.jpg|600px]]
#Rotate and reconstruct
#*Use <code>$ @com:reco_all </code> to reconstruct all slices.
#*Use <code>$ @com:uct_reconstruction_angle </code> to reconstruct selected slices from an RSQ.
#Use the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] to check the sample after the rotated reconstruction:
#:[[File:Rotated_reconstruction.preview.jpg|600px]]

*'''General Usage''':
<pre>
$ @com:reco_all.com P1 P2 P3

P1: Angle in degrees
P2: Sample number
P3: Measurement number

$ @com:uct_reconstruction_angle.com P1 P2 P3 P4 P5

P1: RSQ Filename
P2: Slice number (A – all, start:finish)
P3: Log file of batch job
P4: Delete log file (true/false)
P5: Angle in degrees
</pre>
*The angle of rotation uses the right-hand rule: a counterclockwise rotation is positive and a clockwise rotation is negative.
*The angle of rotation uses a single decimal place.
*By default the reconstruction jobs will be placed in the sceva3_slow queue.
*Both functions are executed from the measurement directory.

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====Reconstruct all slices====
The following examples are for a 19.1 degree counterclockwise rotation of sample 6876, measurement 15417, C0005086.RSQ.
<pre>
$ @com:reco_all.com 19.1 6876 15417
</pre>
*Delete the ISQ file from the measurement directory.

====Reconstruct a selection of slices====
*A valid ISQ must exist.
*There is an offset of 1 slice when designating slice selection.

To reconstruct slices 36 to 41:
<pre>
$ @com:uct_reconstruction_angle.com DK0:MICROCT.DATA.00006876.00015417]C0005086.RSQ 35:40 sys$scratch:reco610.log true 19.1
$ @com:uct_reconstruction_angle.com DK0:MICROCT.DATA.00006876.00015417]C0005086.RSQ 35:40 "" "" 19.1
</pre>
*"" is used as a null input for optional parameters.

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===Other Reconstruction===

====Reconstruct at a new voxel size====
See a script in:
DISK1:[XTREMECT2.EVAL]UPDATE_HEADER.COM

This script includes the following type of information:
$ r ut:updh_voxelsize.exe
DK0:[XTREMECT2.DATA.00000010.00000050]D0000068.RSQ
122
82000
1706
$ r ut:updh_voxelsize.exe
DK0:[XTREMECT2.DATA.00000011.00000054]D0000072.RSQ
122
82000
1706

This is what one would do in a terminal. The only requirement is that this <code>updh_voxelsize.exe</code> cannot be executed as the normal user.
Prior to that, one has to log as calibration, and do:
$ set proc/priv=bypass

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==Manipulate RSQ==

===View RSQ projections and flat field===

It can be very useful to examine the projections that are contained in the RSQ file, as well as to see the flat field correction frames.

In the session manager, double click the RSQ file and the program ximage will open. Or, type:
$ sh sym x
X == "$UM:XIMAGE.EXE"
$ x D0000018.RSQ
Then switch to xz view and go to the second slice (in this order). Then you should see a frame of the none attenuated beam (nothing in the beam, or Scanco calls it the I0 frame). If it is a multi stack measurement then there will be several copys of this frame in this image.

In an RSQ you have for each slice of the detector one dark current line and then the full intensity line followed form the radiographs taken under the different angles (sinogram). In the x direction is the detector line, in the y direction is the rotation angle (except dark and I0) and in the z direction is the z-direction of the scanner. If you switch the view to xz, then you can see the frames as acquired by the detector (or stacked frames all taken under the same rotation angle). Frame 1 is then the dark image and Frame 2 is the full intensity image.

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===Convert RSQ to AIM===
<pre>
$ ipl
ipl> rsq_to_aim in YP_IGFAMOTION_003_6.RSQ
-pos [0 0 0] >
-dim [-1 -1 -1] >
-convert_to_pro [false] > true
-sinogram_not_frames [true] > true
-div_unsigned_by_2 [false] > true

ipl> write
-name [internal_name] > in
-filename [default_file_name] > YP_IGFAMOTION_003_6_rsq.aim
-compress_type [bin] > none
-version_020 [true] >
</pre>

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===Convert RSQ to PSQ===
First, in the terminal turn on the 'advanced questions' mode
<pre>
$ define uct_reconstruction_calibration true
</pre>
Second use the reconstruction EXE to convert RSQ to PSQ
<pre>
$ run UCT_RECONSTRUCTION.EXE
raw file: DISK3:[MICROCT.PROJECTS.YVES.LANDMARK.RAW]filename.RSQ

Give slice number, or 'a' for all
hit return a few times

Write Projection [N]: -> say y and it writes the PSQ and continues with reco
Say p if it shall just produce PSQ and NOT continue with reco!
</pre>
Beam hardening correction can be turned off by doing
<pre>
$ DEFINE UCT_RECONSTRUCTION_CALIBRATION TRUE
$ define uct_disable_bh_correction true
$ deass UCT_BEAMHARD_POWER
$ deass UCT_BEAMHARD_factor
</pre>
and then run <code>uct_reconstruction</code>

The RSQ contains the RAW projection data. The PSQ represents tilted parallel beam projections:

[[Image:CB-Rebinned.gif]]

The rebinning process reduces the number of projections from 836 (1 bright field, 1 dark field and 834 projections spaced at 0.24 deg/proj, spanning 200.16 deg) to 750 (spanning 180 deg) with a resolution of 0.24 deg. In addition to the geometric changes, intensities are adjusted ln(I/I0) and beam hardening correction is applied. After converting a PSQ to AIM with IPL, an image can be reconstructed with Matlab's iradon(), note that only the central slice will be geometrically 'correct', but differences in other slices are small (Circumference of calibration phantom differs less than 1%). in the final reconstruction these effects are accounted for reducing the number of z-slices from 124 (acquired) to 110 in the reconstructed image.

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===Measure RSQ motion artifact===
Based on RSQ data, in-plane translation and rotation, and longitudinal translation can be determined.

The RSQ is first converted to a tilted parallel-beam sinogram. Motion is measured using the bonelab_measuremotion command in the Calgary extension of IPL installed on percy. Copy the motion scripts available in <code>DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]</code> to your COM directory. Here is how they work:

* RSQ_TO_PSQ.COM;1 - (optional) convert RSQ to PSQ, PSQ gets created in the same directory as RSQ. Usage:

<code>$ @rsq_to_psq.com DK0:[BRUNO.DATA.00000162.00009479]C0008921.RSQ</code>

* IPL_MEASUREMOTION.COM;2 - Takes a PSQ and measures motion using Calgary IPL on percy

<pre>
$! example of how to submit a motion measurement
$ SUBMIT/NOPRINT/QUE=SYS$FAST /LOG=SYS$SCRATCH: -
DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]IPL_MEASUREMOTION.COM -
/PARAM=(DISK3:[MICROCT.PROJECTS.DEVEL.RECO_TEST.RAW]PHANTOM_NOMOTION.PSQ) -
/LOG=DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]MEASUREMOTION.LOG
</pre>

Results are save in <code>MEASUREMOTION.LOG</code> and the following section contains all information:
<pre>
/bonelab_measure_motion
-input org
Motion:
Translation = 2.135364
Rotation = 0.024216
Index = 3.694660
Translation weight = 0.943156
Rotation weight = 69.403737
Z_motion = 2.274551

Use the line below with search.
Translation,Rotation,Index,Trans_weight,Rot_weight,Z_motion
2.135364,0.024216,3.694660,0.943156,69.403737,2.274551

Use the line below for DB entry (Index*100).
db_motion_index=369.466034
</pre>

In-plane translation is '''Translation''', in-plane rotation is '''Rotation''' and longitudinal translation is '''Z_motion'''. '''Index''' is the total in-plane motion as used in the IEEE ISBI 2009 paper by linear combination using the weights, not used any more, now we use in-plane translation only. '''db_motion_index''' is the motion index value multiplied by 100 and that could be written to the patient database. Multiplication by 100 is necessary since the motion field in the database is integer only.

For more background on the algorithm look at ''Pauchard Y., et al, Measuring patient motion in HR-pQCT, IEEE ISBI 2009'', and ''Pauchard Y., et.al., Automated quantification of three-dimensional subject motion to monitor image quality in high-resolution peripheral quantitative computed tomography, Phys Med Biol. vol. 56, pp 6523-6543, 2011''. '''IMPORTANT''': The IPL implementation has not been validated against the Matlab implementation used in these publications. Motion Values can be different. Values can be automatically extracted as described below.

* RSQ_MEASUREMOTION.COM;10 - The full deal: creates PSQ and measures motion all in the same directory as the RSQ.
<code>
@DISK3:[MICROCT.PROJECTS.RESCAN.COM]RSQ_MEASUREMOTION.COM DISK3:[MICROCT.PROJECTS.RESCAN.RAW]M0003508.RSQ;1
</code>

Make sure to adjust the line:
<code>$ SCRIPTFILE := DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]IPL_MEASUREMOTION.COM</code>
to the location of your <code>IPL_MEASUREMOTION.COM</code>.

The results are stored in the same directory as the RSQ in <RSQname>MOTION.LOG and can be extracted into motion_all.txt by running the search command:
<pre>search/output=motion_all.txt/window(0,1)/match=OR *motion.log "Translation,","Patient Name "</pre>

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===Update RSQ's Center Information===
<pre>
$ set host 0
username: calibration
password:
$ spb or $ set proc/priv=bypass
$ run [.util]updh_center
Raw-Data-File: enter location of raw data (with directory if necessary)
Center X: [15430]: enter new center value (e.g. 15415)
Press return for all other options.
</pre>

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===Determine RSQ's Centre Calibration Values===
<pre>
$ define uct_reconstruction_calibration true ! Note: do not mistype... or the calibration program will not run
</pre>
In the SAME terminal:
<pre>$ uct_reconstruction dk0:[microct.data.00004026.00004576]c0001344.rsq
Slice-Nr. [0...919] (Neg. to stop): 100
Center [207]: here enter a new number
</pre>
Hit return a few more times to use default values for other options.
<pre>
XtremeCT check these values, that they do not change:
Maximal possible Scan-Distance (mm) = 125.9520
Cropped adjusted Scan-Distance (mm) = 125.9520
See that it does not change, e.g. drop to 124 mm or such...
</pre>
Then do that again, $ uct_reconstruction ....rsq 100 (for the first time, for each file/scan).

Double click on ISQ. slide to slice 101 (!) (100+1, since terminal zero based) compare with image in e.g. slice 100 or 99 (disregard funny half image shift...)

Should already look nicer.

Then try out with e.g. center 230 or so, with e.g. slice 101 (thus slice 102 in Ximage). (now, only one run is necessary)
<pre>
compare against image with center e.g. 200.
continue at libitum until you find the best center, the crispest image.
</pre>
Usually the centre is determined to within about 3 to 5 points (which is 0.3 to 0.5 pixels), so e.g. test 225 and 230, and maybe 228.

Write down your favourite.

If you cannot decide: let Andres know which ISQ slice was reco-ed with which center (in 'Ximage' slice numbers), and I can check - but since remote Ximage is SOOO slow, thanks for only pointing out a few options, I cannot check 20 settings...

Then continue with next diameter scan (the first time for each scan, reco twice again)

The different diameter centers should be a steady function, so all the new center values should be increasing as diameter decreases.

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===Modify RSQ's BHC for in-air scans===
This is necessary because the beam-hardening correction factor assumes scans were done in soft tissue. It is necessary to choose calibrations of 1200 or 700, instead of the default 200.

Currently, the XtremeCT has options for 200 (standard) or 1200 calibration (in air).

To do this, log in as users <code>calibration</code> and then:

<pre>
$ set proc/priv=bypass ! as user calibration; modification of MICROCT user data
$ run ut:UCT_EXT_HEADER_ADD_CALIB.EXE
> Raw-Data-File []: DISK2:[MICROCT.DATA.00000401.00001495]C0001404.RSQ
> ...
> Add another BH-Corr from file again? (Y/N) [N]: ! Enter yes (UCTD:UCT_BH_COEFF_60KV_1200HA_3309.TXT)
</pre>

Then, delete the old ISQ. It must be deleted or else the header information will not be changed. Finally, reconstruct the new ISQ and analyze...

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==Manipulate ISQ==

===Read an ISQ header===
You can either read using the standard tool

$ ctheader C0014141.ISQ
$ sh sym ctheader
CTHEADER == "$UT:CTHEADER.EXE"

Or, use the extended header tool to show the calibration data

$ run ut:uct_ext_header_display.exe

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===Import ISQ===
When you import, please note that the sample number AND measurement number are updated, so meas 10907 is now 10908.

Suppose you have a sample 3000, meas 10000, C0001234.isq, and want to import this into sample 3001, this is what I would do:

To make a copy of the scan (i.e., keep it in sample 3000 and make another copy in 3001)
<pre>
$ cd *3000*10000
$ copy C0001234.isq D0001234.isq, also copy any other files you want imported (RSQ, GOBJs, etc)
$ import

UCT_IMPORT V1.2

---------------

ISQ-file []: D0001234.ISQ

Sample number [0]: 3001

Change File Header name [Y]: Y

Optional: Operator Measurement [0]: 1 (1 = bonelab)

Site 20 Radius L

Optional: Controlfile Nr. [0]: (change if desired)

Execute Rename Command [Y]: Y
</pre>

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==Image Artifacts==
===Ring Artifact===
*Refer to [[Media:Microct_ring_correction.pdf|'''MicroCT Ring Correction''']].

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===Partial Volume Effect===
*Refer to [[Media:Partial_Volume_Effect.pdf|'''Partial Volume Effect''']].

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===Beam Hardening Correction (BHC)===

====Use the right BHC====
*Refer to [[Media:Beam_hardening_correction.pdf|'''Use the right beam hardening correction''']].

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====Understand Scanco BHC====
If you see lines like 'CCD_CORR: Expand BH-corr to1536' etc. etc.:

then we do a polynomial correction:
<pre>
$ dir uctd:*bh_coeff*.txt
</pre>
and you see a file with the scanner ID.

<pre>
--> $ type uctd:UCT_BH_COEFF_60KV_0200HA_3309.TXT

-->
! Function 9 is Addpolynom
Function: 9 A
0: 3 0.00000000 -0.38599902 0.30870225 -0.06162301
--> 0: for all pixels. 3 --> 3rd degree polynom, with factors:
x^0 = 0
x^1 = -0.38...
x^2 = 0.308...
x^3 = -0.061...
</pre>

This polynom is added to the PROJECTION value (not the raw counts).

the BH-corr is doing a 'linearization', e.g. see

http://iospress.metapress.com/content/twcxb9jfk8knhpq2/

for more info.

The values in the middle of the scan are amplified more - not just because of their position, but because the object is thicker there, thus the projection values are higher, thus the correction term is higher.

NOTE : Linearisation, as used by Scanco, will compensate 'soft-tissue' beam hardening (inside of water phantom appears LESS dense). Bone related beam hardening, e.g. soft tissue near skull appearing MORE dense, will NOT generally be compensated. See Kak and Slaney 'Principles of computerized tomogprahic imaging' and Joseph and Spital J Comp Assist Tomo 1978 vol 2 for more information.

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=Evaluation=

==Analysis Topics==

===Cortical thickness analysis in standard evaluation===

!!Note - with ipl v5.42 this should be changed to <code>/dt_cortical_thickness</code>

Use the IPL command <code>/dt_cortex_obj_param</code> to measure cortical thickness using direct methods.

When extracting the results from the database using <code>uct_list</code>, specify the <code>UCT_3D_LIST_W_CTH.TXT</code> template in directory <code>DISK0:[MICROCT_COMMMON.UIL]</code>.

<pre>
$ uct_list
UCT_LIST.EXE Version V5.1
Template-File [UCT_3D_LIST_SHEET]: DISK0:[MICROCT_COMMON.UIL]UCT_3D_LIST_W_CTH.TXT
</pre>

UCT_3D_LIST_W_CTH.TXT is now the default template as of March 2009.

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===Cortical porosity and finite element analysis on XtremeCT===

* This procedure is broken down into 3 separate components
* All Scripts mentioned be copied directly from DISK3:[MICROCT.PROJECTS.KYLE.SCRIPTS]
* Files should be copied from data to projects prior to running analysis (see bonelab procedures.doc on sodor)

1. Autocontour the image 
2. Calculate and extract cortical measurements 
3. Create FE files and run FE 

====Autocontour====
* The main autocontour script is located in the ue: directory, this should NOT be modified!
* The procedure is executed using a "hijack" script [[Media:HIJACK_AUTOCONTOUR.TXT|'''HIJACK_AUTOCONTOUR.TXT''']], but the filename must be changed to .COM or found in the directory mentioned above.
* Files should already have a _SEG.AIM created and should be in the same directory as the raw .AIM file.

* You then create a SUBMIT.COM script as you would for other files. For example:
$ QQ = "SUBMIT/NOPRINT/QUE=SCEVAL_FAST/LOG=SYS$SCRATCH com:HIJACK_AUTOCONTOUR.COM"
$ 'QQ' /PARA=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.MODELS]'''FILENAME'''.AIM

* This command will then create various files for examination and further analysis. These include:
** FILENAME_COMBI.AIM - shows cortical, trabecular, and pores all in different colors
** FILENAME_COMBIPO.AIM - shows only the cortex with porosity as different color
** FILENAME_CRTXFILL.AIM - gives sold mask of cortex, porosity filled (can be used to calculate Ct.Th)
** FILENAME_CRTXPO.AIM - shows only the pores
** FILENAME_TRAB.GOBJ - gobj of trabecular region
** FILENAME_CRTX.GOBJ - gobj of cortical region
** FILENAME_AUTO2.GOBJ - gobj of whole bone region

* Further technical details and references can be found in the following publications:
** Buie, H., Campbell, G., Klinck, R., MacNeil, J., & Boyd, S. (2007). Automatic segmentation of cortical and trabecular compartments based on a dual threshold technique for in vivo micro-CT bone analysis. Bone, 41(4), 505-515.
** K.K. Nishiyama, Macdonald, H., Buie, H., Hanley, D., & Boyd, S. (2010). Postmenopausal Women With Osteopenia Have Higher Cortical Porosity and Thinner Cortices at the Distal Radius and Tibia Than Women With Normal aBMD: An In Vivo HR-pQCT Study. Journal of Bone and Mineral Research, 25(4), 882-890.

====Evaluate Cortex====

*This Step 2 method of doing the cortical analysis is no longer used now that we have the IPL_UPAT_CALGARY_EVAL_XT1.COM or XT2.COM version. The problem with this approach is that it is a Frankenstein of the standard analysis and the advanced analysis. The cortical bone assessment is correct, but the trabecular compartment from the standard analysis is not a perfect match. Instead, we should be using the GOBJs described in IPL_UPAT_CALGARY_EVAL_XT1.COM so that we have a perfect mix.

Nevertheless, we keep this information here for now for posterity.

*After the autocontour is computed we used to call IPL_EVAL_CORTEX.COM that will calculate the cortical parameters:
**Cortical porosity (%)
**Direct cortical thickness (mm)
**Cortical density (mg HA/ccm)

This WAS called as the following:
$ QQ = "SUBMIT/NOPRINT/QUE=SCEVAL_FAST/LOG=SYS$SCRATCH com:IPL_EVAL_CORTEX.COM"
$ 'QQ' /PARA=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.MODELS]'''FILENAME.AIM''' -
/LOG=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.LOG]'''FILENAME'''_EVAL_CRTX.LOG

* The results of this script are outputed into individual log files for each file being evaluated.
* To extract these results into one file use:
$ search/output=output_results_filename.txt *EVAL_CRTX.LOG "!% ov/tv","!> C.Th","!% mean_unit"
*A learn command in the eve editor can be used to extract the specific results desired:
**!% ov/tv is the amount of bone in the cortex (ie. 1- ov/tv = cortical porosity)
**!> C.Th is the direct cortical thickness in mm
**!% mean_unit is the cortical density in mg HA/ccm

====Create and run FE models====

*The most current common FE model to run is a homogeneous model where all elements have the same material properties and the cortex and trabecular regions are labeled separately in order to determine the percentage of load carried by each region.
*The other option is to create a model where the material properties are scaled based on the density values and scripts for this can be found in the COM directory.

*The script IPL_FEM_HOMOGEMOUS_LS.COM will use files created by the autocontour and appropriately label the cortex and trabecular regions as well as remove any disconnected pieces of bone.
$ QQ = "SUBMIT/NOPRINT/QUE=SCEVAL_FAST/LOG=SYS$SCRATCH com:IPL_FEM_HOMOGENOUS_LS.COM"
$ 'QQ' /PARA=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.MODELS]'''FILENAME'''.AIM

*Files will now be created with the suffix _HOM_LS.AIM and can be moved to Mighty-Mac or Mavis for FE analysis. You will require user accounts for these computers and can contact Eric or Steve. If using FTP be sure to transfer the files in binary mode (further documentation on this can be found in this Wiki)

*[[Media:2009-10-15_FEM_Tutorial.pdf|'''FEM tutorial main steps''']] to submit the FE files with a detailed manual is recommended for first time users.
*This is now out of date, but is kept here because it still contains useful information about preparing AIM files and post-processing.
*For running the FE itself, please refer to the current manual at [[FAIM Finite Element Solver]].

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===Cortical midshaft analysis with moment of inertia calculation===

This explains what happens when you type

<pre>
$ midshaft ! or
$ eval_midshaft
</pre>

Draw a rough contour around your slices: open the Contouring Sub-window, double-click on the big image, and it automatically finds the best contour. Then click on 'Selection' 'Forwards', then 'Iterate Forwards'.

Then 'cancel' the contouring sub-window, and start the 3D evaluation. Make sure you have already set the correct threshold, sigma, support in file
<pre>DISK2:[MICROCT.EVAL]IPL_FIXED_BATCH_MIDSHAFT.COM</pre>

When you type

<pre>$ show queue</pre>

you should find a job called UCT_EVALUATION_MIDSHAFT and a SYS$SCRATCH:*_MIDSHAFT_*.LOG

The IPL_FIXED_BATCH_MIDSHAFT.COM by default does not calculate the direct measurement results because you must have many more than 20 slices for these to be valid. You can uncomment these parts of the file if you contoured the whole stack (i.e., stack thickness is >> than cortex thickness).

TILDE: Note that you will see lots of tildes (~) on the result sheets. This is to tell you that, if the measurements were trabecular bone, those values would only be approximate. But now for the cortex, they are actually correct! (see below for more explanation about this) I would now use the tildes to check the 'excel' table that the operator has taken the correct script for the trab. or cort. evaluations for the respective measurements!

So what's the advantage of all this? Now, also VOX-TV is correct! So VOX-TV is the whole area, VOX-BV the doughnut, so TV - BV is the marrow area! And still, TRI-Tb.Th is the cortical thickness (TRI-TV is NOT correct, because the .gobj feature was turned off).

I say 'area' above: depending on how many slices one individual scan has,
VOX-BV (and VOX-TV) might be different for different scans, so you will HAVE to
convert the volumes to area again:

<pre>
volume equals area times height
--> Bone Area = VOX-BV / height = BV / (dim.z * el_size_mm.z)
</pre>

and same for Total area, of course :-)

POROSITY: If you want porosity of the bone itself draw two contours: one around, counter-clockwise, on on the inside, clock-wise (thus a 'negative', excluding contour). Now, TV will be just that ring area, BV will be the bone within that ring area, and BV/TV will be 1 - porosity, thus BV/TV 94% means 6% porosity.

METAPHYSIS: Application of this script to metaphysis scan (with trab. in middle):

<pre>
$ midshaft
</pre>

Draw one contour around the cortex, and in the same slices, a NEGATIVE contour on
the inside (CW contour) to exclude the trabecular bone. You may potentially work with the BP (break-point) system to be able to morph the negative contours, even though there is already an 'outer' contour around the bone in every slice.

Start 3D eval, read out the data-base with <code>$ uct_list</code>.

NOTE: You CANNOT give the .gobj a special name such as c0001234_cortex.gobj if you are using the automatic evaluation button on UCT_EVALUATION. Only after the eval (or midshaft eval) has finished, you may copy it to a more meaningful name, but all of the evaluations are just taking the STANDARD gobj name!

Afterwards (after renaming or copying the _seg.aim to _cortex.aim, and .gobj to _cortex.gobj), you may want to start the very normal eval with normal (inner) contours to evaluate the trabecular compartement.

<pre>
Remember: the values in our 3D result database then are OVERWRITTEN.
</pre>

If you have a large study, I would recommend to run the $ midshaft for ALL
samples, <code>$ uct_list</code> to e.g. <code>sys$scratch:mystudy_cortex.txt</code>,
rename/copy gobj and seg for all, and THEN run the trabecular evaluation for all samples. <code>$ uct_list</code> and you have two nice complete excel sheets.

NOTE ON PLATE MODEL: More explanations of why the plate model is correct

Assume a ring (cortex).

<pre>
Area = thickness * 'middle line'.
'middle line' = average of outer and inner circumference
--> 'middle line' = 0.5 * 'bone surface'

--> thickness = bone volume * 2 / bone surface.
</pre>

And this is nothing else but the 'plate model' formula for Tb.Th!

NORMAL TRABECULAR EVALUATION? And why not just run the 'normal trabecular eval'? Because in the 'normal' TRI calculation, we are EXCLUDING all surfaces that are created artificially by a gobj line that cuts through a trabecula.

However, for the midshaft, this means the whole outer (or even inner, if also
inner contour is there) is SUPPRESSED, because it is touching the gobj line. So
this is where that midshaft script comes in: it turns off that suppression.

MORE EXPLANATIONS: Why the direct DT-Tb.Th* is NOT correct for a scan with
just 12 slices.

If we fill the structure with spheres, those spheres should be bounded by the
width of the cortex, not just by the fact that we only have 12 slices (and even more so, we are always doing 'aim box' suppression with the spheres) if a sphere touches the boundary of the aim box, it is suppressed!

So this is quite crucial for Tb.Sp and Tb.N. To get meaningful Tb.Sp, you would
need a LOT of slices. Also, then, you cannot have the inner contour - otherwise
the negative inner contour will delete the Tb.Sp. spheres.

If you have enough slices, you may opt to turn the <code>/dt_object</code> on again in the
midshaft script (second half). Then DT-Tb.Th* and TRI-Tb.Th just have a slightly different behaviour if there are little pores within the cortex:

<pre>
TRI: the little pore just adds a little BS, thus the influence is not that big.
DT: the little pore cuts the thickness sphere in half, thus at that location, the thickness is halved.
</pre>

MEAN1 and MEAN2: The script is also calculating Mean1 and Mean2 now.

<pre>
Mean1: 'apparent' density, average over whole TV
Mean2: 'tissue' density: average over what was segmented as bone only.
</pre>

These mean values will be in mg HA/ccm if you have the calibration option for bone density installed (and activated for those scans). Remember: the bone has to have some soft-tissue (or equivalent) on the inside, and preferably also on the outside then.

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===Joint Thickness Measurements===
*Sample script to search histogram files for results: [[Media:Summarize_Joint_Th_Measurements.pdf|Summarize Joint Th Measurements]]

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===Scanco Joint Space Width (JSW) analysis===
The scripts published in [https://doi.org/10.21037/qims.2019.12.11 Stok et al. 2020], and released by Scanco, are available for XCT1 and XCT2.

On XCT2 they have been installed as Tasks #112 to #116.

Instructions to run this analysis are available here [[Media:ESD_Joint_Space_Width_v2.3.pdf]].

The full citation for this work is:
<pre>
Stok KS, Burghardt AJ, Boutroy S, Peters MPH, Manske SL, Stadelmann V, Vilayphiou N, van den Bergh JP, Geusens P, Li X, Marotte H, van Rietbergen B, Boyd SK, Barnabe C; SPECTRA Collaboration. Consensus approach for 3D joint space width of metacarpophalangeal joints of rheumatoid arthritis patients using high-resolution peripheral quantitative computed tomography. Quant Imaging Med Surg. 2020 Feb;10(2):314-325. doi: 10.21037/qims.2019.12.11. PMID: 32190559; PMCID: PMC7063288.
</pre>

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==UCT_EVALUATION==

===UCT_EVALUATION SOP===
====Start 3D evaluation from terminal for XtremeCT II====

Logged into the terminal as "xtremect2" you can see the evaluation scripts in <code>IDISK1:[XTREMECT2.EVAL]</code>

The morphological evaluation: Control file #25. It basically runs auto contouring (#23) and then the morphological analysis.
* <code>UCT_EVALUATION_V6_XT2_DT61.COM</code>
* <code>IPLV6_EVAL_CORT.COM</code>
* <code>IPLV6_EVAL_TRAB.COM</code>
* <code>IPLV6_EVAL_TOTAL.COM</code>

* <code>UCT_3D_LIST_CORT_XT2.TXT</code>
* <code>UCT_3D_LIST_TRAB_XT2.TXT</code>
* <code>UCT_3D_LIST_TOTAL_XT2.TXT</code>

Contouring scripts:
* <code>IPLV6_AUTOK.COM</code>: Creates automatically the standard GOBJ. Control file #22.
* <code>IPL_AUTOK_CTTB.COM</code>: Creates automatically the CORT, TRAB and PORE.GOBJ (previously CRTXPO). Control file #23.
* <code>IPLV6_AUTOK_CTTB_CORR.COM</code>: Creates automatically the CORT and PORE.GOBJ, after manual correction on the TRAB.GOBJ. Control file #24.

Laplace- Hamming scripts:
* <code>IPLV6_UPAT_EVAL_LH61_XT1DB.COM</code>
* <code>IPLV6_UPAT_EVAL_LH82_XT1DB.COM</code>

Results will be generated in the <code>IDISK2:[XTREMECT2.RESULTS]</code> directory, in the same way as they are generated for the cortical analysis on XtremeCT I, i.e. using the uct database and appended text files.

Laplace Hamming evaluations will generate results in the upat_list database. The direct measurements will be stored in the uct_list database.

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====Symbols for XtremeCT II vs XtremeCT I====
<code>microct</code> account you get

"MICROCT_BIN" = "DISK1:[MICROCT.]" (LNM$PROCESS_TABLE)
= "DISK0:[MICROCT_COMMON.3309.]"
= "DISK0:[MICROCT_COMMON.]"

for <code>xtremect2</code>

"MICROCT_BIN" = "DISK1:[XTREMECT2.]" (LNM$PROCESS_TABLE)
= "DISK0:[MICROCT_COMMON.]"

So 3309 has its own directory where the software versions for the two scanners are different, e.g.

xtremect: DISK0:[MICROCT_COMMON.][MAIN]IPL_SCANCO_M.EXE
microct: DISK0:[MICROCT_COMMON.3309.][MAIN]IPL_SCANCO_M.EXE

We have defined some symbols for the different ipl versions:

IPL
IPLREG
IPLFE
IPL_BATCH
IPLREG_BATCH
IPLFE_BATCH

In the scripts you can directly use these symbols instead of ipl_scanco_prog (old style).

IPL and IPL_BATCH are different for the two scanners because the newest version is not officially released for XT1.
IPL of the microct account (XT1) cannot read data of the xtremect2 account (XT2). The other way around it works.

IPLREG and IPLREG_BATCH point to <code>$DISK1:[XTREMECT2.MAIN]IPL_SCANCO_REGIS_V107.EXE</code> for both accounts.

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====Start 3D evaluation from terminal for microCTs====

[[Image:Bones2.jpg|20px]] Warning:Do not change <code>uct_evaulation_v4.com</code> and <code>ipl_fixed_batch_v4.com</code> in .eval, but only work on your own file (i.e., eval_steve).

First, an explanation of how the normal evaluation runs by hitting the 'Start 3d' button.
<pre>$ scanco_submit_command ue:uct_evaluation_v4.com/para=(xxx,yyy,zzz,…)</pre>
There are 8 parameters:
*P1: number of print outs of our results sheet
*P2: the ISQ filename
*P3-5: start x (pos x), y, z
*P6-8: dim x, y, z
The parameters p3-p8 come from the white bounding box. The problem is that when you start from the terminal you do not have these. This problem can be overcome by using the <code>isq_to_aim_gobjbox.exe</code> and then give the relevant parameters. You can
<code>$ run um: isq_to_aim_gobjbox.exe </code>
to see what it's asking for.
By using gobjbox you do not need p3-p8. Therefore you can start the evaluation by giving:
<pre>$ scanco_submit_command ue:uct_evaluation_special_josh.com –
/para=(1,dk0:[microct.data.0000275.0000245]c0000332.ISQ)</pre>
*You can make <code>uct_evaluation_special_josh.com</code> such that there is no need for P1 (change p2 to p1 in the script, etc).
*Alternatively to using the gobjbox you could use the normal isq_to_aim, but hard code the dim and pos.
*Then call whatever IPL files you want to call. Look into <code>fixed_batch_v4</code> to see how we turn on the database always on the first line of every IPL part, and how we calculate parameters.

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====Temporarily change evaluation for UCT_EVALUATION====

In a terminal window, we need to redefine the logical that determines which
3D evaluation is associated with the <code>UCT_EVALUATION</code> tool.

For example, typing <code>VOI</code> runs the <code>UCT_EVALUATION</code> tool
by executing <code>UE:UCT_EVALUATION_VOI.COM</code>

Type
<pre>$ show logical UCT_EVALUATION</pre>
and then you can redefine this to point to another evaluation script.
<pre>$ define UCT_EVALUATION UE:UCT_EVALUATION_CUTOUT.COM</pre>

This is only redefined in the particular terminal you are using, and it
will reset to its default in a new terminal. It will also not work if you
try to submit the job to a queue. It only works interactively.

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====Assign special evaluation to UCT_EVALUATION====

'''Warning''': This is for advanced users ONLY. Do not attempt this without contacting Steve!

This will show how to set up <code>$ eval_kyle</code>:
It is easy to set up multiple .COM files for the 3D evalulation tool, one such set-up is already prepared on your computer:
<pre>
$ eval_special
</pre>
will do something similar to <code>$ voi</code> where the normal contour program opens, but if you start the 3D eval, the special script <code>um:uct_evaluation_special.com</code> is called (associated with eval_special), which then in turn calls <code>ipl_fixed_batch_special.com</code>, where you can specify your own set of thresholds, etc.

So it is a daisy chain of files which we will need to follow to set up a special <code>xxx_kyle.com</code> script, and where ever we encounter <code>_special.com</code>, we copy and change it to <code>_kyle.com</code>.

So to set up <code>$ eval_kyle</code> you will need to do the following:

*1. Edit <code>disk1:[microct]microct_setup_user.com</code> (double-click on file), please be careful here, it's very important! (and I hope you have done your 'weekly full backup' regularly, so you could always retrieve a good version of login.com...)

*2. Then, towards to bottom and duplicate the line
<code>$ eval_special :== @com:eval_var.com um:uct_evaluation_special.com</code>
and change duplicate to
<code>$ eval_kyle :== @com:eval_var.com um:uct_evaluation_kyle.com</code>

This will make this command <code>eval_kyle</code> available after you login freshly. Save and Exit.

*3. Then go to <code>disk1:[microct.eval]</code> and copy the file <code>uct_evaluation_special.com</code> to the name <code>uct_evaluation_kyle.com</code> ('Commands', 'Copy ...', BUT CLICK ON THE THREE DOTS and give new output name.
If you do not see the <code>eval_special:</code> go to terminal, <code>$ dir ue:*special*.com</code> and take it from the <code>microct_common</code> directory)

*4. Edit the <code>_kyle.com</code> file: at the top, change <code>ipl_......_special.com</code> to <code>_kyle.com</code>

*5. Copy <code>ipl_fixed_batch_special.com</code> to <code>ipl_fixed_batch_kyle.com</code>

*6. Edit <code>ipl_fixed_batch_kyle.com</code> to your liking. If you want <code>$ eval_kyle</code> to not perform the full evaluation, but only something akin to <code>voi</code>, then, in the steps above, copy <code>uct_eval_voi.com</code> to <code>uct_evaluation_kyle.com</code>, and <code>ipl_voi.com</code> to <code>ipl_fixed_batch_kyle.com</code> (thus you take the <code>voi</code> script as template for the <code>_kyle</code> script).

*7. Then open a new terminal ('applications', 'decterm'), <code>$ eval_kyle</code> should work now!

'''Notes''': When you start the 3D eval, then
<code>$ que</code>
will show you your batch job with your name on it now!

And now a few more explanations how the whole thing works: in all eval programs, hitting 'Start 3d' just submits the logical <code>uct_evaluation</code>, <code>$ show log uct_evaluation</code> shows you that by default, this points to <code>ue:uct_evaluation_v4.com</code>.

Those little <code>voi</code> and <code>eval_steve</code> scripts then just temporarily redefine this logical so that a different script is submitted when you <code>'start 3d eval'</code>.

About the '''corelut eval''': Then we start a whole different eval program: the <code>.exe_corelut</code>. So, if you set up a <code>eval_steve_c</code> (or whatever you want to call it): Produce a <code>eval_var_c.com</code> in the directory commands (maybe copy from microct_common to [microct.commands]), and there, on the last line, instead of starting
<code>$ uct_evaluation</code>
(the normal program), replace by
<code>$ evalc</code>
which starts the <code>.exe_corelut</code> - and because the <code>eval_var.com</code> has over-ridden the <code>uct_evaluation</code> logical just before, then you are starting different script upon starting 3d eval.
NB: we have a logical AND a symbol called <code>uct_evalution</code>. Sorry for confusion. Symbol <code>uct_evaluation</code> starts normal <code>eval</code> program, so this is what you replace by symbol <code>evalc</code> now).

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===UCT_EVALUATION FAQ===
====Warning: Not all required GOBJ files found, Continue anyway?====
This occurs when the chosen evaluation script is looking for a contour file, but can't find it.
*To see what contours the script is looking for go to "File" then "Save GOBJ As...". You can now see the list of required gobj files.
*For some scripts, it may not be necessary to supply a gobj and you can continue with the evaluation without it. For example, the "3D Segmentation of VOI, 1 solid object" applies the contour to isolate the region of interest, however, this may not be necessary if the object of interest can be extracted from thresholding.
[[File:Save_gobj_as.jpg|400px]]

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====Warning: Attempt to access non-existent record CODE: 36====
The scan is most likely still in the process of being reconstructed. Try to access the scan again in a few hours.

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====Error: Insufficient logical unit numbers CODE: 1409716====
Exit the evaluation program and restart it.

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====Error: Process quota exceeded====

[[Image:Process_quota_error.JPG|300px]]

When running UCT_EVALUATION from a dec terminal, an error when starting an evaluation may occur if there are to many dec terminals opened.
*The easy fix for this is to open the terminals from the applications menu in the [[Scanco_User_Instructions#Session_Manager|'''session manager''']] instead of using the dec command.
*Alternatively you can set up a new login script and add <code>/DETACH</code> to the dec definition
<pre>
$ DEC == "CREATE/TERMINAL=DECTERM/DETACH".
</pre>
An example script can be found here @DISK5:[BONELAB.PROJECTS.BUIE]SETUP.COM.

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====Bug: UCT_EVALUATION v6 in customizing EVAL scripts====

<pre>$ run um:uct_k_v6</pre>

The new evaluation tool v6 should be used in place of the older v5. Please see the Documents section of this wiki for a manual on its use.

Known bugs:

When you are producing your own EVAL scripts, and want to call your own ipl file
or such:

The 'EVAL:' keyword in the scripts has the filenames of the
uct_evaluation_v6.com, then the ipl_v6_xxxx.com, then additional filenames (such
as the _prs.com to print and the 3dresults_append.com)

Now, if you are in BASIC mode in the modify window, and you change any of the 3
filename fields, the last of the additional filenames is 'dropped'... ooops...

So please go to Advanced mode and check the long 'EVAL:' keyword that all wished
files are still in the list, otherwise add the last again (most of the time,
that's the useful _3dresult_append.com script...)

Will correct that of course in the next version.

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====Not work: Left mouse button====
When the left mouse button doesn't work in the µCT evaluation program:
*Turn off caps lock.
*For remote sessions, turn of the Num Lock key (this will also allow you to use Ctrl-C and Ctrl-V to copy and paste contours).

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====Not work: Remove and insert keys====

The remove and insert buttons on the keyboard don't work in the µCT evaluation program:
*Turn off caps lock.

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==Evaluation FAQ==

===Customize your evaluation script===
The basic procedure is to create your customized evaluation script is:
#Clear the database of existing results
#Do your evaluation
#Extract the results
#Paste results into excel template.
You could repeat as necessary to evaluate a measurement multiple times and write out the results to a file.
*You must submit all jobs to a single queue!!!

'''1) Start ipl and clear the database of existing results.'''
<pre>
$ IPL_BATCH

/db_clear_eval
-input "IPL_AIM

..
</pre>

'''2) Insert your IPL evaluation.'''

'''3) Extract the results.'''
<pre>$@com:extract_results.com P1 P2</pre>
*P1 is the aim file (including path) and P2 is the result file (including path)

Example:
<pre>
$@com:extract_results.com DISK5:[BONELAB.PROJECTS.BUIE]MYAIM.AIM DISK5:[BONELAB.PROJECTS.BUIE]MYRESULTS.TXT
</pre>
*P2 should be the same for all samples in your project so that results are compiled into a single file.

'''4) Paste results into excel template.'''
*Refer to the [[Media:Extract_Results_Template.xlsx |'''Excel Extract Results Template''']].
*Open your results text file and copy and paste the contents into cell A2. There's no need to use paste special since the sheet is protected.

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===Create your own IPL script===

To make a script that would submit a job to the queue with the command as follows:
<pre>
$ @um:ipl_eval_only.com 'aim_file' 'gobj_file' 'p1' 0
</pre>

you need to create your own IPL file would be translated to the following command:
<pre>
$ submit /noprint /que=sys$slow ue:IPL_VOI_JOSH_M.COM
- /log=sys$scratch:test.log /para=('aim_file','gobj_file','seg_file')
</pre>
The IPL file would look something like this…
<pre>
$ if p1 .EQS. ""
$ THEN
$ write sys$output "Give DK0:[xxx]C0001234_SEG.aim on the line."
$ write sys$output "Or: "
$ write sys$output "Type $ scanco_submit_command um:ipl_eval_autostart/para=(dk0:[xxx]c00123_seg.aim) "
$ exit
$ endif
$
$ gobj_file = p1-F$PARSE(p1,,,"VERSION")-"_SEG.AIM" + ".GOBJ"
$ aim_file = p1-F$PARSE(p1,,,"VERSION")-"_SEG.AIM" + ".AIM"
$
$!
$ @um:ipl_eval_only.com 'aim_file' 'gobj_file' 'p1' 0
$ exit
</pre>

Some more handy IPL sequences are:
<pre>
$ INPUT = F$SEARCH("UCT_MEASUREMENT_DATA:[*.*''P1']*.RSQ",1)
</pre>

and then you just need to give meas. number as P1 (and maybe slice range as p2),
<pre>
$ if p2 .eqs. "" then p2 := A
</pre>
OR, some nice starts are:
<pre>
$ IF P3 .EQS. ""
$ THEN
$ WRITE SYS$OUTPUT "P1: Measurement Number to duplicate"
$ WRITE SYS$OUTPUT "P2: New Sample Number from Database"
$ WRITE SYS$OUTPUT "P3: New Start Letter of ISQ file"
$ WRITE SYS$OUTPUT "P4: Optional: Operator Number"
$ WRITE SYS$OUTPUT "P5: Optional: Controlfile Number"
$ EXIT
$ ENDIF
</pre>
where you say which parameters HAVE to be there (up to p3), and which ones are optional.

All together, the script may look like this:
<pre>
$ IF P1 .EQS. ""
$ THEN
$ WRITE SYS$OUTPUT "P1: Measurement Number to reco"
$ WRITE SYS$OUTPUT "P2: Optional: Slice number N or Range M:N. Auto:All"
$ WRITE SYS$OUTPUT "P3: Optional: Queue. Auto: sys$slow"
$ EXIT
$ ENDIF
$ if p2 .eqs. "" then p2 := A
$ if p3 .eqs. "" then p3 := SYS$SLOW
$ slices = p2
$ quename = p3
$ INPUT = F$SEARCH("UCT_MEASUREMENT_DATA:[*.*''P1']*.RSQ",1)
$ INPUT = INPUT - F$PARSE(INPUT,,,"VERSION")
$ logfile = "sys$scratch:RECO_" + f$PARSE(input,,,"NAME") + ".LOG"
$ submit/noprint/queue='quename' uct_reconstruction_file -
/para=('input','slices','logfile')
$ exit
</pre>
Note that <code>uct_reconstruction_file</code> is a logical that points to <code>um:uct_reconstruction.com</code>.

Logicals are preferred in scripts to make them more universal.

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===Run Scanco cut and match function (on Percy)===

;At DATA DISK:
Run<code>$ upat_list</code>
*mode 1, list mode.
*Select patients and site, etc.
*Select the appropriate template file, e.g. <code>UE:UPAT_TEMPL_CUTMATCH_AUTO_PATTB_CT.TXT</code>
*Output to a file, then run that file.

;At PROJECT DISK:
If you have moved the files to the project directory and renamed them, you can generate a script from:
<pre>
$ @UE:SEARCH_PROJECTS_CUTMATCH.COM
-P1 = filename with device and directory
-P2 = site (RR, RL, TR, TL)
-P3 = output filename
</pre>
For example, if we run:
<pre>
$ @UE:SEARCH_PROJECTS_CUTMATCH.COM DISK3:[MICROCT.PROJECTS.GRACE]GRACE_01_00MTH_RR.AIM RR MYFILE.COM
</pre>
The script will search <code>DISK3:[MICROCT.PROJECTS.GRACE]</code> for files in the form <code>G*RR*.AIM</code> with the same
length as <code>GRACE_01_00MTH_RR</code>, then check sample numbers to determine if the file is a follow-up scan.
*Upat_list is called to obtain position and dimension data for matching slices.
*The output file <code>DISK3:[MICROCT.PROJECTS.GRACE]MYFILE.COM</code> is created to submit and run the cut and match.

Before running, open the file and add <code>$ exit</code> at the end.
<pre>$ @DISK3:[MICROCT.PROJECTS.GRACE]MYFILE.COM</pre>

For multiple files, do something like the following.
<pre>
$ @UE:SEARCH_PROJECTS_CUTMATCH.COM DISK3:[MICROCT.PROJECTS.GRACE]GRACE_01_00MTH_RR.AIM RR MYFILE.COM
$ @UE:SEARCH_PROJECTS_CUTMATCH.COM DISK3:[MICROCT.PROJECTS.GRACE]GRACE_02_00MTH_RR.AIM RR MYFILE.COM
</pre>
Open MYFILE.COM and add <code>$ exit</code> at the end.
<pre>$ @MYFILE.COM</pre>

*The script assumes all follow-ups are provided.
*If follow-up scans are missing, it will be necessary to modify the output file so that the position and dimension data matches the files or update the <code>SEARCH_PROJECTS_CUTMATCH.COM</code> script.

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==IPL FAQ==
===Submit a job to the queue===

<pre>
$ submit/noprint /que=sys$slow ipl_voi_josh_m.com /log=sys$scratch:test.log
</pre>

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===Rotate with turn3d / turn2d===

The turn3d function can be used to perform a single rotation about any axis in 3d. The turnaxis_angle input is the angle between the x, y, and z axes and the line about which the rotation will be performed. The turnangle input is the amount to be rotated about the specified line. To use this function to perform three sequential rotations about the image's original x, y, and z axes requires compensation for the previous rotations.

To rotate an image from the axial view in the z plane to the sagittal view in the z plane:

<pre>
$ipl
/turn3d
-input             in
-output          out
-turnaxis_angles 90 0 90
-turnangle 90
-img_interpol_option 0
</pre>

No interpolation is necessary as this is "pure reformatting" (turning +-90 or 180 degrees around x,y or z axis)

For knee images, to put the femur above the tibia, you further add the step:

<pre>
/turn2d
-input out
-output happyFemur
-turnangle 270
-turnpoint_global_not_local true
-turnpoint -1 -1
-img_interpol_option 0
</pre>

Refer to [[Media:turn3d.pdf |'''turn3d.pdf''']] for further instructions.

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===Noise removal by component labeling===
*Refer to [[Media:ComponentLabeling.pdf|'''Noise removal by using component labeling''']]

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===Create MSQ image and view===

This is based on marching cubes. See <code>IPL_UPAT_EVAL.COM</code> for an example as per below:

<pre>
/read seg C0000214_SEG.AIM

/sup_divide ! careful of the order of inputs here
-input seg
-suppos_pixels_local -1 -1 -1
-supdim_numbers 1 2 1
-subdim_pixels -1 -1 -1
-testoff_pixels 0 0 0

/sub_pick
-input seg
-output segsub
-subpos_numbers 0 1 0

/tri
-input segsub
-output tri
-gobj_filename none
-peel_iter 0
-ip_sigma 0.8
-ip_support 1
-ip_threshold 40
-nr_ave_iter 2
-size_image 512 512
-scale_image 0.800000
-edges false
-nr_views 1 ! Important

/msq_from_aim
-aim_name tri
-msq_filename C0000123_3D.MSQ
</pre>

Then, use <code>UCT_3D</code> to view it. If you click on "animations" it will give you the option to read the MSQ file.

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===db_scanco_activate associate evaluation database===

When <code>/db_scanco_activate</code> is used in the IPL files, the correct association with the evaluation database is through the Index Patient and Index Measurement in the AIM header.

<pre>
Index Patient 3095
Index Measurement 5962
!-------------------------------------------------------------------------------
</pre>

Using IPL
<pre>
$ ipl
$ read in xxx.aim
$ examine in log
$ db true {activates database}
$ dt_object {at end "writing results to database for measurement 1234"}
</pre>

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===dicom_to_aim bug in IPL v5.03===

In IPL, use the /dicom_to_aim function. There is a bug in pre IPL v5.03 which requires that a small AIM be read in before doing the DCM conversion.
<pre>
ipl> read in tmp.aim
ipl> dicom_to_aim
-aim_name [in] >
-dicom_filename [default_file_name] > 4F65038B3986.DCM
-multifile [false] > true
ipl> write in MYFILE.AIM
</pre>

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===Understand "New" DT functions in IPL v5.42===

This applies to:
<pre>/distance_map /dt_ow_thickness /dt_number
/dt_thickness /dt_spacing /dt_cortical_thickness
</pre>

XT1 (old dt) and XT2 (new dt) use 0.5 for assign_epsilon and 0.9 for
ridge_epsilon.

µCT uses 1.8 for assign_epsilon and 0.9 for ridge_epsilon (old dt).

Therefore I recommend to take 0.9 and 1.8 also for the new dt functions
for µCT/vivaCT measurements.

The <code>suppress_boundary</code> feature is new and works as follows:

0: The ridges and spheres are calculated on the full seg AIM, also
outside the gobj. At the end the gobj is applied.

1: The ridges that are on the AIM boundary are not used for the
calculation of the maximal spheres.

2: The ridges are calculated on the full seg aim but then the gobj is
applied to the ridges. This means that at the end there are only spheres
that have the center inside the structure (gobj). The maximal sphere
filling algorithm still accounts for the structure outside the gobj, but
only uses center points inside the gobj.

<code>dt_thickness</code> for example can be used in two different ways in a script:

1) cut out aim - apply threshold - apply gobj - dt_thickness
This way the suppress_boundary options do influence the results
because there are no ridges outside the gobj anyway.

2) cut out aim - apply threshold - dt_thickness (with corresponding gobj)
This calculates the dt on the full aim first and applies then the
gobj and suppress options.

If you examine for example trabecular bone only on a small area bounded
by a gobj then the most accurate way to calculate the dt is to cut out a
much larger area (still containing trabecular bone) and use way 2) above
with suppress_boundary 0.

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===Develop new IPL commands in C===
*Refer to [[Media:IPL programming.doc|'''A short manual on how to develop new IPL commands in C'''.]]

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=Results=

==Extract Results==

===UPAT_LIST command===

*Refer to Scanco specification document on using the [[Media:Specification_upat_print_list_V2.0.pdf | '''Upat_print_list V2.0''']] on XCT2.
*Refer to [[Media:Using_upat.docx |'''Using upat_list Additional Notes''']].

upat_list (version 1.9 on XCT1) is identical to 2.0 except:

:* there is no option for using group codes

:* there is no option for using evaluation types

For all of the available parameters for generating results using upat_list command:
$ upat_list -h

Program: upat_print_list V1.9
Use the following modes to run upat_print_list:
upat_print_list -list for export to spreadsheet, default mode
upat_print_list -print for PostScript output
upat_print_list -show for text output
upat_print_list -advanced to access advanced options interactively
Standard Command-Line Arguments:
-b=<pat_nr> First patient, default = 1
-e=<pat_nr> Last patient
In list & show modes, default = last patient in database
In print mode, default = first patient
-s=<site_code> Site code
In list & show modes, RL RR R* TL TR T* CU *, default = *
In print mode, RL RR TL TR CU, default = RL
-mb=<date> Begin of measurement period, default = 1st measurement date
-me=<date> End of measurement period, default = current date
Dates must be given in VMS format, e.g. 01-JAN-2000
-f=<#_followups> Maximum number of follow-ups to match, default = 19
-t=<file_name> Name of template file
In list mode, default = UPAT_LIST_SHEET
In print mode, default = UPAT_EVAL_SHEETxx
In show mode, default = UPAT_SINGLE
-o=<file_name> Name of output file (in SYS$SCRATCH by default)
In list & print modes, stored in SYS$SCRATCH
In show mode, written to SYS$OUTPUT
-c=<number> Number of Print copies if in print mode. default = 1
-v=<level> Verbosity from 0 (silent) to 2 (verbose), default = 1
-h Print this help and exit
Advanced Command-Line Arguments:
-et=<eval_type> Type code of evaluation, default = 2
-eb=<date> Begin of evaluation period, default = 1st measurement date
-ee=<date> End of evaluation period, default = current date
-tb=<date> Begin of matching period, default = 1st measurement date
-te=<date> End of matching period, default = current date
Dates must be given in VMS format, e.g. 01-JAN-2000
-sk=<#_to_skip> Number of measurements to skip, default = 0
-m=<meas_list> Numbered List of measurements to take, e.g. 0,1,2,5,8
-nomatch Do not match follow up measurement, just take all slices
-sb Begin of Slice Range in % to be evaluated
-se End of Slice Range in % to be evaluated
-q Only take evaluations with quality better than (and including) this.
If positive number: all scans of better quality (incl. this) as well as all non-graded scans are taken.
If negative number: non-graded scans are NOT taken.
-qs Only take Structural evaluations with quality better than (and including) this.
Thus: between -qd and -q: only Density results are printed.
Parameter is disregarded if -qs >= -q.
-ut=<unit_type> 0->default unit, 1->linatt, 2->mg HA/ccm, 3->HU, default = 0
-cd=<density> Value of compact density to use, default = 1200.000000
If no command line arguments are specified, upat_print_list runs interactively.

Note that using "TB" and "TE", you can pull out exact measurements in the specified date range, while using "MB" and "ME", all you get is the latest measurement no matter what date range provided.

For results of all time points for a single site and sample # without matching to Baseline, use:
I.e. the common region will be 100% for all measurements.
$ upat_list -nomatch

From these options, you can write out your own command (vs. using prompts) to give you the specifics you are looking for.

By specifying the CAMOS template of “UPAT_EVAL_CAMOS.PS”, you will get the “Camos” report style. For example:
$ upat_list -nomatch -b=1000 -e=1000 -s=TL -tb=01-MAY-2000 -te=01-AUG-2018 -t=DISK1:[MICROCT.COMMANDS]UPAT_EVAL_CAMOS.PS -c=0 -o=sys$scratch:upat_pat_1000_tl_camos.ps

Note that there are actually many kinds of report templates. These can be found via:
$ dir UU:*.PS

“SCUSA” is a short form for Scanco USA templates. I.e. templates that fit on an 8.5” X 11” page.

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===Extract followup data without slice matching===
Use:
<pre>
$ upat_list -advanced
</pre>
*Choose 'disable slice matching:' -> y.

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===Extract patient results on a slice-by-slice basis===

There is an executable that was specially installed by Andres. Run it as user <code>microct</code>:

<pre>
$ RUN ut:UPAT_EXPORT_MEASUREMENT.EXE
</pre>

Choose from "Style: 0 = default, 1 = raw". Default gives standard patient parameters.

This gives you the .txt file in scratch containing the morphological parameters determined for each slice.

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===UCT_LIST Extract results===

Assuming you've used the <code>SCANCO_SUBMIT_COMMAND</code> to initialize your evaluations (either manually or through the <code>uct_evaluation</code> tool) then you can get all of your results stored into a text file that can be easily imported in Excel.
<pre>$ uct_list</pre>
The output text file will be stored in <code>sys$scratch</code> and you can ftp this to a PC so that it can be imported into excel and further analysis can be performed.

Importing into Excel requires setting a deliminator based on the space.

Customizing the <code>uct_list</code> output.

The default list template is set by the logical <code>UCT_3D_LIST_SHEET</code> which is normally
set to point to <code>UU:UCT_3D_LIST.TXT</code>. See the templates by

<pre>$ dir uu:*.txt</pre>

Almost all the available keywords are in <code>UCT_3D_LIST.TXT</code> enclosed
by \\ and //.

Only when you use the 'show directly on screen mode':
<pre>$ uct_list 1234</pre>
then you need to do this to override the default output:
<pre>
$ def/user uct_3d_single_sheet my-template_file.txt
$ uct_list 1234
</pre>

Some example format files are:
<pre>
UCT_3D_LIST.TXT
UCT_3D_SINGLE.TXT
UCT_3D_LIST_W_CRH.TXT
UCT_3D_MEANS.TXT --> Use this to get the 5 mean values (i.e., calibration)
</pre>

A summary of all the available keywords is available in <code>UU:UCT_3D_SINGLE_SHEET.TXT</code>
<pre>
Name :\\UCTMEASFILENAME//
Sample-Name :\\SAMPLENAME//
Sample-Nr :\\SAMPLENUMBER//
Meas-Nr :\\UCTMEASNR//
Date of Birth :\\SAMPLEDOB//
Sample-Remarks :\\SAMPLEREM//
Meas-Remarks :\\UCTMEASREM//
Meas-NrofSlices :\\UCTMEASNUMSLI//
Direct: -------------------------------------------------------------------
TV : \\VOX_TV//
BV : \\VOX_BV//
BV/TV : \\VOX_BV_TV//
Conn.Dens.: \\UCT_CONN//
SMI : \\MC_SMI//
Tb.N* : \\DT_N//
Tb.Th* : \\DT_TH//
Tb.Sp* : \\DT_SP//
Tb.1/N.SD*: \\DT_N_SD//
Tb.Th.SD* : \\DT_TH_SD//
Tb.Sp.SD* : \\DT_SP_SD//
Lin.Att.1 : \\UCT_MU0// +-\\UCT_MU0_SD//
Lin.Att.2 : \\UCT_MU1// +-\\UCT_MU1_SD//
Lin.Att.3 : \\UCT_MU2// +-\\UCT_MU2_SD//
Lin.Att.4 : \\UCT_MU3// +-\\UCT_MU3_SD//
Lin.Att.5 : \\UCT_MU4// +-\\UCT_MU4_SD//
TRI (Plate Model): --------------------------------------------------------
TV : \\MC_TV//
BV : \\MC_BV//
BS : \\MC_BS//
BV/TV : \\MC_BV_TV//
BS/BV : \\MC_BS_BV//
Tb.Th : \\MC_TH//
Tb.Sp : \\MC_SP//
Tb.N : \\MC_N//
Anisotropy: --------------------------------------------------------------
|H1| : \\MC_H1// H1x: \\MC_H1X// H1y: \\MC_H1Y// H1z: \\MC_H1Z//
|H2| : \\MC_H2// H2x: \\MC_H2X// H2y: \\MC_H2Y// H2z: \\MC_H2Z//
|H3| : \\MC_H3// H3x: \\MC_H3X// H3y: \\MC_H3Y// H3z: \\MC_H3Z//
DA : \\MC_DA//
Dim X : \\VOX_DX//
Dim Y : \\VOX_DY//
Dim Z : \\VOX_DZ//
Pos X : \\VOX_PX//
Pos Y : \\VOX_PY//
Pos Z : \\VOX_PZ//
El-Siz X : \\VOX_ELSX//
El-Siz Y : \\VOX_ELSY//
El-Siz Z : \\VOX_ELSZ//
</pre>

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===Tabulate LOG results from 3D evaluations===

Only use this if you have not used the standard <code>uct_evaluation</code> tool to generate your 3D evaluations (in which case see the HowTo related to the 3D database).
You can tabulate the LOG files:
<pre>$ search xxxx.log "ov "</pre>
Or whatever you want to search for can be stored in a text file
<pre>$ search/output=sys$scratch:ov.txt xxxx.log "ov "</pre>
To search more than one log file, and get the output into one single file:
<pre>$ fda/output=xxx.txt search *.log "ov "</pre>

The fda means 'file do all' and is a script made by Scanco to do one command (search) on a wildcard of files (*.log). Then put all the ov.txt, tv.txt, name.txt etc. files into excel.
Josh has made a .com file that does a similar job as described above.

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===Compile evaluation LOGs into one file===

Call the <code>UE:UCT_EVALUATION_V4_3D_RESULT.COM</code> with the same construction
as <code>$ eval_special</code>. If you need help with this, see the HowTo on this
Wiki site (HowTo: Assign special 3D evaluation to the UCT_EVALUATION tool).

Edit <code>UE:UCT_EVALUATION_V4_3D_RESULT.COM</code> file to call a specific ipl
script as you wish.

When you run the evaluation, you will have three new files created:

:*Two files in the measurement directory (on DK0!) (one with each eval 3D results in its own file, and one <code>APPENDED_ALL.TXT</code> file)
:*Then in sys$scratch, you will have one <code>SYS$SCRATCH:UCT_LIST_ALL_3D_RESULTS.LOG</code> file with ALL 3D evaluations of all measurements.

Note: You may need to edit the <code>SCANCO_SUBMIT_COMMAND</code> to specify a single queue (i.e., /que=sceval$fast)

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==Database==

===Examine patient databases===
This is for advanced users only!

There are two patient databases that get updated every time an evaluation is performed. Below is the name of the database, and the method used to check database values:
<pre>
$ show logical UPAT_EVAL_DATABASE
$ run disk1:[calibration.util]upat_export_measurement.exe ! as microct
</pre>
<pre>
$ show logical UPAT_SLICE_DATABASE
$ set host 0 ! login as user calibration
$ @disk1:[microct]login.com
$ spb
$ run DISK1:[CALIBRATION.UTIL]UPAT_GET_DB_INFO.EXE ! enter '1' to list records
</pre>

In the slice database every evaluation is recorded, but only one is currently active at a time.

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===Manipulate scan sequence===

Upat_list reports the baseline scan and then the percentage change of follow-up scans from the baseline scan. The order of scans in upat_list is determined from the measurement number (not the measurement date). In the case you need to manipulate the baseline and follow-up sequence, you will need to:

[[Image:Bones2.jpg|20px]] Warning: Use this with caution, and as little as possible!! even if the operation is reversible. Database manipulation is sensitive after all.

1. Log in as the "calibration" user (beware which calibration account to use for the different scanners).

How to proceed in the terminal:
$ SPB
$ @DISK1:[MICROCT]LOGIN.COM or $ @DISK1:[XTREMECT2]LOGIN.COM !! don't miss that line, otherwise you would modify the CALIBRATION databases

2. Use the following command to modify the measurement number:

$ RUN DISK1:[CALIBRATION.UTIL]UCT_CORRECT_SAMPLE_FIRST.EXE !! To redefine the very first measurement in the sequence

:* I do mean "First" measurement in the sequence, and not "baseline" measurement. You may have 2 baseline scans, one for radius and one for the tibia, but only one of them is the very "first in the sequence".

$ RUN DISK1:[CALIBRATION.UTIL]UCT_CORRECT_MEAS_PREV_NEXT.EXE !! To redefine the follow-up sequence beyond the first measure

:* The PREV_NEXT utility is a bit tricky to use, as for each measurement you will have to define its "chronological" previous and its next. It is not related to any anatomical site: one might think for example of defining the Radius follow-up sequence for example. It is not the case. The PREV_NEXT sequence will alternate between different anatomical sites, that is how it should be.

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===Add placeholders for missing follow-up scans===
If there is NO scan at a certain time point in a series (i.e. patient did not show up), the program ut:upat_create_meas_placehoder.exe and upat_create_eval_placeholder can insert fake records, so the slice matching and timepoints/visits are still all in order.

The attached file describes how to create an manage placeholders in the case of missing follow-up visits in longitudinal studies. [[Media:SOP_Create_Placeholders_draft.pdf|'''SOP Create Placeholders''']]

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===Disable a database measurement===

It is not possible to delete an evaluation from the database, but it can be disabled.

NOTE: QC results are stored in the UCT database, and there is no tool to disable a UCT database result.

Log in as the normal user (e.g. XTREMECT2). Then in a terminal you may use this simple utility program:
$ RUN UT:UPAT_CORRECT_VALID_FLAG

See below a typical prompt to deactivate an entry:
<pre>
UPAT_CORRECT_VALID_FLAG V2.0

Measurement No. (0 to stop): 1
Evaluation type [2]: 5
Group code [0]: 0

Found evaluation 57 for patient 4: ID003

Value for valid flag (0=invalid, 1=valid) [1]: 0
Value for placeholder flag (0=write results, 1=placeholder) [0]: 0

Measurement No. (0 to stop): 0
</pre>

You can always re-activate the entry, by switching the valid flag from 0 to 1.

Or, to make a scan invalid, you can also login as calibration user.

Point to microct user

$ @DISK1:[MICROCT]LOGIN.COM

Set priviledges to bypass.

$ SPB

Run Correction File
$ run DISK1:[CALIBRATION.UTIL]UPAT_CORRECT_VALID_FLAG.EXE

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===Disable a uct_list database measurement===
You cannot really disable data in the UCT_LIST output. What you can do using IPL is to clear the complete result entry for a given measurement, for example:

$ ipl
/read
-name in
-filename default_file_name
/db_scanco_activate
-write true
/db_clear_eval
-input in

Then UCT_LIST might still report the "disabled" measurement, leaving only the few first meta-data columns non empty. The rest would be cleared.

I must bring your attention to the fact that this sequence is used a lot on XtremeCT I scripts, for the cortical porosity for example.
This means that on XT-I, the UCT_LIST content is highly unstable, as it was used back then while UPAT_LIST was not able to handle those results.
In the future, when new applications come they may delete/overwrite the UCT_LIST entry for a measurement.
That is the rationale for using the TXT output in the RESULTS directory, that at least keeps track of past analyses.
As long as you have a single application on XT-II going through UCT_LIST, calling results on demand with it is fine. Later it might come complicated.

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===Troubleshoot UPAT database===

If there is an error ('inconsistent key change or duplicate key!') in the log file during 'upat_filldb', this is likely caused by too many servers doing UPAT evaluations:

Basically, the UPAT database can not be accessed by 2 evaluation jobs "at the same time", and works on a "1st arrived 1st served" basis. It is actually one reason to have only 1 evaluation at a time running on a single workstation (the usual setup).
In your case (and in mine as well), when you have several workstations clustered together, you can technically run several evaluation jobs at the same time which will eventually access the very same database.
So what happens is that a 1st job executes the /upat_fill_db, and accesses the database for a short amount of time.
During this time, any unfortunate evaluation job trying to access the database will end up in the exact same error as you reported, as their access to the database is restricted. Even though the time window is short, this kind of thing is unavoidable in setup such as ours, and when lots of evaluation are started at the same time.
Here you have no other choice than restarting the evaluation job, in order to update the database (or ultimately you could write a small script just to run the /upat_fill_db command, but I do not think it makes sense).

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===Redirect to a temporary database===

We need to temporarily redefine the logicals UPAT_EVAL_DATABASE and UPAT_SLICE_DATABASE. Normally, the definition is

<pre>
UPAT_EVAL_DATABASE = UCTD:UPAT_EVAL_CALGARY.DAT
UPAT_SLICE_DATABASE = UCTD:UPAT_SLICE_CALGARY.DAT
</pre>

Typically, we submit our jobs to the queue with an IPL script, so within the script we'll have to redefine the name of the database by adding lines such as
<pre>
$ def UPAT_EVAL_DATABASE SYS$SCRATCH:TEMP_UPAT_EVAL_CALGARY.DAT
$ def UPAT_SLICE_DATABASE SYS$SCRATCH:TEMP_UPAT_SLICE_CALGARY.DAT
</pre>
so that the results from the IPL evaluation are redirected to this temporary database.

Then, we need to extract the results from the database. These results are provided on a slice by slice basis (at least with the UPAT data). As user <code>microct</code> in a terminal window, we will again need to redefine the database and then run the program that translates the results to a text file:

<pre>
$ def UPAT_EVAL_DATABASE SYS$SCRATCH:TEMP_UPAT_EVAL_CALGARY.DAT
$ def UPAT_SLICE_DATABASE SYS$SCRATCH:TEMP_UPAT_SLICE_CALGARY.DAT
$ run disk1:[calibration.util]upat_export_measurement.exe ! give the measurement number and output file
</pre>

Or extract the results from the temporary database with:

<pre>
$ def UPAT_EVAL_DATABASE SYS$SCRATCH:TEMP_UPAT_EVAL_CALGARY.DAT
$ def UPAT_SLICE_DATABASE SYS$SCRATCH:TEMP_UPAT_SLICE_CALGARY.DAT

$ def UCT_MEASUREMENT_DATABASE SYS$SCRATCH:UCT_MEASUREMENTS_TORONTOXT.DAT ! only necessary if data came from another system
$ def UCT_SAMPLE_DATABASE SYS$SCRATCH:UCT_SAMPLES_TORONTOXT.DAT ! only necessary if data came from another system

$ upat_list ! choose option [3]show, give the patient number and output file, e.g. sys$scratch:myvalues.txt
</pre>

For an example IPL script that redirects to a temporary database, see Percy:
<pre>
DISK1:[MICROCT.COMMANDS]IPL_UPAT_EVAL_AIMINPUT.COM
</pre>

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===Import from a foreign database===
IF MEASUREMENTS COME FROM A TOTALLY DIFFERENT DATABASE (such as Toronto's XCT):

You will need to redefine the logicals UCT_MEASUREMENT_DATABASE and UCT_SAMPLE_DATABASE
<pre>
def UCT_MEASUREMENT_DATABASE SYS$SCRATCH:UCT_MEASUREMENTS_TORONTOXT.DAT
def UCT_SAMPLE_DATABASE SYS$SCRATCH:UCT_SAMPLES_TORONTOXT.DAT
</pre>

However, it is quite possible that you won't have a copy of the foreign MEASUREMENT and SAMPLE databases. If this is the case, then you must import the ISQ files into our own database. Then, by setting
<pre>
$ define UCT_EVALUATION_DATABASE SYS$SCRATCH:TEMP_EVALUATIONS_CALGARY.DAT
</pre>
you could redirect the results to a temporary database (but normally, if you already imported the data, why not use our own database now).

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===Duplicate as new import to database===

You will need to copy ISQ and GOBJ files to a new designated location. This is done when a screening study is completed to look for potential subjects and then a main longitudinal study is completed under a different study name. 

1. Make a new patient/subject ID 
2. Make a copy of the ISQ. For example: 
<pre>
$ copy DISK2:[microct.DATA.00002584.00008992]*.isq -
DISK2:[microct.DATA.00002696.00009345]*.isq
</pre>
3. Import ISQ into new patient/subject ID number by typing:
<pre>
$ import
</pre>
4. Follow the prompts for the ISQ file names, changing of control file # etc. 
5. Check the data directory to see if ISQ and GOBJ files have been copied properly 
2. In uct_evaluation, open new .ISQ and copied .GOBJ and re-run the evaluation to create .AIM, _SEG.AIM, _CORTEX.AIM, _LHTH_DTH.AIM 
 
3. Copy Scout Views so scanning program will load baseline scout view for followup scans In DISK1:[MICROCT.DATA.SCOUTS], you'll see two series of scout views: one series with the PATIENT # followed by 020 or 021 or 038 or 039, the site code (radius or tibia, left or right respectively) 
Copy the old patient scouts to the new patient #s
For example (using the same old and new #s as above): 
<pre>
$ copy DISK1:[MICROCT.DATA.SCOUTS]00002584021.SCV -
DISK1:[MICROCT.DATA.SCOUTS]00002696021.SCV
</pre>

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===Recover a disappeared due to import===
If you need duplicate a measurement in both the original and new directories, but you forgot copying the measurement before importing as a new. The original measurement will be automatically removed from the original directory. This can be fixed! You will need to copy the measurement back and then fix the header information, as the header will no longer match the original directory.

1. Manually copy all of the associated files for the measurement from the new directory to the original directory:
<pre>
$copy DISK2:[xtremect2.data.00001234.00001234]*.*;* DISK2:[xtremect2.data.00004321.00004321] /log
</pre>
2. Change the header information of the measurement files to those of the original directory. To do this, you will need special software. The use of this software is RESTRICTED. Users must seek special permission to use the software from Steve, Ying, or Anne BEFORE using. Once you have permission, the software can be found here: DISK1:[MICROCT.COMMANDS.FORBIDDEN].

3. Run the software:<pre>
$r [software]
</pre>
4. The software will ask for:
a) the ISQ file
b) the new sample # you would like to give it (i.e. the original directory sample #)
c) the new measurement # you would like to give it (i.e. the original directory measurement #)
c) the new sample name you would like to give it (i.e. the original Study ID)

You can view the header information for a file by using the command:
<pre>
$ctheader [ISQ file]
</pre>

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===Move to fix wrong Study_ID/Sample_No===

Situation: One study participate was assigned in followup scans multiple Study_ID or multiple Sample_No under the same Study_ID.
Action: To correct this mistake and update the database correctly, you get to

1. Return/Restore the RSQ from tape to measurement disk using Move (not Copy) in uct_backup program, otherwise the new location won't have its RAW backup record and thus have no idea where its RSQ was located.

2. When there is no original ISQ in the measurement disk, you will have to reconstruct a new ISQ from this RSQ. If there is an original ISQ there, then skip this step.

3. Import ISQ into a new designated location (correct Study_ID and Sample_No with new Measurement_No).
$ import
Follow the prompts for the ISQ file names, changing of control file # or site # if needed. This action will import RSQ, Gobj and all the files in the folder to the new location.

A reminder is that without an ISQ ready by importing a RSQ only will produce wrong slice no. and site location in the database as shown in the uct_backup.

4. If the ISQ is newly reconstructed (original ISQ could skip this step), the database will show the new reconstruction date & time (not the original scan date & time) as the scan records in the uct_backup. To correct this,

$run ut:uct_correct_meas_measdate

1) To see the original scan date & time: run this command and follow the prompt and input the original measurement No. as the Index, but don't change this by copying and pasting it back in Messdatum/Zeit.

2) To set the new scan date & time: run this command again and input the new measurement No. as the Index, copy & paste the original scan date & time got from 1) in Messdatum/Zeit.

This way will update the database as shown in the uct_backup with the original scan date & time with newly reconstructed ISQ in the correct Study_ID and Sample_No.

5. Backup/Move the RSQ at the new location to tape, so that the new record will have full information of both RAW and IMA.

6. Even though ISQ, RSQ, GOBJ and all other files have been moved over to the new location, you will still need to re-run the evaluation (in uct_evaluation, open ISQ and GOBJ) to create .AIM, _SEG.AIM, _CORTEX.AIM, _LHTH_DTH.AIM ect.

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===Move to fix wrong account used for scanning===

Xtremect2 (on disk2) and xt2recalib (on disk6) accounts share the same databases. However, the definition of DK0 is account specific, ie. the scans are stored on different disks. So when scanning under Xtremect2 account instead of Xt2recalib account, to correct the wrong measurement location you will need to:

#Create the patient directory on disk6:[xtremect2.data], if needed;
#Create the same measurement directory on disk6:[xtremect2.data];
#Create a save set of the measurement folder on disk2:[xtremect2.data] with the isq, rsq, rad and scv files included;
#Unzip the save set in the measurement directory on disk6:[xtremect2.data];
#Delete the measurement directory on disk2:[xtremect2.data] using delete command in the terminal. Caution: Do NOT use the backup program.

[[Image:Bones2.jpg|20px]] Warning: This procedure is specific to this situation between Xtremect2 and Xt2recalib accounts, Microct and Xt1recalib accounts, and vice versa, but not applicable between any other accounts!

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===Update database after RSQ/ISQ restoration===

If you are restoring RSQ or ISQ files from tape (or other source) it might be preferable to do your analysis without resetting the database info.

The database is specific to the user. So, we have to modify the database for <code>microct</code>, and be careful not to modify the <code>calibration</code> (or other users) database. However, we still need to have permissions from <code>calibration</code> in order to do the modification.

When we restore an ISQ or RSQ to disk, the database needs to be updated to ensure it finds it. We have to change the database back to say it's on disk. To do this we need to log in as user <code>calibration</code>.

<pre>
$ set host 0
login as calibXXXX where XXXX is the scanner id (5019 for VivaCT or 2339 for uCT35) or calib3309 or calib3401 (for the XtremeCT and XtremeCTII system, respectively).
password from Steve

$ @ADISK1:[BONELAB]microct_setup_XXXX.com ! XXXX=scanner id, sets the logicals to point to bonelab data for SB group
or
$ @ADISK1:[VIVACT]LOGIN.COM ! sets the logicals to point to microct data for BH group
or
$ @DISK1:[MICROCT]LOGIN.COM ! sets the logicals to point to microct data on the XtremeCT system
or
$ @IDISK1:[XTREMECT2]MICROCT_SETUP.COM ! sets the logicals to point to xtremect2 data on the XtremeCT2 system

$ set proc/priv=bypass or $ spb
$ run DISK1:[CALIBRATION.UTIL]UCT_CORRECT_DIR ! make sure to include the full path to the executable as shown here.
$ run DISK1:[CALIBRATION.UTIL]UCT_CORRECT_MEAS_DIR.EXE ! on xtremect2 system, use this program
</pre>

Note: Only change those items which have to be changed (e.g. just hit RETURN for RAW fields if you only want to change the IMA location. Also, when specifying the directories, use DK0, not DISK2.

<pre>
$ run ut:UCT_CORRECT_DIR.EXE
</pre>

<pre>
Measurement Nr.: 1234
MeasNr. 1234
PatientNr: 268
RAW: RAW004
TP0:00001234_RAW
IMA: IMA002
TP0:00001234_IMA
</pre>

<pre>
RAW-Label: [ RAW004 ]

RAW-Dir : [ TP0:00001234_RAW ]

IMA-Label: [ IMA002 ] DISK
IMA-Dir : [ TP0:00001234_IMA ] DK0:[microct.data.00000456.00001234]

Measurement Nr.: 0
End of program
</pre>

The IMA-label does not matter on disk - but we have to write something to get rid of the IMA002, so 'DISK' makes sense.

Using the standard backup/archiving program, you can archive (MOVE TO) that IMA again to a tape, but use a DIFFERENT TAPE than where the first instance of this scan is on.

Background: Tapes just write file after file, without any directory structure or hierarchy, so the program will always find the first instance (the old dataset) if you try to read it again from that tape.

Note One other option is to change the permissions of UCT_CORRECT_DIR.EXE so that user <code>microct</code> can use it directly. To do this, log in as users <code>calibration</code> and then:

<pre>
$ set proc/priv=bypass ! as user calibration
$ set prot=g:re ut:uct_correct_dir.exe
$ run disk1:[calibration.util]uct_correct_dir ! as user microct
</pre>

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==Other FAQ==

===View Sample info===
<pre>
$ mcr um:uct_info 1234
</pre>
will show you sample-name and date-of-birth of sample-number 1234
<pre>
$ mcr um:uct_info -m 1234
</pre>
will give you some (stupid) info about meas 1234

'''Note:''' If you use this function all the time, put the following into <code>microct_setup_user.com</code>
<pre>
$ uct_info :== $um:uct_info
</pre>
and then the usage info will even be correct.

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===List measurements for data and backup location===

*To generate a list of measurements that are registered in the database, to determine where backups are stored, or if the data is still on disk:

::<code>$ write_info</code>

*Ask you for a range of measurement numbers or sample names.
*Create a <code> sys$scratch:info.txt</code> file.

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===Anonymize patient name and DOB===

Here is the link to [[Media:SOP_Anonymize_patient_name_dob.pdf | Scanco's SOP]] to change a long list of patient's name and/or DOB to de-identify the data.

This does not affect the headers of past RSQ, ISQ or AIM files.

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===Fix a wrong scan site code===

This is done if accidentally scanned using the wrong control file.
For example scan site RR is scanned mistakenly under RL, or TL scanned by mistake using the control file for TR ect.

To see our site codes, e.g. 20 = RL, 21 = RR etc using

<pre>$ show log *eval*</pre>

;Scenario 1:

If the correction commands (uct_correct_meas_site and updh_site) are already in your account (which is the case for the xtremect2 and xt2recalib accounts on the XtremeCT cluster)

$ cd util
$ dir *site*

and you see two programs (uct_correct_meas_site and updh_site). Set priviledge to bypass first

$ spb

$ run uct_correct_meas_site

and enter the meas. number to be corrected and then enter in the correct site code (20 = RL, 21 = RR, 38 = TL, 39 = TR).
*This modifies the database, so the correct site is displayed in the eval program.
*Enter meas. number 0 to exit program.

Then we must also correct the ISQ and RSQ files (has to be restored from tape if not on disk):

$ run updh_site !'updh' = update header</pre>

*Enter the full (i.e. pathname included) ISQ or RSQ filename. For DISK6 data should use DISK6:[xtremect2.data....].
*Then enter the correct site number.

;Scenario 2:

Normally the correction commands (uct_correct_meas_site and updh_site ect.) are only provided in a calibration account to prevent from misusage. We have to login as user calibration to make the change.

$ set host 0
$ username: [enter calibration account, e.g. calib3401]

Then we use the same steps in Scenario 1 to change the site code in both database and ISQ and RSQ files.
*Make sure to <code>logout</code> from user calibration afterwards.

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===Fix for results fail to print/list/show after evaluation===

There are a number of reasons the results may not print:

====Incorrect first measurement number====
When sample information (such as patient name, DOB, remark) is changed DURING scanning, this can over write the 1st Scan measurement number, resulting in the evaluation sheet not being printed, and data not shown when running upat_list. For example, this happens when:

1) open sample program, enter name, hit save, leave program open

2) start scan (which would write correct record with 1st meas. in sample database)

3) in sample program: then only enter DOB, and hit 'save' again in the sample program --> it 'overwrites' the 1st meas. with an empty string again.

If you want to enter DOB after the scan has started, you HAVE to 'Find...' and re-load that patient first (so it correctly loads the 1st meas. entry also). It is best to just not use the sample management program whilst scanning is taking place.

However, if you do encounter this problem, use the following to fix (shown using patient 668 as an example. 1st scan measurement number was 2672):
<pre>
$ set host 0
calibration
xxxxx

$ spb
$ @[microct]microct_setup
$ run [calibration.util]uct_correct_first
$ r UCT_CORRECT_FIRST

Patient Nr.: 668
SampleNr.: 668
First: 0

2672

Patient Nr.:
</pre>
and continue with next non-working patient, give patient number 0 to exit.

$ logout

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====Evaluation completed with results not written to database====
If the first measurement number and DOB are correct... check the .log file of the evaluation... However, if there is no upat*.log file available for that scan, use:

upat_list -v=2 and you will see (for eg sample 594):

<pre>
Found sample 594, CAMOS_0018
Found measurement 2536 made 19-MAR-2007 12:52:58.48
Measurement site RL found in list at index 0
Measurement 2536 within measurement period
ERROR finding evaluation for measurement 2536

No valid evaluation found for measurement 2536
</pre>

So it seems the 3D upat eval never wrote anything to the database for that scan. In this case, you can run:

<pre>
$ @ue:ipl_upat_eval_again_quick.com
</pre>
and let it run for the missing data.
'''NOTE''' it will only need the aim files and gobj files that you still have in your 'models' directory.

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====Incorrect sequence of measurement numbers====
Finally, if none of these options work... check the order of measurement numbers: especially if an import has occured, first check the first measurement number is correct (as above). Then run sys$Scratch:uct_correct_prev_next.exe and correct the order of the measurements: The database keeps a 'daisy' chain of meas. numbers, each meas. knows which one was the previous meas and the next meas.

0 means: no prev. meas (or no next meas) So corrected the order for you like this:

<pre>
$ r UCT_CORRECT_prev_next

Measurement No. (0 to stop) [0]: 2821
MeasNo.: 2821 PatientNo: 723

Previous [0]: <-- leave 0
Next [0]: 2828 <-- give next meas number
Measurement No. (0 to stop) [2828]:
MeasNo.: 2828 PatientNo: 723

Previous [0]: 2821 <-- give prev. meas number
Next [0]: <-- leave 0 for very last meas.

</pre>
Please note: the series of meas. numbers per patient is NOT separate per meas. site, thus radius and tibia meas. are linking to each other. '''Do not mess up!'''

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=Data Management=
==Lab’s Data Responsibility==
*Weekly
#Clean up sys$scratch directory and only keep last week's data.
#Archive RSQ to corresponding tapes.
#*RSQ from temporary tests and non-project (not a formally established project) will NOT be archived unless specifically notified to lab personal.
#Database backup to disks.
*Monthly
#Database backup to corresponding tapes.
#Archive QC RSQ to corresponding tapes.
#Delete QC IMA and only keep last week's data.
*6-monthly
#System backup to corresponding tapes when prompted.
*Yearly
#Data Disk clean up when usage is over 90%.
#*Temporary tests and non-project RSQ and IMA data will be deleted during check up.
#Project Disk clean up when usage is over 90%.
#Winston backups clean up.
*Whenever requested
#Projects backup to Winston server and restoration.
#Projects archive to HOG server and restoration.

[[File:BoneLabDataManagement.JPG|800px]]

[[Image:Bones2.jpg|20px]] Warning: STRONGLY URGE TO DO THE WEEKLY and MONHTLY BACKUP. Two users DID experience disk crashes before, and without the weekly backup, you may still have all scans on the data disk, but without the databases you cannot tell which scans belong the which sample.

*Refer to [[Media:Microct_management.pdf|'''XtremeCT Micro-CT Management SOP''']] or [[Media:Microct_management.docx|'''its Word format''']] for references.

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==HP Server and Disk Array==
===HP References===
*[[Media:Hp-quick-specs-msa30.pdf|'''MSA30 Disk Array Quick Specs''']]
*[[Media:Hp-integrity-rx2620-sceva2-user-service-guide.pdf|'''Integrity RX2620 User Guide''']]
*[[Media:Hp-integrity-rx2660-sceva3-user-service-guide.pdf|'''Integrity RX2660 User Guide''']]

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===HP FAQ===
====Change disk description for $ disks====
Login as the system user and change to the system commands directory.

$ cd scom
$ eve show_disks.com

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==Tape==
[[Image:Bones2.jpg|20px]] Warning: While the tape is running and writing to it, DO NOT LOG OUT, DO NOT INTERRUPT THE PROGRAM! This would make that tape unusable from this point on - you could still read from that tape up to this point, but could not add more scans to this tape.

===Tape Label Convention===
Tape labels are 6 characters in length. For the Bone Imaging Lab projects, the first three letters indicate if the tape is for raw (RAW) or image (IMA) data, and the last three digits are for the tape number.

<pre>
RAW040 = RAW date, tape #040
IMA001 = IMAGE data, tape #001
</pre>

Alternatively, the first two characters may be set to a PI's initials, the third character indicates if the tape is for raw (R) or image (I) data, and the last three digits are for the tape number.

<pre>
SBR040 = Steve Boyd RAW, tape #040 
SBI001 = Steve Boyd IMA, tape #001 
BHR006 = Benedikt Hallgrimsson RAW, tape #006 
BHI017 = Benedikt Hallgrimsson IMA, tape #017 
FJR012 = Frank Jirik RAW, tape #012 
FJI003 = Frank Jirik IMA, tape #003 
</pre>

CaMos raw data is backed up with the following naming:
<pre>
CAMOS1 = CaMos RAW, tape #1
</pre>

When a tape becomes full, start (initialize) a new tape, increasing the tape number by one so that each tape label is unique.

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===Initialize a New Tape===
Put a new tape into the tape drive, then press "Initialize", this will format (erase) everything on the tape. When prompted for a label for the tape, follow the [[Scanco_Administration#Tape_Label_Convention|'''Tape Label Convention''']]. The tape can now be mounted for use. 

[[File:Uct_backup_pic02.jpg|400px]]

===Full Tape===
A tape automatically ejects during a backup procedure if it becomes full.
*Remove the tape and write protect it (orange indicator will be displayed).
*Exit the disk-utility program.
:*Hit <code>ctrl/c</code> to interrupt the program if needed.
*Start a new instance of the program.
*[[Scanco_Administration#Initialize_a_New_Tape|'''Initialize a New Tape''']].
*Backup any remaining files.

[[File:Uct_backup_pic03.jpg]]

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===Tape Drive Setup on XCT cluster===
Both the old and new tape drives are connected to SC3309 (XCT1) and powered on. You do not need to power off one to use another.

New tape in new drive <--> microct, xtremect2, xt2recalib, calib3401, calib3309

:*The 'new' Ultrium 3000 tape drive is for the new tapes and the default tape drive for all other accounts (microct, xtremect2, xt2recalib, calib3309, calib3401).
:*Use the following command to use the old SDLT tape drive no matter which account on the command line:
<pre>
$ uct_backup_sdlt
</pre>

Old tape in old drive <--> xt1recalib

:*The 'old' SDLT tape drive is for the old tapes. You have to log into the default xt1recalib account to recognize this tape drive.
:*Restoring from old tapes in xt1recalib account will restore your data to DISK6:[MICROCT.DATA].
:*By default, xt1recalib account can only see old tape drive, not the new tape drive.
:*Use the following command to use the new tape drive no matter which account on the command line:
<pre>
$ uct_backup_sas
</pre>

*With either of the above commands, you must not "submit" the tape usage jobs to the queue (i.e., cannot run a batch backup from a script), but only run them interactively in the
software. Any job in the queue will use the default tape drive again.

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===Extract from Tape===

====Scripts to Extract from Tape====
Generally, all files on the tape can be extracted, or only specific files.
To extract all files on a tape, for example, a tape received from a collaborator, insert the tape into the drive and do the following:
$ cd ur
$ create/dir [.collaborator]
$ create/dir [.collaborator.com]
$ create/dir [.collaborator.log]
$ create/dir [.collaborator.models]
$ cd ur collaborator models
$ backup/log tp0:*.sav []/by=parent ! be sure you are the user (i.e. 'microct' or 'xtremect2') that has permission
$ backup/log tp0:*.sav DISK4:[BONELAB.PROJECTS.FRAMINGHAM.MODELS...]/by=parent ! The "..." keeps the directory structure. The /by=parent ensures owner of the files is same as parent directory

This will save all the files on the tape to the current directory. Alternatively, if you only want a certain file extracted from the tape, such as an RSQ file, do essentially the same as per above, except with a different final command:
$ backup/log tp0:*.sav/select=*.rsq []/by=parent

The <code>/by=parent</code> part of the command is a qualified for the file owner, and it makes the files that are copied the same owner as the parent directory (nothing to do with how directories are structured). The <code>[...]</code> generates sub-directories.

A custom script is required when extracting data from tape from another micro-CT system or to extract the data to a central location (e.g., a user's directory).
*The script is then submitted to the backup queue of the workstation the tape drive is connected to (i.e., SCEVA3_BACKUP)
*Some example scripts are provided below.

*Extract image data for three scans to a custom folder, maintaining the sample and measurement directory structure:
<pre>
$ mount/foreign tp0
$ backup/log tp0:00001234_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie...]
$ backup/log tp0:00001245_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie...]
$ backup/log tp0:00001238_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie...]
$ dismount tp0
</pre>

*Extract segmented AIM files for three scans to a custom folder without the original directory structure:
<pre>
$ mount/foreign tp0
$ backup/log tp0:00001234_IMA.sav/select=[microct.data...]*seg.aim disk3:[microct.projects.buie]
$ backup/log tp0:00001245_IMA.sav/select=[microct.data...]*seg.aim disk3:[microct.projects.buie]
$ backup/log tp0:00001238_IMA.sav/select=[microct.data...]*seg.aim disk3:[microct.projects.buie]
$ dismount tp0
</pre>

*Extract segmented AIM files for all scans on tape to a custom folder:
<pre>
$ mount/foreign tp0
$ backup/log tp0:*_IMA.sav/select=[microct.data...]*seg.aim disk3:[microct.projects.buie]
$ dismount tp0
</pre>

*Extract raw data for three scans to a custom folder, without the original directory structure:
<pre>
$ mount/foreign tp0
$ backup/log tp0:00001234_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie]
$ backup/log tp0:00001245_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie]
$ backup/log tp0:00001238_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie]
$ dismount tp0
</pre>

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===Tape FAQ===
====Error: Can't mount tape, Medium offline====
This can happen if a tape is interrupted during use (e.g., due to a power failure or system restart while the tape drive is in operation).

#Use the manual eject button to remove the tape from the drive.
#Turn off the tape drive, the switch is on the back of the drive.
#Shutdown the whole micro-CT system.
#Turn on the tape drive.
#Startup the micro-CT system, starting with the server.
#Try to mount the same tape again.

If the above does not work then either the tape or the tape drive is damaged. To determine if it is the drive, take a brand new tape and try to initialize it. Do not use a tape with data on it in the drive unless you are certain the drive is okay.

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====Error: positioning====
This can have two reasons usually:

#The tape is just faulty. Try with a fresh tape.
#A previous tape write operation was interrupted (e.g., a user did an 'End Session', the power went out, or the eject button was pressed on the tape drive, which killed the backup program). In this case the drive did not write the very important 'End of Tape' marker, and now, the tape drive cannot find the current place where it can start adding new data.
*Solution: either take a fresh tape, or if there were only a few scans are on the 'bad' tape, 'Move to Hard Disk' of ALL the scans on that tape, check that the scans have been retrieved well, then initialize that tape again (which will erase everything on the tape!) and archive those scans again.
*IMPORTANT: never interrupt the tape drive while it is running!

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====Error: parity====
Either tape or the tape drive is faulty. Take a fresh tape (potentially from a new batch of tapes), and see if the error persists.
*If yes: have the tape drive repaired.
*Further things to check: for DLT and SDLT tape drives: is the terminator ('dead end') connected on the second SCSI port in the back of the tape drive.

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====Fix: non-responsive tape drive====
This can occur if the user ejects the tape with the little button (and not with the recommended "dismount" button in the uct_backup program). This can also occur if a tape is mounted immediately after one is dismounted. You get the same error for both cases, "medium offline".

:*Check all that all cables are connected.

:*Check that the number on the back of the drive says "5" (use +/- to adjust if necessary)

:*Check that the top connector has a cable connecting to the computer and the bottom one has a terminator.

:*Try turning the tape drive on and off again.

:*Log in as user <code>system</code> (you will need a password from Steve):
<pre>
$ mcr sysman io auto/sele=mk
$ @sys$startup:scanco_setup_devices.com

$ show device tp0
</pre>

If it's online again, then great. If not, then the last resort is to reboot the entire system. If this doesn't work, then shut down the system (see user manual for proper steps) and eject the tape. You may need to turn the computer back on before it will eject. The tape drive should be turned on first (no tape), then the server, and any other computers. Check that the drive is online ($ show device mk). If it is, then test the drive by initializing, mounting and dismounting a brand new tape. If the drive is not online, do not insert any tapes or they will likely get stuck. Log in as system and re-try the command lines shown above.

NOTE: See "Fix a stubborn tape drive" elsewhere in this wiki.

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====Fix: stubborn tape drive====
If the drive cannot be mounted, or it is not visible with
<pre>
$ show device tp0
</pre>
then something went wrong. For example, the server computer was booted while the tape was turned off. It then does not load the driver.

You can 'force load' it - but this will disconnect the scanner for a moment, so only do it while no scan is running:

as user <code>system</code>, on sc3309:
<pre>
$ mcr sysman io auto

$ show dev tp0
</pre>

and you should see it now (otherwise turn on the tape drive, and do again)

Then you'll also have to make it available to all users:
<pre>
$ @sys$startup:scanco_setup_devices.com
</pre>

NOTE: See "Fix a non-responsive tape drive" elsewhere in this wiki.

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====SDLT320 Tape and Tape Drive FAQ====
Please refer to [[Media:Hp-faq-sdlt320-tape-drive-and-sdlt-tapes.pdf|'''SDLT320 Tape and Tape Drive FAQ''']] for details.

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==USB Drive==

===Use a USB drive===
Connect USB to VMS system and format.

Transfer files from the terminal after plugging in the USB device
$ show device dna
Usually the device is dna1 or dna2
$ mount /over=id dna2
$ create/dir dna2:[microct]
$ copy dk0:[microct]
or
$ backup/log dk0:[
and then
$ dismount dna2

Transfer files back again

$ mount /over=id dna2
$ dir dna2:[microct]
$ copy dna2:[microct]myfile.txt disk1:[microct.data.00000702.00001234]

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===USB Device Usage with Scanco Backup/Archive Software===

For illustrated help on Itanium rx2660s , please refer to [[Media:Scanco_TDxxx-USB_Device_Usage.pdf | '''Scanco_TDxxx-USB_Device_Usage.pdf''' ]]

====Initialize procedure====
If an external USB device is to be used to archive measurement data, the USB device must be initialized by Open-
VMS. The data will not be accessible from any other operating system.

- Attach the USB device to the front USB port of the Itanium rx2660.
(note: Itanium rx2620 only supports USB1.1, which will have a very slow transfer rate)

- Open the Scanco backup/archive software.

- Select the correct USB device with the arrow buttons in the “USB Device” section.

- Use the “Initialize<” button in the “USB Device” section to initialize the USB device.

- Confirm the Warning message. Note: All data currently on the device will be erased!

- Enter a six-character label

The USB device will be initialized and mounted.

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====Archive procedure====

- Attach an OpenVMS formatted USB device to the front USB port of the Itanium.
(note: Itanium rx2620 only supports USB1, which will have a very slow transfer rate)

- Open the Scanco backup/archive software.

- Select the correct USB device with the arrow buttons in the “USB Device” section.

- Use the “Mount” button in the “USB Device” section to mount the USB device.

The device label of the mounted USB device will be shown in the “USB Device” section.

- Select the measurement data to be archived.

- Select “Move To:” and “USB/VMS” and click “Start<” to archive the selected data to the USB device.

After the move procedure, the new current location of the measurement data will be shown next to the files path.

- “Dismount” the USB device when done with archiving.

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====Manual file copy procedure====
An OpenVMS formatted USB device can also be mounted and used for file storage using commands in a DECterm.

- Attach an OpenVMS formatted USB device to the front USB port of the Itanium.
(note: Itanium rx2620 only supports USB1, which will have a very slow transfer rate)

- List available devices. The last shown device is usually the attached USB device; dna12 in this example.
$ show device dna

- Mount the USB device using the correct device name
$ mount /over=id dna12

- Create a root directory. Ignore any messages if the directory already exists.
$ create /dir dna12:[microct]

- Copy any wished files to the USB device
$ copy {source files} dna12:[microct] /log

- Dismount the USB device
$ dismount dna12

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====Exporting Files / FAT file system====
If an external USB device is to be used to export measurement data to a Windows or MAC OS, the USB device must be formatted as FAT file system.

- Attach the USB device to the front USB port of the Itanium.
(note: Itanium rx2620 only supports USB1, which will have a very slow transfer rate)

- Open the Scanco backup/archive software.

- Do not “Initialize<” or “Mount” the USB device !

- Select the measurement data to be copied to the USB device, may be even sub-select the wished file type
(TIF files in the example below).

- Select “Copy To:” and “USB/FAT” and click “Start<” to copy the selected data to the USB device.

Once the USB device is connected to Windows or MAC OS, it will show a ZIP file named like the copied measurement
number. This ZIP file contains the same directory structure like the data disk on OpenVMS:

data\sample number\measurement number

In the lowest sub-directory are the copied files, as selected in the backup/archive software (TIF files in this example).

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===Problems with connected USB devices===

Sometimes USB configurations can be problematic, in which case log in as "system" on the server and run

$ dir/date SYS$SYSROOT:[SYSEXE]USB$UCM_DEVICES.DAT

to see whether a file was created recently. If one has, delete that file and reboot the server.

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==CDROM==
===Mount a CDROM===

Device could be <code>dqa0</code> or <code>dqb0</code>. I'm not sure which works:
<pre>
$ mount/foreign dqa0:
</pre>
OR
<pre>
$ mount/override=id dqa0:
</pre>
Then
<pre>
$ dismount dqa0:
</pre>

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==Saveset and Zip files==

===Saveset===

====Saveset Naming Convention====
The Scanco backup program stores raw (RAW) and image (IMA) data as save sets (SAV).
*RAW save sets contain RSQ files and IMA savesets contain all other file types.
*The saveset filename is composed of the 8-digit measurement number plus "_RAW.SAV" for raw data and "_IMA.SAV" for image data.
*For example, the data for a scan with measurement number 1234 would be stored as:
<pre>
00001234_RAW.SAV ? RSQ
00001234_IMA.SAV ? all other files, ISQ, AIM, GOBJ, TXT, SCV, etc.
</pre>

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====Create and Unpack Saveset====
Savesets are OpenVMS backup files, similar to a zip. Use the backup command.
<pre>
$ BACKUP/LOG disk3:[microct.projects.buie...] disk3:[microct.projects]buie2012.sav/sav
!Creates a saveset file of disk3:[microct.projects.buie].
!The ... after the folder indicates to include all subfolders and files.
$ BACKUP/LOG mysaveset.sav/sav disk3:[microct.projects.buie]
!Unpacks the whole saveset to disk3:[microct.projects.buie]
$ BACKUP/LOG mysaveset.sav/sav disk3:[microct.projects.buie...]
!The ... at the end of the output location indicates to unpack the saveset and maintain the original directory structure.
$ BACKUP/LOG mysaveset.sav/sav/select=*.aim disk3:[microct.projects.buie]
!The select flag is used to indicate extraction of only aim file types.
$ BACKUP/LOG mysaveset.sav/sav/select=[microct.data...] disk3:[microct.projects.buie]
!The select flag is used to indicate extraction of the folder data and all subfolders and files.
$ HELP BACKUP !More information on the backup command.
</pre>

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====View Saveset Contents====
To view contents of a saveset (SAV) on disk:
<pre>
$ backup/list upat_print_list_nomatch.sav/sav
</pre>

To view the savesets (SAV) on a tape:
<pre>
$ mount/ov=id tp0:
$ dir/date tp0:*.*
$ dismount tp0:
</pre>

To view contents of a saveset (SAV) on a tape:
<pre>
$ mount/foreign tp0:
$ backup/list tp0:*.* ! OR, backup/list tp0:*.SAV
or
$ backup/list=results.txt tp0:*.* ! save output in results.txt
$ dismount tp0:
</pre>

An idea to get the results of the backup/list into a text file: Run the procedure in a submitted script and save the resulting log file with all the output.

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====Extract a single file from SaveSet====

In a large SaveSet, sometimes we only want one file extracted, not the whole archive extracted. This can be done with

$ backup /log /select=myfile.txt mysaveset.sav /sav disk1:[microct.scratch]

or [] as destination will put the file in the current directory.

This can take a while as it looks through all the saveset. Once it logs that the file has been restored, you may interrupt with F6. Else it goes on looking through the rest of the saveset.

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====Transfer Saveset from microCT to XtremeCT====

You can create a SAV set of your project on the VivaCT and transfer it to the Xtreme system, or vice-versa.
First, create the SAV set using the command:
<pre>
For example:
$ BACKUP/LOG DISK3:[MICROCT.PROJECTS.SB.MYPROJECT...]*.*;* -
SYS$SCRATCH:MYPROJECT.SAV/SAV
</pre>
This creates the MYPROJECT.SAV file in the scratch directory. Now zip the file:
<pre>
$ cd sys$scratch
$ zip "-V" MYPROJECT.ZIP MYPROJECT.SAV (NOTE: must use quotes and a capital V!!!!)
</pre>
FTP the .ZIP file to SODOR ( in binary mode!!!), and then FTP it off onto your destination system (Viva or Xtreme). See the appropriate HowTo for FTP instructions. Once you've FTP'd it, unzip the file:
<pre>
$ unzip MYPROJECT.ZIP
</pre>
Finally, unpack the contents of the .SAV file:
<pre>
$ BACKUP/LOG MYPROJECT.SAV/SAV DISK3:[MICROCT.PROJECTS.MYPROJECT] <--- or whatever destination directory
</pre>
NOTE: transferring a .SAV directly from VMS to VMS should work, but not via any third operating system (like SODOR) - so zipping is always the safe way to make sure it works.

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===Zip===

====Zip and Unzip files====
Use the zip program to add files to a zip archive.
<pre>
$ ZIP myzip.zip myfile.txt;1 !Adds myfile.txt to myzip.zip.
$ ZIP "-V" myzip.zip myfile.txt;1 !Adds myfile.txt;1 to myzip.zip. The "-V" maintains the OpenVMS version number.
$ ZIP "-V" myzip.zip [.subdir...]*.*;* !Adds all files within subdir to myzip.zip, maintaining their version number.
$ ZIP !Displays the help for the zip command.
</pre>

Use the unzip program to unzip an archive.
<pre>
$ UNZIP "-V" myzip.zip !Extracts myzip.zip, maintaining the OpenVMS structure.
$ UNZIP !Displays the help for the unzip command.
</pre>

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====Transfer Zip between Scanco systems====

Files must be zipped before transfer by e-mail or ftp because important attributes will be lost in the transfer otherwise.

To transfer files from system A to B, do the following.

On system A:
<pre>
$ zip "-V" for_calgary.zip uctd:UCT_SAMPLES_TORONTOXT.DAT ! for each filename
$ zip "-V" for_calgary.zip uctd:UCT_MEASUREMENTS_TORONTOXT.DAT
</pre>
This will add both files to the same zip file.

Note: "-V" is very important, it must be capital V!

Transfer the file by e-mail, or by ftp.

On system B:
<pre>
$ unzip -j for_calgary.zip ! to unzip on your end them (-j to 'junk' the original file path)
</pre>

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====Unpack Zip sent by Scanco====
In the .zip file, you'll find a .sav file. Unzip the .zip just by saying

<pre>$ unzip xxxx.zip</pre>

Then:

<pre>$ backup/log xxxx.sav/sav disk3:[steve.devel.temp]</pre>

and it will unpack everything into <code>disk3:[steve.devel.temp]</code>

Or:

<pre>$ backup/list xxxx.sav/sav</pre>

and you see what's in the .sav.

Then:

<pre>$ backup/log xxx.sav/sav/sel=[andres.uct.ipl_for_cust...] disk3:[steve.devel.cipl...]</pre>

and it will create the same diretory tree in steve.devel.cipl as it was when I
packed it into the .sav.

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==Backup and Archive==

===UI Procedures===

====µCT Disk-Utility====
The µCT Disk-Utility Program is used to archive and restore scan data. To start the program type <code>$ uct_backup</code> in a DEC terminal, or use the disk button.

[[File:Uct_backup.jpg|40px]]
*The backup captures both the programs and databases.
*A little helper terminal comes up and gives feedback of every file backed up.
[[File:Uct_backup_pic01.jpg|600px]]

Two possible ways to use <code>UCT_BACKUP</code>:
:* COPY TO -> this does not update the database.
:* MOVE TO -> this updates the database.

Scenario 1:
<pre>
1. Use UCT_BACKUP to 'move' the RSQ to 'tape'
2. Use UCT_BACKUP to 'move' the ISQ to 'garbage'
3. Use UCT_BACKUP to 'move' the remainder (AIM/GOBJ) to 'tape'
</pre>
*At operation 3, the measurement directory will be deleted from the measurement disk.
*The directory will automatically be restored if you restore your data from tape.

Scenario 2:
<pre>
1. Use UCT_BACKUP to 'move' the RSQ to 'tape'
2. Use UCT_BACKUP to 'move' the ISQ to 'garbage'
3. Move all the GOBJ/AIM/etc to a project directory.
4. Generate a .SAV file and put on the IMA tape.
</pre>
*You will have to delete the measurement directories (using UCT_BACKUP if you like).
*The disadvantage of this scenario is that the image data cannot be restored using UCT_BACKUP.

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====Raw Data Backup====
*Ideally 1-2 week after scanning.
*RSQ files are backed up onto RAW tapes (see [[Scanco_Administration#Tape_Label_Convention|'''Tape Label Convention''']]). Put the most recent RAW tape into the tape drive, then press "Mount".
*Show "Current (with RAW)", use the file filter (Measurement: ) to search for your files (e.g., CAMOS) and press enter or press "Update List".
*Select all the files to backup by highlighting them using the left mouse button and ctrl to select individual files or shift to select a range.
*Highlight RAW, choose "Move To" and "Tape". Press "Start...".
*When the backup is complete press "Dismount" to eject the tape.
*If the tape auto-ejected without pressing "Dismount" then the tape is full (see [[Scanco_Administration#Full_Tape|'''Full Tape''']]).
*If you select multiple files, be sure they all need to be backed up, otherwise you will get an error.
:[[File:Uct_backup_pic04.jpg|500px]]

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====Image Data Backup====
*Ideally 1-2 months after scanning, after contouring, onsite analysis and copied image data to project disk.

#'''Delete ISQ After Evaluation'''
#*ISQ files are normally deleted after completing your evaluation since they are very large files and can be reconstructed from the RSQ file.
#*Show "Current (on Disk)", type the beginning of your sample name (e.g., CAMOS) in the file filter and press enter or press "Update List".
#*Select all the files for which you have completed the evaluation (there will be a + sign next to any scan that has been evaluated). #*Highlight IMA, choose "Move To" and "Trash".
#*[[File:Important.JPG|20px]] After you choose the trash symbol, you will now be given the option to select specific file types, choose "Select" and "ISQ". Press "Start...".
#*Only choose one file type to delete at a time. The wildcard (*) indicate all files other than "ISQ" and "AIM" files.
#:[[File:Uct_backup_pic05.jpg|500px]]
#: 
#'''Backup IMAGE Data'''
#*AIM, GOBJ and other evaluation files are backed up onto IMA tapes (see [[Scanco_Administration#Tape_Label_Convention|'''Tape Label Convention''']]).
#*Put the most recent IMA tape into the tape drive, then press "Mount".
#*Show "Current (on Disk)", type in the beginning of your sample names (e.g., CAMOS) in the file filter and press enter or press "Update List".
#*Select all the files to backup by highlighting them using the left mouse button and ctrl to select individual files or shift to select a range.
#*Highlight IMA, choose "Move To" and "Tape". Press "Start...".
#*When the backup is complete press "Dismount" to eject the tape.
#*If the tape auto-ejected without pressing "Dismount" then the tape is full (see [[Scanco_Administration#Full_Tape|'''Full Tape''']]).
#:[[File:Uct_backup_pic06.jpg|500px]]

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====Use 'Script...' button====
Usually, you will start the move/copy by clicking on <code>'Start...'</code> button. The <code>'Script...'</code> button is for advanced users.

*Use of the 'Script...' button will generate a script <code>sys$scratch:archive.com</code>, that you may submit it in batch mode later (e.g. over night) by typing: <pre>$ scanco_submit_command sys$scratch:archive.com/after=23:59</pre>
*In a multi-computer cluster setup, you may want to specify the exact queue name of the computer that has the tape hooked up by giving e.g. <code>/que=sceval_fast</code>.
*Insert a tape, but do NOT mount the tape in the normal program. If necessary: if it's a new tape, [[Scanco_Administration#Initialize_a_New_Tape|'''initialize''']] it as usual.
*The batch job will be started one minute before midnight in the example above. <code>$ show entry</code> will show you that it is holding until then.
*See <code>$ help submit /after</code> and <code>$ help dcl_tips date_time example</code> for more help on this.
*Sample script file (archive.com) restoring the RSQs of measurements 6452 and 6580:
<pre>
$ MOUNT/FOREIGN TP0:
$ UCT_BACKUP_BATCH
ALL
RAW
COPY
DISK
! Meas: SB_BUIE_EX_CTRL_PH_01 (6452)
MEAS
6452
EXECUTE
! Meas: SB_BUIE_EX_CTRL_PH_01 (6580)
MEAS
6580
EXECUTE
EXIT
$ DISMOUNT TP0:
$ EXIT
</pre>

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====Database Backup====

The database (DB) backup should be performed for each user on the system. It should not be performed as user 'calibration' or some derivative. In the case of the XtremeCT2 and XtremeCT cluster, both the 'microct' and 'xtremect2' user accounts must be used to backup their respective DB.

By performing the DB backup, the warning dialog that appears when logging into the system should go away.

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====Operating System (OS) Backup====
If the following error-message appears on the screen then you can click OK to continue your work.

MESSAGE: No recent OS Backup found!
Please perform OS backup (DISK0) in privileged account!
%RMS-W-FNF file not found.
CODE: 268534416
Facility RTL

This message means that no operating system (OS) backup has been performed within the last 6 months. Please perform an OS backup as soon as possible by following the steps below:

1. Make sure there are no scans in progress and that the que is halted from all activity.

2. Log in to the calibration account: Since we have two scanners on the same system, login as either "calib3401" or "calib3309", depending if you need to backup the XtremeCT2 or XtremeCT, respectively. For microCT clusters, (best to do this on SCEVA3) using the username calib5019 and the password (ask Steve for this).

3. Type in the DECterm window:
$ set proc/priv=bypass
Or Set priviledge to bypass by <code>$ spb</code>
$ r um:uct_b Or $ uct_backup

4. You will now see 2 additional buttons on the bottom left that is not seen when logged in as microct user. Push either the button "OS Backup to Disk DK0" or mount the specific OS backup tape and push the "OS Backup to Tape" button.
* A system backup to tape and to DK0 should both be performed.

5. Check the command line & queue to ensure that the backup is being carried out. If you submit the job as 'batch mode' the backup is submitted to SYS$BACKUP queue and allows you to close the backup program and 'end session' without interrupting a running backup. Check with 'show queue' to see the backup job on the queue.

6. Exit the Backup Program and log out of the calibration account.

After a successful OS backup the message above will not appear for the next six months.

Alternatively a system backup can be completed using the command line, without using the uct_backup program. The instructions from Scanco can be found here. The advantage to this method is that you will be able to name the specific backup save set.

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===Using Scripts for Backup/Archive===

====Project Backup/Archive====
*Refer to [[Media:Microct_project_backup.pdf|'''Project Backup SOP''']] or [[Media:Microct_project_backup.docx|''' its Word format''']] for reference.

=====Backup Project=====
Regularly backup projects on a monthly basis using command <code>$ @com:BACKUP_PROJECT.COM</code>
*The script is submitted to the queue and upon completion the log is emailed to the user.
*a SAVset (an OpenVMS file type similar to a zip file), a project info file and a file list are created in DISK5:[BONELAB.PROJECTS.BACKUP] for the microCTs and DISK4:[BONELAB.PROJECTS.ARCHIVE.ARCHIVE] for the XtremeCTs.
*The saveset along with two TXT files created will be automatically SFTP to Winston:\\Backups\backup\
*After the transfer, the saveset file on disk are deleted, leaving only two TXT files on the project disk.
*Only keep the two most recent backups for each project, A or B version name appended on the project name:
:*Backup version "_A" for odd months (Jan, Mar, May, Jul, Sep, Nov), e.g. YZHU_A_OTHER_2017-01-12.SAV
:*Backup version "_B" for even months (Feb, Apr, Jun, Aug, Oct, Dec), e.g. YZHU_B_OTHER_2020-04-08.SAV
*The user MUST verify that the backup completed successfully.
*SAVsets greater than 250 GB cannot be transferred by automatic SFTP, use interactive/manual SFTP instead to transfer to Winston.
*If you are backing up a very large project, please check the server disk space before starting the backup.

<pre>
$ @com:BACKUP_PROJECT.COM
===========================================================
BACKUP PROJECT TOOL V1.2 (XtremeCT)
P1:LOCATION DISK4:[BONELAB.PROJECTS.DUNCAN]
P2:TYPE 1=MOUSE,2=RAT,3=HUMAN,4=OTHER
P3:PROJECT CAMOS
P4:PERSON Ying Zhu
P5:DESCRIPTION A monthly backup
P6:EMAIL me@ucalgary.ca
P7:SFTP y,n
P8:START y,n
</pre>

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=====Restore Project=====
In the commands directory (com) is a BACKUP_RESTORE.COM script which will automatically generate a script to restore a user's project.
*The saveset file has to be moved to Winston:\\Backups\archive folder to be restored.
*The user will be asked if they wish to restore to the original location, or to a new location.
*The script is submitted to the queue and the log from the restore job is emailed to the user.
*The user MUST verify that the job completed successfully.
<pre>
$ @COM:BACKUP_RESTORE.COM
</pre>

=====Delete Project=====
In the commands directory (com) is a BACKUP_DELETE.COM script which will automatically generate a script to delete all the files and subdirectories of a specified path.
*The command script is opened so that the user can check the files to be removed to go ahead.
*You will need to manually delete the root project directory after it's empty.
<pre>
$ @COM:BACKUP_DELETE.COM
</pre>

=====Known Bugs in Project Tools=====
*Long file name won't work (28 letters work but not 32 letters).
*if the user specifies too long a file name, the Project Backup Scripts will fail with the following error:
RMS-E-CRE, ACP file create failed
SYSTEM-W-BADFILENAME, bad file name syntax

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=====Archive Project Saveset to Tape=====
Projects should be stored safely onto a backup tape once complete.

Summary

The following steps summarize the process:
:* Archive the project directory to the tape (detailed instructions below).
:* Change tape to "read only" to protect contents
:* Check tape saveset to ensure proper backup
:* Write name of tape on the project LOG sheet
:* Copy project LOG sheet and bring to Bone Imaging Laboratory "completed" project book
:* Bring copy of tape to the Bone Imaging Laboratory for safe keeping
:* Delete the contents of the project from the disk

In the project, there should be the regular set of directories including DOC, COM, MODELS, LOG. Once the project is stored to tape, ensure that the log sheet for that project include a note stating which tape it was backed up to. Take a photocopy of the log sheet and add it to our Bone Imaging Laboratory project book for COMPLETED projects.

In the following example, a project titled BERN is backed up onto tape. Ideally, the name of the SAV file on tape is the same as the project (i.e., BERN). Note that SAV files must have names with no more than 13 characters (including the .SAV)!

The following example backs the BERN project/directory onto tape IMA001. For large projects and/or critical projects, it is advisable to dedicate an entire tape. The three dots (...) indicate that ALL subfolders of DK0:[MICROCT.PROJECTS.BERN] will be included.

<pre>
$ mount/foreign tp0:

$ backup/log dk0:[microct.projects.bern...]*.*;* tp0:proj_bern.sav - ! writes a saveset to tape
/block=65534 /label=IMA001 -
/media_format=nocompaction ! NEVER use the /rewind option here

$ backup/log tp0:*.sav/select=*.isq DISK4:[BONELAB.PROJECTS.TBONE.ISQ_FROM_TAPE...]/by=parent ! extracts all ISQ files from the tape

$ dismount tp0:
$ dismount tp0: /nounload ! same as previous command, but does not eject the tape (i.e. if you want to read the tape once more)
</pre>

Note that the <code>/rewind</code> option should never be used for backup as it instructs the tape drive to rewind after backup is complete causing a major risk of over writing.

Sometimes it might be handy to exclude certain files. For example, to exclude RSQ files: <code>/excl=*.rsq</code>

A good reference for backup commands and ideas are available in the <code>UM:UCT_MOVE_FILES.COM</code> script which is used by the <code>UCT_BACKUP</code> program. See also the <code>help backup</code> instructions:
<pre>
$ help backup
</pre>

To view the contents of a tape to ensure you've successfully stored your project use the following commands (further details in "HowTo: View save set (SAV) contents"):

To just view if the saveset is on tape (but not its contents):
<pre>
$ mount/ov=id tp0:
$ dir/date tp0:*.*
$ dismount tp0:
</pre>

Note: you can also save the saveset list in a text file using the /output qualifier.

To view the files within a saveset on tape, and save the results in a file called <code>results.txt</code>:
<pre>
$ mount/foreign tp0:
$ backup/list=results.txt tp0:*.*
$ dismount tp0:
</pre>

To delete a set of directories, use the <code>dl</code> command.
<pre>
$ cd ur BERN
$ del *.*;* ! Deletes ALL files in a directory
$ dl *.dir;* ! Will only delete empty directories (not nested directories)
</pre>

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=====Extract Project Saveset from Tape=====
To restore a project, you have two choices:
*1. Login as user <code>calibration</code> and then go to the projects directory. From there:
<pre>
$ spb (bypass priv)
$ backup/log tp0:proj_davison.sav/rewind [*...]
</pre>
This puts all the files back in their original directory structure.

*2. As user <code>microct</code>
<pre>
$ mount/foreign tp0:

$ backup/log tp0:proj_davison.sav/rewind/select=[microct.projects.davison...]
disk2:[microct.projects.davison...]

OR

$ backup/log tp0:*.*/rewind disk3:[microct.projects.vitamink.models]
</pre>
Make sure to write the same path in the /select as the output (except for the
actual disk2 portion). Alternatively, you could unpack it into a slightly different root
directory (i.e., TMP) by changing the output path.

The three dots infers to use the same paths in the saveset as the file structure put onto disk.

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====Scripts to Backup RAW and IMA====
A script can be output from the backup tool to backup and restore data using the backup program.
*When restoring data using this method, choose the COPY to DISK option. The data will be restored to its original location on the data disk.
*You must manually submit the script to the backup queue.
*The command procedures are written to SYS$SCRATCH:ARCHIVE.COM.
*Here is the sample script for backing up RAW data:
<pre>
$ MOUNT/FOREIGN TP0:
$ UCT_BACKUP_BATCH
ALL
RAW
MOVE
TAPE
! Meas: ATHLETE_126 (10565)
MEAS
10565
EXECUTE
! Meas: ATHLETE_126 (10566)
MEAS
10566
EXECUTE
! Meas: ATHLETE_126 (10567)
MEAS
10567
EXECUTE
EXIT
$ DISMOUNT TP0:
$ EXIT
</pre>
*Here is the sample script for backing up IMA data:
<pre>
$ MOUNT/FOREIGN TP0:
$ UCT_BACKUP_BATCH
ALL
IMA
MOVE
TAPE
! Meas: ATHLETE_126 (10565)
MEAS
10565
EXECUTE
! Meas: ATHLETE_126 (10566)
MEAS
10566
EXECUTE
! Meas: ATHLETE_126 (10567)
MEAS
10567
EXECUTE
EXIT
$ DISMOUNT TP0:
$ EXI
</pre>

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====Disk Usage information====
<pre>
$ @COM:DISK_MOUNTIES.COM !Give data disk usage information on an account.
$ eve sys$scratch:disk_mounties_output_summary.txt
</pre>

The template file for summarizing the disk mounties results: [[Media:BoneLab_Data_Disc_Usage.xlsx|'''BoneLab_Data_Disc_Usage.xlsx''']]

To look at the RSQs in the database
<pre>
$ dir/siz dk0:[microct.data...]*.rsq
</pre>
the three dots means all subdirectories.

Other useful commands:

<code>$ ctheader xxxxxx.isq</code>

or

<code>$ ctheader xxxxxx.rsq</code>

shows you header.
<pre>
$ fda command file-wildcard
</pre>
does a 'file do all' of the command on all the given wildcard filenames.
<pre>
$ pipe xxxx | search sys$pipe "patient"
</pre>
is the pipe command in VMS.

So all three combined:
<pre>
$ pipe fda ctheader dk0:[microct.data...]*.rsq | search sys$pipe "patient name"
</pre>
or any other field you want to search for!

If you have a more complex program to run (e.g. with an argument), use the double quotes as follows:
<pre>
pipe fda "aix -l" *.AIM | search sys$pipe "Patient Name"
</pre>

'''Other ideas''':

<pre>$ write_info</pre>

gives you a file <code>sys$scratch:info.txt</code> with info in it (leave defaults to get all samples ever scanned, otherwise 'zoom' in on some samples.)

Check out the <code>search</code> command:
<pre>
$ help search
</pre>
and <code>/match=and</code>
or <code>/match=or</code>

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====Disk Backup====
In the commands directory (com) is a BACKUPDISK script which will automatically generate scripts to backup all the directories on the projects disk.
*As the backup requires significant amounts of space, please check the server disk space before starting the backup.
*Each directory is saved as a separate save set (an OpenVMS file type similar to a zip file) on Winston://Bonelab/Backup/.

<pre>
$ @COM:BACKUPDISK
</pre>

*Refer to [[Media:Microct_disk_backup.pdf|'''Disk Backup SOP''']] or [[Media:Microct_disk_backup.docx|''' its Word format''']] for reference.

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=Process, Printer and System=

==Processes and Jobs==

===Manage jobs in the queue===
Use the DELETE/ENTRY and SET ENTRY commands to manage a batch job.

<pre>
$ SH QUE !Get process info
$ SH QUE /all/by_job_status=executing !Get all executing process info
$ SHOW ENTRY 1131 /full !Get full process info of entry 1131
$ SE 1311 !Get full process info of entry 1131

$ DELETE /ENTRY=251 !Deletes batch job number 251.

$ SET ENTRY 251/PRIORITY=50 !Changes the priority of batch job number 251.
!Default priority is 100 for all jobs, max is 200.
$ SET ENTRY 251/REQUEUE=SCEVAL_FAST !Moves to queue sceval_fast.
!The job cannot be executing to do this, has to be in pending status.
$ SET ENTRY 251/AFTER=TOMORROW !Holds entry 251 until the following day (midnight).

$ HELP SET ENTRY !More information on the SET ENTRY command.
</pre>

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===Control processors # on multi-processor machines===

For example, on the itanium there are two processors. By default, only one takes reconstruction jobs. The other is left for so that evaluations can take place without competing for the CPU.

But if a bottleneck is the reconstruction, it can be switched as user <code>system</code>:

<pre>
$ set que sceva2_slow/job=2
</pre>

so that it will do two reconstruction jobs simultaneously.

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===Create a new queue===
This may be useful to separate jobs for a project. The following will create a queue called BUIE$FAST, which will submit jobs to SCEVAL_FAST and SC3309_FAST.

$ initialize/queue/GENERIC=(SCEVAL_FAST,SC3309_FAST)/OWNER=[SYSTEM] -
/PROTECTION=(S:M,O:D,G:R,W:S)/BATCH/START BUIE$FAST

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===Clear out all entries in a queue===
First create a dummy queue, then merge (i.e., move) all the entries from the queue to be cleared into it, then delete the dummy queue.

Example: Clear out the printer queue.
$ stop/reset printer1
$ initialize/que dummy
$ assign/merge dummy printer1
$ delete/que dummy

Example: Clear out a batch queue, e.g., sys$fast.
$ initialize/que/batch dummy
$ assign/merge dummy sys$fast
$ delete/que dummy

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===Stop and restart queues===
There are three methods. First the nice method.

1. As for the printer queue, a normal user can stop and start other queues.

<pre>
$ stop/que/reset sceval_slow
$ start sceval_slow
</pre>

This kills the current process running. If you want to let the current process complete before stopping the queue, use:
<pre>
$ stop/que/next sceval_slow
</pre>

2. Use the web browser Mozilla.

:*Open mozilla
:*'batch queues'

:*Resize the window so it occupies the right half of the screen

:*Click on 'delete job' once with the MIDDLE mouse button, this will open a new window on the right half of the screen. Ensure the two windows do not overlap, if they do resize the window which contains the batch queues list. Once window locations are correct MIDDLE click on the rest of the jobs which you wish to delete (click on 'Delete Job' in the batch queue list). The reason for locating the widows is because each successive click on 'Delete Job' will open a new window and you don't want it to cover the batch queues list.

:*Then Exit from mozilla, this will delete all the open windows, it may take a bit if you are deleting lots.

3. Now the harsh method.

[[Image:Bones2.jpg|20px]] Warning: Extreme caution! Explicit permission for this change or similar changes must be obtained from Dr. Steven Boyd.

Completely remove the queue and re-generate, as user <code>system</code>

<pre>
$ stop/queue/reset sc3309_slow
$ delete/queue sc3309_slow
</pre>

Then you must restart the queue. To learn how to do this refer to:
<pre>
$ eve sys$startup:dcps_hpljet_ip.com
</pre>

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===Kill hunging processes===

Sometimes jobs need to be stopped manually, such as when FTP or TCPIP is hung. This is done as follows:

Checked processes with
$ show sys
where the FTP jobs are running. Doing it as system with these commands would show all the FTP jobs on all nodes:
$ mcr sysman
SYSMAN> set env /cluster
SYSMAN> do pipe sh sys|sear sys$pipe ftpc
It showed that they all were running on SCEVA1 only. So I logged in there and using the IDs given at the list from above's command:
$ stop/id=29804056
...

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===Check CPU usage and kill a process===
Determine what process is using all the CPU (e.g., SYMBIONT, a print process) using the monitor command, then use the show system command to determin the Pid, which can be used to stop the process.

The print (SYMBIONT) process is known to consume excessive CPU when the clocks are advanced for daylight savings on the alpha systems.
<pre>
$ monitor process/topcpu
$ show system
OpenVMS V7.3-2 on node SCEVAL 6-APR-2009 12:42:22.82 Uptime 124 23:16:08
Pid Process Name State Pri I/O CPU Page flts Pages
20C00081 SWAPPER HIB 16 0 0 01:07:05.63 0 0
20C00087 CLUSTER_SERVER HIB 14 2218 0 00:00:00.54 63 77
20C00088 CONFIGURE HIB 10 23 0 00:00:00.02 54 20
20C00089 LANACP HIBO 13 -- swapped out -- 32
20C0008B FASTPATH_SERVER HIB 10 9 0 00:00:00.01 79 94
20C0008C IPCACP HIB 10 10 0 00:00:00.02 37 28
$ show process/all/id=Pid
$ set host 0
user: system
password:
$ stop/id=Pid
</pre>
*Process Name = BATCH_122 means entry 122 in the queue

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==Printer==

===Set up TCPIP printer queue on a VMS workstation===
$ stop/que/res hpljet
$ tcpip set nohost hpljet
$ tcpip set host "hpljet" /address= xxx.xxx.xxx.xxx
$ start hpljet

Note that many HP printers will not work with OpenVMS. Checking for compatibility is important.

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===Stop and restart the printer queue===

How to fix the printer queue when hung, not working or giving an error.
A full printer queue can seriously affect system performance.
Be sure that the queue is cleaned up from time to time.

<pre>$ show queue</pre>

to first find out the real name of your printer queue.
* Replace "hpljet" and "...dcps_hpljet..." by your own queue (i.e., PRINTER1 for XtremeCT) name below.
* First approach, as normal user <code>microct</code>:
<pre>
$ stop/queue/reset hpljet
$ start/queue hpljet
</pre>

If you need to release a job
$ set entry/release 123

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==System==

===Monitor System===
====Monitor system usage====

<pre>
$ monitor/interval=1 processes/topcpu
$ monitor/interval=1 system
$ show error
$ show system
$ @SCOM:SHOW_DISKS.COM (or simply $ DISKS)
</pre>

The command <code>show error</code> may indicate errors. One or two errors is OK.

To see what processes are running (specific to the machine, not cluster wide).

<pre>
$ show device disk2/file
$ show user /full
</pre>

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====Check status of OpenVMS system====

If when rebooting a VMS system there is a failure, sometimes a message can be repeated many times. The way to stop this repeating message is to press <code>ctrl-C</code> or <code>ctrl-P</code> to get to the <code>>>></code> prompt.

Then show some of the device information, either specifically

>>> show device py*
>>> show device dy*

or in general

>>> show device

which might show more than needed. The output of

>>> show bootdef_dev

can also be useful.

Once settings are all good, you can reboot the system with
>>> init
>>> set bootbios pyb0
>>> boot

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====Check disk status====
Login as the system user on the workstation connected to the disk array that you want to check.

$ run sys$system:msa$util.exe
MSA> set controller

Show the raid volumes (e.g., to check if it failed or is recovering).
MSA> show unit

Locate disks associated with a raid volume (e.g., unit0).
MSA> locate unit0

Accept a failed unit (e.g., unit0) - only for itanium workstations, which use a newer version of OpenVMS.
MSA> accept unit0

Show disk information.
MSA> show disks

Get information on MSA utility functions.
MSA> help

Exit the MSA utility.
MSA> exit

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====Check status of disk array====
To look at the disks in an MSA30 tower:
There are several options to check the status of the disks. One is, if it is installed, to use the command-line utility
<pre>$ mcr msa$util</pre>
as "system". Enter
<pre>
MSA> set controller
MSA> show unit
MSA> show disks
MSA> exit
</pre>

Another is to start the WBEM web interface, which shows the status of the hardware graphically.

It is possible to fix a disk array that hasn't booted by doing the following:

At the login prompt, type 'shutdown'. This will get you to the <code>>>></code> prompt.
There should be a RAID card, for example on Percy, named <code>pya0</code>. Try:
>>> show device
>>> set auto_action halt
>>> init
>>> run bios pya0
>>> set auto_action restart
>>> boot

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====Check disks status in enclosure====

Periodically connect to http://10.148.64.254/ (user name: manage, password same as system password) and check if there are any errors or warnings, like failed disks. You can easily see which disk has failed in the graphical view of "Physical" -> "Enclosure X"

Consider not all web browsers allow connection to this rather old web server. Firefox and Mozilla on the workstations do work fine.

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===Recover System===
====Consistently needs warm-up scanner - Shutter-failsave-Job====

If the scanner is consistently needing to warm-up on consecutive days, and was not powered off, this is likely due to the Shutter-failsave-Job disappearing from the 3309-Batch queue (for XT1). The job must be re-submitted.

The executing file is located in the CALIB3309 ($ um:submit_shutter_test.com) and the command to submit the job is:
<pre>
$ submit/after="tomorrow"/noprint/que=uct_measurement_queue um:submit_shutter_test.com
</pre>

You can check the status by typing:
<pre>
$ show que *3309_batch*/all
</pre>

This job tends to disappear now and then, perhaps because of an abrupt shutdown of the workstation or maybe when stop/pause/re-start the queue. Contact Scanco if this does not resolve.

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====Disk not mounted/unavailable, directory not found, volume not enabled====
Disk is not mounted or is unavailable. Error opening ...., directory not found, volume is not software enabled.
<pre>
%DIRECT-E-OPENIN, error opening DISK4:[MICROCT.PROJECTS]*.*;* as input
-RMS-E-DNF, directory not found
-SYSTEM-F-VOLINV, volume is not software enabled
</pre>
This can happen if communication is broken between workstations, causing the disk mount to time out. Check if this is by showing the devices, then dismount and remount the disk.
<pre>
$ show dev

Device Device Error Volume Free Trans Mnt
Name Status Count Label Space Count Cnt
SC3309$DKA100: Online 0
SC3309$DKD0: Mounted 0 ALPHASYS 3.18GB 642 2
SC3309$DKD1: Mounted 0 AUSER_01 42.84GB 4 2
SC3309$DKD2: Mounted 0 ADATA_01 173.00GB 4 2
SC3309$DKD3: Mounted 0 ADATA_02A 215.80GB 1 2
SC3309$DKD4: Mounted 0 ADATA_02B 215.85GB 1 2
SC3309$DKD5: Mounted 0 ADATA_02C 215.81GB 1 2
SC3309$DQA0: Online 0
SC3309$DQA1: Offline 1
SC3309$DQB0: Offline 1
SC3309$DQB1: Offline 1
SCEVAL$DKA0: Online 0
SCEVAL$DKA1500: Mounted 0 (remote mount) 1
SCEVAL$DKC0: MntVerifyTimeout 0 ADATA_03A 541.62GB 1 2
SCEVAL$DKC1: MntVerifyTimeout 0 ADATA_03B 541.38GB 1 2
SCEVAL$DKC2: MntVerifyTimeout 0 ADATA_03C 541.60GB 1 2
SCEVAL$DQA0: Online 0

$ set host 0
system

$ dismount SCEVAL$DKC0:
$ mount/cluster SCEVAL$DKC0: ADATA_03A
%MOUNT-I-MOUNTED, ADATA_03A mounted on _SCEVAL$DKC0:
$ mount/cluster SCEVAL$DKC1: ADATA_03B
%MOUNT-I-MOUNTED, ADATA_03B mounted on _SCEVAL$DKC1:
$ mount/cluster SCEVAL$DKC2: ADATA_03C
%MOUNT-I-MOUNTED, ADATA_03C mounted on _SCEVAL$DKC2:
$
</pre>

If this does not restore the disk, then shutdown the computer. At the blue screen...
<code>>>> init</code>
Wait for blue screen to return.
<code>>>> run bios pya0</code>
Press F2 at the prompt to accept potential data loss.
Wait for blue screen to return.
<code>>>></code>
Press power button to turn off.
Press power button to turn on.

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====Kill hanging program====

If a program is hunging, it may not be necessary to shut down the system and restart. For example, if the <code>uct_evaluation</code>
program is hung, do the following

<pre>
$ show dev/full microct_scsi

$ stop/id=<Owner process ID> (Replace the <> with the actual ID)

for example:

$ stop/id=2280091C
</pre>

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====Reset the display/GUI====
These commands will terminate the current login session and may restore a frozen or messed up screen. You will need to remotely access the problem workstation either from another micro-ct workstation or using a personal computer.

Use the set host command to connect to the problem workstation (e.g., thomas) using the node name (e.g., sc3309) or the IP address (e.g., thomas.kin.ucalgary.ca).

$ set host sc3309
login: system
password:

Issue the reset display command.
$ @sys$startup:decw$startup restart

At the prompt, type "y".

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====Restart screen server====

If the monitor fails to show the login prompt and displays a blank gray screen...telnet to the computer from another computer (e.g. a PC or so) and login as user system. Run the restart command:

<pre>
$set host gordon.ucalgary.ca. [or other computer name]
$username: system
$password: [system password]
$@sys$startup:decw$startup restart</pre>
confirm (answer "yes" at the prompt) and logout.
<pre>
$y
$logout</pre>

This will kill all programs on your screen, but it will leave all batch jobs running, so if you do a BATCH measurement, this will survive! (but interactive scan will be killed).

If you are restarting a monitor connected to a KVM box, unplug and re-plug in the box.

This command also helps when the mouse/keyboard freezes.

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====Restart Alpha stations====

[[Image:Bones2.jpg|20px]] Warning: Do not do this unless absolutely necessary.

For shutdown

At the login screen, type "shutdown"/no password and hit enter.
Then, you can turn the computer off at the prompt.

Then, you may turn the disk array off (unplug it as there is no power switch).

After you move the computer, power on the disk array and then the computer.

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====Slow/non-responsive computer====

This is usually caused by people logging in via SSH multiple times. The solution involves resetting the SSH/TCPIP daemon.

:*If you are local at the computer:

You will need to log in as user <code>system</code>. ONLY EXPERIENCED USERS SHOULD EVER LOG IN AS SYSTEM!

The system will be extremely slow (it will take 5 minutes just to get a log in prompt). This is expected.

<pre>
$ set host 0 ! user name 'system' and password
$
$ @sys$startup:tcpip$ssh_shutdown ! shutdown SSH
$
$ set host 0 ! user name 'system' and password
$
$ @sys$startup:tcpip$ssh_startup ! restart SSH
</pre>

Alternatively, you can reboot the system to reset the SSH. This is not an appropriate solution and it is solving the problem by hitting it with a jack hammer. Sometimes it is the only choice though.

:*If you are remotely logged in:

You will have to log in as user <code>system</code> and run a script called STOP_START_TCPIP.COM.

This works essentially the same as for the above method, except that since it would be impossible to restart SSH remotely once it is shut down, two separate scripts are called and submitted on SCEVAL_FAST (make sure the queue isn't clogged) separated by a 1 minute delay. The first script called is STOP_TCPIP.COM and the second is START_TCPIP.COM.

To execute this process, you must log in as system, go to the SYS$SCRATCH directory, and interactively execute the script:
<pre>
$ @STOP_START_TCPIP.COM
</pre>

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====Shutdown a workstation remotely====
If a workstation becomes unresponsive, it may be possible to shut it down remotely from another workstation or personal computer, which is preferable over doing a hard power off. These instructions were provided by Mark Blanchard.

'''1. Remote shutdown from another micro-ct workstation'''. MAY NOT WORK FOR CLUSTER SERVER

Login as the system user.

$ set host 0
user: system
password:

Start the system manager.
$ mcr sysman

Set the environment to the workstation to be shutdown (e.g., thomas) using its node name (e.g., sc3309).
SYSMAN>< set env/node=sc3309

Issue the shutdown command. Add a time delay, e.g., 5 min, if you want to give users time to disconnect and the automatic reboot flag if you want to restart.
SYSMAN> shutdown node /min=5 /automatic_reboot

*You need to remain logged into the session running the shutdown until the other node has been shutdown completely!!!

'''2. Remote shutdown from a personal computer'''.

Begin a remote session to the workstation and login as the system user.

Create a detached terminal.
$ create/terminal/detach

On the PC, port 6000 needs to be accessible to the micro-ct workstation and in the X-server's configuration (e.g., in file X0.hosts for Xming).

Issue the shutdown command.
$ shutdown

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====Slow computers - Change RAID battery for Itanium computers====

If computers become sluggish, particularly when saving data after a scan, have Scanco check the batteries in the RAID drive. The batteries in SCEVA3 were changed 2014-11-10. There are two batteries. Order the HP brand (should look like the ones in the image).
*Instructions to open the Itanium work station and access the PCI card: [[Media:HP_rx2660_PCI_card.pdf |'''Change PCI card''']].
*Instructions to change the batteries after accessing the PCI card: [[Media:HP_SA6402_Batteries.pdf |'''Change batteries''']].

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====Frozen computer - "bootstrap failure" on boot up====
The micro-CT computer is frozen or there is a "bootstrap failure" on boot up, This happens to the client computers (those connected to the scanners) when there is interruption in the network. The only option is to restart the computer.

====Crash of XtremeCT II workstation computer====

For a non-responsive monitor and/or a mouse and/or a keyboard of the XtremeCT II workstation (sometimes caused by a lost of connection to server, or an internet outage):

:*1. The first thing to do is to check system logs for any indication of the cause of the issue, if you have the "Administrator" user privilege.
:*2. The next thing to do is to soft-reboot by remote-login and using command line to reboot the workstation, if you have the "system" user privilege.
:*3. If no success, try hard-reboot by pressing the power button as indicated below.
:*4. If no success, try hard-reboot by unplugging both power cords as indicated below.
:*5. If still no success, contact Scanco immediately.
:*6. The last thing to do is to record the issue and any possible reasons.

1. Checking system logs:

:*1) Remotely log into the iLO (the management console of the workstation) using SSH as user "Administrator" with the system password.
Both user/pw are case sensitive. For XtremeCT II workstation (James) it is SSH to 10.148.64.231. For others, consult the network diagram.

A trick: This connection only succeeds through a MAC or PC (via putty) direct login, not through an OpenVMS or Scanco system.
$ ssh -l Administrator 10.148.64.231
:*2) Then you get to a MP> prompt here:

MP MAIN MENU:
CO: Console
VFP: Virtual Front Panel
CM: Command Menu
CL: Console Log
SL: Show Event Logs
HE: Main Help Menu
X: Exit Connection
[sc3401-mp]</> hpiLO->

:*3) Type in 'SL' to show event logs, then you could choose 'E' for system event:

[sc3401-mp]</> hpiLO-> SL
Event Log Viewer Menu:
Log Name Entries % Full Latest Timestamped Entry
-------------------------------------------------------------------------------
E - System Event 1661 58 % 13 Sep 2018 11:17:43
F - Forward Progress 20000 100 % 13 Sep 2018 11:17:43
I - iLO Event 500 100 % 18 Sep 2018 07:46:42
C - Clear SEL and FPL
L - Live Events

Enter menu item or [Ctrl-B] to Quit: E
Log Name Entries % Full Latest Timestamped Entry
-------------------------------------------------------------------------------
E - System Event 1661 58 % 13 Sep 2018 11:17:43
Event Log Navigation Help:
+ View next block (forward in time, e.g. from 3 to 4)
- View previous block (backward in time, e.g. from 3 to 2)
<CR> Continue to the next or previous block
D Dump the entire log
F First entry
L Last entry
J Jump to entry number
H View mode configuration - Hex
K View mode configuration - Keyword
T View mode configuration - Text
A Alert Level Filter options
U Alert Level Unfiltered
? Display this Help menu
Q Quit and return to the Event Log Viewer Menu
Ctrl-B Exit command, and return to the MP Main Menu

:*4) From here you can use - and + to go through the log history back and forth. Not all logs do make a lot of sense though, as they are mainly meant for HPE engineers.
:*5) When finished, use CTRL + b to get back to the main MP> prompt.
:*6) Use MP> co to get to the console, where you see at what stage the booting process is, in case it does not boot properly.
:*7) When finished, use CTRL + b to get back to the main MP> prompt.
:*8) Use MP> x to end the connection.

2. Soft-reboot by remote login:

If a workstation becomes unresponsive, it may be possible to shut it down remotely from another workstation or personal computer, which is preferable over doing a hard-reboot. These instructions were provided by Mark Blanchard.

:*2.A) Remote shutdown from another micro-ct workstation. MAY NOT WORK FOR CLUSTER SERVER

Login as the system user.
$ set host 0
user: system
password:

Start the system manager.
$ mcr sysman

Set the environment to the workstation to be shutdown (e.g., thomas) using its node name (e.g., sc3309).
SYSMAN>< set env/node=sc3309

Issue the shutdown command. Add a time delay, e.g., 5 min, if you want to give users time to disconnect and the automatic reboot flag if you want to restart.
SYSMAN> shutdown node /min=5 /automatic_reboot

You need to remain logged into the session running the shutdown until the other node has been shutdown completely!!!

:*2.B) Remote shutdown from a personal computer.
Begin a remote session to the workstation and login as the system user.

Create a detached terminal.
$ create/terminal/detach

On the PC, port 6000 needs to be accessible to the micro-ct workstation and in the X-server's configuration (e.g., in file X0.hosts for Xming).

Issue the shutdown command.
$ shutdown

3. Hard-reboot by power button:

:*1) Hold the power button until it turns yellow.
:*2) Wait a minutes or two, then press the power button only once and shortly. You will not see anything for a while. Pressing the power button again during this time will turn off the workstation again !
:*3) After about 10~15 min, the workstation would boot up properly.

4. Hard-reboot by unplugging both power cords:

:*1) Hard-reboot by unplugging both the power cords. This will reset the console and controllers.
:*2) Wait for 5~10 minutes, then press the power button only once and shortly. You will not see anything for a while. Pressing the power button again during this time will turn off the workstation again !
:*3) After about 10~15 min, the workstation would boot up properly.

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=Remote Access=

==For Scanco support==
===Send a terminal to a remote computer===

To send a terminal from XCT clusters to Scanco for maintenance, you need to know the ip address for the terminal location.
Such as For Mark Blanchard:

$ set display/create/transport=tcpip/node=193.72.60.24
$ create/terminal/detach

The cursor will disappear for a minute or so, and reappear with the $ prompt indicating sent already.

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==Access VMS filesystem==
===Access XtremeCT VMS filesystem on a Mac===

In finder, select Go --> Connect to Server

This opens up a window that allows you to enter a server address. Enter the following information:
<pre>smb://136.159.130.28</pre>

Click connect. If the internet connection is working, you will then be prompted to enter in login info:

<pre>
USERNAME: xtremect
PASSWORD: uct
</pre>

Select the volumes you want to mount.

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===View XtremeCT VMS filesystem from a Windows PC===

The HP program that allows the VMS file system to be viewed by a PC is called Pathworks (on the VMS system). The following information is needed to connect to the VMS system:

<pre>
USERNAME: xtremect
PASSWORD: uct
WORKGROUP: microct
</pre>

Then, in Windows explorer, while connected in the same network as the VMS station (i.e., .130) enter the following IP address for Thomas (SC3309):

<pre>\\136.159.130.28\</pre>

Alternatively, map the drive.
<pre>
Right click on my computer and choose map network drive.

Folder:
\\136.159.130.28\UCT_DATA1
or
\\136.159.130.28\UCT_DATA2

User name: xtremect@microct
Password: uct
</pre>

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===View VivaCT40/uCT35 VMS filesystem from a Windows PC===

The HP program that allows the VMS file system to be viewed by a PC is called Pathworks (on the VMS system). The following information is needed to connect to the VMS system:

<pre>
USERNAME: vct_40
PASSWORD: uct
WORKGROUP: microct
</pre>

Then, in Windows explorer, while connected in the same network as the VMS station enter the following IP address for SCEVAL:

<pre>\\136.159.74.140\</pre>

Alternatively, map the drive.
<pre>
Right click on my computer and choose map network drive.

Folder:
\\136.159.74.140\SB_DATA
or
\\136.159.74.140\SB_PROJ
or
\\136.159.74.140\BH_DATA
or
\\136.159.74.140\BH_PROJ

User name: vct_40@microct
Password: uct
</pre>

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===Map a Network Drive to the VMS filesystem from Windows===

To do this you must be on the same network as the OpenVMS system. For main campus and the XtremeCT, you will map the drive to Thomas (136.159.130.28), the workstation connected to the scanner.

<pre>
Right click on My Computer and choose Map Network Drive...

Folder: \\136.159.130.28\uct_data1 !FOR THE PROJECTS DISK

and/or

\\136.159.130.28\uct_data2 !FOR THE DATA DISK

User name: microct\xtremect
Password: uct
</pre>

Note: You must use the numerical IP address and not the host name (i.e. thomas.kin.ucalgary.ca).

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==Setup remote access FAQ==
===Access data remotely===
Refer to [[Media:Scanco-faq-accessing-data-remotely.pdf|'''Scanco tutorial on accessing your data remotely''']] for

*A quick refresher course on accessing files
**Web browser
**File sharing
**File transfer protocol (FTP)
*Network file system NFS
*Running Scanco programs remotely

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===Use Hummingbird Exceed for remote access===

*Screen definition
:Server visual = PseudoColor
:Window mode = multiple

*Keyboard input
:Primary = decemus
:Alternate = us

*EVE commands
:select = "end"
:cut = "delete"
:paste = "insert"

:move forward a word = CTRL + right_arrow
:move to start of document = CTRL + up_arrow
:move to end of document = CTRL + down_arrow

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===Use XWin32 for remote access===

Run XWin32. Run Putty and connect to sceval.ucalgary.ca. Use the terminal normally to run programs, which should open with XWin32.

Additional terminal windows can be opened with <code>$ dec</code>

If you try to connect from somewhere other than the university, you will probably get the following error when trying to open a window:

Xlib: connection to "sceval.ucalgary.ca:10.0" refused by server
Xlib: Can not connect to a host on a restricted network
X Toolkit Error: Cannot Open Display
%DWT-F-DWTABORT, xtoolkit fatal error

Type the following at the command prompt to direct the display:

$ set display/create/transport=tcpip/node=Your_IP_Address/server=0

You can find your IP address from: http://www.ip-adress.com/

If you're running XWin32 from off campus and behind a router, forward ports 6000 - 6010 TCP and 177 UDP to your computer.

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===Set up Putty with gold-key access===

Refer [http://bone.wiki/index.php?title=Scanco_User_Instructions#PuTTY_and_Xming '''PuTTY and Xming'''] to download putty.

Set 'keyboard' to Vt400, and 'initial state of numeric keyapad' to 'Application', and now the 'NumLock' key is the gold key (like PF1), and the editor can repeat stuff.

Then

<pre>$ set term/vt100</pre>

to enable the editor in the terminal.

And duplication of a line is:
<pre>
- (which would be PF4) to erase a line,
then twice "numlock, then -" (gold-PF4 is 'restore line')
</pre>

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===SSH tricks===
====RSA and DSA Authentication====

The main advantage of setting up RSA authentication is that you will no longer have to type your password each time you access a host with ssh. There are some technical reasons why RSA and DSA access is more secure than password access.

These instructions work on both Linux and OS-X.

# Create your public/private key pair on your local computer
#* At the command prompt type: ssh-keygen -t rsa
#* You will be asked to create a passphrase.
#* This will create the files .ssh/id_rsa and .ssh/id_rsa.pub . Once you have these files, you never have to repeat this step.
# Copy your public key contents into the .ssh/authorized_keys2 file on the remote server
#* You can email yourself the file .ssh/id_rsa.pub from the local computer.
#* Alternatively, you could do this: ssh username@remoteserver.com 'cat >> ~/.ssh/authorized_keys2' < /Users/Youruser/.ssh/id_rsa.pub

NOTES ABOUT KEYS
Remember, the "authorized_keys" file is a concatenation of public (id_rsa.pub) keys,
and the "id_rsa" is the private key.
Every user on every computer should only have ONE "id_rsa" file,
but can have multiple "id_rsa.pub" files concatenated into
their "authorized_keys" file.

=====SSH Agent=====

SSH-Agent is a tool to store your passphrase so you don't have type it every time.

On OS-X, it is integrated into the system Keychain - you will be asked once if it should remember your passphrase, and after that you don't have to worry about it.

Most Linux systems also have ssh-agent configured to start with every session. You may however have to do this once:
ssh-add ~/.ssh/ida_rsa

====SSH Tunneling====

This is an alternative to VPN through kinesiology. It may come in handy if for some reason VPN is not working.

If you're outside the university system and want to access, for example, svn on mike.kin, which is normally blocked by the university firewall, you can do that with ssh tunneling. Here is an example:

ssh eric@mighty-mac.kin.ucalgary.ca -L 2000:mike.kin.ucalgary.ca:443 -N

Here is what is going on:
* I want to access port 443 (which is https) on mike.kin.ucalgary.ca.
* I have an account on mighty-mac, so I'm using that server to create an ssh tunnel inside the university firewall. I could use any machine I had an account on inside the university system, even mike.kin.ucalgary.ca, the one I'm trying to get to (in fact, that would be best, but for purposes of demonstration I'm using a different machine).
* I'm mapping the local port 2000 to port 443 on mike. Anything I send to localhost:2000 will by sent by ssh or the ssh tunnel to mighty-mac, which will then send it on to port 443 on mike.
* 2000 is a random 4-digit port number. If by some fluke you happen to choose one that is in use, ssh will complain and you will have to try another port number.

Now I can fire up my browser and point it to

https://localhost:200/trac/

And what I get is the trac site on mike.

If I want to get the code, I can do this:

svn checkout https://localhost:2000/svn/numerics88/trunk trunk_tunnel

("trunk_tunnel" is just the directory name where it will end up. It can be named anything, but this will remind me that it only works when the tunnel is up.)

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==Physical connections==
===Connect to VMS station with a serial port cable===

To do this, you will need to connect from a PC using a PC-to-PC (NULL modem) serial cable, 9600 baud. Install PuTTY and connect with the 'serial' option. You will need to know the COM port that is used by the PC to connect the serial cable. You can do this by checking on the PC the [Hardware][Device] settings.

Typical login is "Admin" and password is usually same as the 'system' password.

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===Export VMS display to SUN or LINUX terminal===

<pre>
# - temple
$ - sceval
# xhost +temple.ucalgary.ca
# ssh -X microct@sceval.ucalgary.ca
$ set display /create /transport=tcpip /node=temple.ucalgary.ca
</pre>

NOTE: Do not use <code>xhost+</code>. Always specific exactly which computer is being
allowed X access.

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=Dose=

==Dose Calculations==

===XtremeCT radiation dose===
Some notes about radiation dose to help decide acceptable scanning protocols. These comments are based on scanning an adult (not children having significant red marrow at the scan region).

:*The annual dose limit for the hand for an occupational user is 500 mSv (as per the ICRP), and with the x-ray energy of our XtremeCT that translates to 500 mGy local dose per year. For non-occupational subjects, the limit is generally 10x lower (i.e., our volunteers should not have more than 50 mGy local dose per year).
:*Our scanner delivers a local dose of about 5.3 mGy per scan. However, if we have adjacent scans, there is some overlap due to the penumbra of the x-ray beam which results in about double the local dose (a conservative guess would be 10 mGy) for a ~1mm overlap region. Averaging over the whole scanned regions (overlap and non-overlap regions) we can say that the average delivered local dose is about 7-8 mGy. The local dose is not additive. If we're very conservative, and we take 10 mGy as the local dose, then we could theoretically scan a person 5 times before exceeding the 50 mGy limit based on a tenth of the occupational limit (500 mGy).

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===vivaCT CTDI dose===
====Dose calculation====

Assuming the following settings on the vivaCT for "high mode", we will calculate the CTDI dose.

2000 projections (360 degrees)
0.109 mA
200 ms IT

I calculate the time current value as:

0.109 mA * (0.200 + 0.012) S * 2000 proj= 46.22 mAs

The 0.012 is the integration time between projections.

Taking the proportion of the 68 mAs at 55 kV resulting in 720 mGy (see the document on example
dose calculation on this Wiki site), we have:

46.22 / 68 * 720 = 490 mGy

Since CTDI in air is approximately two times the weighted CTDI, and since our setup is more like in air, we get:

2 * 490 = 980 mGy per scan.

It's always a good idea to look at the time-current product in the control file to get an approximate estimate.

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====Dose chart and example====
*Refer to [[Media:VivaCT dose information-fyi.pdf|'''VivaCT CTDI Dose Calculation Example''']].

We have measured the following CT dose indices (CTDI).
:*CTDIw: Weighted CTDI (chart below)
:*CTDIair: CTDI in air (2 times CTDIw - calculate from chart below).

The detector was placed in the center of a 35 mm PMMA cylinder which was placed in the center of rotation.

<pre>
70kV 300ms 85uA Field of view 38.9mm 1000 Proj./180°: CTDI = 260 mGy
55kV 300ms 109uA Field of view 38.9mm 1000 Proj./180°: CTDI = 220 mGy
45kV 300ms 133uA Field of view 38.9mm 1000 Proj./180°: CTDI = 190 mGy

70kV 300ms 85uA Field of view 30.7mm 1000 Proj./180°: CTDI = 420 mGy
55kV 300ms 109uA Field of view 30.7mm 1000 Proj./180°: CTDI = 350 mGy
45kV 300ms 133uA Field of view 30.7mm 1000 Proj./180°: CTDI = 305 mGy

70kV 300ms 85uA Field of view 21.5mm 1000 Proj./180°: CTDI = 850 mGy
55kV 300ms 109uA Field of view 21.5mm 1000 Proj./180°: CTDI = 720 mGy
45kV 300ms 133uA Field of view 21.5mm 1000 Proj./180°: CTDI = 620 mGy
</pre>

high res = 1000 Proj./180°
medium = 500 Proj./180°
standard = 250 Proj./180°

The CTDI scales linear with the integration time (s), with the current (uA) and number of projections. If you have different settings there, it is easy to calculate the CTDI.

CTDI Definition:
<pre>
Integral from +50mm to -50mm of D(z)/NxT
</pre>
:*where D(z) is the dose profile along a line z which is perpendicular to the tomographic plane
:*N is the number of tomographic sections produced in a single rotation
:*T is the nominal tomographic section thickness

Example: How to estimate how much radiation would be incurred by a mouse scanned at 25
um resolution (medium resolution -- MR) at 55 kVp, 109 uA, 150 ms IT, for about 30 minutes?

If you take your settings you can calculate the CTDI. First thing you have to be aware is that the CTDI is something like the local dose but it takes the cone beam geometry and the not perfect collimation of the x-ray beam into account (The CTDI value is always higher than a local dose measurement with for example TLDs). It does not matter how many stacks you are scanning. The dose you have at one point which is within the volume you are scanning gets the same local dose if you are performing a 1 stack or a 4 stack measurement.

With the 55kVp/109uA HR with 300ms we have a value at the 30.7 mm position of 350 mGy. Because you have MR we can divide the values by a factor of 2; and because you have 150ms instead of 300ms there is an other factor of 2. You would get 87.5 mGy for the position 30.7 mm. Because of the cone beam the dose has a quadratic dependency to the diameter of the field of view. (30.7 mm/25 mm)2 = 1.5. The CTDI value for your settings is in the order of 87.5 mGy * 1.5 = 132 mGy.

Note that for in vivo measurements, we should multiply the result by a factor of two since we are doing the measurement in AIR, not WATER. The charts above are assuming the CTDI done in water.

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==Optimize Scan for Low Dose==
*Refer to [[Media:Scanco-faq-optimization-for-dose.pdf|'''Optimize Scan Protocols for Low Dose''']].

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Scanco Administration

2021-04-06T18:06:25Z

Yingzhu: /* Fix a wrong scan site code */

=OpenVMS=

==OpenVMS References==
*[[Media:OpenVMS Users Manual.PDF| OpenVMS User Manual]]
*[[Media:Vmsfaq.pdf| OpenVMS FAQ]]

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==Unix related==
*[[Media:Vms-unix-commands.pdf| OpenVMS Commands with UNIX equivalents]]

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===Unix filenames on VMS with multiple '.'===

The directory names would have been cvs-1.11.21.dir on Linux. However VMS doesn't allow more than 1 . in the name. If you enter

<pre>$ set process/parse=extended</pre>

in a terminal you'll be able to access these files. You could consider renaming them i.e. cvs-1_11_21.dir.

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===Unix command line basics===
====Twelve Essential Commands====

These are the commands which you have to know in order to be basically functional with a shell (command line).

{|
|-valign="top"
|width="80pt"| <tt>ls</tt>
| List directory contents.

<tt>ls -l</tt> long listing with dates and permissions

<tt>ls -a</tt> list all, including hidden files (hidden files start with a period)

|-valign="top"
| <tt>cd</tt>
| Change directory.

<tt>cd -</tt> change to previous directory

<tt>cd ~</tt> change to home directory

<tt>cd ..</tt> change to parent directory

|-valign="top"
| <tt>pwd</tt>
| Print current (working) directory.
|-valign="top"
| <tt>cp</tt>
| Copy file(s).

<tt>cp -r somedir somedest</tt> Copy recursively (directory and all contents)

|-valign="top"
| <tt>mv</tt>
| Move (or rename) a file (or directory)
|-valign="top"
| <tt>rm</tt>
| Delete (remove) a file.

<tt>rm -r somedir</tt> Delete recursively (directory and all contents)

<tt>rm -ri somedir</tt> Delete recursively, but prompt before each removal

<tt>rm -rf somedir</tt> Delete recursively, never prompt

|-valign="top"
| <tt>mkdir</tt>
| Create directory.
|-valign="top"
| <tt>rmdir</tt>
| Remove (empty) directory.
|-valign="top"
| <tt>cat</tt>
| Print file contents (to console).
|-valign="top"
| <tt>less</tt>
| Scroll through file contents, one page at a time. SPACEBAR to advance a page, B to go back a page, Q to quit, /pattern to search for pattern
|-valign="top"
| <tt>man</tt>
| Get help on <tt>command</tt>. (eg. <tt>man ls</tt> for help on <tt>ls</tt>). You move around in man as you do with less: SPACEBAR is forward a page, and so on.
|-valign="top"
| <tt>exit</tt>
| Close shell (i.e. the terminal). If this is your login shell, you will log out.
|}

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====File names with spaces====

Spaces on the command line separate arguments. Therefore file names containing spaces require special treatment to avoid being interpreted as two separate files. There are a couple of methods. You can use quotes:

cp "file name with spaces" file_name_without_spaces

You can also use the backslash, which indicates that any special significance is to be removed from the following character. Thus a space, instead of being the delimiter for arguments on a command line, is to be interpreted as a regular character.

cp file\ name\ with\ spaces file_name_without_spaces

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====Copying and pasting====

Copying and pasting in a terminal is generally done with the middle mouse button. Just mark the text you want to copy with the mouse, holding down the left mouse button in the usual way. Then move the cursor (which is different than the mouse pointer - move the cursor with arrow keys typically) to where you want to insert and click the middle mouse button (on a wheel mouse the middle button is the wheel).

Tip: You can double-click to mark a whole work, or triple-click to mark a whole line. Remember - you haven't only marked it, you've put it in the clipboard.

Note: This applies to X11, for example on Linux. If using OS-X, just use Option-C and Option-V as usual.

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====Recalling previous commands====

You can scroll though your previous commands (command history) by using the UP and DOWN arrow keys.

A more advanced trick is to use CTRL-R, which is particularly useful when you want to recall a command you used some time ago. Hit CTRL-R and then start typing some fragment of the command you're searching for. The prompt will automatically update to show you the most recent match to the fragment you've typed so far. If you want the matching command previous to the one shown, hit CTRL-R again. Once you've got the previous command you're looking for, hit ENTER to run it again, or start editing it.

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====Be lazy: use TAB to minimize typing====

Some commands and especially some file names can be pretty long. Don't want to type it all? Type the first few letters, then hit TAB. The shell will fill in the rest, as far as there is a unique completion (either command or filename). If there is not a unique completion to the end, you might have to type another character or two and then hit TAB again.

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====Keyboard Shortcuts====

Here are some common command line keyboard shortcuts. Some of these are bash-specific shortcuts, so not all of them will work on all systems.

Note: If you're using OS-X, a number of the editing shortcuts below work in ALL programs in OS-X. (With the sad exception of Microsoft Office, which overrides the system-wide key bindings.)

{|
|+ Table 1. Common editing key bindings
|-
|width="80pt"| <tt>CTRL-A</tt> || Move to the end of the line.
|-
| <tt>CTRL-E</tt> || Move to the beginning of the line.
|-
| <tt>CTRL-F</tt> || Move forward one character.
|-
| <tt>CTRL-B</tt> || Move backward one character.
|-
| <tt>ALT-F</tt> || Move forward one word.
|-
| <tt>ALT-B</tt> || Move backward one word.
|-
| <tt>CTRL-D</tt> || Delete one character forward.
|-
| <tt>CTRL-H</tt> || Delete one character backward.
|-
| <tt>ALT-D</tt> || Delete one word forward.
|-
| <tt>CTRL-W</tt> || Delete one word backwards.
|-
| <tt>CTRL-K</tt> || Delete (Kill) everything from the cursor forwards (to the end of the line).
|-
| <tt>CTRL-U</tt> || Delete everything from the cursor backwards (to the beginning of the line).
|-
| <tt>CTRL-T</tt> || Transpose two characters.
|-
| <tt>ALT-T</tt> || Transpose two words.
|-
| <tt>ESC .</tt> || Insert the last argument (word) from the previous command.
|-
| <tt>CTRL-X-X</tt> || Move between end of line and current cursor position
|}

{|
|+ Table 2. Common control key bindings
|width="80pt"| <tt>CTRL-C</tt> || Terminate the current program, or sometimes cancel some operation.
|-
| <tt>CTRL-\</tt> || Seriously kill the current program! Use only after <tt>CTRL-C</tt> has failed.
|-
| <tt>CTRL-D</tt> || End-of-file. This is often used to signal the end of input, or to exit a program.
|-
| <tt>CTRL-G</tt> || Cancel the current operation. An occasionally useful command to get yourself out of things.
|-
| <tt>CTRL-L</tt> || Redraw the console. Mostly useful if some program running in the background spews a lot of stuff onto your terminal.
|-
| <tt>CTRL-Q</tt> || The only time you need this is if you accidently hit <tt>CTRL-S</tt>. In that case the console is locked until you hit CTRL-Q to unlock it. Apparently once a long long time ago this was actually a useful feature.
|-
| <tt>CTRL-R</tt> || Recall command containing characters. After hitting <tt>CTRL-R</tt>, type the fragment you want to search for. If it returns a command which isn't the one one want, hit <tt>CTRL-R</tt> again to cycle through matches.
|-
| <tt>CTRL-Z</tt> || Suspend the current program and put it in the background. This is very useful once you figure out how it works. Refer to the section on putting jobs in the background.
|}

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====Using scp to copy files between computers====

scp is a secure copy command that works bewteen computers. Typically any computer that supports ssh also supports scp. You must have an actual user account on the target computer, so for example you typically won't be able to scp to mike.kin .

scp works just like the cp command, with a few extra decorations:

scp eric@mighty-mac.kin.ucalgary.ca:Documents/important_file.txt .

In this example the file I want to copy is on the computer mighty-mac.kin.ucalgary.ca, and I used eric@ to specify my user name. You can leave off the user name if it is the same on both computers. The period as the destination is just standard Unix short-hand for the current directory. You can use the -r flag to copy whole directories. For example:

scp -r calculations mighty-mac.kin.ucalgary.ca:Documents/Projects

In this example calculations is a directory containing many files, and possibly subdirectories. This example copies files to mighty-mac instead of from it.

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====Running long calculations====

Here are some useful tips for running long jobs.

=====Getting the prompt back after starting a job=====

Use & at the end of the command. This puts the job in the background. For example:

./myjob someargs &

To see all your background jobs (the ones started in the current shell), enter:

jobs

To bring one of these to the foreground, use:

fg %n

where <tt>n</tt> is the job number (yes it needs a <tt>%</tt> in front of it). To move it to the background again, hit CTRL-Z. This however doesn't just move the job to the background, it suspends it. To get it running again, use

bg %n

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=====Keeping a job running after you log out=====

Use nohup. For example, suppose you want to run <tt>./myjob 20</tt>. In this case, you could use:

nohup nice ./myjob 20 &> output &

There are several things to note here:

* The <tt>&</tt> at the end of the command line is there so you get the command prompt back immediately (see the previous section).
* We have redirected the output to a file out_file with <tt>&> output</tt>. If you don't do this, any output to STDIN (normally the console) will automatically go into a file called <tt>nohup.out</tt>.
* We've niced the job to reduce it's execution priority. This is courteous if you're a multiuser system.

If you want to see what's in nohup.out (or whatever you called it) at any time, you can do the usual

cat nohup.out

Here's another potentially more useful command:

tail -f nohup.out

tail shows you the last few lines of the files. In addition, the -f flag ("follow") means that as lines get added to the file, they are displayed on the screen. This looks just like when you run the program without nohup, except when you hit CTRL-C, the program keeps on running in the background.

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=====Finding out if any of your jobs are still running=====

This command will show all jobs that belong to user "eric":

ps -u eric

Another useful command is "top", which will show interactively which processes are using the most processor cycles.

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=====Terminating a job prematurely=====

If you decide that you want to kill the job before it completes, this is the command:

kill PID

where PID is the actual PID (a number) of the process. You find the PID with 'top' or 'ps -u eric' (replace eric by your user ID of course).

Occasionally a process will decline to terminate when you request it to. This is the more brutal, never-fails method to kill a job immediately:

kill -s KILL PID

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=====Suspending a long-running job and restarting it later=====

First find the PID (process ID) with top or with ps. For example, I might list all jobs belonging to me with:

ps -u eric

To stop the job, send it a STOP signal:

kill -s STOP PID

(replace PID with the actual PID number). It is now no longer running, but it still occupies memory (although the memory it uses will probably be swapped out to disk). When you want to resume execution, give it a CONT signal:

kill -s CONT PID

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==Graphical Applications==

===Calendar - Fix corruption===

Sometimes the calendar file can be corrupted, which is annoying every time you log onto the system.

When we login to a server through a workstation, there is a "File is not a Calendar Datafile." information message pops up.

This means that the calendar database got corrupted during an improper interruption such as a system crash due to a power outage.

To fix this, you will need to login to the Server through the Workstation

Once logged in:
cd xdefaults
dir *calendar*.dat /date

Delete the calendar file for the workstation, such as the following James workstation:
del decw$calendar_sc3401.dat

Once logged out and logged in again, you will be asked if you want to create a new calendar file.
Say "yes" there and a new calendar will open.

In the calendar window menu "options" -> "general" set the "start iconized" -> apply and "ok", then "options" -> "save settings".

So next time you log in, the calendar window will be minimized in the right lower corner.

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===Session Manager - Create a customized button===
The session manager part to enable the double-click on the AIM file:
Session Manager, 'Options', 'Menu', enter new item
SAP
with command:
<pre>
@decw$user_defaults:sap$vue
</pre>
Then move that menu point into 'Applications' menu.
Also:
'Options', 'File types', Create 'AIM' file type.
Move 'rename', 'copy', 'purge' etc. into menu, Select 'SAP', click on
'Change double click', and also move SAP into menu.

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===EVE Editor===

====Launch EVE editor====

On the command line
$ edit/display=decwindows/tpu fname.txt

Or to set it up permanently, edit <code>DISK1:[MICROCT]MICROCT_SETUP_USER.COM</code> to include

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====Configure EVE editor====

The following file, called <code>tpu.dat</code>, should be installed in <code>disk1:[microct.xdefaults]:</code>
<pre>
#
# DECTPU V3.1 1993-04-22 15:50 defaults
# CHANGED B.KOLLER 21-JUN-90
#
# Copyright (c) 1993 Digital Equipment Corporation. All rights reserved.
#
#
# The following are all the resource names that DECTPU supports.
#
Tpu.Tpu$MainWindow.Title: DECTPU Copyright © Digital Equipment Corporation 1992. All Rights Reserved.
Tpu.Tpu$MainWindow.ApplicationTitle: DECTPU
Tpu.Tpu$MainWindow.IconName: DECTPU
Tpu.Tpu$MainWindow.X: 610
Tpu.Tpu$MainWindow.Y: 0
#
# The following resource names are commented out so that users can specify
# *rows and *columns and have DECTPU obey those directives. If DECTPU finds
# finds no resource names governing the number of rows and columns it should
# have, it uses 24 rows and 80 columns.
#
#
Tpu.Tpu$MainWindow.Columns: 80
Tpu.Tpu$MainWindow.Rows: 56
*EVE_MENU_BAR*background: #ADADADADADAD
Tpu*XmScrollBar*background: #ADADADADADAD
Tpu*XmDialogShell*background: #ADADADADADAD
Tpu*XmMenuShell*background: #ADADADADADAD
*background: white
Tpu*condensedFont: OFF
Tpu*fontSetSelection: 0

# 0 = big font
# 1 = little font
# 2 = GS font (German Standard)
# 3 = Fine font (used only for non-latin 1 fonts?)
</pre>

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====EVE editor Commands====

* mark -> ctrl-space
* delete -> remove (delete)
* insert -> insert here (insert)
* learn -> ctrl-k (ctrl-r to stop)
* The right 'alt' key on the PC accesses the menu for EVE.

{| class="wikitable"
| copy
| <code><PF1><Remove></code> on VMS
|-
| paste
| <code><Insert Here></code> on VMS or <code> <ctrl><insert></code> on PC
|-
| cut
| <code><Remove> </code> on VMS or <code><delete> </code> on PC
|-
| learn
| <code><CTRL><K></code>
|-
| stop
| <code><CTRL><R> </code> (then give a key sequence such as <code><CTRL><Q></code>)
|-
| repeat
| <code><PF1><#><(CTRL-Q)> </code> (the <code>CTRL-Q </code> depends on the given key sequence).
|-
| find next
| <code><PF3></code>
|-
| enter search string
| <code><PF1><PF3></code>
|-
| replace string
| <code><PF1><S></code>
|-
| margins
| Mouse click bottom of window type: <code>set right 999</code>
|-
| kill line
| <code><PF4></code>
|-
| kill word
| - (minus key on number pad)
|-
| advance next line
| <code>0</code> (zero on number pad)
|-
| select text
| <code><CTRL><SPACE></code>
|}

*To avoid having the EVE editor automatically create multiple lines from a long input sequence set the margins [FORMAT - SET MARGINS] to some high number eg. 500.

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====Use Commands Remotely with XWin32====

Default key settings:

{| class="wikitable"
| remove (cut) and append to previous paste buffer
| <code>9</code> (nine on number pad)
|-
| paste
| <code><insert></code>
|-
| learn
| <code><CTRL><K></code>
|-
| stop
| <code><CTRL><R></code> (then give a key sequence such as <code><CTRL><Q></code>)
|-
| repeat
| <code><CTRL>-Q</code> or given key sequence
|-
| kill word
| - (minus key on number pad)
|-
| advance next line
| <code>0</code> (zero on number pad)
|-
| go to end of line
| <code>2</code> (two on number pad) or <code><CTRL><E></code>
|-
| go to start of line
| <code><backspace> or <CTRL><H></code>
|-
| go to start of word
| <code>1</code> (one on number pad)
|-
| delete line to left of cursor
| <code><CTRL></code>
|-
| turn on/off select text
| <code><CTRL><SPACE> or .</code> (on number pad)
|-
| select all text
| <code><CTRL><O></code>
|-
| turn on/off overstrike
| <code><CTRL><A></code>
|-
| save and exit
| <code><CTRL><Z></code>
|-
| enter command
| <code><CTRL></code>
|}

You may find it useful to define keys. For example, define keys to cut, copy and paste:

*To Cut <code><CTRL><X></code>:
:<code><CTRL></code> (enter command)
:Command: <code>define key=Ctrl/x cut</code>

*To Copy <code><CTRL><C></code>:
:<code><CTRL></code> (enter command)
:Command: <code>define key=Ctrl/c copy</code>

*To Paste <code><CTRL><V></code>:
:<code><CTRL></code> (enter command)
:Command: <code>define key=Ctrl/v paste</code>

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====Use terminal based editor (EVE)====
<pre>
$ edit file.txt
</pre>
If you are using this from a remote terminal, you will need to initiate a vt100 terminal.
<pre>
$ set term /vt100
</pre>
Some useful commands:
:* ctrl-z -> exit with save
:* ctrl-y -> kill without saving
:* do-key, then type 'quit' or 'exit' (what is the do key on a remote terminal?)
:* PF2 -> shows special keypad functions
:* GoldKey -> PF1

====Use EVE editor Remotely====
For remote sessions, once used $ EVE to start the text editor, press Ctrl-B to bring up a command line at the bottom of the screen.

*Command: @eveconfig

This will set backspace to delete normally.
*Ctrl-X cut
*Ctrl-C copy
*Ctrl-V paste
*Ctrl-S save file
*Ctrl-L learn command
*Ctrl-F find next
*Ctrl-Q quit
*Ctrl-O open
*Ctrl-space to select

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===Scout Views===
====View scout views in two locations====
Go to scout view directory
<pre>
XtremeCT side:
$ cd DISK1:[MICROCT.DATA.SCOUTS]

VivaCT side:
$ cd ADISK1:[VIVACT.DATA.SCOUTS]</pre>

Use the program ximage
<pre>$ x asdf.SCV</pre>

For XtremeCT users, 2 sets of scout views are saved. Scout views can be viewed from the main scouts directory (above) and in the data directory under specific patient and measurement numbers. For example using patient #: 2795 and meas#:9933:
$ cd DISK2:[MICROCT.DATA.00002795.00009933]
$ x C00008848.SCV

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====Reuse old scout views====
Reference SCV files are not overwritten. When you Save a new reference within the scout view Dialog, it writes a new version that is read by the measurement program.

If you want to return to an old scout view reference, you will have to manipulate files manually.

Typically all the scouts are accessible here:
DISK1:[MICROCT.DATA.SCOUTS]0000PPPPSS.SCV

PPPP being the patient number, and SS the Site Code number [i.e. 20,21,38,39 = RL, RR, TL, TR].

Assuming you have only version;1 and ;2 what you can do is to rename/delete version;2, so that it is not read anymore by the measurement program.
Or copy version;1 as version;3, but this is rather messy.

Note: Do not look in the measurement directories. There are copies of the SCV files, but those are not the one called by the measurement program.

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==File Operations==

===Copy and Move===
====Copy files between accounts/users====

As user <code>system</code> you can copy files between accounts (e.g., microct and devel). There is no need to set user/priv=bypass as this is set by default as user system.

If you want to copy between two users (i.e. normal users, not calibration or system), then you can only write on the user directories for which you are logged in. So, if you want
to copy files from account xtremect2 to microct, you need to log into microct account and copy the file from xtremect2 to microct

If you want to use the backup command for copying multiple subdirectories with
the three dots (e.g., <code>disk2:[microct.data.00000034...]</code>) then you HAVE to put an <code>/owner=devel</code> at the end:

<pre>
$ backup/log disk2:[microct.data.00000034...] -
disk2:[devel.data.00000034...]/own=devel
</pre>

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====Move a directory on the same device====

You can simply use the rename command to move a directory on the same device, but you need to set DELETE protection for the file owner for this to work
$ set prot=o:rwed <dir>.dir
$ ren <dir>.dir new:[parent.directory]
$ set prot=o:rwe new:[parent.directory]<dir>.dir

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====Move a whole directory structure with BACKUP command====

Sometimes we want to move entire directories. For example, moving a measurement directory from DISK2 to DISK6, or moving a project to another disk.

Here is how to move a project:
$ BACKUP DISK2:[MICROCT.PROJECTS...] DISK3:[MICROCT.PROJECTS...]/VERIFY

Note the use of <code>...</code> in both places.

If you move a data measurement, you could do it as follows:
$ BACKUP DISK2:[XTREMECT2.DATA...] DISK6:[XTREMECT2.DATA...]/LOG/VERIFY

In both cases, you can add a <code>/DELETE</code> command to so that it deletes after the move is completed and verified.
$ BACKUP/VERIFY/DELETE DISK2:[XTREMECT2.DATA...] DISK6:[XTREMECT2.DATA...]/LOG/VERIFY

Alternatively, you can simply check that the move was successful, and then delete the original files:
$ delete disk2:[microctt.projects...]*.*;*
$ dl disk2:[microctt.projects...]*.dir ! A for all; do until sub-dirs are gone

Note that I've misspelled "microctt" on purpose as these commands are VERY dangerous. You could wipe out a lot of data by accident. Be careful!

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====Fix corrupted VMS files when moved to or from a PC====

We start by getting good file format/attributes from a good aim/isq/gobj, etc.

$ ana/rms/fdl/out=correct.fdl good.aim

Then we edit the file correct.fdl, leaving only 5 lines:
RECORD
BLOCK_SPAN yes
CARRIAGE_CONTROL none
FORMAT fixed
SIZE 512

Now we have to set the file attributes of the affected aim (isq, gobi) file:

$ set file/attr=lrl=514 bad.aim ! Yes, 514
$ set file/attr=lrl=514 *.AIM ! do a bunch at a time

Finally we create a fixed file

$ convert/fdl=correct.fdl/trunc bad.aim converted.aim

This process discards the superfluous 2 bytes, usually caused by transferring to/from a PC.

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===Delete===

====Delete older versions of files====
Use the PURGE command.[[Image:Bones2.jpg|20px]] Warning: Extreme caution!
<pre>
$ PURGE !Removes older versions of all files in the directory! CAREFUL!!!!
$ PURGE myfile.aim !Removes older versions of myfile.aim.
$ PURGE /KEEP=3 !Removes all but the three most recent versions of all files.
$ HELP PURGE !More information on the PURGE command.
</pre>

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====Undelete Files====

The Disk/File Utility (DFU) will allow you to restore files that have been deleted, however, you will only be able to do so if the disk space hasn't been overwritten. This means that unless all scanning and access to the disk is stopped, you likely only have a couple of hours at most to undelete the files. 
 
Login as the system user and start the disk file utility program, DFU. 
<pre>
$ dfu
DFU> undelete diskX: /file=myfile OR undelete filepath/filename
</pre>
 
For example, suppose we want to restore an RSQ (C0001234.RSQ) that was deleted from the BH data disk (disk2): 
<pre>
DFU> undelete disk2:/file=C0001234.RSQ
</pre>
If the file can be undeleted successfully (i.e., without corruption), then you will be asked if you wish to restore the file. Type "y" or "n". 
When done restoring desired files, to get out of dfu:
<pre>
DFU> exit
$ logout
</pre>
 
*The undelete function will lock access to the disk while it searches for a file and until you respond "y" or "n" to restoring it. This means that all programs and commands trying to access the disk (i.e., by other people using the system) will appear to freeze momentarily until the disk is unlocked.
*If you search for a specific file, the lock period will be very short (maybe 15-30 seconds). If you search for files in general (e.g., *.RSQ), the lock period will be longer (maybe 5 to 10 minutes).
*You cannot search specific locations for files (i.e., a folder on a disk).
*Files are restored to their original location on disk.
*More information on DFU can be found here: http://digiater.nl/dfu.html

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====Delete a directory====
Use the DL command (this calls the script $ @SCOM:DL.COM), but first remove all files from the directory.
[[Image:Bones2.jpg|20px]] Warning: Extreme caution!
<pre>
$ DEL [.subdir...]*.*;* !Deletes all files in subdir. CAREFUL!!!
$ DL subdir.dir; !Deletes subdir.dir with confirmation.
$ DL disk:[dir.subdir...]*.dir !* for all; do until subdirs are gone.
</pre>

Use the DELETE command, but first remove all files from the directory and set file protections to enable deletion of the directory.
<pre>
$ SET FILE/PROT=O:RWED [.subdir...]*.*;* !Changes protections so you can delete the files. O is short for OWNER and RWED refers to Read, Write, Edit, Delete.
$ DEL [.subdir...]*.*;* !Deletes all files in subdir. CAREFUL!!!
$ SET FILE/PROTECTION=O:RWED subdir.dir !Changes protections so you can delete the subdirectory subdir.dir.
$ DEL subdir.dir; !Deletes the subdirectory.
</pre>

If the file cannot be deleted to due a permission error
<pre>
$ purge 12_RAD_FX.AIM
%PURGE-W-FILNOTPUR, error deleting DISK4:[BONELAB.PROJECTS.MULTILOAD.CAMOS]12_RAD_FX.AIM;1
-RMS-E-FLK, file currently locked by another user
</pre>
Do the following:
<pre>
$ set ho 0 ! log in as calibration
$ spb
$ del DISK4:[BONELAB.PROJECTS.MULTILOAD.CAMOS]12_RAD_FX.AIM;1
$ logout
</pre>

If that still doesn't work, then maybe you need to kill a process first:
<pre>
$ show device disk4 /file ! shows all the files currently involved in a process
$ set ho 0 ! log in as 'system'
$ stop /id=2081F1EC
$ del DISK4:[BONELAB.PROJECTS.MULTILOAD.CAMOS]12_RAD_FX.AIM;1
$ logout
</pre>

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===Authorizations===

====Can not access a Projects directory====
In principal, all Scanco user accounts (even including the calibration ones) should have read and write access to the Projects directories. While it (denied reading or writing access to a Project folder) did happen for a reason (used different accounts to create a file or a subfolder within a Projects folder), you could let lab administrator know and carefully run the following command to overwrite the authority, or switch to microct or xtremct2 account to perform as a walkaround.

<pre>
$ set file/prot=(g:rwe,o:rwe) disk4:[bonelab.projects.danielle...]*.*;*
</pre>

To avoid this happening again, make use always using the same account consistently to create all files and subfolders within their Project folder.

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==Administrative Commands==

===Query commands===
====Check licenses on VMS system====

This can be used to see what educational licenses (and other licenses) are currently on the system:

<pre>
$ SHOW LICENSE
</pre>

To apply for an educational license go to http://www.openvmsedu.com

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====Check MAC address of VMS system====
You can check them using the command
$ mcr lancp sh dev/char
For example, the result on percy.kin.ucalgary.ca gives

Device Characteristics EIA0:
Value Characteristic
----- --------------
1500 Device buffer size
Normal Controller mode
External Internal loopback mode
00-02-A5-20-29-99 Hardware LAN address
Multicast address list
CSMA/CD Communication medium
FF-FF-FF-FF-FF-FF Current LAN address
128 Minimum receive buffers
256 Maximum receive buffers
Yes Full duplex enable
Yes Full duplex operational
TwistedPair Line media type
100 Line speed (mbps)
Disabled/No Failset Logical LAN state
0 Failover priority

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===Update commands===

====Change hosts====
<pre>
$ mcr latcp show service * ! and if it shows you SCTHIN:
$ set host scthin ! or
$ set host scthin/lat
</pre>

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====Update OpenVMS Licenses====
This needs to be done on all the Calgary workstations, XtremeCT, vivaCT40/uCT35, and uCT100. 
Request licenses from HP:
*School Identification (for U of C): 855803-9502
*License type: OpenVMS VAX/Alpha (uCT100: OpenVMW Integrity) Layered Products? (Or try others)
*Member of DSPP or AlicanceONE: No
*Do you use a VAX or Alpha Emulator: No

On every workstation, you need to check which licenses are loaded and update those with a termination date.
<pre>
$ show license

Active licenses on node SCEVA3:

------- Product ID -------- ---- Rating ----- -- Version --
Product Producer Units PCL Activ Version Release Termination
C DEC 0 0 100 0.0 (none) 1-OCT-2012
CMS DEC 0 0 100 0.0 (none) 1-OCT-2012
CXX-V DEC 0 0 100 0.0 (none) 1-OCT-2012
FORTRAN DEC 0 0 100 0.0 (none) 1-OCT-2012
LSE DEC 0 0 100 0.0 (none) 1-OCT-2012
MMS DEC 0 0 100 0.0 (none) 1-OCT-2012
VMSCLUSTER DEC 0 0 100 0.0 (none) 1-OCT-2012
OPENVMS-I64-FOE HP 4 1 0 0.0 (none) (none)
</pre>

*HP will provide you with a script file ([[media:Openvms_license_update_hp.docx |'''Example script from HP''' ]]) containing a large number of licenses.
*Modify the script to contain only the relevant licenses and load the licenses ([[Media:Openvms_license_update.docx |'''Example modified script''']]).
*Login as user: system
*Re-check the licenses on the workstation to ensure that the termination date has been updated.
*The date after expiry, if cannot log in, then there is a problem with the VMS Cluster license, which was installed by Scanco. Contact Mark Blanchard (mblanchard@scanco.ch) about this problem.

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====Understanding how to set default parameters with OpenVMS====

Here is how the files all hang together...

LOGIN.COM is called automatically during login and calls
::MICROCT_SETUP.COM, which sets the scanner ID, data device, etc. This file calls
::::MICROCT_SETUP_COMMON.COM to create general settings. This file is located in DISK0:[MICROCT_COMMON] and calls
::::::MICROCT_FE.COM, if present, to setup the environment for Bert's FE program
::::::MICROCT_SETUP_SITE_SPECIFIC.COM to create local settings for all accounts (e.g. ICALC)
::::::MICROCT_SETUP_COMMON_*.COM, if present, typically to create application-specific settings for all accounts
::::::MICROCT_SETUP_GROUP_*.COM, if present, to create local settings for specific groups (e.g. group 3401)
::MICROCT_SETUP_USER.COM to create user-specific settings.

Note that the $UM designation is the MAIN directory, and the location of the binary files. To see a list:

$ dir DISK0:[MICROCT_COMMON.MAIN]

This is where you'll find IPL_SCANCO_FE.EXE, IPL_SCANCO_M.EXE, etc.

Lots of stuff here:

Directory DISK0:[MICROCT_COMMON]

3309.DIR;1 DATABASE.DIR;1 DEMO.DIR;1 EVAL.DIR;1
MAIN.DIR;1 TEMPLATES.DIR;1 TIPS.DIR;1 UIL.DIR;1
UTIL.DIR;1 WWW.DIR;1

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====Edit Symbol====

=====Edit SCANCO_SUBMIT_COMMAND=====

*Check the current setting:
<pre>
$ show sym *submit*
</pre>

In directory <code>DISK2:[MICROCT]MICROCT_SETUP_USER.COM</code> add the following line:
<pre>
$ SCANCO_SUBMIT_COMMAND :== SUBMIT/NOPRINT/QUE=SYS$SLOW /NOTIFY/LOG=SYS$SCRATCH:
</pre>
Then end session and log in again. Definition of the symbol in the
<code>MICRO_SETUP_USER.COM</code> supersedes the standard setting.

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=====Edit AIX=====

[[Image:Bones2.jpg|20px]] Warning: Extreme caution! Explicit permission for this change or similar changes must be obtained from Dr. Steven Boyd.

Log in as user calibration (Xtremect: calibration; VivaCT40: calib5019; uCT35: calib2339), the password is the same as for the system user.
Set priviledges to bypass.
$ set proc/priv=bypass
Or
$ spb
Change to the MICROCT_COMMANDS directory.
$ cdc
$ sea *.com aix
$ eve microct_setup_common.com
Edit the file which is called <code>MICROCT_SETUP_COMMON.COM</code>

''Another example'': To make the backspace/insert keys work properly, edit the <code>login.com</code> and insert the line
<pre>
$ set terminal/insert
</pre>
Anywhere suitable.

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====Setup Time====
=====Change system date and time=====
The OpenVMS system should adjust for daylight savings, however, this is currently incorrect for the alpha systems. The alpha systems will need to be manually moved forward in March and moved back in April. To do this, you will need to login as system
<pre>
$ set host 0
user: system
password:
$ show time
$ set time=dd-mmm-yyyy:hh:mm:ss/cluster !/cluster to change the time on all computers at once
$ set time=01-APR-2012:18:00/cluster !Example: Set the system to April 1, 2012, 6 pm.
</pre>

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=====Set time zone=====
As user system:

$ @sys$startup:utc$time_setup
Choose "CANADA" from the menu.
Choose "MOUNTAIN" from the menu.

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=====Disable Distributed Time Synchronization Service (DTSS)=====
DTSS will automatically adjust the clocks for daylight savings (i.e., 2am to 1am on the 2nd Sunday in March, 2am to 3am on the 1st Sunday in November). As user system:

$ mcr ncl disable dtss
$ mcr ncl delete dtss
$ eve sys$startup:sylogicals.com

Add line to disable DTSS
$ DEFINE/SYSTEM/EXEC NET$DISABLE_DTSS TRUE
Save and exit.
Now re-set the time zone.

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=====Configure Network Time Protocol (NTP) server to synchronize clocks=====
*NTP must be configured for each node (computer). Login as user system.
NTP can only synchronize the system clock if the error is less than 1000 seconds.

Synchronize the system clock to UofC's NTP server (ensures time is correct to within 1000s):

$ mcr sys$system:tcpip$ntpdate ntp.cpsc.ucalgary.ca

Enable NTP:

$ cd sys$startup
$ @tcpip$config
3 - Server components
12 - NTP
1 – Enable service on this node
E – Exit menu
E – Exit configuration procedure
N – don’t start service

Create the NTP configuration file:

$ sys$sysroot:[tcpip$ntp]
$ copy/log tcpip$ntp.template tcpip$ntp.conf
$ eve tcpip$ntp.conf

Comment out existing peer and server entries (# for comments).
Add entries for local servers.
server ntp.cpsc.ucalgary.ca
server ntp1.cpsc.ucalgary.ca
Save and exit.

Start NTP:

$ @sys$startup:tcpip$ntp_startup

Check the log:

$ type/cont/int=1 sys$sysroot:[tcpip$ntp]tcpip$ntp_run.log

Sample log file:

$ Set NoOn
$ VERIFY = F$VERIFY(F$TRNLNM("SYLOGIN_VERIFY"))
11 Apr 09:22:34 ntp[547708872]: ntpd version = 4.1.0
11 Apr 09:22:34 ntp[547708872]: precision = 976 usec
11 Apr 09:22:34 ntp[547708872]: drift file 'SYS$SPECIFIC:[TCPIP$NTP]TCPIP$NTP.DRIFT' does not exist: no such file or directory
11 Apr 09:22:34 ntp[547708872]: will attempt to create drift file

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====Setup Email====
=====Setup email server=====
The SMTP protocol is not enabled by default. If you use <code>tcpip$config</code> you can switch on the mail server under Client Components. As system:

$ set host 0
user: system
password:
$ @SYS$MANAGER:TCPIP$CONFIG
Or
$ @tcpip$config
-> 2 (client components)
-> 6 (SMTP)
-> 2 (Enable & Start services)

*Select option 2 (client components) from the menu.
*Select option 6 (SMTP) from the next menu to enable and start it.

Since your smtp server is not registered anywhere, it can be that emails sent from this server will be filtered out as spam on the way to your mailbox. In that case you would need a so called MX record for your mail server. Contact UofC IT to resolve this issue.

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=====Send an email=====
Example: Send an email without an attachment.
$ mail sys$scratch:email_message.txt/subject="email subject" "hbuie@ucalgary.ca,mkan@ucalgary.ca"

Example: Send an email with an attachment.
$ MIME :== $MIME.EXE
$ MIME MIME> NEW /NOEDIT sys$scratch:file.txt
MIME> ADD /TEXT thisattached.txt
MIME> ADD /BINARY thatattached.zip
MIME> ADD /MESSAGE this_is_written.txt
MIME> SAVE
MIME> EXIT
$ MAIL /SUBJECT="MIME-encoded Message" - sys$scratch:file.txt "hbuie@ucalgary.ca,mkan@ucalgary.ca"
$
*MIME> ADD /TEXT *.txt does not work

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===Action commands===
====Send a message to terminals====
<pre>
$ reply /all "Merry Christmas to Bone Imaging Lab!"

Reply received on SCEVA2 from user XTREMECT2 at _SCEVA2$FTA8473: 09:21:58
Merry Christmas to Bone Imaging Lab!

4 terminals have been notified on SCEVA2.
$
1 terminal has been notified on SCSRV2.
$
1 terminal has been notified on SC3309.
$
3 terminals have been notified on SCEVA1.
$
</pre>

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====<code>mcr</code> vs <code>run</code> command====

The command <code>mcr</code> is the same as <code>run</code>, but only with mcr you can hand over 'in-line' parameters to an .exe file:

<pre>$ run ut:ctheader.exe c000124.isq</pre>
does not work, but you have to say
<pre>$ mcr ut:ctheader.exe c000124.isq</pre>

But funnily if you define a symbol in <code>microct_setup_user.com</code> (or <code>login.com</code>),

<pre>$ ctheader :== $ut:ctheader.exe</pre>

with just neither run nor mcr, but the 'funny' $ sign, then you can also hand over the ISQ name in-line.

Small detail with big effect...

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====File Do All (fda) - apply a command to a set of files====

<code>$ fda ctheader dk0:[microct.data.0001234...]*.isq </code>

to see the header of all isq files of sample 1234 (the three dots ... means all subdirectories)

Or:

<code>$ fda aix dk0:[microct.data.0001234.00005678]*.aim</code>

to see the processing log of all aim files of scan 5678

Wildcard "*" means multiple characters, "%" is for ONE character:

<code>$ fda aix dk0:[microct.data...]C%%%%%%%.aim</code>

(yes, 7 %'s)

to show the aim header of the gray-scale c0000135.aim (etc) files only, and NOT from the _seg.aims also.

[[Image:Bones2.jpg|20px]] Warning: CAUTION! Always test the wildcard expression first with

<code>$ dir dk0:[xxx...]*.aim </code>

The 'file do all' fda command can even be combined with a pipe, or an /output qualifier:

<code>$ pipe fda aix dk0:[microct...]*.aim | search sys$pipe "Slope" </code>

will show you all "Slopes" in a row. (but you may not see which slope belongs to which aim file anymore...)

or:

<code>$ fda/output=sys$scratch:all_headers.log aix dk0:[microct...]*.aim</code>

will write all the output into the .log file - which you can then either edit, or
<code>$ search sys$scratch:all_headers.log "String"</code>

or whatever you want.

Another example with output:

<pre>$ pipe fda type *.log | search sys$pipe "BV/TV" /output=BVTV.txt</pre>

"fda" is our self-written script, so you may have to try-n-error a bit...

<code>$ fda command file_wildcard [Optional: further parameters]</code>

If the command consists of multiple words with spaces inbetween (e.g. mcr ut:xxx.exe), then enclose the command in double-quotes

<code>$ fda "mcr ut:uct_ext_header_display" dk0:[microct...]*.isq 8</code>

Grab more than one line using pipe and search command:

<code>$ pipe fda aix *.aim | search sys$pipe "dim", "pos", "name"</code>

*The further parameters may not contain wildcards - so unfortunately, the fda can NOT be used to 'adaptively' rename a whole bunch of files.

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====Make commands available to all users with symbols or paths====

DCL$PATH is one way to do that, WE don't use it...
<pre>
$ def dcl$path disk1:[microct.main],disk1:[microct.util]
</pre>
then, if you type
<code>
$ uct_t
</code>
it will first try to

<code>
$ @uct_t.com
</code>
and then
<code>
$ r uct_t.exe
</code>

however, we usually define it by giving full path:

<pre>
$ progx :== $disk1:[microct.main]progx.exe
$ com_proc_x :== @disk1:[microct.main]procedure.com
</pre>

then, you can just type the shortcut ('symbol' in VMS language)

We use the 'cd' to set the default path, you may also use this in your command procedure:

<code>proc.com</code>:

<pre>
$ cd 'p1'
$ dir *.*/size

$ define COM disk1:[microct.commands]
$ p :== @COM:PROC.COM
</pre>

these both go into <code>login.com</code>, but see the Wiki entry above to confirm exactly where...

then, you can just type:

<pre>
$ p disk4:[microct.data.0000007.000009]*.ISQ
</pre>

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=Calibration and QC=

==System Updates==
{| class="wikitable"
|-
! scope="row"| XtremeCT II
|
*22-OCT-2020: Recalibration
*01-OCT-2020: Recalibration
*31-JUL-2020: Pixel Correction
*21-Feb-2019: New X-ray source, recalibration
*28-Apr-2016: Recalibration
*04-Nov-2014: Recalibration
*21-May-2014: New Daily QC Phantom (Scanco concluded minimal differences from previous)
|-
! scope="row"| XtremeCT I
|
|-
! scope="row"| vivaCT80
|
*20-OCT-2020: Filter changer replaced, Recalibration
|-
! scope="row"| vivaCT40
|
*20-OCT-2020: New x-ray source, Recalibration
*09-NOV-2010: Recalibration (70KV energy only)
*01-NOV-2010: New x-ray source, Pixel Correction, Recalibration
|-
! scope="row"| µCT35
|
*20-OCT-2020: New x-ray source, Recalibration
*15-JUN-2011: Recalibration
*21-MAR-2011: Recalibration
*10-FEB-2011: Recalibration
*26-NOV-2010: Pixel Correction
*29-OCT-2010: Recalibration
|}

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==Calibration and Conversion==
===Attenuation measured by µCT===
A micro-CT 3D image of an object is basically a 3D map of local x-ray absorption in the object. The reconstruction from multiple angular views provides information on how much x-ray absorption is happening within each cubic voxel element of the scanned volume.

It is important to understand what is meant by “density” in a µCT image. The reconstructed grey-scale intensity of each image voxel does not relate directly to mass density alone, thus do not expect it to correspond with measurements of weight per volume, e.g. g.cm-3. The primary entity that is measured is x-ray absorption, defined as the x-ray linear attenuation coefficient in units of
1/distance, specifically, 1/cm. This is determined both by mass density and x-ray mass attenuation coefficient which is determined by the elemental composition of the material. The x-ray linear attenuation coefficients of typical material is shown blow.

[[File:Mu_comparison.JPG|thumb|center|600px|X-ray linear attenuation coefficient µ of typical material (image curtesy of Dr. Ying Zhu)]]

The images we obtain from the scanner are in a special scanner manufacturer format called AIM files. Each voxel in these images contains a scaled linear attenuation value (mu-value) to save disk space.

{| class="wikitable"
|-
! scope="col"| Symbol
! scope="col"| Name
! scope="col"| Unit
! scope="col"| Value Range
! scope='col'| Meaning or Comments
|-
! scope="row"| µ
| x-ray linear attenuation coefficient
| 1/cm
| µ > 0
| A constant that describes the fraction of attenuated incident photons in a monoenergetic beam per unit thickness of a material
|-
! scope="row"| mu_value
| linear attenuation in Scanco images
| 1/cm
| -8～8 typically
| mu value represented in Scanco images
|-
! scope="row"| pixel_Scanco
| pixel intensity value in Scanco images
| -
| −32768～32767
| Original format of Scanco images in 16-bit signed
|-
! scope="row"| pixel_uint
| pixel intensity value in converted Scanco images
| -
| 0～65535
| Converted format of Scanco images in 16-bit unsigned, using the same slope (unscaled) but an updated intercept
|}

<pre>
pixel_Scanco = mu-value * scaling_factor
</pre>

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===Calibration by BMD===
When we know that the x-ray absorption of a material is dominated by one specific material, then we can relate the measured x-ray linear attenuation coefficient (mu_value) to the mass density of that material. The calibration of [[Scanco_User_Instructions#Descriptive_Statistics_.28Mean.2C_Median.2C_SD.29_of_Calibrated_Voxel_Values| '''Bone Mineral Density (BMD)''']] is an example of this. We assume that the x-ray attenuation within mineralized tissues such as bone, dentine and enamel is dominated by, and can be approximated as, the x-ray attenuation of the mineral compound calcium hydroxyapatite (CaHA) which has the formula Ca5(PO4)3(OH).

Then we obtain “phantoms” with two or more known mass concentrations of CaHA. By linking these mass concentrations of CaHA with measured mu_value in the micro-CT images, we can establish calibration linking the two quantities, allowing us to infer from the micro-CT measured linear attenuation coefficient (mu_value) in a mineralized tissue, to the density of CaHA in mg.cm-3.

*The assumption of linear correlation between the two quantities is based on a well-applied beam hardening correction and the phantoms' diameter matching with the size of bone within the sample.

*This calibration system could be used to calibrate measurement of other substances apart from CaHA and bone, where x-ray absorption is known to be dominated by a certain substance and phantoms can be prepared with known concentrations of that substance.

{| class="wikitable"
|-
! scope="col"| Symbol
! scope="col"| Name
! scope="col"| Unit
! scope="col"| Value Range
! scope='col'| Meaning or Comments
|-
! scope="row"| BMD
| Bone Mineral Density
| mg HA/ccm
| 0～3000
| Volumetric density of calcium hydroxyapatite (CaHA) in a biological tissue in terms of mg/cm^3
|-
! scope="row"| BMD_value
| Bone Mineral Density in Scanco images
| mg HA/ccm
| -1500～3000 typically
| BMD value in Scanco images
|}

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===Conversion between Attenuation and Bone Density===
<pre>
BMD_value = mu-value * slope + intercept

mu-value = (BMD_value – intercept) / slope

pixel_Scanco = scaling_factor * (BMD_value – intercept) / slope

</pre>

For example, to convert mu_value of 1.7923 (1/cm) to BMD (mg HA/ccm):
<pre>
BMD_value = 1.7923 * 3.67162994e+02 + -2.06399002e+02 = 451.667 (mg HA/ccm)
</pre>

For example, to convert the lower threshold of 125 mg HA/ccm that is in the IPL script to pixel intensity in Scanco images:
<pre>
pixel_Scanco = 4096 * (125 - -2.06399002e+02) / 3.67162994e+02 = 3697
</pre>

*You could get the scaling_factor, intercept and slope values from the AIM header of your scan by using aix -l command:
[[File:Aix.JPG|400px]]

*Reference: [[Media:Jbmr.141.pdf|Bouxsein ML, Boyd SK, Christiansen BA, Guldberg RE, Jepsen KJ, Müller R, Guidelines for assessment of bone microstructure in rodents using micro-computed tomography. J Bone Miner Res. 25(7): 1468-86. 2010.]]

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===Convert CT numbers to mg HA/ccm / Houndsfield units (HU)===

The two byte numbers (short) can be converted to mu values by first dividing by mu_scaling which is probably 4096 (uCT35, vivaCT40) or 8192 (XtremeCT).

Houndsfield units (HU)

Here is the conversion formula from mu (lin.att. in 1/cm, our original, 'physical' image numbers) to HU:

<pre>HU(pixel) = -1000 + mu(pixel) * 1000/mu(water)</pre>

so the mu(water) is the 'constant' that is needed for this conversion of any pixel value mu(pixel) to HU of that pixel.

divide the 2-byte numbers in our dicom/aim/isq files by 4096 to get mu. (4096 --> 'mu_scaling' in our headers). E.g. you see
gray-scale number 8192 in our files --> mu = 2 [1/cm].

A reasonable result for the uCT35 is:

<pre>HU = (CT / 4096) * 1718.19 - 1000</pre>

and that means 1000/mu(water) = 1718.19 --> mu(water) = 0.58299 which is a reasonable number.

mg HA/ccm

<pre>
mg HA/ccm = (AIM/mu_scaling) * slope + intercept
mg HA/ccm = (AIM/4096) * 295.494 - 189.695 ! vivaCT40
mg HA/ccm = (AIM/4096) * 256.51 - 172.99 ! uCT35
mg HA/ccm = (AIM/8192) * 1402.549 - 340.953 ! XtremeCT
</pre>

These numbers are available in the AIM header, or the ISQ header (<code>$ run ut:ctheader</code>).

To look up slope, intercept and mu_scaling, check either the AIM header
<pre>$ aix C1234567.AIM</pre>
or
<pre>$ run ut:uct_update_calibration</pre>
and look at a record, and you'll find slope and intercept and mu-water.

<pre>
vivaCT40
!----------------------------------------------------------------------
Mu_Scaling 4096
Calibration Data 55 kVp, 200mg HA wedge, 4096 scaling
Calib. default unit type 2 (Density)
Density: unit mg HA/ccm
Density: slope 2.95493988e+02
Density: intercept -1.89695007e+02
HU: mu water 0.58200
!----------------------------------------------------------------------
</pre>
<pre>
XtremeCT
!-------------------------------------------------------------------------------
Mu_Scaling 8192
Calibration Data 60kVp, BH: 200 mg HA/ccm, Scaling 8192
Calib. default unit type 2 (Density)
Density: unit mg HA/ccm
Density: slope 1.40254895e+03
Density: intercept -3.40953003e+02
HU: mu water 0.23900
!-------------------------------------------------------------------------------
</pre>

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===Calibration FAQ===
====Change brightness scaling====
*Refer to [[Media:Mu-scaling.pdf|'''Change the brightness scaling''']].

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====Update a scan after pixel correction====
Contact Lab personnel with system-level priviledges to perform
<pre>
$ set host 0
! Username: calib2339 (µCT35)
! Username: calib5019 (vivaCT40)
$ spb ! set priviledge bypass to write in other user accounts
$ run ut:pixel_corr_apply

PIXEL_CORR_APPLY Version 1.5
Scanner ID from UCTD:UCT_SCANNER_2339.DAT : 2339 !2339 for µCT 35, 5019 for vivaCT 40
Is this Scanner ID correct ? [?]: y
Give RSQ-Filename (leave empty to exit) []: DISK4:[BONELAB.DATA.00005283.00011668]C0005128.RSQ
...
...
Copy .RSQ to _CORRECTED.RSQ befor correction ? [?]: y

$ logout
</pre>

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====Update calibration in ISQ====
If DICOM files are converted to ISQ with IPL and then used for patient evaluation, the calibration data in the ISQ header needs to be present and correct. If this information is missing, utilizing upat_list to extract the values will say 'Error: Density calibration not valid'. In order to add calibration data to an ISQ file, do the following as user calibration:
<pre>
$set proc/priv=bypass ! gain read/write access to the files
$mcr ut:uct_ext_header_add_calib ! provide ISQ file name and header type (I chose [2])
</pre>

If you need to adjust the calibration of a file, without changing the system calibration data, copy the calibration database into a different directory, e.g. sys$scratch. Then, add a new calibration record to this temporary calibration database. This way your new, temporary values will not show up in the scan program.

$ copy uctd:uct_calibration_3401.dat sys$scratch:

Define the following logical in a terminal MAKE SURE TO DO THIS!!!!

$ def UCT_CALIBRATION_DATABASE sys$scratch:uct_calibration_3401.dat

Run uct_update_calibration and click trough the current calibration record (always enter).

$ r ut:UCT_UPDATE_CALIBRATION.EXE
select current calibration record
enter...

$ r ut:UCT_UPDATE_CALIBRATION.EXE

Then select the last number (New Record), copy all values from above, change slope and intercept.

Then use

$ mcr ut:uct_ext_header_add_calib

for ISQ and RSQ.

At the end, close the terminal!

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==Quality Control (QC)==
===Scope===
*Only Authorized XCT and µCT Operators are permitted to perform QC scans, including both scan acquisition and analysis.
*Authorization is a formal process. If you are not sure whether you have or should have authorization, speak to Dr. Boyd or Dr. Hallgrimsson or the MoJo Operations Manager.
*Authorized XCT and µCT Operators are responsible for ensuring a QC schedule is maintained.
*Only the manufacturer can calibrate the scanner! QC only checks the calibration.

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===Overview===
*Micro-CT systems cannot directly measure the density of a material, however, the density is linearly correlated to the x-ray absorption (assuming a proper beam-hardening correction is applied), which can be measured by micro-CT. Density is therefore determined by measuring a reference material of known density (i.e., a phantom) to define a conversion function to relate x-ray absorption to density. Quality control of density and structural measurements for the micro-CT systems is achieved through weekly checks of phantom values to their reference values and recalibrating the system (i.e., defining a new conversion function) as necessary.

*Performing QC is essential to the:
# Safety of our study participants and lab members
# Validity of our research data

[[File:QC_phantom.jpg|thumb|center|600px|Scanco Medical quality control phantom (a) and its CT scans of the density QC1 (b) and the structural QC2 (c)]]

*Reference: Koller B, Laib A (2007) Calibration of micro-CT data for quantifying bone mineral and biomaterial density and microarchitecture. In: Advanced bioimaging technologies in assessment of the quality of bone and scaffold materials: techniques and applications. Springer, pp 79-84.

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===Density QC1===
QC1 measures the density of 5 different rods of known hydroxyapatite (HA) densities within the QC phantom: approximately 0, 100, 200, 400, and 800 mg HA/cm3. This tests 3 things:

# That the scanner’s last calibration is still valid. This is done by comparing daily QC values to an acceptable range.
# The presence of drifts and shifts in the calibration. This is done by plotting daily QC results over time and using Shewart’s Controls to mathematically look for drifts and shifts. (Shewart’s Controls replaces visual assessment.)
# The correct functioning of scanner hardware and electrical components. This is done by visual inspection for image artifacts.

*QC1 is checked daily or 3 times a week on XtremeCT scanners whenever used and weekly on microCT scanners.

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===Structural QC2===
QC2 measures the volume of 3 fine aluminum rods within the QC phantom (Al rod volume measurement). This tests for:

# Alignment of the gantry (or stability of architectural parameters)
# The correct functioning of scanner hardware and electrical components. This is done by visual inspection for image artifacts.

*QC2 is checked weekly on both XtremeCT and microCT scanners.

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===QC Scan Instructions===
*XtremeCT QC Scan Instructions: Boyd Drive:\02 - Operations\01 - Scanner QC, Specifications, & Maintenance\QC Workflows\QC 001.2 - XCT Quality Control.docx
*[[Media:Calibration-instructions-for-uct35.pdf |µCT35 QC Instructions]] or [[Media:uCT35_Calibration.pdf|µCT35 QC another Instructions]]
*[[Media:Calibration-instructions-for-vivact40.pdf |VivaCT40 QC Instructions]] or [[Media:VivaCT40_Calibration.pdf| VivaCT40 QC another Instructions]]

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===Print out QC reports===
After running a QC1 or QC2 analysis, the results are output to:
*DISK4:[BONELAB.PROJECTS.QC] for XtremeCT QC results
*DISK3:[MICROCT.PROJECTS.CALIBRATION] for microCT QC results performed by BH lab
:*login with microct account
*DISK5:[BONELAB.PROJECTS.CALIBRATION] for microCT QC results performed by Bone Imaging lab
:*RESULTS_QC1_UCT35.TXT;2
:*RESULTS_QC1_VIVACT.TXT;4
:*RESULTS_QC2_UCT35.TXT;2
:*RESULTS_QC2_VIVACT.TXT;2

As usual as [[Scanco_User_Instructions#Print_out_report_sheets|'''print out report sheets''']], you use
$ upat_list
When it asks for a template, you can select for a graphical report
template = UU:UCT_EVAL_PHANTOM_SCANCO.PS
or for a text output
template = UU:UCT_3D_LIST.TXT

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===System Stability and Precision===
System Stability and Precision here is based on the QC measurement, QC1 for density variations and QC2 for structure variations.
{| class="wikitable"
|-
! scope="col"| System Stability and Precision
! scope="col"| XtremeCT
! scope="col"| vivaCT40
! scope="col"| µCT35
|-
! scope="row"| Long Term Precision
|
*QC1: ± 8mg HA/cm3
*QC2: ± 2.0%
|
*QC1: ± 0.4%
*QC2: ± 0.7%
(Ref term: 26-NOV-2010 to 8-APR-2011)
|
*QC1: ± 1.0%
*QC2: ± 1.6%
(Ref term: 26-NOV-2010 to 8-APR-2011)
|-
! scope="row"| Short Term Precision
|
*QC1: ± 8mg HA/cm3
*QC2: ± 2.0%
|
*QC1: ± 0.4%
*QC2: ± 0.9%
(Ref term: 4-MAR-2011 to 8-APR-2011)
|
*QC1: ± 1.0%
*QC2: ± 0.7%
(Ref term: 6-MAR-2011 to 8-APR-2011)
|}

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===QC FAQ===
====Determine calibration drift for microCT QC1====
The microCT QC1 analyses provide an estimate of the calibration drift by considering 'mean5' values. Use <code>$ uct_list</code> and make sure to use UU:UCT_3D_MEANS.TXT as the template. Then give the measurement numbers of the QC1 measurements (or all of them and remove what's not needed later).

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====Update QC1 contours====
If the QC contours don't line up on the phantom, then the contours need to be updated on the system. Normally this should not happen unless the phantom has become loose - if this is the case, re-fix it.

1. Login as user system. Do not use the <code>$ set host 0 </code> command since you will not be able to open windows for program. 
2. Run the login script for the user that does the QC scans so that Scanco logicals point to that scan database.
$ @adisk1:[microct]login.com on the XtremeCT cluster
$ @adisk1:[microct]login.com on the vivaCT cluster
$ @disk1:[microct]login.com on the µCT100 cluster

3. Run the evaluation program.
$ uct_evaluation
4. Load the most recent QC scan and locate the contours. File-->Load Gobj... Filter: <code>uctd:*.GOBJ</code>. Locate the contours for the phantom: <code> UCT_PHANTOM_KP_HA_XXXX_Y.GOBJ </code> where XXXX corresponds with the scanner ID (XtremeCT 3309, vivaCT 5019, µCT35 2339, µCT100 6002) and Y corresponds with the rod number (1-5 and results mean1 - mean5. 

5. Adjust the contours to centre on the rods.
Load a contour.
Move the contour on the first slice to be centred on the rod.
Copy the contour.
Delete the contours on slices 2 to the end.
Paste the contour on the last slice.
Morph between the two contours.
Save the contours. They should be saved to (A)DISK0:[000000.MICROCT_COMMON.DATABASE].
6. Perform a new QC scan as the standard (i.e., microct) user. Check that the contours line up for the evaluation. Evaluate and check the results.

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====Update Gobj for QC1 Analysis====
Refer to [[Media:Fix_QC1_gobj.pdf| '''Fix QC1 Gobj''' ]] for instructions.

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====Update XtremeCT QC1 calibration====
This procedure needs to be done for each beam hardening correction (e.g., QC1 with 200 mg HA/cm3, QC1 with 1200 mg HA/cm3) and for each scan energy.

1. Perform 3 back-to-back QC1 scans, which ensures the x-ray tube is very warm. 
2. Evaluate the last QC1 scan. 
3. After the evaluation is done, determine parameters for the new calibration
<pre>
$ uct_calib_phantom
UCT_CALIB_PHANTOM Version V1.0

Reading UCTD:UCT_CALIB_PHANTOM_KP_HA_3309.TXT
Phantom Type in file: 6
Phantom Number in file: 304
Voltage in file: 0
No of Materials in file: 1
With each, no of steps: 5
and mus: 1.000000
No. of Cylinders: 5
Measurement No. (0 to Stop) [0]: 11404

Mus: 0.2382 0.3163 0.3823 0.5358 0.8112
*****************************************************
Calibration: Slope Intercept: 1398.628 -339.819
Enter in Calibration Records if wished.
*****************************************************
Measurement No. (0 to Stop) [0]:
End of program
$
</pre>

4. Save the above screen output in a file called CALIB_3309_YYYY-MM-DD.TXT.

5. Now update the calibration. For most settings, you will use the default value by pressing return. You need to choose the correct calibration record, the one that corresponds with the energy and beam hardening correction used in the QC1 scans you did. Next, you need to update the slope, intercept, and mu water values to those determined in step 3 (copy and paste values to avoid typos). The new values should be similar to the old ones. Finally, if you have not made any mistakes, then save the record.
<pre>
$ run ut:uct_update_calibration
UCT_UPDATE_CALIBRATION V2.5

IDX Calib/Rec. Description
1 1/42 60kVp, BH: 200 mg HA/ccm, Scaling 8192
2 2/43 60kVp, BH: 1200 mg HA/ccm, Scaling 4096
3 3/0 New Record
Choose Calibration Record (IDX): [2]: 1
Valid Flag [1]:
Scanner-ID [3309]:
Energy [V] [59400]:
Intensity [µA] [0]:
Description [60kVp, BH: 200 mg HA/ccm, Scaling 8192]:

Antiring Enable [0]:

Beamhardening Enable [1]:
Beamhardening Coeff file [MICROCT_COMMON:[DATABASE]UCT_BH_COEFF_60KV_0200HA_3309.TXT;5]:
Beamhardening Checksum [0]:
CCD_CORR: Read to mem: 500 bytes to correct 1 pixels (588 bytes allocated)

Default unit type (1=µ, 2=mg, 3=HU, 4=Custom) [2]:
µ Enable [1]:
µ-scaling [8192]:

Density Enable [1]:
Density units [mg HA/ccm]:
Density Slope [1402.549]: 1398.628
Density Intercept [-340.953]: -339.819

HU Enable [1]:
µ of water [0.239]: 0.2382

CUSTOM Enable [0]:

HW Filter Code [0]:
HW Filter Description []:

Save Record ? [Y]: Y
End of program
$
</pre>

6. Save the above screen output in a file called CALIB_3309_YYYY-MM-DD_ENTERED.TXT. Send both text files to support@scanco.ch for them to archive.

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====Update microCT QC1 calibration====
Refer to [[Media:QC1_Calibration_Update.pdf|'''QC1 Calibration Update''']] for instructions for the VivaCT40 and uCT35.

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====Update a scan with new calibration or BHC====
If the QC1 range was out of range but it was not possible to update the system calibration before scanning, you can update the scan with the new density calibration (i.e., slope and intercept). It is also possible to change the beam hardening correction that is applied (e.g., from 200 mg HA/cm3 to 1200 mg HA/cm3).

{| class="wikitable"
|-
! scope="col"| Type of Update ||RSQ||ISQ||AIM
|-
|QC1 was out of range, need new slope and intercept
(e.g., after updating the system calibration)
|Yes||Yes||No, Create New
|-
|Change beam hardening correction type
(e.g., 200 mg HA/cm3 to 1200 mg HA/cm3)
|Yes||No, Reconstruct||No, Create New
|}

Use the UCT_EXT_HEADER_ADD_CALIB program to update an RSQ and, if appropriate, repeat for the ISQ.
*Use default values for all prompts except those commented after !.
<pre>
$ mcr ut:uct_ext_header_add_calib

UCT_EXT_HEADER_ADD_CALIB V 1.1
Raw-Data-File []: !give the name of the RSQ/ISQ with full path if not in that directory

Reading Raw Data ...
IDX Calib Description
1 1 45 kVp, 200mg HA wedge, 4096 scaling
2 2 55 kVp, 200mg HA wedge, 4096 scaling
3 3 70 kVp, 200mg HA wedge, 4096 scaling
4 4 General, non-bone-density-calibrated scan, scale 4096
5 5 45 kVp, BH: 1200 mg HA/ccm, Scaling 4096
6 6 55 kVp, BH: 1200 mg HA/ccm, Scaling 4096
7 7 70 kVp, BH: 1200 mg HA/ccm, Scaling 4096

Calibration Record No [0]: !specify the new calibration, e.g. 6

Calibration No. 6
Description 55 kVp, BH: 1200 mg HA/ccm, Scaling 4096
Scanner-ID 5019
Energy [V] 55000
Antiring Enable 0
Beamhardening Enable 1
Beamhardening Coeff file UCTD:UCT_BH_COEFF_55KV_1200HA_5019.TXT
Default unit type (1=µ, 2=mg, 3=HU, 4=Custom) 2
Same type already found. Setting old to invalid
SUCCESS: calib hext written
updating header...
SUCCESS: Header successfully updated.

Calib record indicates that BH-Corr is usually applied.
Info: There is a BH-Corr corr already in hext.
Add another BH-Corr from file again? (Y/N) [N]: Y
</pre>

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====Update a scan with new QC1 calibration====
Refer to [[Media:Update_Scan_with_new_QC1.pdf|'''Update Scan with new QC1''']] for instructions.

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====Fix: un-centered QC1 Gobj====
The contour for the QC1 scan is not centered on the on hydroxyapatite rod, which will result in erroneous low density values.

This can occur for a couple of reasons:
*The metal spindle has come loose on the phantom, in which case re-glue it and update the contours
*The slot on the phantom's spindle was not correctly aligned
*For the vivaCT 40, the sample bed was not pushed to the right before locking it in place
[[File:Phantom_not_pushed_right.jpg|600px]]

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====Fix: rods in QC2 images====
The QC2 scan has aluminum rods AND hydroxyapatite rods. This happens because the slot on the phantom's spindle was not correctly aligned and the phantom positioning is off slightly. Adjust the phantom and re-scan.

[[File:Phantom_spindle_not_in_right.jpg|600px]]

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=Scanning=

==Scanner User Manual==
For XtremeCTs:

* [[Media:Scanco - Manual_XtremeCTII_2.5.pdf |XtremeCT II User's Guide V2.5]]
* [[Media:XtremeCT User Guide XCT I.pdf |XtremeCT I User's Guide V6.4]]

For microCTs:
* [[Media:Manual_vivaCT_80.pdf |VivaCT80 User's Guide V1.5]]
* [[Media:scanco-manual-vivact40.pdf |VivaCT40 User's Guide V4.05]]
* [[Media:Scanco-manual-uct35.pdf |MicroCT35 User's Guide V4.05]]

==Scanco's FAQ==
Navigate to the manufacturer [http://www.scanco.ch/index.php?id=customer_login Scanco Medical FAQ].

* Username: users@scanco.ch
* Password: basser5dorf

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==Scan==
===Scan SOP===
====Image Quality====
*Refer to [[Media:Scanco-faq-image-quality.pdf|'''Image Quality: Resolution vs. Noise''']] by Scanco Medical.

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====Optimize Control File Settings====
*Refer to [[Media:ControlFileSettingsUserMeeting2014Final.pdf|'''Optimize Control File Settings''']] with regards to resolution, contrast and scan time.

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====Scan materials of different densities====
*Refer to [[Media:UM_HongKong_DifferentDensityMaterials.pdf|'''Scan materials of different densities''']].

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====Optimize Scan for Soft and Adipose Tissue Separability====
*Refer to [[Media:Scanco-faq-adipose-vs-soft-tissue.pdf|'''Scan Protocol Optimization for Soft and Adipose Tissue Separability''']].

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====Measure multiple samples in one scan====

This quite often happens when you want to scan 6 rat bones, for example, but using our six-gun sample holder you scan them in one go. But, you want to analyse them separately, so you have to import the ISQ multiple times as new MEASUREMENTS into each SAMPLE.

There are two options: manual and auto. Read this entire HowTo before proceeding. There is significant potential for mistakes!

<pre>
$ @com:import_manual.com

P1: Measurement Number to duplicate
P2: New Sample Number from Database
P3: New Start Letter of ISQ file
P4: Optional: Operator Number
P5: Optional: Controlfile Number
</pre>

So:

<pre>$ @com:import_manual.com 1234 342 D</pre>

will copy the ISQ from measurement 1234, import it into the database to sample 342, give some feedback lines with 'old' and the new samplename, CHECK IT, and at the end it gives the feedback line on the terminal which you take with the mouse and drop to rename the data over to the new location.

IMPORTANT: BE VERY SURE NOT TO MIX UP MEASUREMENT AND SAMPLE NUMBER !!!

This distiction needs to be VERY clear in your mind! Of course, you can duplicate one scan and give it to the same samplenumber again (e.g. to evaluate different parts of the same sample, and each has its database
entry).

Please build up some system so you see immediately that the right meas. goes to the right sample. E.g. all four bones in one scan have the same part in the name, distinct from other 4 bones. If there is any trace of a doubt later on that somebody MAY have messed up the samples in this duplication step, you'll most probably have to start from scratch again...

Of course, I'll have to make you aware that Scanco declines all responsibility - this program is NOT in the normal user-friendly, quite fool-proof Scanco controlbox, but it's up to you to use it carefully, and not on Friday night when you're sleepy and mistakenly mix up sample and meas. numbers...

The new startletter I built in so you always know which one was the 'original' measurement (which has an RSQ), and which are the duplicated ones.

Backup
And the organization of how you know which duplicated scan is which part is
completely up to you - as well as how you want to handle the backup - our
software allows you to back-up each duplicated scan (but this might be an
overkill, since it's the same ISQ always) so you may choose to delete the
duplicated ISQ by hand in the session manager (only keep the 'original' ISQ), and only backup the .gobj, .aim and _seg.aim etc. (but then you will need to know not to get scared if you retrieve a scan, and the ISQ is missing...) (Or you just 'move to trash' the duplicated scans to nicely delete them with the backup program if you want to remove them completely (but you still have the 3D results in the evaluation database))

Autosubmit

<pre>$ import_autosubmit.com</pre>

Please use the manual one for a while. Then, if you feel comfortable, use the autosubmit one (which also does the last command automatically, the renaming of the isq to the new location.) Because it goes into a batch que, you can quickly submit all duplications, and do not have to wait for the whole file-copying like in the manual one.

One thing you should check there:
$ show que sys$fast/full

This needs to be one single queue (/job_limit=1). In a clustered enviroment,
this might be a '/generic=' que that then gives the jobs to multiple queues in the cluster. This is NOT good. If this is the case, please edit the autosubmit script, and replace sys$fast in the following line at the end by ONE of the generic fast queues, e.g. SC4240_FAST or whatever the name is (preferrable the one computer where also the data disk DK0 is sitting:

<pre>
$!
$ SUBMIT/NOPRINT/QUE=SYS$FAST/DELETE/NOTIFY/LOG=SYS$SCRATCH: 'COMMANDFILE'
$!
</pre>

(Reason: if multiple uct_imports would run at exactly totally the very same time, both jobs might get the same new measurement number... bad...)

I also suggest to add the following line to your login.com

<pre>$ dupl*icate :== @com:import_autosubmit.com</pre>

then you can just start it with

<pre>$ dupl 1234 342 D</pre>

And I also recommend to put into login.com:

<pre>
$ check_dup :== search sys$scratch:import*.log """ name:""
</pre>

(yes, with all these double-quotes)

Then use it to check the feedback that the right scans were given to the right samples.

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===Scan FAQ===
====Unlock a locked controlfile====
If you accidentally locked a controlfile, it is possible to unlock it so that it can again be modified.

Login as the calibration user (Xtremect: calibration; VivaCT40: calib5019; uCT35: calib2339), the password is the same as for the system user, Set priviledges to bypass.
$ spb

Set the controlfile database to the microct, or other, user where the controlfile is locked.
*The file is usually located on (a)disk1:[username.database] and may be accessible using the uctd logical.
*The database file contains the scanner ID (e.g., 3309 for the XtremeCT, note there's no SC before 3309).
$ def uct_controlfiles_database adisk1:[microct.database]uct_controlfiles_3309.dat
$ run ut:uct_upd_controlfiles

Choose the controlfile.Use T and F to indicate true and false.
*YOU MUST SAY YES TO UPDATE CTRL-FILE! There is a bug so do this even if you make a mistake.

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====Warning: Selected operator is not an operator CODE: 24====
You must enter an operator name in the micro-CT control panel.
*You only need to enter the beginning part of your operator name (e.g., Bo for Bone Imaging Lab) or your operator number.
*You can also press "Edit..." and then press the "Find..." and press "OK" to show a list of all the operators that have been registered.

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====Warning: Error assigning IO-channel for UCT_ACQ_LINE, device already allocated to another user CODE: 2112====
Only one person can be given control of the scanner at any time. Most likely the scanning program is already open. Check the minimized icons on the desktop.

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====Error: ROT (M1) end switch detected, Motor stopped CODE: 3031====
We're not sure why motor errors occur occasionally. The solution is to exit the scanning program and turn off the scanner (the switch is on the side of the machine). Wait 30 seconds. Turn the scanner on again. Re-start the scanning program. Wait for the scanner to warm up (20 min).

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====Error: Acquisition error, Buffer overrun CODE: 1005====
This error occurs if the computer hooked up to the scanner is overloaded and does not accept the stream of CT data quickly enough. Check that no large calculations are running interactively (e.g., loading a large dataset into the 3D viewer while the scan is running). If you happen to be there at the very exact second when the buffer overrun happens, do the following:
<pre>
$ show user/node/full !check how many users/processes there are
$ monitor system/int=1 !check the process that is using the most cpu and page file quota
</pre>
Advise lab personal of the problem. If nobody is around, put the output of the above commands into a text document, stop the queues for the computer, and repeat the scan.
<pre>
$ stop/que/next sc5019_fast !for the vivaCT 40
$ stop/que/next sc5019_slow !for the vivaCT 40

$ stop/que/next sceva2_fast !for the µCT35
$ stop/que/next sceva2_slow !for the µCT35
</pre>
When finished, restart the queues that you stopped by <code>$ start/que queue_name </code>.

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====Error: Shutter fail safety test timeout CODE: 2101====
This happens if the scanning program has accidentally be left on overnight and the shutter fail safe test cannot be performed. Ensure that uct_tomography is closed at the end of the day and the scanner computer is logged out at the end of the day to avoid this error.

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====Error: Input error detected, Z protection detected CODE: 4001====
This means the big plate that you can see through the gantry has moved or been touched, activating one of the Z protection switches. This can happen during positioning a patient for a tibia scan if the person's leg isn't pushed into the scanner straight. The cast can potentially touch the plates and cause this error.

In the rare case where this error occurs spontaneously during or at the end of a scan, or during a precalibration, one of the switches may have become activated due to the position of the Z plate. To determine the position(s) this error is triggered, do the following:
<pre>
$ set host 0 Username: calibration Password:

$ sdl
$ spb
$ run um:ccd_2d
</pre>
The Scanco test programs will open. First click on the Reset Z button (upper left corner). Then move the Z slider all the way to the right and hit move. If the Z-protection error appears, record exactly which Z position triggers the error (should be a red number on the left hand side of the slider). When you are done with this test, hit Reset Z again, wait until the motor comes to a complete stop (max. 15 seconds), close the software and in the same terminal by <code>$ logout </code>.

Contact Scanco regarding this error and provide the details from running the ccd program. They will provide further instructions on how to proceed and fix the problem.

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====Fatal: CCD frame timeout, HOTLink reframing CODE: 1007====
Take a screenshot of the error message and email Scanco immediately. Message indicates that X-ray tube is arcing. Try and warm up the X-ray tube again, and notify Scanco if there is any abnormal activity and whether the tube was able to warm up.

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====Fatal: Invalid Scanner ID CODE: 24====
You have logged in with the incorrect user name. End the session and login with the correct user name (vivaCT 40: vivact or invivo; µCT 35: microct or invitro).

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====Fatal: Unable to create shared memory, global page table full CODE: 196====
The temporary fix is to reboot the system. But before you restart, if you have system access, do the following and save the output to a text to send to Scanco.
<pre>
$ set host 0
Username: system
Password:

$ search sys$system:agen$feedback.dat gblpages
$ write sys$output f$getsyi("contig_gblpages")
$ write sys$output f$getsyi("free_gblsects")
</pre>

==Reconstruction==

===Standard Reconstruction===
Scans are automatically submitted for reconstruction, so manual submission is usually only necessary if there was a problem during reconstruction (e.g., a power failure).

*To reconstruct all slices from the RSQ, first delete or rename the old ISQ.
*To reconstruct a selection of slices, a valid ISQ must exist. There is an offset of 1 slice when designating slice selection.
'''General Usage for Interactive Reconstruction''':
<pre>
$ uct_reconstruction P1 P2 P3

P1: RSQ Filename
P2: Slice number (A – all, start:finish)
P3: Log file of batch job
</pre>
'''General Usage for Non-interactive Reconstruction''':
$ submit/noprint/que=sys$slow um:uct_reconstruction.com/params=(DISK2:MICROCT.DATA.00000610.00002449]C000####.RSQ , a)
*Normally jobs are submitted to sys$slow queue instead of running them interactively.

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====Reconstruct a selection of slices====
Here are examples of how to reconstruct a single RSQ file: C0007655.RSQ, sample 4111 and measurement 9899. 
To reconstruct slices 101 to 201 and submit the job to the sys$slow queue:
<pre>
$ submit/noprint/que=sys$slow um:uct_reconstruction.com /log=sys$scratch:reco4111.log/para=(dk0:[microct.data.00004111.00009899]C0007655.rsq, 100:200, sys$scratch:reco4111.log)
</pre>
*The command must be all on one line (or use hyphen), and it wants the 3 parameters: filename, slices, and log.file name

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====Reconstruct all slices====
To reconstruct all slices, use “a” for all slices and submit the job to the sys$slow queue:
<pre>
$ delete C0007655.ISQ;*
$ submit/noprint/que=sys$slow um:uct_reconstruction.com/log=sys$scratch:reco4111.log/para=(dk0:[microct.data.00004111.00009899]C0007655.rsq, a, sys$scratch:reco4111.log)
</pre>
*The .log filename is up to you, as long as it's the same at both places.
*Give full pathname for RSQ file.

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====Reconstruct multiple files====
For multiple files, create a script and submit the job to the sys$slow queue. For example,
<pre>
$ cd sys$scratch
$ eve reco_all.com
</pre>
Or open editor (command 'Edit'), put the following lines in the file and save it as .e.g sys$scratch:reco_all.com:
<pre>
$ uct_reconstruction dk0:[microct.data.00004111.00009899]C0007655.rsq a
$ uct_reconstruction dk0:[microct.data.00004111.00009900]C0007656.rsq a
$ uct_reconstruction dk0:[microct.data.00004111.00009001]C0007657.rsq a
$ exit
</pre>
Save the script and exit the text editor, then submit the job (e.g. to sys$slow):
<pre>
$ submit/noprint/que=sys$slow/log=sys$scratch:reco4111.log sys$scratch:reco_all.com
All the files will be reconstructed as a single job, with one log file.
</pre>

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====Batch reconstruction on XtremeCT2====
The reconstruction software available for the XT2 supports the /batch syntax that replaces reco_all.com.
You can split a manual reconstruction into several jobs using

$ uct_reconstruction DK0:[XTREMECT2.DATA.00001234.00005678]D0123456.RSQ a/batch=16

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====Update to uct_reconstruction V6.2-5, March 2019====

As of March 2019, we should only use uct_reconstruction v6.2-5 on xtremect2.
For studies with baseline and follow-up scans overlapping this time, the old version (V6.2-2) can still be accessed using
<pre>
$ uct_old_recon
</pre>
Changing reconstruction versions can lead to small systematic differences in the result parameters of a trabecular bone analysis. The old version should only be accessed by those who absolutely need to use it. (Scanco recommends re-reconstructing all measurements of a study with version 6.2-5 instead).

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=== Rotated Reconstruction (about z-axis)===
#Use the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] to measure the angle for the rotated reconstruction.
#*To start the program type <code>$ uct_evaluation </code> in a DEC terminal, or use the graph button.
#*Load your sample and select the angle measurement button.
#*Drag the ends and the intersection of the green lines to measure the desired rotation angle.
#:[[File:Angle meas.preview.jpg|600px]]
#Rotate and reconstruct
#*Use <code>$ @com:reco_all </code> to reconstruct all slices.
#*Use <code>$ @com:uct_reconstruction_angle </code> to reconstruct selected slices from an RSQ.
#Use the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] to check the sample after the rotated reconstruction:
#:[[File:Rotated_reconstruction.preview.jpg|600px]]

*'''General Usage''':
<pre>
$ @com:reco_all.com P1 P2 P3

P1: Angle in degrees
P2: Sample number
P3: Measurement number

$ @com:uct_reconstruction_angle.com P1 P2 P3 P4 P5

P1: RSQ Filename
P2: Slice number (A – all, start:finish)
P3: Log file of batch job
P4: Delete log file (true/false)
P5: Angle in degrees
</pre>
*The angle of rotation uses the right-hand rule: a counterclockwise rotation is positive and a clockwise rotation is negative.
*The angle of rotation uses a single decimal place.
*By default the reconstruction jobs will be placed in the sceva3_slow queue.
*Both functions are executed from the measurement directory.

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====Reconstruct all slices====
The following examples are for a 19.1 degree counterclockwise rotation of sample 6876, measurement 15417, C0005086.RSQ.
<pre>
$ @com:reco_all.com 19.1 6876 15417
</pre>
*Delete the ISQ file from the measurement directory.

====Reconstruct a selection of slices====
*A valid ISQ must exist.
*There is an offset of 1 slice when designating slice selection.

To reconstruct slices 36 to 41:
<pre>
$ @com:uct_reconstruction_angle.com DK0:MICROCT.DATA.00006876.00015417]C0005086.RSQ 35:40 sys$scratch:reco610.log true 19.1
$ @com:uct_reconstruction_angle.com DK0:MICROCT.DATA.00006876.00015417]C0005086.RSQ 35:40 "" "" 19.1
</pre>
*"" is used as a null input for optional parameters.

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===Other Reconstruction===

====Reconstruct at a new voxel size====
See a script in:
DISK1:[XTREMECT2.EVAL]UPDATE_HEADER.COM

This script includes the following type of information:
$ r ut:updh_voxelsize.exe
DK0:[XTREMECT2.DATA.00000010.00000050]D0000068.RSQ
122
82000
1706
$ r ut:updh_voxelsize.exe
DK0:[XTREMECT2.DATA.00000011.00000054]D0000072.RSQ
122
82000
1706

This is what one would do in a terminal. The only requirement is that this <code>updh_voxelsize.exe</code> cannot be executed as the normal user.
Prior to that, one has to log as calibration, and do:
$ set proc/priv=bypass

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==Manipulate RSQ==

===View RSQ projections and flat field===

It can be very useful to examine the projections that are contained in the RSQ file, as well as to see the flat field correction frames.

In the session manager, double click the RSQ file and the program ximage will open. Or, type:
$ sh sym x
X == "$UM:XIMAGE.EXE"
$ x D0000018.RSQ
Then switch to xz view and go to the second slice (in this order). Then you should see a frame of the none attenuated beam (nothing in the beam, or Scanco calls it the I0 frame). If it is a multi stack measurement then there will be several copys of this frame in this image.

In an RSQ you have for each slice of the detector one dark current line and then the full intensity line followed form the radiographs taken under the different angles (sinogram). In the x direction is the detector line, in the y direction is the rotation angle (except dark and I0) and in the z direction is the z-direction of the scanner. If you switch the view to xz, then you can see the frames as acquired by the detector (or stacked frames all taken under the same rotation angle). Frame 1 is then the dark image and Frame 2 is the full intensity image.

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===Convert RSQ to AIM===
<pre>
$ ipl
ipl> rsq_to_aim in YP_IGFAMOTION_003_6.RSQ
-pos [0 0 0] >
-dim [-1 -1 -1] >
-convert_to_pro [false] > true
-sinogram_not_frames [true] > true
-div_unsigned_by_2 [false] > true

ipl> write
-name [internal_name] > in
-filename [default_file_name] > YP_IGFAMOTION_003_6_rsq.aim
-compress_type [bin] > none
-version_020 [true] >
</pre>

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===Convert RSQ to PSQ===
First, in the terminal turn on the 'advanced questions' mode
<pre>
$ define uct_reconstruction_calibration true
</pre>
Second use the reconstruction EXE to convert RSQ to PSQ
<pre>
$ run UCT_RECONSTRUCTION.EXE
raw file: DISK3:[MICROCT.PROJECTS.YVES.LANDMARK.RAW]filename.RSQ

Give slice number, or 'a' for all
hit return a few times

Write Projection [N]: -> say y and it writes the PSQ and continues with reco
Say p if it shall just produce PSQ and NOT continue with reco!
</pre>
Beam hardening correction can be turned off by doing
<pre>
$ DEFINE UCT_RECONSTRUCTION_CALIBRATION TRUE
$ define uct_disable_bh_correction true
$ deass UCT_BEAMHARD_POWER
$ deass UCT_BEAMHARD_factor
</pre>
and then run <code>uct_reconstruction</code>

The RSQ contains the RAW projection data. The PSQ represents tilted parallel beam projections:

[[Image:CB-Rebinned.gif]]

The rebinning process reduces the number of projections from 836 (1 bright field, 1 dark field and 834 projections spaced at 0.24 deg/proj, spanning 200.16 deg) to 750 (spanning 180 deg) with a resolution of 0.24 deg. In addition to the geometric changes, intensities are adjusted ln(I/I0) and beam hardening correction is applied. After converting a PSQ to AIM with IPL, an image can be reconstructed with Matlab's iradon(), note that only the central slice will be geometrically 'correct', but differences in other slices are small (Circumference of calibration phantom differs less than 1%). in the final reconstruction these effects are accounted for reducing the number of z-slices from 124 (acquired) to 110 in the reconstructed image.

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===Measure RSQ motion artifact===
Based on RSQ data, in-plane translation and rotation, and longitudinal translation can be determined.

The RSQ is first converted to a tilted parallel-beam sinogram. Motion is measured using the bonelab_measuremotion command in the Calgary extension of IPL installed on percy. Copy the motion scripts available in <code>DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]</code> to your COM directory. Here is how they work:

* RSQ_TO_PSQ.COM;1 - (optional) convert RSQ to PSQ, PSQ gets created in the same directory as RSQ. Usage:

<code>$ @rsq_to_psq.com DK0:[BRUNO.DATA.00000162.00009479]C0008921.RSQ</code>

* IPL_MEASUREMOTION.COM;2 - Takes a PSQ and measures motion using Calgary IPL on percy

<pre>
$! example of how to submit a motion measurement
$ SUBMIT/NOPRINT/QUE=SYS$FAST /LOG=SYS$SCRATCH: -
DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]IPL_MEASUREMOTION.COM -
/PARAM=(DISK3:[MICROCT.PROJECTS.DEVEL.RECO_TEST.RAW]PHANTOM_NOMOTION.PSQ) -
/LOG=DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]MEASUREMOTION.LOG
</pre>

Results are save in <code>MEASUREMOTION.LOG</code> and the following section contains all information:
<pre>
/bonelab_measure_motion
-input org
Motion:
Translation = 2.135364
Rotation = 0.024216
Index = 3.694660
Translation weight = 0.943156
Rotation weight = 69.403737
Z_motion = 2.274551

Use the line below with search.
Translation,Rotation,Index,Trans_weight,Rot_weight,Z_motion
2.135364,0.024216,3.694660,0.943156,69.403737,2.274551

Use the line below for DB entry (Index*100).
db_motion_index=369.466034
</pre>

In-plane translation is '''Translation''', in-plane rotation is '''Rotation''' and longitudinal translation is '''Z_motion'''. '''Index''' is the total in-plane motion as used in the IEEE ISBI 2009 paper by linear combination using the weights, not used any more, now we use in-plane translation only. '''db_motion_index''' is the motion index value multiplied by 100 and that could be written to the patient database. Multiplication by 100 is necessary since the motion field in the database is integer only.

For more background on the algorithm look at ''Pauchard Y., et al, Measuring patient motion in HR-pQCT, IEEE ISBI 2009'', and ''Pauchard Y., et.al., Automated quantification of three-dimensional subject motion to monitor image quality in high-resolution peripheral quantitative computed tomography, Phys Med Biol. vol. 56, pp 6523-6543, 2011''. '''IMPORTANT''': The IPL implementation has not been validated against the Matlab implementation used in these publications. Motion Values can be different. Values can be automatically extracted as described below.

* RSQ_MEASUREMOTION.COM;10 - The full deal: creates PSQ and measures motion all in the same directory as the RSQ.
<code>
@DISK3:[MICROCT.PROJECTS.RESCAN.COM]RSQ_MEASUREMOTION.COM DISK3:[MICROCT.PROJECTS.RESCAN.RAW]M0003508.RSQ;1
</code>

Make sure to adjust the line:
<code>$ SCRIPTFILE := DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]IPL_MEASUREMOTION.COM</code>
to the location of your <code>IPL_MEASUREMOTION.COM</code>.

The results are stored in the same directory as the RSQ in <RSQname>MOTION.LOG and can be extracted into motion_all.txt by running the search command:
<pre>search/output=motion_all.txt/window(0,1)/match=OR *motion.log "Translation,","Patient Name "</pre>

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===Update RSQ's Center Information===
<pre>
$ set host 0
username: calibration
password:
$ spb or $ set proc/priv=bypass
$ run [.util]updh_center
Raw-Data-File: enter location of raw data (with directory if necessary)
Center X: [15430]: enter new center value (e.g. 15415)
Press return for all other options.
</pre>

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===Determine RSQ's Centre Calibration Values===
<pre>
$ define uct_reconstruction_calibration true ! Note: do not mistype... or the calibration program will not run
</pre>
In the SAME terminal:
<pre>$ uct_reconstruction dk0:[microct.data.00004026.00004576]c0001344.rsq
Slice-Nr. [0...919] (Neg. to stop): 100
Center [207]: here enter a new number
</pre>
Hit return a few more times to use default values for other options.
<pre>
XtremeCT check these values, that they do not change:
Maximal possible Scan-Distance (mm) = 125.9520
Cropped adjusted Scan-Distance (mm) = 125.9520
See that it does not change, e.g. drop to 124 mm or such...
</pre>
Then do that again, $ uct_reconstruction ....rsq 100 (for the first time, for each file/scan).

Double click on ISQ. slide to slice 101 (!) (100+1, since terminal zero based) compare with image in e.g. slice 100 or 99 (disregard funny half image shift...)

Should already look nicer.

Then try out with e.g. center 230 or so, with e.g. slice 101 (thus slice 102 in Ximage). (now, only one run is necessary)
<pre>
compare against image with center e.g. 200.
continue at libitum until you find the best center, the crispest image.
</pre>
Usually the centre is determined to within about 3 to 5 points (which is 0.3 to 0.5 pixels), so e.g. test 225 and 230, and maybe 228.

Write down your favourite.

If you cannot decide: let Andres know which ISQ slice was reco-ed with which center (in 'Ximage' slice numbers), and I can check - but since remote Ximage is SOOO slow, thanks for only pointing out a few options, I cannot check 20 settings...

Then continue with next diameter scan (the first time for each scan, reco twice again)

The different diameter centers should be a steady function, so all the new center values should be increasing as diameter decreases.

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===Modify RSQ's BHC for in-air scans===
This is necessary because the beam-hardening correction factor assumes scans were done in soft tissue. It is necessary to choose calibrations of 1200 or 700, instead of the default 200.

Currently, the XtremeCT has options for 200 (standard) or 1200 calibration (in air).

To do this, log in as users <code>calibration</code> and then:

<pre>
$ set proc/priv=bypass ! as user calibration; modification of MICROCT user data
$ run ut:UCT_EXT_HEADER_ADD_CALIB.EXE
> Raw-Data-File []: DISK2:[MICROCT.DATA.00000401.00001495]C0001404.RSQ
> ...
> Add another BH-Corr from file again? (Y/N) [N]: ! Enter yes (UCTD:UCT_BH_COEFF_60KV_1200HA_3309.TXT)
</pre>

Then, delete the old ISQ. It must be deleted or else the header information will not be changed. Finally, reconstruct the new ISQ and analyze...

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==Manipulate ISQ==

===Read an ISQ header===
You can either read using the standard tool

$ ctheader C0014141.ISQ
$ sh sym ctheader
CTHEADER == "$UT:CTHEADER.EXE"

Or, use the extended header tool to show the calibration data

$ run ut:uct_ext_header_display.exe

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===Import ISQ===
When you import, please note that the sample number AND measurement number are updated, so meas 10907 is now 10908.

Suppose you have a sample 3000, meas 10000, C0001234.isq, and want to import this into sample 3001, this is what I would do:

To make a copy of the scan (i.e., keep it in sample 3000 and make another copy in 3001)
<pre>
$ cd *3000*10000
$ copy C0001234.isq D0001234.isq, also copy any other files you want imported (RSQ, GOBJs, etc)
$ import

UCT_IMPORT V1.2

---------------

ISQ-file []: D0001234.ISQ

Sample number [0]: 3001

Change File Header name [Y]: Y

Optional: Operator Measurement [0]: 1 (1 = bonelab)

Site 20 Radius L

Optional: Controlfile Nr. [0]: (change if desired)

Execute Rename Command [Y]: Y
</pre>

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==Image Artifacts==
===Ring Artifact===
*Refer to [[Media:Microct_ring_correction.pdf|'''MicroCT Ring Correction''']].

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===Partial Volume Effect===
*Refer to [[Media:Partial_Volume_Effect.pdf|'''Partial Volume Effect''']].

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===Beam Hardening Correction (BHC)===

====Use the right BHC====
*Refer to [[Media:Beam_hardening_correction.pdf|'''Use the right beam hardening correction''']].

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====Understand Scanco BHC====
If you see lines like 'CCD_CORR: Expand BH-corr to1536' etc. etc.:

then we do a polynomial correction:
<pre>
$ dir uctd:*bh_coeff*.txt
</pre>
and you see a file with the scanner ID.

<pre>
--> $ type uctd:UCT_BH_COEFF_60KV_0200HA_3309.TXT

-->
! Function 9 is Addpolynom
Function: 9 A
0: 3 0.00000000 -0.38599902 0.30870225 -0.06162301
--> 0: for all pixels. 3 --> 3rd degree polynom, with factors:
x^0 = 0
x^1 = -0.38...
x^2 = 0.308...
x^3 = -0.061...
</pre>

This polynom is added to the PROJECTION value (not the raw counts).

the BH-corr is doing a 'linearization', e.g. see

http://iospress.metapress.com/content/twcxb9jfk8knhpq2/

for more info.

The values in the middle of the scan are amplified more - not just because of their position, but because the object is thicker there, thus the projection values are higher, thus the correction term is higher.

NOTE : Linearisation, as used by Scanco, will compensate 'soft-tissue' beam hardening (inside of water phantom appears LESS dense). Bone related beam hardening, e.g. soft tissue near skull appearing MORE dense, will NOT generally be compensated. See Kak and Slaney 'Principles of computerized tomogprahic imaging' and Joseph and Spital J Comp Assist Tomo 1978 vol 2 for more information.

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=Evaluation=

==Analysis Topics==

===Cortical thickness analysis in standard evaluation===

!!Note - with ipl v5.42 this should be changed to <code>/dt_cortical_thickness</code>

Use the IPL command <code>/dt_cortex_obj_param</code> to measure cortical thickness using direct methods.

When extracting the results from the database using <code>uct_list</code>, specify the <code>UCT_3D_LIST_W_CTH.TXT</code> template in directory <code>DISK0:[MICROCT_COMMMON.UIL]</code>.

<pre>
$ uct_list
UCT_LIST.EXE Version V5.1
Template-File [UCT_3D_LIST_SHEET]: DISK0:[MICROCT_COMMON.UIL]UCT_3D_LIST_W_CTH.TXT
</pre>

UCT_3D_LIST_W_CTH.TXT is now the default template as of March 2009.

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===Cortical porosity and finite element analysis on XtremeCT===

* This procedure is broken down into 3 separate components
* All Scripts mentioned be copied directly from DISK3:[MICROCT.PROJECTS.KYLE.SCRIPTS]
* Files should be copied from data to projects prior to running analysis (see bonelab procedures.doc on sodor)

1. Autocontour the image 
2. Calculate and extract cortical measurements 
3. Create FE files and run FE 

====Autocontour====
* The main autocontour script is located in the ue: directory, this should NOT be modified!
* The procedure is executed using a "hijack" script [[Media:HIJACK_AUTOCONTOUR.TXT|'''HIJACK_AUTOCONTOUR.TXT''']], but the filename must be changed to .COM or found in the directory mentioned above.
* Files should already have a _SEG.AIM created and should be in the same directory as the raw .AIM file.

* You then create a SUBMIT.COM script as you would for other files. For example:
$ QQ = "SUBMIT/NOPRINT/QUE=SCEVAL_FAST/LOG=SYS$SCRATCH com:HIJACK_AUTOCONTOUR.COM"
$ 'QQ' /PARA=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.MODELS]'''FILENAME'''.AIM

* This command will then create various files for examination and further analysis. These include:
** FILENAME_COMBI.AIM - shows cortical, trabecular, and pores all in different colors
** FILENAME_COMBIPO.AIM - shows only the cortex with porosity as different color
** FILENAME_CRTXFILL.AIM - gives sold mask of cortex, porosity filled (can be used to calculate Ct.Th)
** FILENAME_CRTXPO.AIM - shows only the pores
** FILENAME_TRAB.GOBJ - gobj of trabecular region
** FILENAME_CRTX.GOBJ - gobj of cortical region
** FILENAME_AUTO2.GOBJ - gobj of whole bone region

* Further technical details and references can be found in the following publications:
** Buie, H., Campbell, G., Klinck, R., MacNeil, J., & Boyd, S. (2007). Automatic segmentation of cortical and trabecular compartments based on a dual threshold technique for in vivo micro-CT bone analysis. Bone, 41(4), 505-515.
** K.K. Nishiyama, Macdonald, H., Buie, H., Hanley, D., & Boyd, S. (2010). Postmenopausal Women With Osteopenia Have Higher Cortical Porosity and Thinner Cortices at the Distal Radius and Tibia Than Women With Normal aBMD: An In Vivo HR-pQCT Study. Journal of Bone and Mineral Research, 25(4), 882-890.

====Evaluate Cortex====

*This Step 2 method of doing the cortical analysis is no longer used now that we have the IPL_UPAT_CALGARY_EVAL_XT1.COM or XT2.COM version. The problem with this approach is that it is a Frankenstein of the standard analysis and the advanced analysis. The cortical bone assessment is correct, but the trabecular compartment from the standard analysis is not a perfect match. Instead, we should be using the GOBJs described in IPL_UPAT_CALGARY_EVAL_XT1.COM so that we have a perfect mix.

Nevertheless, we keep this information here for now for posterity.

*After the autocontour is computed we used to call IPL_EVAL_CORTEX.COM that will calculate the cortical parameters:
**Cortical porosity (%)
**Direct cortical thickness (mm)
**Cortical density (mg HA/ccm)

This WAS called as the following:
$ QQ = "SUBMIT/NOPRINT/QUE=SCEVAL_FAST/LOG=SYS$SCRATCH com:IPL_EVAL_CORTEX.COM"
$ 'QQ' /PARA=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.MODELS]'''FILENAME.AIM''' -
/LOG=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.LOG]'''FILENAME'''_EVAL_CRTX.LOG

* The results of this script are outputed into individual log files for each file being evaluated.
* To extract these results into one file use:
$ search/output=output_results_filename.txt *EVAL_CRTX.LOG "!% ov/tv","!> C.Th","!% mean_unit"
*A learn command in the eve editor can be used to extract the specific results desired:
**!% ov/tv is the amount of bone in the cortex (ie. 1- ov/tv = cortical porosity)
**!> C.Th is the direct cortical thickness in mm
**!% mean_unit is the cortical density in mg HA/ccm

====Create and run FE models====

*The most current common FE model to run is a homogeneous model where all elements have the same material properties and the cortex and trabecular regions are labeled separately in order to determine the percentage of load carried by each region.
*The other option is to create a model where the material properties are scaled based on the density values and scripts for this can be found in the COM directory.

*The script IPL_FEM_HOMOGEMOUS_LS.COM will use files created by the autocontour and appropriately label the cortex and trabecular regions as well as remove any disconnected pieces of bone.
$ QQ = "SUBMIT/NOPRINT/QUE=SCEVAL_FAST/LOG=SYS$SCRATCH com:IPL_FEM_HOMOGENOUS_LS.COM"
$ 'QQ' /PARA=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.MODELS]'''FILENAME'''.AIM

*Files will now be created with the suffix _HOM_LS.AIM and can be moved to Mighty-Mac or Mavis for FE analysis. You will require user accounts for these computers and can contact Eric or Steve. If using FTP be sure to transfer the files in binary mode (further documentation on this can be found in this Wiki)

*[[Media:2009-10-15_FEM_Tutorial.pdf|'''FEM tutorial main steps''']] to submit the FE files with a detailed manual is recommended for first time users.
*This is now out of date, but is kept here because it still contains useful information about preparing AIM files and post-processing.
*For running the FE itself, please refer to the current manual at [[FAIM Finite Element Solver]].

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===Cortical midshaft analysis with moment of inertia calculation===

This explains what happens when you type

<pre>
$ midshaft ! or
$ eval_midshaft
</pre>

Draw a rough contour around your slices: open the Contouring Sub-window, double-click on the big image, and it automatically finds the best contour. Then click on 'Selection' 'Forwards', then 'Iterate Forwards'.

Then 'cancel' the contouring sub-window, and start the 3D evaluation. Make sure you have already set the correct threshold, sigma, support in file
<pre>DISK2:[MICROCT.EVAL]IPL_FIXED_BATCH_MIDSHAFT.COM</pre>

When you type

<pre>$ show queue</pre>

you should find a job called UCT_EVALUATION_MIDSHAFT and a SYS$SCRATCH:*_MIDSHAFT_*.LOG

The IPL_FIXED_BATCH_MIDSHAFT.COM by default does not calculate the direct measurement results because you must have many more than 20 slices for these to be valid. You can uncomment these parts of the file if you contoured the whole stack (i.e., stack thickness is >> than cortex thickness).

TILDE: Note that you will see lots of tildes (~) on the result sheets. This is to tell you that, if the measurements were trabecular bone, those values would only be approximate. But now for the cortex, they are actually correct! (see below for more explanation about this) I would now use the tildes to check the 'excel' table that the operator has taken the correct script for the trab. or cort. evaluations for the respective measurements!

So what's the advantage of all this? Now, also VOX-TV is correct! So VOX-TV is the whole area, VOX-BV the doughnut, so TV - BV is the marrow area! And still, TRI-Tb.Th is the cortical thickness (TRI-TV is NOT correct, because the .gobj feature was turned off).

I say 'area' above: depending on how many slices one individual scan has,
VOX-BV (and VOX-TV) might be different for different scans, so you will HAVE to
convert the volumes to area again:

<pre>
volume equals area times height
--> Bone Area = VOX-BV / height = BV / (dim.z * el_size_mm.z)
</pre>

and same for Total area, of course :-)

POROSITY: If you want porosity of the bone itself draw two contours: one around, counter-clockwise, on on the inside, clock-wise (thus a 'negative', excluding contour). Now, TV will be just that ring area, BV will be the bone within that ring area, and BV/TV will be 1 - porosity, thus BV/TV 94% means 6% porosity.

METAPHYSIS: Application of this script to metaphysis scan (with trab. in middle):

<pre>
$ midshaft
</pre>

Draw one contour around the cortex, and in the same slices, a NEGATIVE contour on
the inside (CW contour) to exclude the trabecular bone. You may potentially work with the BP (break-point) system to be able to morph the negative contours, even though there is already an 'outer' contour around the bone in every slice.

Start 3D eval, read out the data-base with <code>$ uct_list</code>.

NOTE: You CANNOT give the .gobj a special name such as c0001234_cortex.gobj if you are using the automatic evaluation button on UCT_EVALUATION. Only after the eval (or midshaft eval) has finished, you may copy it to a more meaningful name, but all of the evaluations are just taking the STANDARD gobj name!

Afterwards (after renaming or copying the _seg.aim to _cortex.aim, and .gobj to _cortex.gobj), you may want to start the very normal eval with normal (inner) contours to evaluate the trabecular compartement.

<pre>
Remember: the values in our 3D result database then are OVERWRITTEN.
</pre>

If you have a large study, I would recommend to run the $ midshaft for ALL
samples, <code>$ uct_list</code> to e.g. <code>sys$scratch:mystudy_cortex.txt</code>,
rename/copy gobj and seg for all, and THEN run the trabecular evaluation for all samples. <code>$ uct_list</code> and you have two nice complete excel sheets.

NOTE ON PLATE MODEL: More explanations of why the plate model is correct

Assume a ring (cortex).

<pre>
Area = thickness * 'middle line'.
'middle line' = average of outer and inner circumference
--> 'middle line' = 0.5 * 'bone surface'

--> thickness = bone volume * 2 / bone surface.
</pre>

And this is nothing else but the 'plate model' formula for Tb.Th!

NORMAL TRABECULAR EVALUATION? And why not just run the 'normal trabecular eval'? Because in the 'normal' TRI calculation, we are EXCLUDING all surfaces that are created artificially by a gobj line that cuts through a trabecula.

However, for the midshaft, this means the whole outer (or even inner, if also
inner contour is there) is SUPPRESSED, because it is touching the gobj line. So
this is where that midshaft script comes in: it turns off that suppression.

MORE EXPLANATIONS: Why the direct DT-Tb.Th* is NOT correct for a scan with
just 12 slices.

If we fill the structure with spheres, those spheres should be bounded by the
width of the cortex, not just by the fact that we only have 12 slices (and even more so, we are always doing 'aim box' suppression with the spheres) if a sphere touches the boundary of the aim box, it is suppressed!

So this is quite crucial for Tb.Sp and Tb.N. To get meaningful Tb.Sp, you would
need a LOT of slices. Also, then, you cannot have the inner contour - otherwise
the negative inner contour will delete the Tb.Sp. spheres.

If you have enough slices, you may opt to turn the <code>/dt_object</code> on again in the
midshaft script (second half). Then DT-Tb.Th* and TRI-Tb.Th just have a slightly different behaviour if there are little pores within the cortex:

<pre>
TRI: the little pore just adds a little BS, thus the influence is not that big.
DT: the little pore cuts the thickness sphere in half, thus at that location, the thickness is halved.
</pre>

MEAN1 and MEAN2: The script is also calculating Mean1 and Mean2 now.

<pre>
Mean1: 'apparent' density, average over whole TV
Mean2: 'tissue' density: average over what was segmented as bone only.
</pre>

These mean values will be in mg HA/ccm if you have the calibration option for bone density installed (and activated for those scans). Remember: the bone has to have some soft-tissue (or equivalent) on the inside, and preferably also on the outside then.

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===Joint Thickness Measurements===
*Sample script to search histogram files for results: [[Media:Summarize_Joint_Th_Measurements.pdf|Summarize Joint Th Measurements]]

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===Scanco Joint Space Width (JSW) analysis===
The scripts published in [https://doi.org/10.21037/qims.2019.12.11 Stok et al. 2020], and released by Scanco, are available for XCT1 and XCT2.

On XCT2 they have been installed as Tasks #112 to #116.

Instructions to run this analysis are available here [[Media:ESD_Joint_Space_Width_v2.3.pdf]].

The full citation for this work is:
<pre>
Stok KS, Burghardt AJ, Boutroy S, Peters MPH, Manske SL, Stadelmann V, Vilayphiou N, van den Bergh JP, Geusens P, Li X, Marotte H, van Rietbergen B, Boyd SK, Barnabe C; SPECTRA Collaboration. Consensus approach for 3D joint space width of metacarpophalangeal joints of rheumatoid arthritis patients using high-resolution peripheral quantitative computed tomography. Quant Imaging Med Surg. 2020 Feb;10(2):314-325. doi: 10.21037/qims.2019.12.11. PMID: 32190559; PMCID: PMC7063288.
</pre>

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==UCT_EVALUATION==

===UCT_EVALUATION SOP===
====Start 3D evaluation from terminal for XtremeCT II====

Logged into the terminal as "xtremect2" you can see the evaluation scripts in <code>IDISK1:[XTREMECT2.EVAL]</code>

The morphological evaluation: Control file #25. It basically runs auto contouring (#23) and then the morphological analysis.
* <code>UCT_EVALUATION_V6_XT2_DT61.COM</code>
* <code>IPLV6_EVAL_CORT.COM</code>
* <code>IPLV6_EVAL_TRAB.COM</code>
* <code>IPLV6_EVAL_TOTAL.COM</code>

* <code>UCT_3D_LIST_CORT_XT2.TXT</code>
* <code>UCT_3D_LIST_TRAB_XT2.TXT</code>
* <code>UCT_3D_LIST_TOTAL_XT2.TXT</code>

Contouring scripts:
* <code>IPLV6_AUTOK.COM</code>: Creates automatically the standard GOBJ. Control file #22.
* <code>IPL_AUTOK_CTTB.COM</code>: Creates automatically the CORT, TRAB and PORE.GOBJ (previously CRTXPO). Control file #23.
* <code>IPLV6_AUTOK_CTTB_CORR.COM</code>: Creates automatically the CORT and PORE.GOBJ, after manual correction on the TRAB.GOBJ. Control file #24.

Laplace- Hamming scripts:
* <code>IPLV6_UPAT_EVAL_LH61_XT1DB.COM</code>
* <code>IPLV6_UPAT_EVAL_LH82_XT1DB.COM</code>

Results will be generated in the <code>IDISK2:[XTREMECT2.RESULTS]</code> directory, in the same way as they are generated for the cortical analysis on XtremeCT I, i.e. using the uct database and appended text files.

Laplace Hamming evaluations will generate results in the upat_list database. The direct measurements will be stored in the uct_list database.

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====Symbols for XtremeCT II vs XtremeCT I====
<code>microct</code> account you get

"MICROCT_BIN" = "DISK1:[MICROCT.]" (LNM$PROCESS_TABLE)
= "DISK0:[MICROCT_COMMON.3309.]"
= "DISK0:[MICROCT_COMMON.]"

for <code>xtremect2</code>

"MICROCT_BIN" = "DISK1:[XTREMECT2.]" (LNM$PROCESS_TABLE)
= "DISK0:[MICROCT_COMMON.]"

So 3309 has its own directory where the software versions for the two scanners are different, e.g.

xtremect: DISK0:[MICROCT_COMMON.][MAIN]IPL_SCANCO_M.EXE
microct: DISK0:[MICROCT_COMMON.3309.][MAIN]IPL_SCANCO_M.EXE

We have defined some symbols for the different ipl versions:

IPL
IPLREG
IPLFE
IPL_BATCH
IPLREG_BATCH
IPLFE_BATCH

In the scripts you can directly use these symbols instead of ipl_scanco_prog (old style).

IPL and IPL_BATCH are different for the two scanners because the newest version is not officially released for XT1.
IPL of the microct account (XT1) cannot read data of the xtremect2 account (XT2). The other way around it works.

IPLREG and IPLREG_BATCH point to <code>$DISK1:[XTREMECT2.MAIN]IPL_SCANCO_REGIS_V107.EXE</code> for both accounts.

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====Start 3D evaluation from terminal for microCTs====

[[Image:Bones2.jpg|20px]] Warning:Do not change <code>uct_evaulation_v4.com</code> and <code>ipl_fixed_batch_v4.com</code> in .eval, but only work on your own file (i.e., eval_steve).

First, an explanation of how the normal evaluation runs by hitting the 'Start 3d' button.
<pre>$ scanco_submit_command ue:uct_evaluation_v4.com/para=(xxx,yyy,zzz,…)</pre>
There are 8 parameters:
*P1: number of print outs of our results sheet
*P2: the ISQ filename
*P3-5: start x (pos x), y, z
*P6-8: dim x, y, z
The parameters p3-p8 come from the white bounding box. The problem is that when you start from the terminal you do not have these. This problem can be overcome by using the <code>isq_to_aim_gobjbox.exe</code> and then give the relevant parameters. You can
<code>$ run um: isq_to_aim_gobjbox.exe </code>
to see what it's asking for.
By using gobjbox you do not need p3-p8. Therefore you can start the evaluation by giving:
<pre>$ scanco_submit_command ue:uct_evaluation_special_josh.com –
/para=(1,dk0:[microct.data.0000275.0000245]c0000332.ISQ)</pre>
*You can make <code>uct_evaluation_special_josh.com</code> such that there is no need for P1 (change p2 to p1 in the script, etc).
*Alternatively to using the gobjbox you could use the normal isq_to_aim, but hard code the dim and pos.
*Then call whatever IPL files you want to call. Look into <code>fixed_batch_v4</code> to see how we turn on the database always on the first line of every IPL part, and how we calculate parameters.

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====Temporarily change evaluation for UCT_EVALUATION====

In a terminal window, we need to redefine the logical that determines which
3D evaluation is associated with the <code>UCT_EVALUATION</code> tool.

For example, typing <code>VOI</code> runs the <code>UCT_EVALUATION</code> tool
by executing <code>UE:UCT_EVALUATION_VOI.COM</code>

Type
<pre>$ show logical UCT_EVALUATION</pre>
and then you can redefine this to point to another evaluation script.
<pre>$ define UCT_EVALUATION UE:UCT_EVALUATION_CUTOUT.COM</pre>

This is only redefined in the particular terminal you are using, and it
will reset to its default in a new terminal. It will also not work if you
try to submit the job to a queue. It only works interactively.

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====Assign special evaluation to UCT_EVALUATION====

'''Warning''': This is for advanced users ONLY. Do not attempt this without contacting Steve!

This will show how to set up <code>$ eval_kyle</code>:
It is easy to set up multiple .COM files for the 3D evalulation tool, one such set-up is already prepared on your computer:
<pre>
$ eval_special
</pre>
will do something similar to <code>$ voi</code> where the normal contour program opens, but if you start the 3D eval, the special script <code>um:uct_evaluation_special.com</code> is called (associated with eval_special), which then in turn calls <code>ipl_fixed_batch_special.com</code>, where you can specify your own set of thresholds, etc.

So it is a daisy chain of files which we will need to follow to set up a special <code>xxx_kyle.com</code> script, and where ever we encounter <code>_special.com</code>, we copy and change it to <code>_kyle.com</code>.

So to set up <code>$ eval_kyle</code> you will need to do the following:

*1. Edit <code>disk1:[microct]microct_setup_user.com</code> (double-click on file), please be careful here, it's very important! (and I hope you have done your 'weekly full backup' regularly, so you could always retrieve a good version of login.com...)

*2. Then, towards to bottom and duplicate the line
<code>$ eval_special :== @com:eval_var.com um:uct_evaluation_special.com</code>
and change duplicate to
<code>$ eval_kyle :== @com:eval_var.com um:uct_evaluation_kyle.com</code>

This will make this command <code>eval_kyle</code> available after you login freshly. Save and Exit.

*3. Then go to <code>disk1:[microct.eval]</code> and copy the file <code>uct_evaluation_special.com</code> to the name <code>uct_evaluation_kyle.com</code> ('Commands', 'Copy ...', BUT CLICK ON THE THREE DOTS and give new output name.
If you do not see the <code>eval_special:</code> go to terminal, <code>$ dir ue:*special*.com</code> and take it from the <code>microct_common</code> directory)

*4. Edit the <code>_kyle.com</code> file: at the top, change <code>ipl_......_special.com</code> to <code>_kyle.com</code>

*5. Copy <code>ipl_fixed_batch_special.com</code> to <code>ipl_fixed_batch_kyle.com</code>

*6. Edit <code>ipl_fixed_batch_kyle.com</code> to your liking. If you want <code>$ eval_kyle</code> to not perform the full evaluation, but only something akin to <code>voi</code>, then, in the steps above, copy <code>uct_eval_voi.com</code> to <code>uct_evaluation_kyle.com</code>, and <code>ipl_voi.com</code> to <code>ipl_fixed_batch_kyle.com</code> (thus you take the <code>voi</code> script as template for the <code>_kyle</code> script).

*7. Then open a new terminal ('applications', 'decterm'), <code>$ eval_kyle</code> should work now!

'''Notes''': When you start the 3D eval, then
<code>$ que</code>
will show you your batch job with your name on it now!

And now a few more explanations how the whole thing works: in all eval programs, hitting 'Start 3d' just submits the logical <code>uct_evaluation</code>, <code>$ show log uct_evaluation</code> shows you that by default, this points to <code>ue:uct_evaluation_v4.com</code>.

Those little <code>voi</code> and <code>eval_steve</code> scripts then just temporarily redefine this logical so that a different script is submitted when you <code>'start 3d eval'</code>.

About the '''corelut eval''': Then we start a whole different eval program: the <code>.exe_corelut</code>. So, if you set up a <code>eval_steve_c</code> (or whatever you want to call it): Produce a <code>eval_var_c.com</code> in the directory commands (maybe copy from microct_common to [microct.commands]), and there, on the last line, instead of starting
<code>$ uct_evaluation</code>
(the normal program), replace by
<code>$ evalc</code>
which starts the <code>.exe_corelut</code> - and because the <code>eval_var.com</code> has over-ridden the <code>uct_evaluation</code> logical just before, then you are starting different script upon starting 3d eval.
NB: we have a logical AND a symbol called <code>uct_evalution</code>. Sorry for confusion. Symbol <code>uct_evaluation</code> starts normal <code>eval</code> program, so this is what you replace by symbol <code>evalc</code> now).

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===UCT_EVALUATION FAQ===
====Warning: Not all required GOBJ files found, Continue anyway?====
This occurs when the chosen evaluation script is looking for a contour file, but can't find it.
*To see what contours the script is looking for go to "File" then "Save GOBJ As...". You can now see the list of required gobj files.
*For some scripts, it may not be necessary to supply a gobj and you can continue with the evaluation without it. For example, the "3D Segmentation of VOI, 1 solid object" applies the contour to isolate the region of interest, however, this may not be necessary if the object of interest can be extracted from thresholding.
[[File:Save_gobj_as.jpg|400px]]

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====Warning: Attempt to access non-existent record CODE: 36====
The scan is most likely still in the process of being reconstructed. Try to access the scan again in a few hours.

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====Error: Insufficient logical unit numbers CODE: 1409716====
Exit the evaluation program and restart it.

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====Error: Process quota exceeded====

[[Image:Process_quota_error.JPG|300px]]

When running UCT_EVALUATION from a dec terminal, an error when starting an evaluation may occur if there are to many dec terminals opened.
*The easy fix for this is to open the terminals from the applications menu in the [[Scanco_User_Instructions#Session_Manager|'''session manager''']] instead of using the dec command.
*Alternatively you can set up a new login script and add <code>/DETACH</code> to the dec definition
<pre>
$ DEC == "CREATE/TERMINAL=DECTERM/DETACH".
</pre>
An example script can be found here @DISK5:[BONELAB.PROJECTS.BUIE]SETUP.COM.

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====Bug: UCT_EVALUATION v6 in customizing EVAL scripts====

<pre>$ run um:uct_k_v6</pre>

The new evaluation tool v6 should be used in place of the older v5. Please see the Documents section of this wiki for a manual on its use.

Known bugs:

When you are producing your own EVAL scripts, and want to call your own ipl file
or such:

The 'EVAL:' keyword in the scripts has the filenames of the
uct_evaluation_v6.com, then the ipl_v6_xxxx.com, then additional filenames (such
as the _prs.com to print and the 3dresults_append.com)

Now, if you are in BASIC mode in the modify window, and you change any of the 3
filename fields, the last of the additional filenames is 'dropped'... ooops...

So please go to Advanced mode and check the long 'EVAL:' keyword that all wished
files are still in the list, otherwise add the last again (most of the time,
that's the useful _3dresult_append.com script...)

Will correct that of course in the next version.

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====Not work: Left mouse button====
When the left mouse button doesn't work in the µCT evaluation program:
*Turn off caps lock.
*For remote sessions, turn of the Num Lock key (this will also allow you to use Ctrl-C and Ctrl-V to copy and paste contours).

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====Not work: Remove and insert keys====

The remove and insert buttons on the keyboard don't work in the µCT evaluation program:
*Turn off caps lock.

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==Evaluation FAQ==

===Customize your evaluation script===
The basic procedure is to create your customized evaluation script is:
#Clear the database of existing results
#Do your evaluation
#Extract the results
#Paste results into excel template.
You could repeat as necessary to evaluate a measurement multiple times and write out the results to a file.
*You must submit all jobs to a single queue!!!

'''1) Start ipl and clear the database of existing results.'''
<pre>
$ IPL_BATCH

/db_clear_eval
-input "IPL_AIM

..
</pre>

'''2) Insert your IPL evaluation.'''

'''3) Extract the results.'''
<pre>$@com:extract_results.com P1 P2</pre>
*P1 is the aim file (including path) and P2 is the result file (including path)

Example:
<pre>
$@com:extract_results.com DISK5:[BONELAB.PROJECTS.BUIE]MYAIM.AIM DISK5:[BONELAB.PROJECTS.BUIE]MYRESULTS.TXT
</pre>
*P2 should be the same for all samples in your project so that results are compiled into a single file.

'''4) Paste results into excel template.'''
*Refer to the [[Media:Extract_Results_Template.xlsx |'''Excel Extract Results Template''']].
*Open your results text file and copy and paste the contents into cell A2. There's no need to use paste special since the sheet is protected.

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===Create your own IPL script===

To make a script that would submit a job to the queue with the command as follows:
<pre>
$ @um:ipl_eval_only.com 'aim_file' 'gobj_file' 'p1' 0
</pre>

you need to create your own IPL file would be translated to the following command:
<pre>
$ submit /noprint /que=sys$slow ue:IPL_VOI_JOSH_M.COM
- /log=sys$scratch:test.log /para=('aim_file','gobj_file','seg_file')
</pre>
The IPL file would look something like this…
<pre>
$ if p1 .EQS. ""
$ THEN
$ write sys$output "Give DK0:[xxx]C0001234_SEG.aim on the line."
$ write sys$output "Or: "
$ write sys$output "Type $ scanco_submit_command um:ipl_eval_autostart/para=(dk0:[xxx]c00123_seg.aim) "
$ exit
$ endif
$
$ gobj_file = p1-F$PARSE(p1,,,"VERSION")-"_SEG.AIM" + ".GOBJ"
$ aim_file = p1-F$PARSE(p1,,,"VERSION")-"_SEG.AIM" + ".AIM"
$
$!
$ @um:ipl_eval_only.com 'aim_file' 'gobj_file' 'p1' 0
$ exit
</pre>

Some more handy IPL sequences are:
<pre>
$ INPUT = F$SEARCH("UCT_MEASUREMENT_DATA:[*.*''P1']*.RSQ",1)
</pre>

and then you just need to give meas. number as P1 (and maybe slice range as p2),
<pre>
$ if p2 .eqs. "" then p2 := A
</pre>
OR, some nice starts are:
<pre>
$ IF P3 .EQS. ""
$ THEN
$ WRITE SYS$OUTPUT "P1: Measurement Number to duplicate"
$ WRITE SYS$OUTPUT "P2: New Sample Number from Database"
$ WRITE SYS$OUTPUT "P3: New Start Letter of ISQ file"
$ WRITE SYS$OUTPUT "P4: Optional: Operator Number"
$ WRITE SYS$OUTPUT "P5: Optional: Controlfile Number"
$ EXIT
$ ENDIF
</pre>
where you say which parameters HAVE to be there (up to p3), and which ones are optional.

All together, the script may look like this:
<pre>
$ IF P1 .EQS. ""
$ THEN
$ WRITE SYS$OUTPUT "P1: Measurement Number to reco"
$ WRITE SYS$OUTPUT "P2: Optional: Slice number N or Range M:N. Auto:All"
$ WRITE SYS$OUTPUT "P3: Optional: Queue. Auto: sys$slow"
$ EXIT
$ ENDIF
$ if p2 .eqs. "" then p2 := A
$ if p3 .eqs. "" then p3 := SYS$SLOW
$ slices = p2
$ quename = p3
$ INPUT = F$SEARCH("UCT_MEASUREMENT_DATA:[*.*''P1']*.RSQ",1)
$ INPUT = INPUT - F$PARSE(INPUT,,,"VERSION")
$ logfile = "sys$scratch:RECO_" + f$PARSE(input,,,"NAME") + ".LOG"
$ submit/noprint/queue='quename' uct_reconstruction_file -
/para=('input','slices','logfile')
$ exit
</pre>
Note that <code>uct_reconstruction_file</code> is a logical that points to <code>um:uct_reconstruction.com</code>.

Logicals are preferred in scripts to make them more universal.

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===Run Scanco cut and match function (on Percy)===

;At DATA DISK:
Run<code>$ upat_list</code>
*mode 1, list mode.
*Select patients and site, etc.
*Select the appropriate template file, e.g. <code>UE:UPAT_TEMPL_CUTMATCH_AUTO_PATTB_CT.TXT</code>
*Output to a file, then run that file.

;At PROJECT DISK:
If you have moved the files to the project directory and renamed them, you can generate a script from:
<pre>
$ @UE:SEARCH_PROJECTS_CUTMATCH.COM
-P1 = filename with device and directory
-P2 = site (RR, RL, TR, TL)
-P3 = output filename
</pre>
For example, if we run:
<pre>
$ @UE:SEARCH_PROJECTS_CUTMATCH.COM DISK3:[MICROCT.PROJECTS.GRACE]GRACE_01_00MTH_RR.AIM RR MYFILE.COM
</pre>
The script will search <code>DISK3:[MICROCT.PROJECTS.GRACE]</code> for files in the form <code>G*RR*.AIM</code> with the same
length as <code>GRACE_01_00MTH_RR</code>, then check sample numbers to determine if the file is a follow-up scan.
*Upat_list is called to obtain position and dimension data for matching slices.
*The output file <code>DISK3:[MICROCT.PROJECTS.GRACE]MYFILE.COM</code> is created to submit and run the cut and match.

Before running, open the file and add <code>$ exit</code> at the end.
<pre>$ @DISK3:[MICROCT.PROJECTS.GRACE]MYFILE.COM</pre>

For multiple files, do something like the following.
<pre>
$ @UE:SEARCH_PROJECTS_CUTMATCH.COM DISK3:[MICROCT.PROJECTS.GRACE]GRACE_01_00MTH_RR.AIM RR MYFILE.COM
$ @UE:SEARCH_PROJECTS_CUTMATCH.COM DISK3:[MICROCT.PROJECTS.GRACE]GRACE_02_00MTH_RR.AIM RR MYFILE.COM
</pre>
Open MYFILE.COM and add <code>$ exit</code> at the end.
<pre>$ @MYFILE.COM</pre>

*The script assumes all follow-ups are provided.
*If follow-up scans are missing, it will be necessary to modify the output file so that the position and dimension data matches the files or update the <code>SEARCH_PROJECTS_CUTMATCH.COM</code> script.

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==IPL FAQ==
===Submit a job to the queue===

<pre>
$ submit/noprint /que=sys$slow ipl_voi_josh_m.com /log=sys$scratch:test.log
</pre>

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===Rotate with turn3d / turn2d===

The turn3d function can be used to perform a single rotation about any axis in 3d. The turnaxis_angle input is the angle between the x, y, and z axes and the line about which the rotation will be performed. The turnangle input is the amount to be rotated about the specified line. To use this function to perform three sequential rotations about the image's original x, y, and z axes requires compensation for the previous rotations.

To rotate an image from the axial view in the z plane to the sagittal view in the z plane:

<pre>
$ipl
/turn3d
-input             in
-output          out
-turnaxis_angles 90 0 90
-turnangle 90
-img_interpol_option 0
</pre>

No interpolation is necessary as this is "pure reformatting" (turning +-90 or 180 degrees around x,y or z axis)

For knee images, to put the femur above the tibia, you further add the step:

<pre>
/turn2d
-input out
-output happyFemur
-turnangle 270
-turnpoint_global_not_local true
-turnpoint -1 -1
-img_interpol_option 0
</pre>

Refer to [[Media:turn3d.pdf |'''turn3d.pdf''']] for further instructions.

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===Noise removal by component labeling===
*Refer to [[Media:ComponentLabeling.pdf|'''Noise removal by using component labeling''']]

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===Create MSQ image and view===

This is based on marching cubes. See <code>IPL_UPAT_EVAL.COM</code> for an example as per below:

<pre>
/read seg C0000214_SEG.AIM

/sup_divide ! careful of the order of inputs here
-input seg
-suppos_pixels_local -1 -1 -1
-supdim_numbers 1 2 1
-subdim_pixels -1 -1 -1
-testoff_pixels 0 0 0

/sub_pick
-input seg
-output segsub
-subpos_numbers 0 1 0

/tri
-input segsub
-output tri
-gobj_filename none
-peel_iter 0
-ip_sigma 0.8
-ip_support 1
-ip_threshold 40
-nr_ave_iter 2
-size_image 512 512
-scale_image 0.800000
-edges false
-nr_views 1 ! Important

/msq_from_aim
-aim_name tri
-msq_filename C0000123_3D.MSQ
</pre>

Then, use <code>UCT_3D</code> to view it. If you click on "animations" it will give you the option to read the MSQ file.

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===db_scanco_activate associate evaluation database===

When <code>/db_scanco_activate</code> is used in the IPL files, the correct association with the evaluation database is through the Index Patient and Index Measurement in the AIM header.

<pre>
Index Patient 3095
Index Measurement 5962
!-------------------------------------------------------------------------------
</pre>

Using IPL
<pre>
$ ipl
$ read in xxx.aim
$ examine in log
$ db true {activates database}
$ dt_object {at end "writing results to database for measurement 1234"}
</pre>

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===dicom_to_aim bug in IPL v5.03===

In IPL, use the /dicom_to_aim function. There is a bug in pre IPL v5.03 which requires that a small AIM be read in before doing the DCM conversion.
<pre>
ipl> read in tmp.aim
ipl> dicom_to_aim
-aim_name [in] >
-dicom_filename [default_file_name] > 4F65038B3986.DCM
-multifile [false] > true
ipl> write in MYFILE.AIM
</pre>

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===Understand "New" DT functions in IPL v5.42===

This applies to:
<pre>/distance_map /dt_ow_thickness /dt_number
/dt_thickness /dt_spacing /dt_cortical_thickness
</pre>

XT1 (old dt) and XT2 (new dt) use 0.5 for assign_epsilon and 0.9 for
ridge_epsilon.

µCT uses 1.8 for assign_epsilon and 0.9 for ridge_epsilon (old dt).

Therefore I recommend to take 0.9 and 1.8 also for the new dt functions
for µCT/vivaCT measurements.

The <code>suppress_boundary</code> feature is new and works as follows:

0: The ridges and spheres are calculated on the full seg AIM, also
outside the gobj. At the end the gobj is applied.

1: The ridges that are on the AIM boundary are not used for the
calculation of the maximal spheres.

2: The ridges are calculated on the full seg aim but then the gobj is
applied to the ridges. This means that at the end there are only spheres
that have the center inside the structure (gobj). The maximal sphere
filling algorithm still accounts for the structure outside the gobj, but
only uses center points inside the gobj.

<code>dt_thickness</code> for example can be used in two different ways in a script:

1) cut out aim - apply threshold - apply gobj - dt_thickness
This way the suppress_boundary options do influence the results
because there are no ridges outside the gobj anyway.

2) cut out aim - apply threshold - dt_thickness (with corresponding gobj)
This calculates the dt on the full aim first and applies then the
gobj and suppress options.

If you examine for example trabecular bone only on a small area bounded
by a gobj then the most accurate way to calculate the dt is to cut out a
much larger area (still containing trabecular bone) and use way 2) above
with suppress_boundary 0.

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===Develop new IPL commands in C===
*Refer to [[Media:IPL programming.doc|'''A short manual on how to develop new IPL commands in C'''.]]

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=Results=

==Extract Results==

===UPAT_LIST command===

*Refer to Scanco specification document on using the [[Media:Specification_upat_print_list_V2.0.pdf | '''Upat_print_list V2.0''']] on XCT2.
*Refer to [[Media:Using_upat.docx |'''Using upat_list Additional Notes''']].

upat_list (version 1.9 on XCT1) is identical to 2.0 except:

:* there is no option for using group codes

:* there is no option for using evaluation types

For all of the available parameters for generating results using upat_list command:
$ upat_list -h

Program: upat_print_list V1.9
Use the following modes to run upat_print_list:
upat_print_list -list for export to spreadsheet, default mode
upat_print_list -print for PostScript output
upat_print_list -show for text output
upat_print_list -advanced to access advanced options interactively
Standard Command-Line Arguments:
-b=<pat_nr> First patient, default = 1
-e=<pat_nr> Last patient
In list & show modes, default = last patient in database
In print mode, default = first patient
-s=<site_code> Site code
In list & show modes, RL RR R* TL TR T* CU *, default = *
In print mode, RL RR TL TR CU, default = RL
-mb=<date> Begin of measurement period, default = 1st measurement date
-me=<date> End of measurement period, default = current date
Dates must be given in VMS format, e.g. 01-JAN-2000
-f=<#_followups> Maximum number of follow-ups to match, default = 19
-t=<file_name> Name of template file
In list mode, default = UPAT_LIST_SHEET
In print mode, default = UPAT_EVAL_SHEETxx
In show mode, default = UPAT_SINGLE
-o=<file_name> Name of output file (in SYS$SCRATCH by default)
In list & print modes, stored in SYS$SCRATCH
In show mode, written to SYS$OUTPUT
-c=<number> Number of Print copies if in print mode. default = 1
-v=<level> Verbosity from 0 (silent) to 2 (verbose), default = 1
-h Print this help and exit
Advanced Command-Line Arguments:
-et=<eval_type> Type code of evaluation, default = 2
-eb=<date> Begin of evaluation period, default = 1st measurement date
-ee=<date> End of evaluation period, default = current date
-tb=<date> Begin of matching period, default = 1st measurement date
-te=<date> End of matching period, default = current date
Dates must be given in VMS format, e.g. 01-JAN-2000
-sk=<#_to_skip> Number of measurements to skip, default = 0
-m=<meas_list> Numbered List of measurements to take, e.g. 0,1,2,5,8
-nomatch Do not match follow up measurement, just take all slices
-sb Begin of Slice Range in % to be evaluated
-se End of Slice Range in % to be evaluated
-q Only take evaluations with quality better than (and including) this.
If positive number: all scans of better quality (incl. this) as well as all non-graded scans are taken.
If negative number: non-graded scans are NOT taken.
-qs Only take Structural evaluations with quality better than (and including) this.
Thus: between -qd and -q: only Density results are printed.
Parameter is disregarded if -qs >= -q.
-ut=<unit_type> 0->default unit, 1->linatt, 2->mg HA/ccm, 3->HU, default = 0
-cd=<density> Value of compact density to use, default = 1200.000000
If no command line arguments are specified, upat_print_list runs interactively.

Note that using "TB" and "TE", you can pull out exact measurements in the specified date range, while using "MB" and "ME", all you get is the latest measurement no matter what date range provided.

For results of all time points for a single site and sample # without matching to Baseline, use:
I.e. the common region will be 100% for all measurements.
$ upat_list -nomatch

From these options, you can write out your own command (vs. using prompts) to give you the specifics you are looking for.

By specifying the CAMOS template of “UPAT_EVAL_CAMOS.PS”, you will get the “Camos” report style. For example:
$ upat_list -nomatch -b=1000 -e=1000 -s=TL -tb=01-MAY-2000 -te=01-AUG-2018 -t=DISK1:[MICROCT.COMMANDS]UPAT_EVAL_CAMOS.PS -c=0 -o=sys$scratch:upat_pat_1000_tl_camos.ps

Note that there are actually many kinds of report templates. These can be found via:
$ dir UU:*.PS

“SCUSA” is a short form for Scanco USA templates. I.e. templates that fit on an 8.5” X 11” page.

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===Extract followup data without slice matching===
Use:
<pre>
$ upat_list -advanced
</pre>
*Choose 'disable slice matching:' -> y.

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===Extract patient results on a slice-by-slice basis===

There is an executable that was specially installed by Andres. Run it as user <code>microct</code>:

<pre>
$ RUN ut:UPAT_EXPORT_MEASUREMENT.EXE
</pre>

Choose from "Style: 0 = default, 1 = raw". Default gives standard patient parameters.

This gives you the .txt file in scratch containing the morphological parameters determined for each slice.

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===UCT_LIST Extract results===

Assuming you've used the <code>SCANCO_SUBMIT_COMMAND</code> to initialize your evaluations (either manually or through the <code>uct_evaluation</code> tool) then you can get all of your results stored into a text file that can be easily imported in Excel.
<pre>$ uct_list</pre>
The output text file will be stored in <code>sys$scratch</code> and you can ftp this to a PC so that it can be imported into excel and further analysis can be performed.

Importing into Excel requires setting a deliminator based on the space.

Customizing the <code>uct_list</code> output.

The default list template is set by the logical <code>UCT_3D_LIST_SHEET</code> which is normally
set to point to <code>UU:UCT_3D_LIST.TXT</code>. See the templates by

<pre>$ dir uu:*.txt</pre>

Almost all the available keywords are in <code>UCT_3D_LIST.TXT</code> enclosed
by \\ and //.

Only when you use the 'show directly on screen mode':
<pre>$ uct_list 1234</pre>
then you need to do this to override the default output:
<pre>
$ def/user uct_3d_single_sheet my-template_file.txt
$ uct_list 1234
</pre>

Some example format files are:
<pre>
UCT_3D_LIST.TXT
UCT_3D_SINGLE.TXT
UCT_3D_LIST_W_CRH.TXT
UCT_3D_MEANS.TXT --> Use this to get the 5 mean values (i.e., calibration)
</pre>

A summary of all the available keywords is available in <code>UU:UCT_3D_SINGLE_SHEET.TXT</code>
<pre>
Name :\\UCTMEASFILENAME//
Sample-Name :\\SAMPLENAME//
Sample-Nr :\\SAMPLENUMBER//
Meas-Nr :\\UCTMEASNR//
Date of Birth :\\SAMPLEDOB//
Sample-Remarks :\\SAMPLEREM//
Meas-Remarks :\\UCTMEASREM//
Meas-NrofSlices :\\UCTMEASNUMSLI//
Direct: -------------------------------------------------------------------
TV : \\VOX_TV//
BV : \\VOX_BV//
BV/TV : \\VOX_BV_TV//
Conn.Dens.: \\UCT_CONN//
SMI : \\MC_SMI//
Tb.N* : \\DT_N//
Tb.Th* : \\DT_TH//
Tb.Sp* : \\DT_SP//
Tb.1/N.SD*: \\DT_N_SD//
Tb.Th.SD* : \\DT_TH_SD//
Tb.Sp.SD* : \\DT_SP_SD//
Lin.Att.1 : \\UCT_MU0// +-\\UCT_MU0_SD//
Lin.Att.2 : \\UCT_MU1// +-\\UCT_MU1_SD//
Lin.Att.3 : \\UCT_MU2// +-\\UCT_MU2_SD//
Lin.Att.4 : \\UCT_MU3// +-\\UCT_MU3_SD//
Lin.Att.5 : \\UCT_MU4// +-\\UCT_MU4_SD//
TRI (Plate Model): --------------------------------------------------------
TV : \\MC_TV//
BV : \\MC_BV//
BS : \\MC_BS//
BV/TV : \\MC_BV_TV//
BS/BV : \\MC_BS_BV//
Tb.Th : \\MC_TH//
Tb.Sp : \\MC_SP//
Tb.N : \\MC_N//
Anisotropy: --------------------------------------------------------------
|H1| : \\MC_H1// H1x: \\MC_H1X// H1y: \\MC_H1Y// H1z: \\MC_H1Z//
|H2| : \\MC_H2// H2x: \\MC_H2X// H2y: \\MC_H2Y// H2z: \\MC_H2Z//
|H3| : \\MC_H3// H3x: \\MC_H3X// H3y: \\MC_H3Y// H3z: \\MC_H3Z//
DA : \\MC_DA//
Dim X : \\VOX_DX//
Dim Y : \\VOX_DY//
Dim Z : \\VOX_DZ//
Pos X : \\VOX_PX//
Pos Y : \\VOX_PY//
Pos Z : \\VOX_PZ//
El-Siz X : \\VOX_ELSX//
El-Siz Y : \\VOX_ELSY//
El-Siz Z : \\VOX_ELSZ//
</pre>

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===Tabulate LOG results from 3D evaluations===

Only use this if you have not used the standard <code>uct_evaluation</code> tool to generate your 3D evaluations (in which case see the HowTo related to the 3D database).
You can tabulate the LOG files:
<pre>$ search xxxx.log "ov "</pre>
Or whatever you want to search for can be stored in a text file
<pre>$ search/output=sys$scratch:ov.txt xxxx.log "ov "</pre>
To search more than one log file, and get the output into one single file:
<pre>$ fda/output=xxx.txt search *.log "ov "</pre>

The fda means 'file do all' and is a script made by Scanco to do one command (search) on a wildcard of files (*.log). Then put all the ov.txt, tv.txt, name.txt etc. files into excel.
Josh has made a .com file that does a similar job as described above.

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===Compile evaluation LOGs into one file===

Call the <code>UE:UCT_EVALUATION_V4_3D_RESULT.COM</code> with the same construction
as <code>$ eval_special</code>. If you need help with this, see the HowTo on this
Wiki site (HowTo: Assign special 3D evaluation to the UCT_EVALUATION tool).

Edit <code>UE:UCT_EVALUATION_V4_3D_RESULT.COM</code> file to call a specific ipl
script as you wish.

When you run the evaluation, you will have three new files created:

:*Two files in the measurement directory (on DK0!) (one with each eval 3D results in its own file, and one <code>APPENDED_ALL.TXT</code> file)
:*Then in sys$scratch, you will have one <code>SYS$SCRATCH:UCT_LIST_ALL_3D_RESULTS.LOG</code> file with ALL 3D evaluations of all measurements.

Note: You may need to edit the <code>SCANCO_SUBMIT_COMMAND</code> to specify a single queue (i.e., /que=sceval$fast)

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==Database==

===Examine patient databases===
This is for advanced users only!

There are two patient databases that get updated every time an evaluation is performed. Below is the name of the database, and the method used to check database values:
<pre>
$ show logical UPAT_EVAL_DATABASE
$ run disk1:[calibration.util]upat_export_measurement.exe ! as microct
</pre>
<pre>
$ show logical UPAT_SLICE_DATABASE
$ set host 0 ! login as user calibration
$ @disk1:[microct]login.com
$ spb
$ run DISK1:[CALIBRATION.UTIL]UPAT_GET_DB_INFO.EXE ! enter '1' to list records
</pre>

In the slice database every evaluation is recorded, but only one is currently active at a time.

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===Manipulate scan sequence===

Upat_list reports the baseline scan and then the percentage change of follow-up scans from the baseline scan. The order of scans in upat_list is determined from the measurement number (not the measurement date). In the case you need to manipulate the baseline and follow-up sequence, you will need to:

[[Image:Bones2.jpg|20px]] Warning: Use this with caution, and as little as possible!! even if the operation is reversible. Database manipulation is sensitive after all.

1. Log in as the "calibration" user (beware which calibration account to use for the different scanners).

How to proceed in the terminal:
$ SPB
$ @DISK1:[MICROCT]LOGIN.COM or $ @DISK1:[XTREMECT2]LOGIN.COM !! don't miss that line, otherwise you would modify the CALIBRATION databases

2. Use the following command to modify the measurement number:

$ RUN DISK1:[CALIBRATION.UTIL]UCT_CORRECT_SAMPLE_FIRST.EXE !! To redefine the very first measurement in the sequence

:* I do mean "First" measurement in the sequence, and not "baseline" measurement. You may have 2 baseline scans, one for radius and one for the tibia, but only one of them is the very "first in the sequence".

$ RUN DISK1:[CALIBRATION.UTIL]UCT_CORRECT_MEAS_PREV_NEXT.EXE !! To redefine the follow-up sequence beyond the first measure

:* The PREV_NEXT utility is a bit tricky to use, as for each measurement you will have to define its "chronological" previous and its next. It is not related to any anatomical site: one might think for example of defining the Radius follow-up sequence for example. It is not the case. The PREV_NEXT sequence will alternate between different anatomical sites, that is how it should be.

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===Add placeholders for missing follow-up scans===
If there is NO scan at a certain time point in a series (i.e. patient did not show up), the program ut:upat_create_meas_placehoder.exe and upat_create_eval_placeholder can insert fake records, so the slice matching and timepoints/visits are still all in order.

The attached file describes how to create an manage placeholders in the case of missing follow-up visits in longitudinal studies. [[Media:SOP_Create_Placeholders_draft.pdf|'''SOP Create Placeholders''']]

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===Disable a database measurement===

It is not possible to delete an evaluation from the database, but it can be disabled.

NOTE: QC results are stored in the UCT database, and there is no tool to disable a UCT database result.

Log in as the normal user (e.g. XTREMECT2). Then in a terminal you may use this simple utility program:
$ RUN UT:UPAT_CORRECT_VALID_FLAG

See below a typical prompt to deactivate an entry:
<pre>
UPAT_CORRECT_VALID_FLAG V2.0

Measurement No. (0 to stop): 1
Evaluation type [2]: 5
Group code [0]: 0

Found evaluation 57 for patient 4: ID003

Value for valid flag (0=invalid, 1=valid) [1]: 0
Value for placeholder flag (0=write results, 1=placeholder) [0]: 0

Measurement No. (0 to stop): 0
</pre>

You can always re-activate the entry, by switching the valid flag from 0 to 1.

Or, to make a scan invalid, you can also login as calibration user.

Point to microct user

$ @DISK1:[MICROCT]LOGIN.COM

Set priviledges to bypass.

$ SPB

Run Correction File
$ run DISK1:[CALIBRATION.UTIL]UPAT_CORRECT_VALID_FLAG.EXE

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===Disable a uct_list database measurement===
You cannot really disable data in the UCT_LIST output. What you can do using IPL is to clear the complete result entry for a given measurement, for example:

$ ipl
/read
-name in
-filename default_file_name
/db_scanco_activate
-write true
/db_clear_eval
-input in

Then UCT_LIST might still report the "disabled" measurement, leaving only the few first meta-data columns non empty. The rest would be cleared.

I must bring your attention to the fact that this sequence is used a lot on XtremeCT I scripts, for the cortical porosity for example.
This means that on XT-I, the UCT_LIST content is highly unstable, as it was used back then while UPAT_LIST was not able to handle those results.
In the future, when new applications come they may delete/overwrite the UCT_LIST entry for a measurement.
That is the rationale for using the TXT output in the RESULTS directory, that at least keeps track of past analyses.
As long as you have a single application on XT-II going through UCT_LIST, calling results on demand with it is fine. Later it might come complicated.

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===Troubleshoot UPAT database===

If there is an error ('inconsistent key change or duplicate key!') in the log file during 'upat_filldb', this is likely caused by too many servers doing UPAT evaluations:

Basically, the UPAT database can not be accessed by 2 evaluation jobs "at the same time", and works on a "1st arrived 1st served" basis. It is actually one reason to have only 1 evaluation at a time running on a single workstation (the usual setup).
In your case (and in mine as well), when you have several workstations clustered together, you can technically run several evaluation jobs at the same time which will eventually access the very same database.
So what happens is that a 1st job executes the /upat_fill_db, and accesses the database for a short amount of time.
During this time, any unfortunate evaluation job trying to access the database will end up in the exact same error as you reported, as their access to the database is restricted. Even though the time window is short, this kind of thing is unavoidable in setup such as ours, and when lots of evaluation are started at the same time.
Here you have no other choice than restarting the evaluation job, in order to update the database (or ultimately you could write a small script just to run the /upat_fill_db command, but I do not think it makes sense).

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===Redirect to a temporary database===

We need to temporarily redefine the logicals UPAT_EVAL_DATABASE and UPAT_SLICE_DATABASE. Normally, the definition is

<pre>
UPAT_EVAL_DATABASE = UCTD:UPAT_EVAL_CALGARY.DAT
UPAT_SLICE_DATABASE = UCTD:UPAT_SLICE_CALGARY.DAT
</pre>

Typically, we submit our jobs to the queue with an IPL script, so within the script we'll have to redefine the name of the database by adding lines such as
<pre>
$ def UPAT_EVAL_DATABASE SYS$SCRATCH:TEMP_UPAT_EVAL_CALGARY.DAT
$ def UPAT_SLICE_DATABASE SYS$SCRATCH:TEMP_UPAT_SLICE_CALGARY.DAT
</pre>
so that the results from the IPL evaluation are redirected to this temporary database.

Then, we need to extract the results from the database. These results are provided on a slice by slice basis (at least with the UPAT data). As user <code>microct</code> in a terminal window, we will again need to redefine the database and then run the program that translates the results to a text file:

<pre>
$ def UPAT_EVAL_DATABASE SYS$SCRATCH:TEMP_UPAT_EVAL_CALGARY.DAT
$ def UPAT_SLICE_DATABASE SYS$SCRATCH:TEMP_UPAT_SLICE_CALGARY.DAT
$ run disk1:[calibration.util]upat_export_measurement.exe ! give the measurement number and output file
</pre>

Or extract the results from the temporary database with:

<pre>
$ def UPAT_EVAL_DATABASE SYS$SCRATCH:TEMP_UPAT_EVAL_CALGARY.DAT
$ def UPAT_SLICE_DATABASE SYS$SCRATCH:TEMP_UPAT_SLICE_CALGARY.DAT

$ def UCT_MEASUREMENT_DATABASE SYS$SCRATCH:UCT_MEASUREMENTS_TORONTOXT.DAT ! only necessary if data came from another system
$ def UCT_SAMPLE_DATABASE SYS$SCRATCH:UCT_SAMPLES_TORONTOXT.DAT ! only necessary if data came from another system

$ upat_list ! choose option [3]show, give the patient number and output file, e.g. sys$scratch:myvalues.txt
</pre>

For an example IPL script that redirects to a temporary database, see Percy:
<pre>
DISK1:[MICROCT.COMMANDS]IPL_UPAT_EVAL_AIMINPUT.COM
</pre>

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===Import from a foreign database===
IF MEASUREMENTS COME FROM A TOTALLY DIFFERENT DATABASE (such as Toronto's XCT):

You will need to redefine the logicals UCT_MEASUREMENT_DATABASE and UCT_SAMPLE_DATABASE
<pre>
def UCT_MEASUREMENT_DATABASE SYS$SCRATCH:UCT_MEASUREMENTS_TORONTOXT.DAT
def UCT_SAMPLE_DATABASE SYS$SCRATCH:UCT_SAMPLES_TORONTOXT.DAT
</pre>

However, it is quite possible that you won't have a copy of the foreign MEASUREMENT and SAMPLE databases. If this is the case, then you must import the ISQ files into our own database. Then, by setting
<pre>
$ define UCT_EVALUATION_DATABASE SYS$SCRATCH:TEMP_EVALUATIONS_CALGARY.DAT
</pre>
you could redirect the results to a temporary database (but normally, if you already imported the data, why not use our own database now).

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===Duplicate as new import to database===

You will need to copy ISQ and GOBJ files to a new designated location. This is done when a screening study is completed to look for potential subjects and then a main longitudinal study is completed under a different study name. 

1. Make a new patient/subject ID 
2. Make a copy of the ISQ. For example: 
<pre>
$ copy DISK2:[microct.DATA.00002584.00008992]*.isq -
DISK2:[microct.DATA.00002696.00009345]*.isq
</pre>
3. Import ISQ into new patient/subject ID number by typing:
<pre>
$ import
</pre>
4. Follow the prompts for the ISQ file names, changing of control file # etc. 
5. Check the data directory to see if ISQ and GOBJ files have been copied properly 
2. In uct_evaluation, open new .ISQ and copied .GOBJ and re-run the evaluation to create .AIM, _SEG.AIM, _CORTEX.AIM, _LHTH_DTH.AIM 
 
3. Copy Scout Views so scanning program will load baseline scout view for followup scans In DISK1:[MICROCT.DATA.SCOUTS], you'll see two series of scout views: one series with the PATIENT # followed by 020 or 021 or 038 or 039, the site code (radius or tibia, left or right respectively) 
Copy the old patient scouts to the new patient #s
For example (using the same old and new #s as above): 
<pre>
$ copy DISK1:[MICROCT.DATA.SCOUTS]00002584021.SCV -
DISK1:[MICROCT.DATA.SCOUTS]00002696021.SCV
</pre>

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===Recover a disappeared due to import===
If you need duplicate a measurement in both the original and new directories, but you forgot copying the measurement before importing as a new. The original measurement will be automatically removed from the original directory. This can be fixed! You will need to copy the measurement back and then fix the header information, as the header will no longer match the original directory.

1. Manually copy all of the associated files for the measurement from the new directory to the original directory:
<pre>
$copy DISK2:[xtremect2.data.00001234.00001234]*.*;* DISK2:[xtremect2.data.00004321.00004321] /log
</pre>
2. Change the header information of the measurement files to those of the original directory. To do this, you will need special software. The use of this software is RESTRICTED. Users must seek special permission to use the software from Steve, Ying, or Anne BEFORE using. Once you have permission, the software can be found here: DISK1:[MICROCT.COMMANDS.FORBIDDEN].

3. Run the software:<pre>
$r [software]
</pre>
4. The software will ask for:
a) the ISQ file
b) the new sample # you would like to give it (i.e. the original directory sample #)
c) the new measurement # you would like to give it (i.e. the original directory measurement #)
c) the new sample name you would like to give it (i.e. the original Study ID)

You can view the header information for a file by using the command:
<pre>
$ctheader [ISQ file]
</pre>

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===Move to fix wrong Study_ID/Sample_No===

Situation: One study participate was assigned in followup scans multiple Study_ID or multiple Sample_No under the same Study_ID.
Action: To correct this mistake and update the database correctly, you get to

1. Return/Restore the RSQ from tape to measurement disk using Move (not Copy) in uct_backup program, otherwise the new location won't have its RAW backup record and thus have no idea where its RSQ was located.

2. When there is no original ISQ in the measurement disk, you will have to reconstruct a new ISQ from this RSQ. If there is an original ISQ there, then skip this step.

3. Import ISQ into a new designated location (correct Study_ID and Sample_No with new Measurement_No).
$ import
Follow the prompts for the ISQ file names, changing of control file # or site # if needed. This action will import RSQ, Gobj and all the files in the folder to the new location.

A reminder is that without an ISQ ready by importing a RSQ only will produce wrong slice no. and site location in the database as shown in the uct_backup.

4. If the ISQ is newly reconstructed (original ISQ could skip this step), the database will show the new reconstruction date & time (not the original scan date & time) as the scan records in the uct_backup. To correct this,

$run ut:uct_correct_meas_measdate

1) To see the original scan date & time: run this command and follow the prompt and input the original measurement No. as the Index, but don't change this by copying and pasting it back in Messdatum/Zeit.

2) To set the new scan date & time: run this command again and input the new measurement No. as the Index, copy & paste the original scan date & time got from 1) in Messdatum/Zeit.

This way will update the database as shown in the uct_backup with the original scan date & time with newly reconstructed ISQ in the correct Study_ID and Sample_No.

5. Backup/Move the RSQ at the new location to tape, so that the new record will have full information of both RAW and IMA.

6. Even though ISQ, RSQ, GOBJ and all other files have been moved over to the new location, you will still need to re-run the evaluation (in uct_evaluation, open ISQ and GOBJ) to create .AIM, _SEG.AIM, _CORTEX.AIM, _LHTH_DTH.AIM ect.

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===Move to fix wrong account used for scanning===

Xtremect2 (on disk2) and xt2recalib (on disk6) accounts share the same databases. However, the definition of DK0 is account specific, ie. the scans are stored on different disks. So when scanning under Xtremect2 account instead of Xt2recalib account, to correct the wrong measurement location you will need to:

#Create the patient directory on disk6:[xtremect2.data], if needed;
#Create the same measurement directory on disk6:[xtremect2.data];
#Create a save set of the measurement folder on disk2:[xtremect2.data] with the isq, rsq, rad and scv files included;
#Unzip the save set in the measurement directory on disk6:[xtremect2.data];
#Delete the measurement directory on disk2:[xtremect2.data] using delete command in the terminal. Caution: Do NOT use the backup program.

[[Image:Bones2.jpg|20px]] Warning: This procedure is specific to this situation between Xtremect2 and Xt2recalib accounts, Microct and Xt1recalib accounts, and vice versa, but not applicable between any other accounts!

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===Update database after RSQ/ISQ restoration===

If you are restoring RSQ or ISQ files from tape (or other source) it might be preferable to do your analysis without resetting the database info.

The database is specific to the user. So, we have to modify the database for <code>microct</code>, and be careful not to modify the <code>calibration</code> (or other users) database. However, we still need to have permissions from <code>calibration</code> in order to do the modification.

When we restore an ISQ or RSQ to disk, the database needs to be updated to ensure it finds it. We have to change the database back to say it's on disk. To do this we need to log in as user <code>calibration</code>.

<pre>
$ set host 0
login as calibXXXX where XXXX is the scanner id (5019 for VivaCT or 2339 for uCT35) or calib3309 or calib3401 (for the XtremeCT and XtremeCTII system, respectively).
password from Steve

$ @ADISK1:[BONELAB]microct_setup_XXXX.com ! XXXX=scanner id, sets the logicals to point to bonelab data for SB group
or
$ @ADISK1:[VIVACT]LOGIN.COM ! sets the logicals to point to microct data for BH group
or
$ @DISK1:[MICROCT]LOGIN.COM ! sets the logicals to point to microct data on the XtremeCT system
or
$ @IDISK1:[XTREMECT2]MICROCT_SETUP.COM ! sets the logicals to point to xtremect2 data on the XtremeCT2 system

$ set proc/priv=bypass or $ spb
$ run DISK1:[CALIBRATION.UTIL]UCT_CORRECT_DIR ! make sure to include the full path to the executable as shown here.
$ run DISK1:[CALIBRATION.UTIL]UCT_CORRECT_MEAS_DIR.EXE ! on xtremect2 system, use this program
</pre>

Note: Only change those items which have to be changed (e.g. just hit RETURN for RAW fields if you only want to change the IMA location. Also, when specifying the directories, use DK0, not DISK2.

<pre>
$ run ut:UCT_CORRECT_DIR.EXE
</pre>

<pre>
Measurement Nr.: 1234
MeasNr. 1234
PatientNr: 268
RAW: RAW004
TP0:00001234_RAW
IMA: IMA002
TP0:00001234_IMA
</pre>

<pre>
RAW-Label: [ RAW004 ]

RAW-Dir : [ TP0:00001234_RAW ]

IMA-Label: [ IMA002 ] DISK
IMA-Dir : [ TP0:00001234_IMA ] DK0:[microct.data.00000456.00001234]

Measurement Nr.: 0
End of program
</pre>

The IMA-label does not matter on disk - but we have to write something to get rid of the IMA002, so 'DISK' makes sense.

Using the standard backup/archiving program, you can archive (MOVE TO) that IMA again to a tape, but use a DIFFERENT TAPE than where the first instance of this scan is on.

Background: Tapes just write file after file, without any directory structure or hierarchy, so the program will always find the first instance (the old dataset) if you try to read it again from that tape.

Note One other option is to change the permissions of UCT_CORRECT_DIR.EXE so that user <code>microct</code> can use it directly. To do this, log in as users <code>calibration</code> and then:

<pre>
$ set proc/priv=bypass ! as user calibration
$ set prot=g:re ut:uct_correct_dir.exe
$ run disk1:[calibration.util]uct_correct_dir ! as user microct
</pre>

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==Other FAQ==

===View Sample info===
<pre>
$ mcr um:uct_info 1234
</pre>
will show you sample-name and date-of-birth of sample-number 1234
<pre>
$ mcr um:uct_info -m 1234
</pre>
will give you some (stupid) info about meas 1234

'''Note:''' If you use this function all the time, put the following into <code>microct_setup_user.com</code>
<pre>
$ uct_info :== $um:uct_info
</pre>
and then the usage info will even be correct.

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===List measurements for data and backup location===

*To generate a list of measurements that are registered in the database, to determine where backups are stored, or if the data is still on disk:

::<code>$ write_info</code>

*Ask you for a range of measurement numbers or sample names.
*Create a <code> sys$scratch:info.txt</code> file.

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===Anonymize patient name and DOB===

Here is the link to [[Media:SOP_Anonymize_patient_name_dob.pdf | Scanco's SOP]] to change a long list of patient's name and/or DOB to de-identify the data.

This does not affect the headers of past RSQ, ISQ or AIM files.

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===Fix a wrong scan site code===

This is done if accidentally scanned using the wrong control file.
For example scan site RR is scanned mistakenly under RL, or TL scanned by mistake using the control file for TR ect.

To see our site codes, e.g. 20 = RL, 21 = RR etc using

<pre>$ show log *eval*</pre>

;Scenario 1:

If the correction commands (uct_correct_meas_site and updh_site) are already in your account (which is the case for the xtremect2 and xt2recalib accounts on the XtremeCT cluster)

$ cd util
$ dir *site*

and you see two programs (uct_correct_meas_site and updh_site). Set priviledge to bypass first

$ spb

$ run uct_correct_meas_site

and enter the meas. number to be corrected and then enter in the correct site code (20 = RL, 21 = RR, 38 = TL, 39 = TR).
*This modifies the database, so the correct site is displayed in the eval program.
*Enter meas. number 0 to exit program.

Then we must also correct the ISQ and RSQ files (has to be restored from tape if not on disk):

$ run updh_site !'updh' = update header</pre>

*Enter the full (i.e. pathname included) ISQ or RSQ filename. For DISK6 data should use DISK6:[xtremect2.data....].
*Then enter the correct site number.

;Scenario 2:

Normally the correction commands (uct_correct_meas_site and updh_site ect.) are only provided in a calibration account to prevent from misusage. We have to login as user calibration to make the change.

$ set host 0
$ username: [enter calibration account, e.g. calib3401]

Then we use the same steps in Scenario 1 to change the site code in both database and ISQ and RSQ files.
*Make sure to <code>logout</code> from user calibration afterwards.

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===Fix for results fail to print/list/show after evaluation===

There are a number of reasons the results may not print:

====Incorrect first measurement number====
When sample information (such as patient name, DOB, remark) is changed DURING scanning, this can over write the 1st Scan measurement number, resulting in the evaluation sheet not being printed, and data not shown when running upat_list. For example, this happens when:

1) open sample program, enter name, hit save, leave program open

2) start scan (which would write correct record with 1st meas. in sample database)

3) in sample program: then only enter DOB, and hit 'save' again in the sample program --> it 'overwrites' the 1st meas. with an empty string again.

If you want to enter DOB after the scan has started, you HAVE to 'Find...' and re-load that patient first (so it correctly loads the 1st meas. entry also). It is best to just not use the sample management program whilst scanning is taking place.

However, if you do encounter this problem, use the following to fix (shown using patient 668 as an example. 1st scan measurement number was 2672):
<pre>
$ set host 0
calibration
xxxxx

$ spb
$ @[microct]microct_setup
$ run [calibration.util]uct_correct_first
$ r UCT_CORRECT_FIRST

Patient Nr.: 668
SampleNr.: 668
First: 0

2672

Patient Nr.:
</pre>
and continue with next non-working patient, give patient number 0 to exit.

$ logout

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====Evaluation completed with results not written to database====
If the first measurement number and DOB are correct... check the .log file of the evaluation... However, if there is no upat*.log file available for that scan, use:

upat_list -v=2 and you will see (for eg sample 594):

<pre>
Found sample 594, CAMOS_0018
Found measurement 2536 made 19-MAR-2007 12:52:58.48
Measurement site RL found in list at index 0
Measurement 2536 within measurement period
ERROR finding evaluation for measurement 2536

No valid evaluation found for measurement 2536
</pre>

So it seems the 3D upat eval never wrote anything to the database for that scan. In this case, you can run:

<pre>
$ @ue:ipl_upat_eval_again_quick.com
</pre>
and let it run for the missing data.
'''NOTE''' it will only need the aim files and gobj files that you still have in your 'models' directory.

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====Incorrect sequence of measurement numbers====
Finally, if none of these options work... check the order of measurement numbers: especially if an import has occured, first check the first measurement number is correct (as above). Then run sys$Scratch:uct_correct_prev_next.exe and correct the order of the measurements: The database keeps a 'daisy' chain of meas. numbers, each meas. knows which one was the previous meas and the next meas.

0 means: no prev. meas (or no next meas) So corrected the order for you like this:

<pre>
$ r UCT_CORRECT_prev_next

Measurement No. (0 to stop) [0]: 2821
MeasNo.: 2821 PatientNo: 723

Previous [0]: <-- leave 0
Next [0]: 2828 <-- give next meas number
Measurement No. (0 to stop) [2828]:
MeasNo.: 2828 PatientNo: 723

Previous [0]: 2821 <-- give prev. meas number
Next [0]: <-- leave 0 for very last meas.

</pre>
Please note: the series of meas. numbers per patient is NOT separate per meas. site, thus radius and tibia meas. are linking to each other. '''Do not mess up!'''

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=Data Management=
==Lab’s Data Responsibility==
*Weekly
#Clean up sys$scratch directory and only keep last week's data.
#Archive RSQ to corresponding tapes.
#*RSQ from temporary tests and non-project (not a formally established project) will NOT be archived unless specifically notified to lab personal.
#Database backup to disks.
*Monthly
#Database backup to corresponding tapes.
#Archive QC RSQ to corresponding tapes.
#Delete QC IMA and only keep last week's data.
*6-monthly
#System backup to corresponding tapes when prompted.
*Yearly
#Data Disk clean up when usage is over 90%.
#*Temporary tests and non-project RSQ and IMA data will be deleted during check up.
#Project Disk clean up when usage is over 90%.
#Winston backups clean up.
*Whenever requested
#Projects backup to Winston server and restoration.
#Projects archive to HOG server and restoration.

[[File:BoneLabDataManagement.JPG|800px]]

[[Image:Bones2.jpg|20px]] Warning: STRONGLY URGE TO DO THE WEEKLY and MONHTLY BACKUP. Two users DID experience disk crashes before, and without the weekly backup, you may still have all scans on the data disk, but without the databases you cannot tell which scans belong the which sample.

*Refer to [[Media:Microct_management.pdf|'''XtremeCT Micro-CT Management SOP''']] or [[Media:Microct_management.docx|'''its Word format''']] for references.

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==HP Server and Disk Array==
===HP References===
*[[Media:Hp-quick-specs-msa30.pdf|'''MSA30 Disk Array Quick Specs''']]
*[[Media:Hp-integrity-rx2620-sceva2-user-service-guide.pdf|'''Integrity RX2620 User Guide''']]
*[[Media:Hp-integrity-rx2660-sceva3-user-service-guide.pdf|'''Integrity RX2660 User Guide''']]

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===HP FAQ===
====Change disk description for $ disks====
Login as the system user and change to the system commands directory.

$ cd scom
$ eve show_disks.com

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==Tape==
[[Image:Bones2.jpg|20px]] Warning: While the tape is running and writing to it, DO NOT LOG OUT, DO NOT INTERRUPT THE PROGRAM! This would make that tape unusable from this point on - you could still read from that tape up to this point, but could not add more scans to this tape.

===Tape Label Convention===
Tape labels are 6 characters in length. For the Bone Imaging Lab projects, the first three letters indicate if the tape is for raw (RAW) or image (IMA) data, and the last three digits are for the tape number.

<pre>
RAW040 = RAW date, tape #040
IMA001 = IMAGE data, tape #001
</pre>

Alternatively, the first two characters may be set to a PI's initials, the third character indicates if the tape is for raw (R) or image (I) data, and the last three digits are for the tape number.

<pre>
SBR040 = Steve Boyd RAW, tape #040 
SBI001 = Steve Boyd IMA, tape #001 
BHR006 = Benedikt Hallgrimsson RAW, tape #006 
BHI017 = Benedikt Hallgrimsson IMA, tape #017 
FJR012 = Frank Jirik RAW, tape #012 
FJI003 = Frank Jirik IMA, tape #003 
</pre>

CaMos raw data is backed up with the following naming:
<pre>
CAMOS1 = CaMos RAW, tape #1
</pre>

When a tape becomes full, start (initialize) a new tape, increasing the tape number by one so that each tape label is unique.

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===Initialize a New Tape===
Put a new tape into the tape drive, then press "Initialize", this will format (erase) everything on the tape. When prompted for a label for the tape, follow the [[Scanco_Administration#Tape_Label_Convention|'''Tape Label Convention''']]. The tape can now be mounted for use. 

[[File:Uct_backup_pic02.jpg|400px]]

===Full Tape===
A tape automatically ejects during a backup procedure if it becomes full.
*Remove the tape and write protect it (orange indicator will be displayed).
*Exit the disk-utility program.
:*Hit <code>ctrl/c</code> to interrupt the program if needed.
*Start a new instance of the program.
*[[Scanco_Administration#Initialize_a_New_Tape|'''Initialize a New Tape''']].
*Backup any remaining files.

[[File:Uct_backup_pic03.jpg]]

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===Tape Drive Setup on XCT cluster===
Both the old and new tape drives are connected to SC3309 (XCT1) and powered on. You do not need to power off one to use another.

New tape in new drive <--> microct, xtremect2, xt2recalib, calib3401, calib3309

:*The 'new' Ultrium 3000 tape drive is for the new tapes and the default tape drive for all other accounts (microct, xtremect2, xt2recalib, calib3309, calib3401).
:*Use the following command to use the old SDLT tape drive no matter which account on the command line:
<pre>
$ uct_backup_sdlt
</pre>

Old tape in old drive <--> xt1recalib

:*The 'old' SDLT tape drive is for the old tapes. You have to log into the default xt1recalib account to recognize this tape drive.
:*Restoring from old tapes in xt1recalib account will restore your data to DISK6:[MICROCT.DATA].
:*By default, xt1recalib account can only see old tape drive, not the new tape drive.
:*Use the following command to use the new tape drive no matter which account on the command line:
<pre>
$ uct_backup_sas
</pre>

*With either of the above commands, you must not "submit" the tape usage jobs to the queue (i.e., cannot run a batch backup from a script), but only run them interactively in the
software. Any job in the queue will use the default tape drive again.

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===Extract from Tape===

====Scripts to Extract from Tape====
Generally, all files on the tape can be extracted, or only specific files.
To extract all files on a tape, for example, a tape received from a collaborator, insert the tape into the drive and do the following:
$ cd ur
$ create/dir [.collaborator]
$ create/dir [.collaborator.com]
$ create/dir [.collaborator.log]
$ create/dir [.collaborator.models]
$ cd ur collaborator models
$ backup/log tp0:*.sav []/by=parent ! be sure you are the user (i.e. 'microct' or 'xtremect2') that has permission
$ backup/log tp0:*.sav DISK4:[BONELAB.PROJECTS.FRAMINGHAM.MODELS...]/by=parent ! The "..." keeps the directory structure. The /by=parent ensures owner of the files is same as parent directory

This will save all the files on the tape to the current directory. Alternatively, if you only want a certain file extracted from the tape, such as an RSQ file, do essentially the same as per above, except with a different final command:
$ backup/log tp0:*.sav/select=*.rsq []/by=parent

The <code>/by=parent</code> part of the command is a qualified for the file owner, and it makes the files that are copied the same owner as the parent directory (nothing to do with how directories are structured). The <code>[...]</code> generates sub-directories.

A custom script is required when extracting data from tape from another micro-CT system or to extract the data to a central location (e.g., a user's directory).
*The script is then submitted to the backup queue of the workstation the tape drive is connected to (i.e., SCEVA3_BACKUP)
*Some example scripts are provided below.

*Extract image data for three scans to a custom folder, maintaining the sample and measurement directory structure:
<pre>
$ mount/foreign tp0
$ backup/log tp0:00001234_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie...]
$ backup/log tp0:00001245_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie...]
$ backup/log tp0:00001238_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie...]
$ dismount tp0
</pre>

*Extract segmented AIM files for three scans to a custom folder without the original directory structure:
<pre>
$ mount/foreign tp0
$ backup/log tp0:00001234_IMA.sav/select=[microct.data...]*seg.aim disk3:[microct.projects.buie]
$ backup/log tp0:00001245_IMA.sav/select=[microct.data...]*seg.aim disk3:[microct.projects.buie]
$ backup/log tp0:00001238_IMA.sav/select=[microct.data...]*seg.aim disk3:[microct.projects.buie]
$ dismount tp0
</pre>

*Extract segmented AIM files for all scans on tape to a custom folder:
<pre>
$ mount/foreign tp0
$ backup/log tp0:*_IMA.sav/select=[microct.data...]*seg.aim disk3:[microct.projects.buie]
$ dismount tp0
</pre>

*Extract raw data for three scans to a custom folder, without the original directory structure:
<pre>
$ mount/foreign tp0
$ backup/log tp0:00001234_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie]
$ backup/log tp0:00001245_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie]
$ backup/log tp0:00001238_IMA.sav/select=[microct.data...] disk3:[microct.projects.buie]
$ dismount tp0
</pre>

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===Tape FAQ===
====Error: Can't mount tape, Medium offline====
This can happen if a tape is interrupted during use (e.g., due to a power failure or system restart while the tape drive is in operation).

#Use the manual eject button to remove the tape from the drive.
#Turn off the tape drive, the switch is on the back of the drive.
#Shutdown the whole micro-CT system.
#Turn on the tape drive.
#Startup the micro-CT system, starting with the server.
#Try to mount the same tape again.

If the above does not work then either the tape or the tape drive is damaged. To determine if it is the drive, take a brand new tape and try to initialize it. Do not use a tape with data on it in the drive unless you are certain the drive is okay.

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====Error: positioning====
This can have two reasons usually:

#The tape is just faulty. Try with a fresh tape.
#A previous tape write operation was interrupted (e.g., a user did an 'End Session', the power went out, or the eject button was pressed on the tape drive, which killed the backup program). In this case the drive did not write the very important 'End of Tape' marker, and now, the tape drive cannot find the current place where it can start adding new data.
*Solution: either take a fresh tape, or if there were only a few scans are on the 'bad' tape, 'Move to Hard Disk' of ALL the scans on that tape, check that the scans have been retrieved well, then initialize that tape again (which will erase everything on the tape!) and archive those scans again.
*IMPORTANT: never interrupt the tape drive while it is running!

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====Error: parity====
Either tape or the tape drive is faulty. Take a fresh tape (potentially from a new batch of tapes), and see if the error persists.
*If yes: have the tape drive repaired.
*Further things to check: for DLT and SDLT tape drives: is the terminator ('dead end') connected on the second SCSI port in the back of the tape drive.

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====Fix: non-responsive tape drive====
This can occur if the user ejects the tape with the little button (and not with the recommended "dismount" button in the uct_backup program). This can also occur if a tape is mounted immediately after one is dismounted. You get the same error for both cases, "medium offline".

:*Check all that all cables are connected.

:*Check that the number on the back of the drive says "5" (use +/- to adjust if necessary)

:*Check that the top connector has a cable connecting to the computer and the bottom one has a terminator.

:*Try turning the tape drive on and off again.

:*Log in as user <code>system</code> (you will need a password from Steve):
<pre>
$ mcr sysman io auto/sele=mk
$ @sys$startup:scanco_setup_devices.com

$ show device tp0
</pre>

If it's online again, then great. If not, then the last resort is to reboot the entire system. If this doesn't work, then shut down the system (see user manual for proper steps) and eject the tape. You may need to turn the computer back on before it will eject. The tape drive should be turned on first (no tape), then the server, and any other computers. Check that the drive is online ($ show device mk). If it is, then test the drive by initializing, mounting and dismounting a brand new tape. If the drive is not online, do not insert any tapes or they will likely get stuck. Log in as system and re-try the command lines shown above.

NOTE: See "Fix a stubborn tape drive" elsewhere in this wiki.

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====Fix: stubborn tape drive====
If the drive cannot be mounted, or it is not visible with
<pre>
$ show device tp0
</pre>
then something went wrong. For example, the server computer was booted while the tape was turned off. It then does not load the driver.

You can 'force load' it - but this will disconnect the scanner for a moment, so only do it while no scan is running:

as user <code>system</code>, on sc3309:
<pre>
$ mcr sysman io auto

$ show dev tp0
</pre>

and you should see it now (otherwise turn on the tape drive, and do again)

Then you'll also have to make it available to all users:
<pre>
$ @sys$startup:scanco_setup_devices.com
</pre>

NOTE: See "Fix a non-responsive tape drive" elsewhere in this wiki.

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====SDLT320 Tape and Tape Drive FAQ====
Please refer to [[Media:Hp-faq-sdlt320-tape-drive-and-sdlt-tapes.pdf|'''SDLT320 Tape and Tape Drive FAQ''']] for details.

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==USB Drive==

===Use a USB drive===
Connect USB to VMS system and format.

Transfer files from the terminal after plugging in the USB device
$ show device dna
Usually the device is dna1 or dna2
$ mount /over=id dna2
$ create/dir dna2:[microct]
$ copy dk0:[microct]
or
$ backup/log dk0:[
and then
$ dismount dna2

Transfer files back again

$ mount /over=id dna2
$ dir dna2:[microct]
$ copy dna2:[microct]myfile.txt disk1:[microct.data.00000702.00001234]

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===USB Device Usage with Scanco Backup/Archive Software===

For illustrated help on Itanium rx2660s , please refer to [[Media:Scanco_TDxxx-USB_Device_Usage.pdf | '''Scanco_TDxxx-USB_Device_Usage.pdf''' ]]

====Initialize procedure====
If an external USB device is to be used to archive measurement data, the USB device must be initialized by Open-
VMS. The data will not be accessible from any other operating system.

- Attach the USB device to the front USB port of the Itanium rx2660.
(note: Itanium rx2620 only supports USB1.1, which will have a very slow transfer rate)

- Open the Scanco backup/archive software.

- Select the correct USB device with the arrow buttons in the “USB Device” section.

- Use the “Initialize<” button in the “USB Device” section to initialize the USB device.

- Confirm the Warning message. Note: All data currently on the device will be erased!

- Enter a six-character label

The USB device will be initialized and mounted.

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====Archive procedure====

- Attach an OpenVMS formatted USB device to the front USB port of the Itanium.
(note: Itanium rx2620 only supports USB1, which will have a very slow transfer rate)

- Open the Scanco backup/archive software.

- Select the correct USB device with the arrow buttons in the “USB Device” section.

- Use the “Mount” button in the “USB Device” section to mount the USB device.

The device label of the mounted USB device will be shown in the “USB Device” section.

- Select the measurement data to be archived.

- Select “Move To:” and “USB/VMS” and click “Start<” to archive the selected data to the USB device.

After the move procedure, the new current location of the measurement data will be shown next to the files path.

- “Dismount” the USB device when done with archiving.

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====Manual file copy procedure====
An OpenVMS formatted USB device can also be mounted and used for file storage using commands in a DECterm.

- Attach an OpenVMS formatted USB device to the front USB port of the Itanium.
(note: Itanium rx2620 only supports USB1, which will have a very slow transfer rate)

- List available devices. The last shown device is usually the attached USB device; dna12 in this example.
$ show device dna

- Mount the USB device using the correct device name
$ mount /over=id dna12

- Create a root directory. Ignore any messages if the directory already exists.
$ create /dir dna12:[microct]

- Copy any wished files to the USB device
$ copy {source files} dna12:[microct] /log

- Dismount the USB device
$ dismount dna12

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====Exporting Files / FAT file system====
If an external USB device is to be used to export measurement data to a Windows or MAC OS, the USB device must be formatted as FAT file system.

- Attach the USB device to the front USB port of the Itanium.
(note: Itanium rx2620 only supports USB1, which will have a very slow transfer rate)

- Open the Scanco backup/archive software.

- Do not “Initialize<” or “Mount” the USB device !

- Select the measurement data to be copied to the USB device, may be even sub-select the wished file type
(TIF files in the example below).

- Select “Copy To:” and “USB/FAT” and click “Start<” to copy the selected data to the USB device.

Once the USB device is connected to Windows or MAC OS, it will show a ZIP file named like the copied measurement
number. This ZIP file contains the same directory structure like the data disk on OpenVMS:

data\sample number\measurement number

In the lowest sub-directory are the copied files, as selected in the backup/archive software (TIF files in this example).

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===Problems with connected USB devices===

Sometimes USB configurations can be problematic, in which case log in as "system" on the server and run

$ dir/date SYS$SYSROOT:[SYSEXE]USB$UCM_DEVICES.DAT

to see whether a file was created recently. If one has, delete that file and reboot the server.

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==CDROM==
===Mount a CDROM===

Device could be <code>dqa0</code> or <code>dqb0</code>. I'm not sure which works:
<pre>
$ mount/foreign dqa0:
</pre>
OR
<pre>
$ mount/override=id dqa0:
</pre>
Then
<pre>
$ dismount dqa0:
</pre>

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==Saveset and Zip files==

===Saveset===

====Saveset Naming Convention====
The Scanco backup program stores raw (RAW) and image (IMA) data as save sets (SAV).
*RAW save sets contain RSQ files and IMA savesets contain all other file types.
*The saveset filename is composed of the 8-digit measurement number plus "_RAW.SAV" for raw data and "_IMA.SAV" for image data.
*For example, the data for a scan with measurement number 1234 would be stored as:
<pre>
00001234_RAW.SAV ? RSQ
00001234_IMA.SAV ? all other files, ISQ, AIM, GOBJ, TXT, SCV, etc.
</pre>

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====Create and Unpack Saveset====
Savesets are OpenVMS backup files, similar to a zip. Use the backup command.
<pre>
$ BACKUP/LOG disk3:[microct.projects.buie...] disk3:[microct.projects]buie2012.sav/sav
!Creates a saveset file of disk3:[microct.projects.buie].
!The ... after the folder indicates to include all subfolders and files.
$ BACKUP/LOG mysaveset.sav/sav disk3:[microct.projects.buie]
!Unpacks the whole saveset to disk3:[microct.projects.buie]
$ BACKUP/LOG mysaveset.sav/sav disk3:[microct.projects.buie...]
!The ... at the end of the output location indicates to unpack the saveset and maintain the original directory structure.
$ BACKUP/LOG mysaveset.sav/sav/select=*.aim disk3:[microct.projects.buie]
!The select flag is used to indicate extraction of only aim file types.
$ BACKUP/LOG mysaveset.sav/sav/select=[microct.data...] disk3:[microct.projects.buie]
!The select flag is used to indicate extraction of the folder data and all subfolders and files.
$ HELP BACKUP !More information on the backup command.
</pre>

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====View Saveset Contents====
To view contents of a saveset (SAV) on disk:
<pre>
$ backup/list upat_print_list_nomatch.sav/sav
</pre>

To view the savesets (SAV) on a tape:
<pre>
$ mount/ov=id tp0:
$ dir/date tp0:*.*
$ dismount tp0:
</pre>

To view contents of a saveset (SAV) on a tape:
<pre>
$ mount/foreign tp0:
$ backup/list tp0:*.* ! OR, backup/list tp0:*.SAV
or
$ backup/list=results.txt tp0:*.* ! save output in results.txt
$ dismount tp0:
</pre>

An idea to get the results of the backup/list into a text file: Run the procedure in a submitted script and save the resulting log file with all the output.

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====Extract a single file from SaveSet====

In a large SaveSet, sometimes we only want one file extracted, not the whole archive extracted. This can be done with

$ backup /log /select=myfile.txt mysaveset.sav /sav disk1:[microct.scratch]

or [] as destination will put the file in the current directory.

This can take a while as it looks through all the saveset. Once it logs that the file has been restored, you may interrupt with F6. Else it goes on looking through the rest of the saveset.

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====Transfer Saveset from microCT to XtremeCT====

You can create a SAV set of your project on the VivaCT and transfer it to the Xtreme system, or vice-versa.
First, create the SAV set using the command:
<pre>
For example:
$ BACKUP/LOG DISK3:[MICROCT.PROJECTS.SB.MYPROJECT...]*.*;* -
SYS$SCRATCH:MYPROJECT.SAV/SAV
</pre>
This creates the MYPROJECT.SAV file in the scratch directory. Now zip the file:
<pre>
$ cd sys$scratch
$ zip "-V" MYPROJECT.ZIP MYPROJECT.SAV (NOTE: must use quotes and a capital V!!!!)
</pre>
FTP the .ZIP file to SODOR ( in binary mode!!!), and then FTP it off onto your destination system (Viva or Xtreme). See the appropriate HowTo for FTP instructions. Once you've FTP'd it, unzip the file:
<pre>
$ unzip MYPROJECT.ZIP
</pre>
Finally, unpack the contents of the .SAV file:
<pre>
$ BACKUP/LOG MYPROJECT.SAV/SAV DISK3:[MICROCT.PROJECTS.MYPROJECT] <--- or whatever destination directory
</pre>
NOTE: transferring a .SAV directly from VMS to VMS should work, but not via any third operating system (like SODOR) - so zipping is always the safe way to make sure it works.

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===Zip===

====Zip and Unzip files====
Use the zip program to add files to a zip archive.
<pre>
$ ZIP myzip.zip myfile.txt;1 !Adds myfile.txt to myzip.zip.
$ ZIP "-V" myzip.zip myfile.txt;1 !Adds myfile.txt;1 to myzip.zip. The "-V" maintains the OpenVMS version number.
$ ZIP "-V" myzip.zip [.subdir...]*.*;* !Adds all files within subdir to myzip.zip, maintaining their version number.
$ ZIP !Displays the help for the zip command.
</pre>

Use the unzip program to unzip an archive.
<pre>
$ UNZIP "-V" myzip.zip !Extracts myzip.zip, maintaining the OpenVMS structure.
$ UNZIP !Displays the help for the unzip command.
</pre>

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====Transfer Zip between Scanco systems====

Files must be zipped before transfer by e-mail or ftp because important attributes will be lost in the transfer otherwise.

To transfer files from system A to B, do the following.

On system A:
<pre>
$ zip "-V" for_calgary.zip uctd:UCT_SAMPLES_TORONTOXT.DAT ! for each filename
$ zip "-V" for_calgary.zip uctd:UCT_MEASUREMENTS_TORONTOXT.DAT
</pre>
This will add both files to the same zip file.

Note: "-V" is very important, it must be capital V!

Transfer the file by e-mail, or by ftp.

On system B:
<pre>
$ unzip -j for_calgary.zip ! to unzip on your end them (-j to 'junk' the original file path)
</pre>

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====Unpack Zip sent by Scanco====
In the .zip file, you'll find a .sav file. Unzip the .zip just by saying

<pre>$ unzip xxxx.zip</pre>

Then:

<pre>$ backup/log xxxx.sav/sav disk3:[steve.devel.temp]</pre>

and it will unpack everything into <code>disk3:[steve.devel.temp]</code>

Or:

<pre>$ backup/list xxxx.sav/sav</pre>

and you see what's in the .sav.

Then:

<pre>$ backup/log xxx.sav/sav/sel=[andres.uct.ipl_for_cust...] disk3:[steve.devel.cipl...]</pre>

and it will create the same diretory tree in steve.devel.cipl as it was when I
packed it into the .sav.

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==Backup and Archive==

===UI Procedures===

====µCT Disk-Utility====
The µCT Disk-Utility Program is used to archive and restore scan data. To start the program type <code>$ uct_backup</code> in a DEC terminal, or use the disk button.

[[File:Uct_backup.jpg|40px]]
*The backup captures both the programs and databases.
*A little helper terminal comes up and gives feedback of every file backed up.
[[File:Uct_backup_pic01.jpg|600px]]

Two possible ways to use <code>UCT_BACKUP</code>:
:* COPY TO -> this does not update the database.
:* MOVE TO -> this updates the database.

Scenario 1:
<pre>
1. Use UCT_BACKUP to 'move' the RSQ to 'tape'
2. Use UCT_BACKUP to 'move' the ISQ to 'garbage'
3. Use UCT_BACKUP to 'move' the remainder (AIM/GOBJ) to 'tape'
</pre>
*At operation 3, the measurement directory will be deleted from the measurement disk.
*The directory will automatically be restored if you restore your data from tape.

Scenario 2:
<pre>
1. Use UCT_BACKUP to 'move' the RSQ to 'tape'
2. Use UCT_BACKUP to 'move' the ISQ to 'garbage'
3. Move all the GOBJ/AIM/etc to a project directory.
4. Generate a .SAV file and put on the IMA tape.
</pre>
*You will have to delete the measurement directories (using UCT_BACKUP if you like).
*The disadvantage of this scenario is that the image data cannot be restored using UCT_BACKUP.

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====Raw Data Backup====
*Ideally 1-2 week after scanning.
*RSQ files are backed up onto RAW tapes (see [[Scanco_Administration#Tape_Label_Convention|'''Tape Label Convention''']]). Put the most recent RAW tape into the tape drive, then press "Mount".
*Show "Current (with RAW)", use the file filter (Measurement: ) to search for your files (e.g., CAMOS) and press enter or press "Update List".
*Select all the files to backup by highlighting them using the left mouse button and ctrl to select individual files or shift to select a range.
*Highlight RAW, choose "Move To" and "Tape". Press "Start...".
*When the backup is complete press "Dismount" to eject the tape.
*If the tape auto-ejected without pressing "Dismount" then the tape is full (see [[Scanco_Administration#Full_Tape|'''Full Tape''']]).
*If you select multiple files, be sure they all need to be backed up, otherwise you will get an error.
:[[File:Uct_backup_pic04.jpg|500px]]

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====Image Data Backup====
*Ideally 1-2 months after scanning, after contouring, onsite analysis and copied image data to project disk.

#'''Delete ISQ After Evaluation'''
#*ISQ files are normally deleted after completing your evaluation since they are very large files and can be reconstructed from the RSQ file.
#*Show "Current (on Disk)", type the beginning of your sample name (e.g., CAMOS) in the file filter and press enter or press "Update List".
#*Select all the files for which you have completed the evaluation (there will be a + sign next to any scan that has been evaluated). #*Highlight IMA, choose "Move To" and "Trash".
#*[[File:Important.JPG|20px]] After you choose the trash symbol, you will now be given the option to select specific file types, choose "Select" and "ISQ". Press "Start...".
#*Only choose one file type to delete at a time. The wildcard (*) indicate all files other than "ISQ" and "AIM" files.
#:[[File:Uct_backup_pic05.jpg|500px]]
#: 
#'''Backup IMAGE Data'''
#*AIM, GOBJ and other evaluation files are backed up onto IMA tapes (see [[Scanco_Administration#Tape_Label_Convention|'''Tape Label Convention''']]).
#*Put the most recent IMA tape into the tape drive, then press "Mount".
#*Show "Current (on Disk)", type in the beginning of your sample names (e.g., CAMOS) in the file filter and press enter or press "Update List".
#*Select all the files to backup by highlighting them using the left mouse button and ctrl to select individual files or shift to select a range.
#*Highlight IMA, choose "Move To" and "Tape". Press "Start...".
#*When the backup is complete press "Dismount" to eject the tape.
#*If the tape auto-ejected without pressing "Dismount" then the tape is full (see [[Scanco_Administration#Full_Tape|'''Full Tape''']]).
#:[[File:Uct_backup_pic06.jpg|500px]]

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====Use 'Script...' button====
Usually, you will start the move/copy by clicking on <code>'Start...'</code> button. The <code>'Script...'</code> button is for advanced users.

*Use of the 'Script...' button will generate a script <code>sys$scratch:archive.com</code>, that you may submit it in batch mode later (e.g. over night) by typing: <pre>$ scanco_submit_command sys$scratch:archive.com/after=23:59</pre>
*In a multi-computer cluster setup, you may want to specify the exact queue name of the computer that has the tape hooked up by giving e.g. <code>/que=sceval_fast</code>.
*Insert a tape, but do NOT mount the tape in the normal program. If necessary: if it's a new tape, [[Scanco_Administration#Initialize_a_New_Tape|'''initialize''']] it as usual.
*The batch job will be started one minute before midnight in the example above. <code>$ show entry</code> will show you that it is holding until then.
*See <code>$ help submit /after</code> and <code>$ help dcl_tips date_time example</code> for more help on this.
*Sample script file (archive.com) restoring the RSQs of measurements 6452 and 6580:
<pre>
$ MOUNT/FOREIGN TP0:
$ UCT_BACKUP_BATCH
ALL
RAW
COPY
DISK
! Meas: SB_BUIE_EX_CTRL_PH_01 (6452)
MEAS
6452
EXECUTE
! Meas: SB_BUIE_EX_CTRL_PH_01 (6580)
MEAS
6580
EXECUTE
EXIT
$ DISMOUNT TP0:
$ EXIT
</pre>

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====Database Backup====

The database (DB) backup should be performed for each user on the system. It should not be performed as user 'calibration' or some derivative. In the case of the XtremeCT2 and XtremeCT cluster, both the 'microct' and 'xtremect2' user accounts must be used to backup their respective DB.

By performing the DB backup, the warning dialog that appears when logging into the system should go away.

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====Operating System (OS) Backup====
If the following error-message appears on the screen then you can click OK to continue your work.

MESSAGE: No recent OS Backup found!
Please perform OS backup (DISK0) in privileged account!
%RMS-W-FNF file not found.
CODE: 268534416
Facility RTL

This message means that no operating system (OS) backup has been performed within the last 6 months. Please perform an OS backup as soon as possible by following the steps below:

1. Make sure there are no scans in progress and that the que is halted from all activity.

2. Log in to the calibration account: Since we have two scanners on the same system, login as either "calib3401" or "calib3309", depending if you need to backup the XtremeCT2 or XtremeCT, respectively. For microCT clusters, (best to do this on SCEVA3) using the username calib5019 and the password (ask Steve for this).

3. Type in the DECterm window:
$ set proc/priv=bypass
Or Set priviledge to bypass by <code>$ spb</code>
$ r um:uct_b Or $ uct_backup

4. You will now see 2 additional buttons on the bottom left that is not seen when logged in as microct user. Push either the button "OS Backup to Disk DK0" or mount the specific OS backup tape and push the "OS Backup to Tape" button.
* A system backup to tape and to DK0 should both be performed.

5. Check the command line & queue to ensure that the backup is being carried out. If you submit the job as 'batch mode' the backup is submitted to SYS$BACKUP queue and allows you to close the backup program and 'end session' without interrupting a running backup. Check with 'show queue' to see the backup job on the queue.

6. Exit the Backup Program and log out of the calibration account.

After a successful OS backup the message above will not appear for the next six months.

Alternatively a system backup can be completed using the command line, without using the uct_backup program. The instructions from Scanco can be found here. The advantage to this method is that you will be able to name the specific backup save set.

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===Using Scripts for Backup/Archive===

====Project Backup/Archive====
*Refer to [[Media:Microct_project_backup.pdf|'''Project Backup SOP''']] or [[Media:Microct_project_backup.docx|''' its Word format''']] for reference.

=====Backup Project=====
Regularly backup projects on a monthly basis using command <code>$ @com:BACKUP_PROJECT.COM</code>
*The script is submitted to the queue and upon completion the log is emailed to the user.
*a SAVset (an OpenVMS file type similar to a zip file), a project info file and a file list are created in DISK5:[BONELAB.PROJECTS.BACKUP] for the microCTs and DISK4:[BONELAB.PROJECTS.ARCHIVE.ARCHIVE] for the XtremeCTs.
*The saveset along with two TXT files created will be automatically SFTP to Winston:\\Backups\backup\
*After the transfer, the saveset file on disk are deleted, leaving only two TXT files on the project disk.
*Only keep the two most recent backups for each project, A or B version name appended on the project name:
:*Backup version "_A" for odd months (Jan, Mar, May, Jul, Sep, Nov), e.g. YZHU_A_OTHER_2017-01-12.SAV
:*Backup version "_B" for even months (Feb, Apr, Jun, Aug, Oct, Dec), e.g. YZHU_B_OTHER_2020-04-08.SAV
*The user MUST verify that the backup completed successfully.
*SAVsets greater than 250 GB cannot be transferred by automatic SFTP, use interactive/manual SFTP instead to transfer to Winston.
*If you are backing up a very large project, please check the server disk space before starting the backup.

<pre>
$ @com:BACKUP_PROJECT.COM
===========================================================
BACKUP PROJECT TOOL V1.2 (XtremeCT)
P1:LOCATION DISK4:[BONELAB.PROJECTS.DUNCAN]
P2:TYPE 1=MOUSE,2=RAT,3=HUMAN,4=OTHER
P3:PROJECT CAMOS
P4:PERSON Ying Zhu
P5:DESCRIPTION A monthly backup
P6:EMAIL me@ucalgary.ca
P7:SFTP y,n
P8:START y,n
</pre>

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=====Restore Project=====
In the commands directory (com) is a BACKUP_RESTORE.COM script which will automatically generate a script to restore a user's project.
*The saveset file has to be moved to Winston:\\Backups\archive folder to be restored.
*The user will be asked if they wish to restore to the original location, or to a new location.
*The script is submitted to the queue and the log from the restore job is emailed to the user.
*The user MUST verify that the job completed successfully.
<pre>
$ @COM:BACKUP_RESTORE.COM
</pre>

=====Delete Project=====
In the commands directory (com) is a BACKUP_DELETE.COM script which will automatically generate a script to delete all the files and subdirectories of a specified path.
*The command script is opened so that the user can check the files to be removed to go ahead.
*You will need to manually delete the root project directory after it's empty.
<pre>
$ @COM:BACKUP_DELETE.COM
</pre>

=====Known Bugs in Project Tools=====
*Long file name won't work (28 letters work but not 32 letters).
*if the user specifies too long a file name, the Project Backup Scripts will fail with the following error:
RMS-E-CRE, ACP file create failed
SYSTEM-W-BADFILENAME, bad file name syntax

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=====Archive Project Saveset to Tape=====
Projects should be stored safely onto a backup tape once complete.

Summary

The following steps summarize the process:
:* Archive the project directory to the tape (detailed instructions below).
:* Change tape to "read only" to protect contents
:* Check tape saveset to ensure proper backup
:* Write name of tape on the project LOG sheet
:* Copy project LOG sheet and bring to Bone Imaging Laboratory "completed" project book
:* Bring copy of tape to the Bone Imaging Laboratory for safe keeping
:* Delete the contents of the project from the disk

In the project, there should be the regular set of directories including DOC, COM, MODELS, LOG. Once the project is stored to tape, ensure that the log sheet for that project include a note stating which tape it was backed up to. Take a photocopy of the log sheet and add it to our Bone Imaging Laboratory project book for COMPLETED projects.

In the following example, a project titled BERN is backed up onto tape. Ideally, the name of the SAV file on tape is the same as the project (i.e., BERN). Note that SAV files must have names with no more than 13 characters (including the .SAV)!

The following example backs the BERN project/directory onto tape IMA001. For large projects and/or critical projects, it is advisable to dedicate an entire tape. The three dots (...) indicate that ALL subfolders of DK0:[MICROCT.PROJECTS.BERN] will be included.

<pre>
$ mount/foreign tp0:

$ backup/log dk0:[microct.projects.bern...]*.*;* tp0:proj_bern.sav - ! writes a saveset to tape
/block=65534 /label=IMA001 -
/media_format=nocompaction ! NEVER use the /rewind option here

$ backup/log tp0:*.sav/select=*.isq DISK4:[BONELAB.PROJECTS.TBONE.ISQ_FROM_TAPE...]/by=parent ! extracts all ISQ files from the tape

$ dismount tp0:
$ dismount tp0: /nounload ! same as previous command, but does not eject the tape (i.e. if you want to read the tape once more)
</pre>

Note that the <code>/rewind</code> option should never be used for backup as it instructs the tape drive to rewind after backup is complete causing a major risk of over writing.

Sometimes it might be handy to exclude certain files. For example, to exclude RSQ files: <code>/excl=*.rsq</code>

A good reference for backup commands and ideas are available in the <code>UM:UCT_MOVE_FILES.COM</code> script which is used by the <code>UCT_BACKUP</code> program. See also the <code>help backup</code> instructions:
<pre>
$ help backup
</pre>

To view the contents of a tape to ensure you've successfully stored your project use the following commands (further details in "HowTo: View save set (SAV) contents"):

To just view if the saveset is on tape (but not its contents):
<pre>
$ mount/ov=id tp0:
$ dir/date tp0:*.*
$ dismount tp0:
</pre>

Note: you can also save the saveset list in a text file using the /output qualifier.

To view the files within a saveset on tape, and save the results in a file called <code>results.txt</code>:
<pre>
$ mount/foreign tp0:
$ backup/list=results.txt tp0:*.*
$ dismount tp0:
</pre>

To delete a set of directories, use the <code>dl</code> command.
<pre>
$ cd ur BERN
$ del *.*;* ! Deletes ALL files in a directory
$ dl *.dir;* ! Will only delete empty directories (not nested directories)
</pre>

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=====Extract Project Saveset from Tape=====
To restore a project, you have two choices:
*1. Login as user <code>calibration</code> and then go to the projects directory. From there:
<pre>
$ spb (bypass priv)
$ backup/log tp0:proj_davison.sav/rewind [*...]
</pre>
This puts all the files back in their original directory structure.

*2. As user <code>microct</code>
<pre>
$ mount/foreign tp0:

$ backup/log tp0:proj_davison.sav/rewind/select=[microct.projects.davison...]
disk2:[microct.projects.davison...]

OR

$ backup/log tp0:*.*/rewind disk3:[microct.projects.vitamink.models]
</pre>
Make sure to write the same path in the /select as the output (except for the
actual disk2 portion). Alternatively, you could unpack it into a slightly different root
directory (i.e., TMP) by changing the output path.

The three dots infers to use the same paths in the saveset as the file structure put onto disk.

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====Scripts to Backup RAW and IMA====
A script can be output from the backup tool to backup and restore data using the backup program.
*When restoring data using this method, choose the COPY to DISK option. The data will be restored to its original location on the data disk.
*You must manually submit the script to the backup queue.
*The command procedures are written to SYS$SCRATCH:ARCHIVE.COM.
*Here is the sample script for backing up RAW data:
<pre>
$ MOUNT/FOREIGN TP0:
$ UCT_BACKUP_BATCH
ALL
RAW
MOVE
TAPE
! Meas: ATHLETE_126 (10565)
MEAS
10565
EXECUTE
! Meas: ATHLETE_126 (10566)
MEAS
10566
EXECUTE
! Meas: ATHLETE_126 (10567)
MEAS
10567
EXECUTE
EXIT
$ DISMOUNT TP0:
$ EXIT
</pre>
*Here is the sample script for backing up IMA data:
<pre>
$ MOUNT/FOREIGN TP0:
$ UCT_BACKUP_BATCH
ALL
IMA
MOVE
TAPE
! Meas: ATHLETE_126 (10565)
MEAS
10565
EXECUTE
! Meas: ATHLETE_126 (10566)
MEAS
10566
EXECUTE
! Meas: ATHLETE_126 (10567)
MEAS
10567
EXECUTE
EXIT
$ DISMOUNT TP0:
$ EXI
</pre>

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====Disk Usage information====
<pre>
$ @COM:DISK_MOUNTIES.COM !Give data disk usage information on an account.
$ eve sys$scratch:disk_mounties_output_summary.txt
</pre>

The template file for summarizing the disk mounties results: [[Media:BoneLab_Data_Disc_Usage.xlsx|'''BoneLab_Data_Disc_Usage.xlsx''']]

To look at the RSQs in the database
<pre>
$ dir/siz dk0:[microct.data...]*.rsq
</pre>
the three dots means all subdirectories.

Other useful commands:

<code>$ ctheader xxxxxx.isq</code>

or

<code>$ ctheader xxxxxx.rsq</code>

shows you header.
<pre>
$ fda command file-wildcard
</pre>
does a 'file do all' of the command on all the given wildcard filenames.
<pre>
$ pipe xxxx | search sys$pipe "patient"
</pre>
is the pipe command in VMS.

So all three combined:
<pre>
$ pipe fda ctheader dk0:[microct.data...]*.rsq | search sys$pipe "patient name"
</pre>
or any other field you want to search for!

If you have a more complex program to run (e.g. with an argument), use the double quotes as follows:
<pre>
pipe fda "aix -l" *.AIM | search sys$pipe "Patient Name"
</pre>

'''Other ideas''':

<pre>$ write_info</pre>

gives you a file <code>sys$scratch:info.txt</code> with info in it (leave defaults to get all samples ever scanned, otherwise 'zoom' in on some samples.)

Check out the <code>search</code> command:
<pre>
$ help search
</pre>
and <code>/match=and</code>
or <code>/match=or</code>

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====Disk Backup====
In the commands directory (com) is a BACKUPDISK script which will automatically generate scripts to backup all the directories on the projects disk.
*As the backup requires significant amounts of space, please check the server disk space before starting the backup.
*Each directory is saved as a separate save set (an OpenVMS file type similar to a zip file) on Winston://Bonelab/Backup/.

<pre>
$ @COM:BACKUPDISK
</pre>

*Refer to [[Media:Microct_disk_backup.pdf|'''Disk Backup SOP''']] or [[Media:Microct_disk_backup.docx|''' its Word format''']] for reference.

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=Process, Printer and System=

==Processes and Jobs==

===Manage jobs in the queue===
Use the DELETE/ENTRY and SET ENTRY commands to manage a batch job.

<pre>
$ SH QUE !Get process info
$ SH QUE /all/by_job_status=executing !Get all executing process info
$ SHOW ENTRY 1131 /full !Get full process info of entry 1131
$ SE 1311 !Get full process info of entry 1131

$ DELETE /ENTRY=251 !Deletes batch job number 251.

$ SET ENTRY 251/PRIORITY=50 !Changes the priority of batch job number 251.
!Default priority is 100 for all jobs, max is 200.
$ SET ENTRY 251/REQUEUE=SCEVAL_FAST !Moves to queue sceval_fast.
!The job cannot be executing to do this, has to be in pending status.
$ SET ENTRY 251/AFTER=TOMORROW !Holds entry 251 until the following day (midnight).

$ HELP SET ENTRY !More information on the SET ENTRY command.
</pre>

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===Control processors # on multi-processor machines===

For example, on the itanium there are two processors. By default, only one takes reconstruction jobs. The other is left for so that evaluations can take place without competing for the CPU.

But if a bottleneck is the reconstruction, it can be switched as user <code>system</code>:

<pre>
$ set que sceva2_slow/job=2
</pre>

so that it will do two reconstruction jobs simultaneously.

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===Create a new queue===
This may be useful to separate jobs for a project. The following will create a queue called BUIE$FAST, which will submit jobs to SCEVAL_FAST and SC3309_FAST.

$ initialize/queue/GENERIC=(SCEVAL_FAST,SC3309_FAST)/OWNER=[SYSTEM] -
/PROTECTION=(S:M,O:D,G:R,W:S)/BATCH/START BUIE$FAST

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===Clear out all entries in a queue===
First create a dummy queue, then merge (i.e., move) all the entries from the queue to be cleared into it, then delete the dummy queue.

Example: Clear out the printer queue.
$ stop/reset printer1
$ initialize/que dummy
$ assign/merge dummy printer1
$ delete/que dummy

Example: Clear out a batch queue, e.g., sys$fast.
$ initialize/que/batch dummy
$ assign/merge dummy sys$fast
$ delete/que dummy

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===Stop and restart queues===
There are three methods. First the nice method.

1. As for the printer queue, a normal user can stop and start other queues.

<pre>
$ stop/que/reset sceval_slow
$ start sceval_slow
</pre>

This kills the current process running. If you want to let the current process complete before stopping the queue, use:
<pre>
$ stop/que/next sceval_slow
</pre>

2. Use the web browser Mozilla.

:*Open mozilla
:*'batch queues'

:*Resize the window so it occupies the right half of the screen

:*Click on 'delete job' once with the MIDDLE mouse button, this will open a new window on the right half of the screen. Ensure the two windows do not overlap, if they do resize the window which contains the batch queues list. Once window locations are correct MIDDLE click on the rest of the jobs which you wish to delete (click on 'Delete Job' in the batch queue list). The reason for locating the widows is because each successive click on 'Delete Job' will open a new window and you don't want it to cover the batch queues list.

:*Then Exit from mozilla, this will delete all the open windows, it may take a bit if you are deleting lots.

3. Now the harsh method.

[[Image:Bones2.jpg|20px]] Warning: Extreme caution! Explicit permission for this change or similar changes must be obtained from Dr. Steven Boyd.

Completely remove the queue and re-generate, as user <code>system</code>

<pre>
$ stop/queue/reset sc3309_slow
$ delete/queue sc3309_slow
</pre>

Then you must restart the queue. To learn how to do this refer to:
<pre>
$ eve sys$startup:dcps_hpljet_ip.com
</pre>

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===Kill hunging processes===

Sometimes jobs need to be stopped manually, such as when FTP or TCPIP is hung. This is done as follows:

Checked processes with
$ show sys
where the FTP jobs are running. Doing it as system with these commands would show all the FTP jobs on all nodes:
$ mcr sysman
SYSMAN> set env /cluster
SYSMAN> do pipe sh sys|sear sys$pipe ftpc
It showed that they all were running on SCEVA1 only. So I logged in there and using the IDs given at the list from above's command:
$ stop/id=29804056
...

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===Check CPU usage and kill a process===
Determine what process is using all the CPU (e.g., SYMBIONT, a print process) using the monitor command, then use the show system command to determin the Pid, which can be used to stop the process.

The print (SYMBIONT) process is known to consume excessive CPU when the clocks are advanced for daylight savings on the alpha systems.
<pre>
$ monitor process/topcpu
$ show system
OpenVMS V7.3-2 on node SCEVAL 6-APR-2009 12:42:22.82 Uptime 124 23:16:08
Pid Process Name State Pri I/O CPU Page flts Pages
20C00081 SWAPPER HIB 16 0 0 01:07:05.63 0 0
20C00087 CLUSTER_SERVER HIB 14 2218 0 00:00:00.54 63 77
20C00088 CONFIGURE HIB 10 23 0 00:00:00.02 54 20
20C00089 LANACP HIBO 13 -- swapped out -- 32
20C0008B FASTPATH_SERVER HIB 10 9 0 00:00:00.01 79 94
20C0008C IPCACP HIB 10 10 0 00:00:00.02 37 28
$ show process/all/id=Pid
$ set host 0
user: system
password:
$ stop/id=Pid
</pre>
*Process Name = BATCH_122 means entry 122 in the queue

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==Printer==

===Set up TCPIP printer queue on a VMS workstation===
$ stop/que/res hpljet
$ tcpip set nohost hpljet
$ tcpip set host "hpljet" /address= xxx.xxx.xxx.xxx
$ start hpljet

Note that many HP printers will not work with OpenVMS. Checking for compatibility is important.

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===Stop and restart the printer queue===

How to fix the printer queue when hung, not working or giving an error.
A full printer queue can seriously affect system performance.
Be sure that the queue is cleaned up from time to time.

<pre>$ show queue</pre>

to first find out the real name of your printer queue.
* Replace "hpljet" and "...dcps_hpljet..." by your own queue (i.e., PRINTER1 for XtremeCT) name below.
* First approach, as normal user <code>microct</code>:
<pre>
$ stop/queue/reset hpljet
$ start/queue hpljet
</pre>

If you need to release a job
$ set entry/release 123

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==System==

===Monitor System===
====Monitor system usage====

<pre>
$ monitor/interval=1 processes/topcpu
$ monitor/interval=1 system
$ show error
$ show system
$ @SCOM:SHOW_DISKS.COM (or simply $ DISKS)
</pre>

The command <code>show error</code> may indicate errors. One or two errors is OK.

To see what processes are running (specific to the machine, not cluster wide).

<pre>
$ show device disk2/file
$ show user /full
</pre>

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====Check status of OpenVMS system====

If when rebooting a VMS system there is a failure, sometimes a message can be repeated many times. The way to stop this repeating message is to press <code>ctrl-C</code> or <code>ctrl-P</code> to get to the <code>>>></code> prompt.

Then show some of the device information, either specifically

>>> show device py*
>>> show device dy*

or in general

>>> show device

which might show more than needed. The output of

>>> show bootdef_dev

can also be useful.

Once settings are all good, you can reboot the system with
>>> init
>>> set bootbios pyb0
>>> boot

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====Check disk status====
Login as the system user on the workstation connected to the disk array that you want to check.

$ run sys$system:msa$util.exe
MSA> set controller

Show the raid volumes (e.g., to check if it failed or is recovering).
MSA> show unit

Locate disks associated with a raid volume (e.g., unit0).
MSA> locate unit0

Accept a failed unit (e.g., unit0) - only for itanium workstations, which use a newer version of OpenVMS.
MSA> accept unit0

Show disk information.
MSA> show disks

Get information on MSA utility functions.
MSA> help

Exit the MSA utility.
MSA> exit

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====Check status of disk array====
To look at the disks in an MSA30 tower:
There are several options to check the status of the disks. One is, if it is installed, to use the command-line utility
<pre>$ mcr msa$util</pre>
as "system". Enter
<pre>
MSA> set controller
MSA> show unit
MSA> show disks
MSA> exit
</pre>

Another is to start the WBEM web interface, which shows the status of the hardware graphically.

It is possible to fix a disk array that hasn't booted by doing the following:

At the login prompt, type 'shutdown'. This will get you to the <code>>>></code> prompt.
There should be a RAID card, for example on Percy, named <code>pya0</code>. Try:
>>> show device
>>> set auto_action halt
>>> init
>>> run bios pya0
>>> set auto_action restart
>>> boot

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====Check disks status in enclosure====

Periodically connect to http://10.148.64.254/ (user name: manage, password same as system password) and check if there are any errors or warnings, like failed disks. You can easily see which disk has failed in the graphical view of "Physical" -> "Enclosure X"

Consider not all web browsers allow connection to this rather old web server. Firefox and Mozilla on the workstations do work fine.

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===Recover System===
====Consistently needs warm-up scanner - Shutter-failsave-Job====

If the scanner is consistently needing to warm-up on consecutive days, and was not powered off, this is likely due to the Shutter-failsave-Job disappearing from the 3309-Batch queue (for XT1). The job must be re-submitted.

The executing file is located in the CALIB3309 ($ um:submit_shutter_test.com) and the command to submit the job is:
<pre>
$ submit/after="tomorrow"/noprint/que=uct_measurement_queue um:submit_shutter_test.com
</pre>

You can check the status by typing:
<pre>
$ show que *3309_batch*/all
</pre>

This job tends to disappear now and then, perhaps because of an abrupt shutdown of the workstation or maybe when stop/pause/re-start the queue. Contact Scanco if this does not resolve.

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====Disk not mounted/unavailable, directory not found, volume not enabled====
Disk is not mounted or is unavailable. Error opening ...., directory not found, volume is not software enabled.
<pre>
%DIRECT-E-OPENIN, error opening DISK4:[MICROCT.PROJECTS]*.*;* as input
-RMS-E-DNF, directory not found
-SYSTEM-F-VOLINV, volume is not software enabled
</pre>
This can happen if communication is broken between workstations, causing the disk mount to time out. Check if this is by showing the devices, then dismount and remount the disk.
<pre>
$ show dev

Device Device Error Volume Free Trans Mnt
Name Status Count Label Space Count Cnt
SC3309$DKA100: Online 0
SC3309$DKD0: Mounted 0 ALPHASYS 3.18GB 642 2
SC3309$DKD1: Mounted 0 AUSER_01 42.84GB 4 2
SC3309$DKD2: Mounted 0 ADATA_01 173.00GB 4 2
SC3309$DKD3: Mounted 0 ADATA_02A 215.80GB 1 2
SC3309$DKD4: Mounted 0 ADATA_02B 215.85GB 1 2
SC3309$DKD5: Mounted 0 ADATA_02C 215.81GB 1 2
SC3309$DQA0: Online 0
SC3309$DQA1: Offline 1
SC3309$DQB0: Offline 1
SC3309$DQB1: Offline 1
SCEVAL$DKA0: Online 0
SCEVAL$DKA1500: Mounted 0 (remote mount) 1
SCEVAL$DKC0: MntVerifyTimeout 0 ADATA_03A 541.62GB 1 2
SCEVAL$DKC1: MntVerifyTimeout 0 ADATA_03B 541.38GB 1 2
SCEVAL$DKC2: MntVerifyTimeout 0 ADATA_03C 541.60GB 1 2
SCEVAL$DQA0: Online 0

$ set host 0
system

$ dismount SCEVAL$DKC0:
$ mount/cluster SCEVAL$DKC0: ADATA_03A
%MOUNT-I-MOUNTED, ADATA_03A mounted on _SCEVAL$DKC0:
$ mount/cluster SCEVAL$DKC1: ADATA_03B
%MOUNT-I-MOUNTED, ADATA_03B mounted on _SCEVAL$DKC1:
$ mount/cluster SCEVAL$DKC2: ADATA_03C
%MOUNT-I-MOUNTED, ADATA_03C mounted on _SCEVAL$DKC2:
$
</pre>

If this does not restore the disk, then shutdown the computer. At the blue screen...
<code>>>> init</code>
Wait for blue screen to return.
<code>>>> run bios pya0</code>
Press F2 at the prompt to accept potential data loss.
Wait for blue screen to return.
<code>>>></code>
Press power button to turn off.
Press power button to turn on.

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====Kill hanging program====

If a program is hunging, it may not be necessary to shut down the system and restart. For example, if the <code>uct_evaluation</code>
program is hung, do the following

<pre>
$ show dev/full microct_scsi

$ stop/id=<Owner process ID> (Replace the <> with the actual ID)

for example:

$ stop/id=2280091C
</pre>

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====Reset the display/GUI====
These commands will terminate the current login session and may restore a frozen or messed up screen. You will need to remotely access the problem workstation either from another micro-ct workstation or using a personal computer.

Use the set host command to connect to the problem workstation (e.g., thomas) using the node name (e.g., sc3309) or the IP address (e.g., thomas.kin.ucalgary.ca).

$ set host sc3309
login: system
password:

Issue the reset display command.
$ @sys$startup:decw$startup restart

At the prompt, type "y".

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====Restart screen server====

If the monitor fails to show the login prompt and displays a blank gray screen...telnet to the computer from another computer (e.g. a PC or so) and login as user system. Run the restart command:

<pre>
$set host gordon.ucalgary.ca. [or other computer name]
$username: system
$password: [system password]
$@sys$startup:decw$startup restart</pre>
confirm (answer "yes" at the prompt) and logout.
<pre>
$y
$logout</pre>

This will kill all programs on your screen, but it will leave all batch jobs running, so if you do a BATCH measurement, this will survive! (but interactive scan will be killed).

If you are restarting a monitor connected to a KVM box, unplug and re-plug in the box.

This command also helps when the mouse/keyboard freezes.

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====Restart Alpha stations====

[[Image:Bones2.jpg|20px]] Warning: Do not do this unless absolutely necessary.

For shutdown

At the login screen, type "shutdown"/no password and hit enter.
Then, you can turn the computer off at the prompt.

Then, you may turn the disk array off (unplug it as there is no power switch).

After you move the computer, power on the disk array and then the computer.

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====Slow/non-responsive computer====

This is usually caused by people logging in via SSH multiple times. The solution involves resetting the SSH/TCPIP daemon.

:*If you are local at the computer:

You will need to log in as user <code>system</code>. ONLY EXPERIENCED USERS SHOULD EVER LOG IN AS SYSTEM!

The system will be extremely slow (it will take 5 minutes just to get a log in prompt). This is expected.

<pre>
$ set host 0 ! user name 'system' and password
$
$ @sys$startup:tcpip$ssh_shutdown ! shutdown SSH
$
$ set host 0 ! user name 'system' and password
$
$ @sys$startup:tcpip$ssh_startup ! restart SSH
</pre>

Alternatively, you can reboot the system to reset the SSH. This is not an appropriate solution and it is solving the problem by hitting it with a jack hammer. Sometimes it is the only choice though.

:*If you are remotely logged in:

You will have to log in as user <code>system</code> and run a script called STOP_START_TCPIP.COM.

This works essentially the same as for the above method, except that since it would be impossible to restart SSH remotely once it is shut down, two separate scripts are called and submitted on SCEVAL_FAST (make sure the queue isn't clogged) separated by a 1 minute delay. The first script called is STOP_TCPIP.COM and the second is START_TCPIP.COM.

To execute this process, you must log in as system, go to the SYS$SCRATCH directory, and interactively execute the script:
<pre>
$ @STOP_START_TCPIP.COM
</pre>

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====Shutdown a workstation remotely====
If a workstation becomes unresponsive, it may be possible to shut it down remotely from another workstation or personal computer, which is preferable over doing a hard power off. These instructions were provided by Mark Blanchard.

'''1. Remote shutdown from another micro-ct workstation'''. MAY NOT WORK FOR CLUSTER SERVER

Login as the system user.

$ set host 0
user: system
password:

Start the system manager.
$ mcr sysman

Set the environment to the workstation to be shutdown (e.g., thomas) using its node name (e.g., sc3309).
SYSMAN>< set env/node=sc3309

Issue the shutdown command. Add a time delay, e.g., 5 min, if you want to give users time to disconnect and the automatic reboot flag if you want to restart.
SYSMAN> shutdown node /min=5 /automatic_reboot

*You need to remain logged into the session running the shutdown until the other node has been shutdown completely!!!

'''2. Remote shutdown from a personal computer'''.

Begin a remote session to the workstation and login as the system user.

Create a detached terminal.
$ create/terminal/detach

On the PC, port 6000 needs to be accessible to the micro-ct workstation and in the X-server's configuration (e.g., in file X0.hosts for Xming).

Issue the shutdown command.
$ shutdown

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====Slow computers - Change RAID battery for Itanium computers====

If computers become sluggish, particularly when saving data after a scan, have Scanco check the batteries in the RAID drive. The batteries in SCEVA3 were changed 2014-11-10. There are two batteries. Order the HP brand (should look like the ones in the image).
*Instructions to open the Itanium work station and access the PCI card: [[Media:HP_rx2660_PCI_card.pdf |'''Change PCI card''']].
*Instructions to change the batteries after accessing the PCI card: [[Media:HP_SA6402_Batteries.pdf |'''Change batteries''']].

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====Frozen computer - "bootstrap failure" on boot up====
The micro-CT computer is frozen or there is a "bootstrap failure" on boot up, This happens to the client computers (those connected to the scanners) when there is interruption in the network. The only option is to restart the computer.

====Crash of XtremeCT II workstation computer====

For a non-responsive monitor and/or a mouse and/or a keyboard of the XtremeCT II workstation (sometimes caused by a lost of connection to server, or an internet outage):

:*1. The first thing to do is to check system logs for any indication of the cause of the issue, if you have the "Administrator" user privilege.
:*2. The next thing to do is to soft-reboot by remote-login and using command line to reboot the workstation, if you have the "system" user privilege.
:*3. If no success, try hard-reboot by pressing the power button as indicated below.
:*4. If no success, try hard-reboot by unplugging both power cords as indicated below.
:*5. If still no success, contact Scanco immediately.
:*6. The last thing to do is to record the issue and any possible reasons.

1. Checking system logs:

:*1) Remotely log into the iLO (the management console of the workstation) using SSH as user "Administrator" with the system password.
Both user/pw are case sensitive. For XtremeCT II workstation (James) it is SSH to 10.148.64.231. For others, consult the network diagram.

A trick: This connection only succeeds through a MAC or PC (via putty) direct login, not through an OpenVMS or Scanco system.
$ ssh -l Administrator 10.148.64.231
:*2) Then you get to a MP> prompt here:

MP MAIN MENU:
CO: Console
VFP: Virtual Front Panel
CM: Command Menu
CL: Console Log
SL: Show Event Logs
HE: Main Help Menu
X: Exit Connection
[sc3401-mp]</> hpiLO->

:*3) Type in 'SL' to show event logs, then you could choose 'E' for system event:

[sc3401-mp]</> hpiLO-> SL
Event Log Viewer Menu:
Log Name Entries % Full Latest Timestamped Entry
-------------------------------------------------------------------------------
E - System Event 1661 58 % 13 Sep 2018 11:17:43
F - Forward Progress 20000 100 % 13 Sep 2018 11:17:43
I - iLO Event 500 100 % 18 Sep 2018 07:46:42
C - Clear SEL and FPL
L - Live Events

Enter menu item or [Ctrl-B] to Quit: E
Log Name Entries % Full Latest Timestamped Entry
-------------------------------------------------------------------------------
E - System Event 1661 58 % 13 Sep 2018 11:17:43
Event Log Navigation Help:
+ View next block (forward in time, e.g. from 3 to 4)
- View previous block (backward in time, e.g. from 3 to 2)
<CR> Continue to the next or previous block
D Dump the entire log
F First entry
L Last entry
J Jump to entry number
H View mode configuration - Hex
K View mode configuration - Keyword
T View mode configuration - Text
A Alert Level Filter options
U Alert Level Unfiltered
? Display this Help menu
Q Quit and return to the Event Log Viewer Menu
Ctrl-B Exit command, and return to the MP Main Menu

:*4) From here you can use - and + to go through the log history back and forth. Not all logs do make a lot of sense though, as they are mainly meant for HPE engineers.
:*5) When finished, use CTRL + b to get back to the main MP> prompt.
:*6) Use MP> co to get to the console, where you see at what stage the booting process is, in case it does not boot properly.
:*7) When finished, use CTRL + b to get back to the main MP> prompt.
:*8) Use MP> x to end the connection.

2. Soft-reboot by remote login:

If a workstation becomes unresponsive, it may be possible to shut it down remotely from another workstation or personal computer, which is preferable over doing a hard-reboot. These instructions were provided by Mark Blanchard.

:*2.A) Remote shutdown from another micro-ct workstation. MAY NOT WORK FOR CLUSTER SERVER

Login as the system user.
$ set host 0
user: system
password:

Start the system manager.
$ mcr sysman

Set the environment to the workstation to be shutdown (e.g., thomas) using its node name (e.g., sc3309).
SYSMAN>< set env/node=sc3309

Issue the shutdown command. Add a time delay, e.g., 5 min, if you want to give users time to disconnect and the automatic reboot flag if you want to restart.
SYSMAN> shutdown node /min=5 /automatic_reboot

You need to remain logged into the session running the shutdown until the other node has been shutdown completely!!!

:*2.B) Remote shutdown from a personal computer.
Begin a remote session to the workstation and login as the system user.

Create a detached terminal.
$ create/terminal/detach

On the PC, port 6000 needs to be accessible to the micro-ct workstation and in the X-server's configuration (e.g., in file X0.hosts for Xming).

Issue the shutdown command.
$ shutdown

3. Hard-reboot by power button:

:*1) Hold the power button until it turns yellow.
:*2) Wait a minutes or two, then press the power button only once and shortly. You will not see anything for a while. Pressing the power button again during this time will turn off the workstation again !
:*3) After about 10~15 min, the workstation would boot up properly.

4. Hard-reboot by unplugging both power cords:

:*1) Hard-reboot by unplugging both the power cords. This will reset the console and controllers.
:*2) Wait for 5~10 minutes, then press the power button only once and shortly. You will not see anything for a while. Pressing the power button again during this time will turn off the workstation again !
:*3) After about 10~15 min, the workstation would boot up properly.

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=Remote Access=

==For Scanco support==
===Send a terminal to a remote computer===

To send a terminal from XCT clusters to Scanco for maintenance, you need to know the ip address for the terminal location.
Such as For Mark Blanchard:

$ set display/create/transport=tcpip/node=193.72.60.24
$ create/terminal/detach

The cursor will disappear for a minute or so, and reappear with the $ prompt indicating sent already.

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==Access VMS filesystem==
===Access XtremeCT VMS filesystem on a Mac===

In finder, select Go --> Connect to Server

This opens up a window that allows you to enter a server address. Enter the following information:
<pre>smb://136.159.130.28</pre>

Click connect. If the internet connection is working, you will then be prompted to enter in login info:

<pre>
USERNAME: xtremect
PASSWORD: uct
</pre>

Select the volumes you want to mount.

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===View XtremeCT VMS filesystem from a Windows PC===

The HP program that allows the VMS file system to be viewed by a PC is called Pathworks (on the VMS system). The following information is needed to connect to the VMS system:

<pre>
USERNAME: xtremect
PASSWORD: uct
WORKGROUP: microct
</pre>

Then, in Windows explorer, while connected in the same network as the VMS station (i.e., .130) enter the following IP address for Thomas (SC3309):

<pre>\\136.159.130.28\</pre>

Alternatively, map the drive.
<pre>
Right click on my computer and choose map network drive.

Folder:
\\136.159.130.28\UCT_DATA1
or
\\136.159.130.28\UCT_DATA2

User name: xtremect@microct
Password: uct
</pre>

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===View VivaCT40/uCT35 VMS filesystem from a Windows PC===

The HP program that allows the VMS file system to be viewed by a PC is called Pathworks (on the VMS system). The following information is needed to connect to the VMS system:

<pre>
USERNAME: vct_40
PASSWORD: uct
WORKGROUP: microct
</pre>

Then, in Windows explorer, while connected in the same network as the VMS station enter the following IP address for SCEVAL:

<pre>\\136.159.74.140\</pre>

Alternatively, map the drive.
<pre>
Right click on my computer and choose map network drive.

Folder:
\\136.159.74.140\SB_DATA
or
\\136.159.74.140\SB_PROJ
or
\\136.159.74.140\BH_DATA
or
\\136.159.74.140\BH_PROJ

User name: vct_40@microct
Password: uct
</pre>

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===Map a Network Drive to the VMS filesystem from Windows===

To do this you must be on the same network as the OpenVMS system. For main campus and the XtremeCT, you will map the drive to Thomas (136.159.130.28), the workstation connected to the scanner.

<pre>
Right click on My Computer and choose Map Network Drive...

Folder: \\136.159.130.28\uct_data1 !FOR THE PROJECTS DISK

and/or

\\136.159.130.28\uct_data2 !FOR THE DATA DISK

User name: microct\xtremect
Password: uct
</pre>

Note: You must use the numerical IP address and not the host name (i.e. thomas.kin.ucalgary.ca).

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==Setup remote access FAQ==
===Access data remotely===
Refer to [[Media:Scanco-faq-accessing-data-remotely.pdf|'''Scanco tutorial on accessing your data remotely''']] for

*A quick refresher course on accessing files
**Web browser
**File sharing
**File transfer protocol (FTP)
*Network file system NFS
*Running Scanco programs remotely

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===Use Hummingbird Exceed for remote access===

*Screen definition
:Server visual = PseudoColor
:Window mode = multiple

*Keyboard input
:Primary = decemus
:Alternate = us

*EVE commands
:select = "end"
:cut = "delete"
:paste = "insert"

:move forward a word = CTRL + right_arrow
:move to start of document = CTRL + up_arrow
:move to end of document = CTRL + down_arrow

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===Use XWin32 for remote access===

Run XWin32. Run Putty and connect to sceval.ucalgary.ca. Use the terminal normally to run programs, which should open with XWin32.

Additional terminal windows can be opened with <code>$ dec</code>

If you try to connect from somewhere other than the university, you will probably get the following error when trying to open a window:

Xlib: connection to "sceval.ucalgary.ca:10.0" refused by server
Xlib: Can not connect to a host on a restricted network
X Toolkit Error: Cannot Open Display
%DWT-F-DWTABORT, xtoolkit fatal error

Type the following at the command prompt to direct the display:

$ set display/create/transport=tcpip/node=Your_IP_Address/server=0

You can find your IP address from: http://www.ip-adress.com/

If you're running XWin32 from off campus and behind a router, forward ports 6000 - 6010 TCP and 177 UDP to your computer.

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===Set up Putty with gold-key access===

Refer [http://bone.wiki/index.php?title=Scanco_User_Instructions#PuTTY_and_Xming '''PuTTY and Xming'''] to download putty.

Set 'keyboard' to Vt400, and 'initial state of numeric keyapad' to 'Application', and now the 'NumLock' key is the gold key (like PF1), and the editor can repeat stuff.

Then

<pre>$ set term/vt100</pre>

to enable the editor in the terminal.

And duplication of a line is:
<pre>
- (which would be PF4) to erase a line,
then twice "numlock, then -" (gold-PF4 is 'restore line')
</pre>

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===SSH tricks===
====RSA and DSA Authentication====

The main advantage of setting up RSA authentication is that you will no longer have to type your password each time you access a host with ssh. There are some technical reasons why RSA and DSA access is more secure than password access.

These instructions work on both Linux and OS-X.

# Create your public/private key pair on your local computer
#* At the command prompt type: ssh-keygen -t rsa
#* You will be asked to create a passphrase.
#* This will create the files .ssh/id_rsa and .ssh/id_rsa.pub . Once you have these files, you never have to repeat this step.
# Copy your public key contents into the .ssh/authorized_keys2 file on the remote server
#* You can email yourself the file .ssh/id_rsa.pub from the local computer.
#* Alternatively, you could do this: ssh username@remoteserver.com 'cat >> ~/.ssh/authorized_keys2' < /Users/Youruser/.ssh/id_rsa.pub

NOTES ABOUT KEYS
Remember, the "authorized_keys" file is a concatenation of public (id_rsa.pub) keys,
and the "id_rsa" is the private key.
Every user on every computer should only have ONE "id_rsa" file,
but can have multiple "id_rsa.pub" files concatenated into
their "authorized_keys" file.

=====SSH Agent=====

SSH-Agent is a tool to store your passphrase so you don't have type it every time.

On OS-X, it is integrated into the system Keychain - you will be asked once if it should remember your passphrase, and after that you don't have to worry about it.

Most Linux systems also have ssh-agent configured to start with every session. You may however have to do this once:
ssh-add ~/.ssh/ida_rsa

====SSH Tunneling====

This is an alternative to VPN through kinesiology. It may come in handy if for some reason VPN is not working.

If you're outside the university system and want to access, for example, svn on mike.kin, which is normally blocked by the university firewall, you can do that with ssh tunneling. Here is an example:

ssh eric@mighty-mac.kin.ucalgary.ca -L 2000:mike.kin.ucalgary.ca:443 -N

Here is what is going on:
* I want to access port 443 (which is https) on mike.kin.ucalgary.ca.
* I have an account on mighty-mac, so I'm using that server to create an ssh tunnel inside the university firewall. I could use any machine I had an account on inside the university system, even mike.kin.ucalgary.ca, the one I'm trying to get to (in fact, that would be best, but for purposes of demonstration I'm using a different machine).
* I'm mapping the local port 2000 to port 443 on mike. Anything I send to localhost:2000 will by sent by ssh or the ssh tunnel to mighty-mac, which will then send it on to port 443 on mike.
* 2000 is a random 4-digit port number. If by some fluke you happen to choose one that is in use, ssh will complain and you will have to try another port number.

Now I can fire up my browser and point it to

https://localhost:200/trac/

And what I get is the trac site on mike.

If I want to get the code, I can do this:

svn checkout https://localhost:2000/svn/numerics88/trunk trunk_tunnel

("trunk_tunnel" is just the directory name where it will end up. It can be named anything, but this will remind me that it only works when the tunnel is up.)

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==Physical connections==
===Connect to VMS station with a serial port cable===

To do this, you will need to connect from a PC using a PC-to-PC (NULL modem) serial cable, 9600 baud. Install PuTTY and connect with the 'serial' option. You will need to know the COM port that is used by the PC to connect the serial cable. You can do this by checking on the PC the [Hardware][Device] settings.

Typical login is "Admin" and password is usually same as the 'system' password.

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===Export VMS display to SUN or LINUX terminal===

<pre>
# - temple
$ - sceval
# xhost +temple.ucalgary.ca
# ssh -X microct@sceval.ucalgary.ca
$ set display /create /transport=tcpip /node=temple.ucalgary.ca
</pre>

NOTE: Do not use <code>xhost+</code>. Always specific exactly which computer is being
allowed X access.

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=Dose=

==Dose Calculations==

===XtremeCT radiation dose===
Some notes about radiation dose to help decide acceptable scanning protocols. These comments are based on scanning an adult (not children having significant red marrow at the scan region).

:*The annual dose limit for the hand for an occupational user is 500 mSv (as per the ICRP), and with the x-ray energy of our XtremeCT that translates to 500 mGy local dose per year. For non-occupational subjects, the limit is generally 10x lower (i.e., our volunteers should not have more than 50 mGy local dose per year).
:*Our scanner delivers a local dose of about 5.3 mGy per scan. However, if we have adjacent scans, there is some overlap due to the penumbra of the x-ray beam which results in about double the local dose (a conservative guess would be 10 mGy) for a ~1mm overlap region. Averaging over the whole scanned regions (overlap and non-overlap regions) we can say that the average delivered local dose is about 7-8 mGy. The local dose is not additive. If we're very conservative, and we take 10 mGy as the local dose, then we could theoretically scan a person 5 times before exceeding the 50 mGy limit based on a tenth of the occupational limit (500 mGy).

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===vivaCT CTDI dose===
====Dose calculation====

Assuming the following settings on the vivaCT for "high mode", we will calculate the CTDI dose.

2000 projections (360 degrees)
0.109 mA
200 ms IT

I calculate the time current value as:

0.109 mA * (0.200 + 0.012) S * 2000 proj= 46.22 mAs

The 0.012 is the integration time between projections.

Taking the proportion of the 68 mAs at 55 kV resulting in 720 mGy (see the document on example
dose calculation on this Wiki site), we have:

46.22 / 68 * 720 = 490 mGy

Since CTDI in air is approximately two times the weighted CTDI, and since our setup is more like in air, we get:

2 * 490 = 980 mGy per scan.

It's always a good idea to look at the time-current product in the control file to get an approximate estimate.

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====Dose chart and example====
*Refer to [[Media:VivaCT dose information-fyi.pdf|'''VivaCT CTDI Dose Calculation Example''']].

We have measured the following CT dose indices (CTDI).
:*CTDIw: Weighted CTDI (chart below)
:*CTDIair: CTDI in air (2 times CTDIw - calculate from chart below).

The detector was placed in the center of a 35 mm PMMA cylinder which was placed in the center of rotation.

<pre>
70kV 300ms 85uA Field of view 38.9mm 1000 Proj./180°: CTDI = 260 mGy
55kV 300ms 109uA Field of view 38.9mm 1000 Proj./180°: CTDI = 220 mGy
45kV 300ms 133uA Field of view 38.9mm 1000 Proj./180°: CTDI = 190 mGy

70kV 300ms 85uA Field of view 30.7mm 1000 Proj./180°: CTDI = 420 mGy
55kV 300ms 109uA Field of view 30.7mm 1000 Proj./180°: CTDI = 350 mGy
45kV 300ms 133uA Field of view 30.7mm 1000 Proj./180°: CTDI = 305 mGy

70kV 300ms 85uA Field of view 21.5mm 1000 Proj./180°: CTDI = 850 mGy
55kV 300ms 109uA Field of view 21.5mm 1000 Proj./180°: CTDI = 720 mGy
45kV 300ms 133uA Field of view 21.5mm 1000 Proj./180°: CTDI = 620 mGy
</pre>

high res = 1000 Proj./180°
medium = 500 Proj./180°
standard = 250 Proj./180°

The CTDI scales linear with the integration time (s), with the current (uA) and number of projections. If you have different settings there, it is easy to calculate the CTDI.

CTDI Definition:
<pre>
Integral from +50mm to -50mm of D(z)/NxT
</pre>
:*where D(z) is the dose profile along a line z which is perpendicular to the tomographic plane
:*N is the number of tomographic sections produced in a single rotation
:*T is the nominal tomographic section thickness

Example: How to estimate how much radiation would be incurred by a mouse scanned at 25
um resolution (medium resolution -- MR) at 55 kVp, 109 uA, 150 ms IT, for about 30 minutes?

If you take your settings you can calculate the CTDI. First thing you have to be aware is that the CTDI is something like the local dose but it takes the cone beam geometry and the not perfect collimation of the x-ray beam into account (The CTDI value is always higher than a local dose measurement with for example TLDs). It does not matter how many stacks you are scanning. The dose you have at one point which is within the volume you are scanning gets the same local dose if you are performing a 1 stack or a 4 stack measurement.

With the 55kVp/109uA HR with 300ms we have a value at the 30.7 mm position of 350 mGy. Because you have MR we can divide the values by a factor of 2; and because you have 150ms instead of 300ms there is an other factor of 2. You would get 87.5 mGy for the position 30.7 mm. Because of the cone beam the dose has a quadratic dependency to the diameter of the field of view. (30.7 mm/25 mm)2 = 1.5. The CTDI value for your settings is in the order of 87.5 mGy * 1.5 = 132 mGy.

Note that for in vivo measurements, we should multiply the result by a factor of two since we are doing the measurement in AIR, not WATER. The charts above are assuming the CTDI done in water.

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==Optimize Scan for Low Dose==
*Refer to [[Media:Scanco-faq-optimization-for-dose.pdf|'''Optimize Scan Protocols for Low Dose''']].

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