Revision as of 19:39, 22 December 2020

How To Section 1 - Micro-CT Scanning

Micro-CT Scanning

Scanco Setting Possibilites

E (kVp): 50, 60 70

I (uA): 80, 160

Integration time (ms): 100, 200, 350

Settings Suggestions for SkyScan bone scanning

email, forwarded from Phil Salmon, phil.salmon@skyscan.be

Here are some guidelines for scanning bone. You will in due course be able to fine tune the scan settings for your own samples.

Get the best magnification that you can, but have at least most of your object perimeter contained within the borders of your field of view. Technically it is possible to scan an internal region at high magnification with much of the object outside the field, but in practice this decreases the signal/noise ratio. For example if you are interested primarily in trabecular bone, it is OK if some small parts of the cortical perimeter move out of the field during scanning.
N.B. Always check your object at several angles before launching the scan - e.g. 45, 90,135, 180 degree views, to check that it is rotating as symmetrically as possible).
Voltage: What species bone are you studying? If it is anything larger than a rat I should stay with the maximum 100 kV unless you have very small samples and require maximum resolution. For mouse bones a general range is 50-68 kV. Remember that you will need to make a new background or "flat field" correction when you change tube voltage or current.
Current: Again for large bones leave this at maximum. However for small samples you could make use of the smaller source spot size option. If your machine is the 100kV 1072, then at full voltage and current (power=10W) the spot size is 8 um.
However, when the power falls below 4W the spot size decreases to 5um (this happens automatically). If the sample x-ray absorption is still OK at a setting with power < 4W, you will get optimum spatial resolution.
Exposure time. Exposure time is set automatically.
Frame averaging and step size. As you increase frame averaging and decrease rotation step, resolution will increase but so will scan time. So use the maximum values that time allows.
Filter. I always use 1mm Al for bone, even small mouse samples. "Filter 2 and 3" actually contain no filter. So your options are 1mm Al or no filter.
Some notes on dataset reconstruction:
- Set beam hardening and ring artifact reduction on the minimum settings that are visibly necessary.
- Set smoothing to minimum or off.
- Set the “cross-section to image�? upper limit just a little above the top end of the grey spectrum of the sample to optimise contrast in the reconstructed images. I usually put the lower limit halfway down the upper slope of the peak of background - some background will facilitate dataset thresholding (see next comment).
You can use the threshold module in the program 3d-calculator to get the optimum thresholding to binary images.
Download this from here if you don’t have it yet.

Corrections for Ring Artifacts and Filter Use

email, forwarded from Alexander Sasov, sasov@skyscan.be

If ring artifacts appear only when you scan with a filter, you should acquire new flat-field reference for that particular filter and save it. Possible reasons for the rings are switching to another voltage or current or exposure, some particles in the filter surface, cracks or just small changes in the x-ray spectrum of the source, which normally appear in several years of usage.
Normally one should acquire new flat-field references t wice per year or in the case of the appearance of strong ring artifacts. Another reason to acquire new flat-field references is a system operation with new voltage/current/exposure. Don't forget to save new flat-field references directly after acquisition.

Specimen Holders

email, forwarded from SkyScan

Scanning area for one scan in 1072-instrument can be max.20mm in diameter and 18-19mm in length. Also possible to scan the big objects up to 38mm in diameter with twice scanning time. Object can move +/-10mm for positioning of scanning area or to scan up to 30-35mm in length by several partial scans with automatic connection to one continuous set of cross sections.

Physical object length may be up to 45-50mm, but only 30-35mm can be scanned.

How To Section 2 - VMS Commands

Tables

Table 1 - Login and Software

xuct	login password
eve, lse, e	text editors
spa corelut	spawn a process
uct	main program
uct_evaluation
uct_3d
uct_backup
aix C0000104.AIM	examine an AIM
aio 13	AIM filtrations (list of procedures)
sap	2d AIM viewing tool
sap -s aimfile.aim	Opens the given AIM in sap.
pwindow /nowait	capture a window as TIF, GIF, etc.
viza /nowait	3d viewer (requires mcubes result)
mcubes	marching cubes
help `arg`
sh sym `arg`
aimod	to alter the dim, pos, el_size_mm, etc of an aim. Use ‘e’ to end input parameters.

Table 2 - Commands and Aliases

ds	directory, with file sizes
dh	directory, with whole path
dh0	for all the files in lower directories beginning with ‘0’.
-	to continue command to next line
sh sym dd	shows symbol value {executable, path}
sh log ud	shows a logical value {path}
dec	delete file (with confirmation)
del	delete file (no confirmation)
decisq	delete ISQ file
sh dev ud (sdud)	report disk space (38881940 blocks equals ~19GB)
sdur	report disk space on measurement disk
onjane	set display to jane (jane.ethz.ch)
onblund	set display to blund (blund.ethz.ch)
cd scratch	view scratch directory (e.g. see MEASUREMENT_233.LOG;1)
sh que reco	show reconstruction queue (also, sq reco)
sh que meas	show measurement queue
sh que eval	show evaluation queue
del /entry=#	delete a process off queue (use see to view entry numbers)
tp0	tape drive for backups
sh dev tp0 /full	shows all information about tape drive (including if somebody has mounted it).
purge filename	deletes all files except for the latest version.
v1 filename	renames the latest version to version 1.
dsg	type from project directory (ur) to get a report of disk space used by all projects.
term	opens a new terminal (new blund terminal).
sb 1217	show batch info after you know the process id from the `see` command.
sb 1217/cont	shows the continuous cpu usage. Type `e` to exit.
qm	In a busy terminal, type `qm s "this is done"` to send a mail to myself.
qmm	Type `qmm s “this is done”` to put a mail on measurement queue (`m`).
qme	Type `qme s “this is done”` to put a mail on evaluation queue (`e`).
qmr	Type `qmr s “this is done”` to put a mail on reconstruction queue (`r`).
beep	Makes a beep sound!
se ipl	To look at just the jobs with IPL in the job name.
read_meas	Takes a measurement number and reports info on it (i.e. backup tape name etc).
sh que /all $mou	Show printer queue.
sm	show memory
monitor/interval=1processes/topcpu	Every 1 second update the cpu usage. Use ctrl-Z to quit. Type `monitor/interval=1 processes/topcpu`
ss	show current system processes
show proc	to see who is user
stop `jobname`	to kill a process
onlocal	make display on the local machine (i.e. if you’re at blund, display is at blund). or `SET DISP/CREATE/TRANSPORT=TCPIP/NODE=SCAPULA.EE.ETHZ.CH`
dk40	sets disk to DISK40
dk50	sets disk to DISK50
help lex	returns the possible lexical commands for script files (e.g. `F$SEARCH`)
move files	`rename myfiles. [.TEMP]`
move files	`rename myfiles. [-], rename myfiles. [-.-]`
see	see current processes (`show entry/by=executing /full`)
se ipl/full	see ipl processes on queue
ss	show system processes
stop <`proc id`>	kill a system process (i.e. `stop UCT_LUT7BB8`)
move	move or rename a file
copy	duplicate file
rename	move/copy files
rename test.dir [-]	to move up
rename test.dir [.models]	change name to models
more	view file contents
ud *224 0	goto DISK40:[DATA.UCT.00000224.00000404]
lo	logout
ur	goto DISK40:[DATA.UCT.PROJECTS]
or	goto OBL projects
ret	return to previous directory
tup	check utility processing
v1	reduces to newest file
dd	directory, with dates
d	refresh

Table 3 - File Definitions

RSQ	raw image file (contains projection data), created with scan
ISQ	reconstructed file (contains slice data), created from RSQ
AIM	discretized CT results, extracted from ISQ.
RAW	raw data (RSQ)
IMA	image data (AIM, ISQ, GOBJ).

Table 4 - Reconstruction and Batch Jobs

fan_reko_all [] 9.6	reconstruct ISQ from RSQ in directory [] with a reconstruction angle of 9.6 (righthand-rule).
fan_reko 9.6 [] 22 10	reconstruct ISQ from RSQ, angle 9.6, directory [], first slice number, number of slices (optional queue name). Must reconstruct at least 2 slices. Get reconstruction angle from uct_evaluation (atan).
fan_reco	interactive reconstruction of single slices from RSQ data.
subut MEASUREMENT_92.COM;1 /que=BLUND_MEASURE submeas #sample
	submit a batch job

Table 5 - Directory and File Organization

data

DISK40:[DATA.UCT.00000224.00000404]

C0000274.ISQ;1 {after reconstructing all slices}
C0000274.RSQ;1 {measurement output}

C0000274.AIM;1 {extracted from ISQ}

projects

DISK40:[DATA.UCT.PROJECTS.JAX]
00000216.DIR;1

DISK40: [DATA.UCT.PROJECTS.JAX.00000216.00000354]

C0000229.AIM;1

C0000229_GFILT.AIM;1

C0000229_THRES.AIM;1

00000217.DIR;1 {more data files as above, etc.}
COM.DIR;1

DISK40:[DATA.UCT.PROJECTS.JAX.COM]

EVAL.COM;1

IPL_SCANCO_V4.COM;1

UCT_EVALUATION_FULL.COM;1

DOC.DIR;1

Directory DISK40:[DATA.UCT.PROJECTS.JAX.DOC.IMG]

2D.DIR;1 {images from SAP usually}

3D.DIR;1 {images from viza usually}

LANDMARKS.DIR;1 {other images}

LOG.DIR;1 {evalution processing logs}

Table 6 - AIO Procedures

AIO Procedures

1. Different mathematical procedures.

2. Different mask procedures.

3. Exchange a slice with another slice in the AIM.

4. Reduce an AIM with cardinal reduction factors.

5. Calculate the relative positions of two AIMs.

6. Thresholding an AIM.

7. Thresholding and inverting an AIM.

8. Fill AIM with ramp function.

9. Calculate morphometric parameters from AIM.

10. Convert BID image to AIM with only one slice.

11. Mirror slices in AIM.

12. Interleaf slices in AIM.

13. Gaussian filtration of AIM.

14. Read single slice in AIM and convert to BID image.

15. Select AIM subimage (or MINIMAL).

16. SIBA bone remodeling module.

17. Flip, flop or flup AIM.

18. Convert AIM from YZ or XZ to XY representation.

19. Segmentation of AIM using region growing.

20. Segmentation of AIM using local thresholding.

21. Select cylindrical subvolume from AIM.

22. Calculate fist and second area moments from AIM.

Table 7 - EVE Editor Commands

gold key	`<PF1>`
copy	`<PF1><Remove>` on VMS
paste	`<Insert Here>` on VMS or `<ctrl><insert>` on PC
cut	`<Remove>` on VMS or `<delete>` on PC
learn	`<CTRL><K>`
stop	`<CTRL><R>` (then give a key sequence such as `<CTRL><Q>`)
repeat	`<PF1><#><(CTRL-Q)>` (the `CTRL-Q` depends on the given key sequence).
find next	`<PF3>`
enter search string	`<PF1><PF3>`
replace string	`<PF1><S>`
margins	Mouse click bottom of window type: `set right 999`
kill line	`<PF4>`
kill word	- (minus key on number pad)
advance next line	`0` (zero on number pad)
select text	`<CTRL><SPACE>`
Further reference at `DISK1:[RAM.EDIT]TPU.ACCEL` where some of Ralph’s definitions are described.

Project How To's

How To: Set up a new project

Step 1: Make directories

In DISK40:[DATA.UCT.PROJECTS] make a directory HERZOG.
Make COM, LOG, DOC directories. DOC can have IMG. IMG can have 2D and 3D.

Step 2: Copy files

Copy some of the COM files from another project. Especially EVAL.COM and EVALUATION.COM.
EVAL.COM is the main file that calls EVALUATION.COM

Step 3: Create a symbol

Go to: cd DISK1:[UCT]
Edit: eve LOGIN.COM
Add logical HERZOG in alphabetical order.
Add EVAL_HERZOG :== @UCT-DATA-R:[HERZOG.COM]EVAL.COM HERZOG
Type rulog to update the symbols.

How To: Process a project

Record specimens to be scanned on a project sheet.
Scan
Create directory in projects: COM, LOG, MODELS, DOC
Create EVAL.COM
Do evaluation (will move the output AIMs to the projects directory)
Backup RSQs.
Rename the AIMs and place in MODELS.
Backup AIMs fromUD (measurement disk). Note that we don’t backup ISQs. These can be made again from the RSQs and take much more disk space than the AIMs that have been cutout from them.
Generate 2D images.

How To: Evaluate a project (PRE)

This is done in 2 steps: AIM extraction, AIM filtration.
Run the evaluation as user XUCT so that enough memory can be allocated for the job. To login as xuct on blund, type blund (see HowTo:).
EVAL_HERZOG G 245 (runs the evaluation, with option G, on sample 245).
When uct_evaluation tool pops up, click cancel to get sample 245.
Select the <evaluation 3D> button, select <ROI>, then <start evaluation>.
Then exit.
To look at the latest UCT_EVALUATION.LOG, go to cd scratch
Once the AIM has been successfully extracted (it’ll be located in the measurement directory), start the second part of the analysis by typing: EVAL_HERZOG SE 245 or EVAL_HERZOG 245. With no options defaults to GSE, and since option G is already processed, it skips to options SE.

- Option S starts SAP with which the user can check that the AIM captures the data of interest.

- Once you exit from SAP, the file is Gaussian filtered (option E in script), renamed to the PROJECTS directory, and the original ISQ file in the measurement directory is deleted.

Once the two steps of evaluation are finished, the filtered aims should be renamed to meaningful project names (see renaming HowTo's).
If anything goes wrong in the evaluation, goto the LOG directory in the HERZOG project to see the problem.

How To: Evaluate a project (POST)

This is done typically once the original data has been pre-processed (i.e., cutout and filtered).
Create a script file with the exact name: SUBMIT_ALL_IPL.COM

- This file usually contains references to various steps in the evaluation such as trabecular morphological evaluation, cortical evaluation, mask generation, etc. These might be named TRAB, CORT, MASK or, if all three steps are to be performed, use ALL.

Create an IPL procedure file (as opposed to interactive use of IPL). Remember to use the two dots (..) after the IPL procedure! This file might be named IPL_TRAB_SUBMIT_ALL.COM for example. One of these files is necessary for each of the possible evaluations (trab, cort, mask).
Test the procedures by submitting only one job.

- From the COM directory, type SAI TRAB NORMAL-01. This will submit the file that contains the string NORMAL-01 to be evaluated using the IPL procedure that TRAB refers to in the SUBMIT_ALL_IPL.COM file.

Submit the project for evaluation using SAI ALL. Or, if only one part of the evaluation is to be performed SAI TRAB.
Look in the LOG directory for the results from the evaluation.

How To: Measure reconstruction angle and align an image axially

The ISQ generated from the RSQ can be re-aligned axially.
Measure the reconstruction angle:

- Start uct_evaluation and load the ISQ image.

- Launch corelut from uct_evaluation (<lut>, <modify>, <option cursor>, <position>).

- Click <draw line> and <show>.

- <shift> to draw line, <mb2> to store line (don’t forget to uncheck the show line button).

- View reconstruction angle in corelut window. Follow right-hand rule.

Generate a new ISQ with: fan_reko_all [directory] -12.6

How To: Rename the AIMs from the data base and move to MODELS

Do this from the COM directory of the particular project: ur michigan
Type: r2m 404 421 (these are the measurement numbers). Makes a file called REN2MODELS.COM.
if you want to rename also GOBJ + THRES + FILT aims, type r2m ALL (+meas #)
Edit the COM file. Change xx.yy to MICHIGAN (capitals). Change “right�? to “r�? and “left�? to “l�? so that all files are the same length.
@REN2MODELS.COM (moves the files to the MODELS directory).
Test that the AIMs were properly moved to the MODELS directory by typing: dh0 (tests no files in 000... from projects directory).
Delete the empty directories: dec0

How To: Create 2D or 3D images

Always rename the images from their system-given name to a meaningful project name.
Manually, start corelut. Set colormap to black and white (#2).

Option 1: Manual

Start sap and pwindows.

Option 2: Automatic

Generate an SAP.COM file using @ut:create_sap-pw.com or “csp�?
Edit SAP.COM. Then start with @SAP.COM XY.
Make XY, YZ and XZ 2d images, and some detail images. Always close pwindows before sap. The next AIM will be automatically loaded.
Always save as TIFFs. Powerpoint is able to make invisible background with TIFFs only.
Rename the TIFF files to TIF (one ‘F’) so that programs such as Adobe Photoshop will recognize the files.
Look at TIFFs using xv filename or i disp filename (image magick).

How To: Compile LOG files from IPL evaluation

Concatenate the log files into one long file and place it in the log directory.

- app/new ipl_trab*.log [-.doc]calgary_bear_trab.log

In the doc directory, use the tabulating program to extract the results.

- taball calgary_bear (it looks for a file ending in ‘_trab’ extension).

Instead of taball, individual IPL evaluation results can be tabulated. Type tab to get the usage.

Tape

How To: Tape is allocated to another user

Before using tape, test with sh dev tp0 /full
Status online allocated or offline. Should be online before using.
If somebody else is using the tape, wait.
If you are the one using the tape, make sure you dismount tp0 or dismount tp0/nounload from the same window you mounted the tape.
If there is a serious error in getting the tape use back, then logout of blund completely (<exit> button on CDE at top of screen) and log back (xuct).
Any currently running queued jobs, including current measurements, will not be affected by the logout.

How To: Deal with a full backup tape

Option 1: From an archive script

Wait for the script to fail after typing no for the request for volume 2 tape by the program.
dismount tp0 to remove tape.
Insert new tape, initialize with uct_backup, and start script again so that it includes only those filesthat were not already backed up on the previous tape (check the measurement directories).

Option 2: From the uct_backup utility

Resume the operation on a new backup tape.
To abort the uct_backup utility, type ctrl-y. It is very slow. Be patient!
Insert the new tape.
With uct_backup, initialize the tape. Name is RAW007 (max 6 characters).
Continue backing up after mounting the new tape.

Option 3: From bltp utility.

Type ctrl-y.

How To: Initialize a new backup tape

Put new tape in drive.
Start uct_backup
Select <initialize> before <mount>.
An alternative to using uct_backup is to type at the command line: init tp0 BE0007

How To: Archive (RSQ and AIM) files with a batch job

RAW = RSQ, IMA = AIM.
Create an ARCHIVE.COM file and put it in the COM directory. Always add any files that have been backed up for the project to this file so that restoration is simply a matter of changing this file.
Automatic generation of the ARCHIVE.COM file is possible using the command: archive

- start_date: copy and paste date of the first measured file (12-DEC-2001).

- end_date: Last measured file.

- RAW data only: N

- *seg.aim: N

edit the ARCHIVE.COM to include only the files that you want backed up. The version of ARCHIVE.COM can be temporarily modified at any time to:

- archive the IMA files (AIMs).

- restore either the IMA or RAW files from tape.

@ARCHIVE.COM from the COM directory to execute the backup once the appropriate RAW/IMA tape is in the drive.
Note the tape number on the project sheet.

How To: Archive the RSQ (and AIM) files with the uct_backup tool

Step 1: Tape in drive

Type sh dev tp0 to ensure nobody else is using the drive (should not be mounted).
Put RAW006 in drive.
Door up to insert tape.
Door down to close.
Wait for flashing light to stop. Indicates tape is loaded.

Step 2: Back up utility

Start uct_backup
Click on <mount>/code>


Click on file to backup in window and file type (i.e. RSQ).
Select <move to> (from disk to tape), or <copy to> (from tape to disk).
Check that we are moving to tape, not trash!
Click <start>
Click <yes>
Then minimize the window. Never re-open the minimized window during the backup process. It will open automatically when done.
Note the tape label on the project sheet.


Step 3: Remove tape
Click on <unmount>.
Wait for green light, then pop open the door. Done!

HowTo: Delete a measurement

Option 1: Permanent deletion (i.e., a failed measurement)
Use uct_backup
Then move to the trash bin. Click on the all box.
Type exit.
This removes the measurement from the micro-CT database and prevents future confusion.
Option 2: Delete a restored RSQ (i.e., a good measurement was restored from backup tape)
Confirm that the RSQ is stored on tape (read_meas).
Delete the file manually (i.e., del SOME.RSQ).

HowTo: Archive a project

Do this once MODELS has been created.
In the project directory, type bltp to remind yourself how to use the command.
Choose an appropriate name for the SAV name. It must be 13 characters max, and must not be the same name as another sav file on the backup tape.
Type: bltp HERZOG HERZOG_NORMAL BE0002 (project name, SAV name, tape label).
If only backing up the MODELS directory, type: bltp HERZOG.MODELS HERZOG_NORMAL BE0002
Creates a BCK directory and puts the SAV (equivalent to a tar) filename in that directory.
Use quick mail in the busy terminal to notify myself when the backup is complete.
Type to dismount the tape once done: dismount tp0
This command does not delete anything from the disk. That is up to you to decide.
-Usually the AIM GFILT data should be deleted to save space, but keep the thresholded AIMs as they are much smaller files.

How To: Restore a project

Insert the backup tape into the drive.
Check what SAV name (in the project BCK directory) includes the files that you want to restore.
Type: blud HERZOG_NORMAL or blud MICH_BAT01 to restore that SAV batch.
Restored files are automatically put into their original directories.

ProcessHowTo: Convert an AIM to a stack of TIFFs

Convert AIM to BID with aimio.
Convert BID to TIFF with imagemagick.
Make a COM file to do this automatically.

HowTo: Reduce resolution of an AIM

Use: aio filein.aim fileout.aim 4 (4 refers to cardinal reduction factor).
x = 1, y = 13, z = 1, no average.

HowTo: Switch the XY axis of an AIM

Use: aio filein.aim fileout.aim 18
Or, use the 64 bit option available in IPL. See the utility command files (cd ut com) for some options.

HowTo: Filter the AIM data

Filter with either support of 1 or 2. Use support of 1 when the data is very good and we don’t want to loose any spatial resolution. Use support of 2 when the data is a little bit sketchy.

HowTo: Use the 64-bit procedures

Refer to the Scanco manual to learn about the different procedures.
Must be on BLUND (the 64-bit system).
Step 1: Example: To flip an AIM
To make it from XZ to XY orientation, we’ll use ipl_flip.
Go to: cd ut com (to see the command procedures. i.e. IPL stuff).
Make a procedure here by copying an old one.
Set the appropriate variables. See manual to see which are necessary.
Execute the procedure interactively: @ut:ipl_flip MICHIGAN...860..._GFILT.AIM 
<outputaim> XZ (we want XZ to be moved into XY orienation).
Execute the procedure on a queue: subut ipl_flip []MICHIGAN...860..._GFILT.AIM[]MICHIGAN...860..._GFILT_FLIP.AIM XZ

HowTo: Use SAP effectively

Sub-selecting an AIM
- [MANAGEMENT:Superior image:New] Set position and sub-dimension
- [MANAGEMENT:Sub-image selection:Apply] Mouse: click selected part in overview.
Measuring distances and/or mouse position
- Each click of the mouse in the image window results in an output to the terminal window
- Terminal output includes position of mouse click (both in mm and voxels)
-Two subsequent mouse clicks results in the distance between two points output in the 2nd click.
Mouse control
- Left button double click: select image
- Middle button double click: show sequential images from selected (before and after)
- Right button double click: show menu.

HowTo: Select a threshold

Should be as deep a threshold possible without creating fragments.
Threshold given as a value between 1 and 1000.
A common value is 224 of a possible 1000 (22.4%).
Work with a representative sub-aim (see HowTo:) approximately 100 voxels cubed.
Option 1: Mcubes and Viza
Select the threshold after ensuring there aren’t too many fragments.
Note that the value given here is twice the threshold value that should be used. For some reason, if you choose 40% threshold in mcubes, that number corresponds to a real threshold (for use in IPL commands) of 20% or 200.
Option 2: SAP
Read in the Gaussian filtered aim [Processing:segmentation:procedures].
Threshold only.
With different thresholds, switch between the original data and the thresholded data until satisfactory. Try other planes too!
Go to maximum threshold until bonds are broken.

HowTo: Run IPL in interactive mode

On VMS system, start the 64 bit version with ipl64 (ipl starts 32 bit version).
To read a file: read in DISK40:[DATA.UCT.PROJECTS.HERZOG.MODELS]MYAIM.AIM 
or, type read and fill in the blanks as asked.
The command gobj will find the first IPL command that starts with gobj (gobj_maskaimpeel_ow in this case).
See the IPL manual for all the available commands.
See the sample IPL script command files in this manual.

HowTo: Extract part of amask

If a mask contains, for example, values 63 and 127 (each representing a different part of the image), then the mask of each component can be extracted using thresholding.
The lower perm and upper perm control the thresholding.
Note that if this mask is to be used in an IPL procedure, it must be written to file before it can be used (the IPL gobj command is special and only accepts input from a file. Internal files in IPL are not allowed).
Option 1: To get the 127 value
Threshold in IPL with lower perm equal 600 and upper perm equal 1000.
Upper refers the maximum possible value (in case of code>char/code> it is 127, in case of short it is 32k). Therefore, for a char file, setting lower perm to 600 passes values above 76.2 only (0.6 x 127).

Option 2: To get the 63 value

Threshold in IPL with lower perm equal 100 and upper perm equal 800.
Setting upper perm to 800 is a trick that, in the case of a char file, passes data that only has a maximum of 101.6 (0.8 x 127).
Choosing a lower perm of 100 in the case of a char file passes data that is greater than 12.7 (0.1 x 127).

Trouble-ShootingHowTo: Get the correct colour map to display

Problem: The colour map isn’t giving the correct colours.
Close all corelut applications in all windows (1, 2, 3, 4) and try the uct_evaluation tool again.

HowTo: Add a new command

Go to directory RAM.COMMANDS.
Add command to evelog.
Use rlog to register the command.

HowTo: Kill a string of processes

The process needs a LOG file in order to run. We can rename the LOG file to LOGO temporarily, then delete the most recent process on the queue. All the rest of processes will fail.
The ren LOGO to LOG.

HowTo: Log in as XUCT in a terminal window

Type blund.
User and password: xuct, password.
Type onlocal to set display to blund (see Commands and Aliases section if this option is not implemented).
To login as a micro-CT user, type the user last name in capitals in bold, and the rest should be automatically updated: BOYD

HowTo: Move files to other systems

Option 1: FTP
ftpmich (give anonymous as login and password).
Type: cd c:\\users\anonymous
or, cd f:\\anonymous\\zuerich or (cd “f:\anonymous\zuerich“)
Type: cd zuerich
Option 2: cp
Type: cp2mich zuerich /bin MICHIGAN*.AIM

HowTo: View TIFFS or GIFSUse either xv filename.tiff or i disp filename.tiff

HowTo: Generate a text file

If, for example, we wanted a text file of all the processes running on the reconstruction queue so that we can create a COM file to kill a number of processes, type
- sh que *reco* /output=queuekiller.com
Then, edit queuekiller.com so that the COM file could be executed.
Then execute with @queuekiller.com

HowTo: Subselect a minimal AIM

Type: aio mydata.aim * minimal 15
Or, replace the * with an output filename if different than the input name.
Give the extra offset in X equal 0, in Y equal 0, and in Z equal 0.

HowTo: Set logicals and symbols on OpenVMS

The logicals and symbols should be defined in the user account, rather than the microct_common account so it only overrides YOUR settings, but not of anybody else on the same computer (i.e., user calibration).
In DISK1:[MICROCT]MICROCT_SETUP_USER.COM input your special settings.

For example, to override the current IPL evaluation script that is used by uct_evaluation, do the following in the file:$ define uct_evaluation ue:xxxxx.com

RecordsHowTo: Michigan project sheetMichigan Pic

Sample COM Files

 Sample COM Files

Scanco AIM File Format(this section has been uploaded as a Word document. Click the link below.) Scanco Aim File Format DocumentSample COM FilesHowTo: Example ipl_scanco_v64.com pre-processing

$!

$! _/_/_/ _/_/_/ _/

$! _/ _/ _/ _/ Image Processing Language 

$! _/ _/_/_/ _/

$! _/ _/ _/ (c) Andres Laib, IBT/ETH Z¸rich

$! _/_/_/ _/ _/_/_/_/

$!

$!

$!

$! IPL Batch Scanco

$!

$! Segmentation with gauss filter and thresholding.

$! The segmented volume is saved compressed to file.

$!

$!

$ define log_file 'p1'

$ define org_file 'p2'

$ define gobj_file 'p3'.GOBJ

$ define gau_file 'p3'_GFILT.AIM

$ define seg_file 'p3'_THRES.AIM

$!

$ show log log_file

$ show log org_file

$ show log gobj_file

$ show log gau_file

$ show log seg_file

$!

$!

$ ipl_scanco_prog := $um:ipl_scanco_m64.exe

$!

$ ON ERROR THEN EXIT

$!

$ ipl_scanco_prog

/db_scanco_activate true

! read, threshold and vox gfilt aim file

/read org org_file

/sup_divide org

-supdim_numbers 4 4 4

-testoff_pixels 1 1 1

/gauss_lp org gau

 -sigma 1.2

-support 1

/del org

/write gau gau_file

/vox_scanco_param

-input gau

..

$ ON ERROR THEN CONTINUE

$! ENDIF

$!------------------------------------------------------------------------------

$ ENDCOM:

$ IF F$SEARCH("gau_file") .NES. ""

$ THEN

$ org = F$SEARCH("org_file")

$! IF org .NES. "" THEN DELETE/NOCONFIRM 'org'

$ ENDIF

$ EXIT

HowTo: Example ipl_scanco_v64.com post-processing


$!

$! _/_/_/ _/_/_/ _/

$! _/ _/ _/ _/ Image Processing Language

$! _/ _/_/_/ _/

$! _/ _/ _/ (c) Andres Laib, IBT/ETH Zrich

$! _/_/_/ _/ _/_/_/_/

$!

$!

$!

$! IPL Batch Scanco

$!

$! Segmentation with gauss filter and thresholding.

$! The segmented volume is saved compressed to file.

$!

$!

$ define log_file ‘p1’

$ define org_file ‘p2’.AIM

$ define gobj_file ‘p2’.GOBJ

$ define gau_file ‘p2’_GFILT.AIM

$ define seg_file ‘p2’_THRES.AIM

$!

$ show log log_file

$ show log org_file

$ show log gobj_file

$ show log gau_file

$ show log seg_file

$!

$!

$ ipl_scanco_prog := $um:ipl_scanco_m64.exe

$!

$ ON ERROR THEN EXIT

$!

$!------------------------------------------------------------------------------

$!Gauss filter, cutout with GOBJ, and threshold

$!------------------------------------------------------------------------------

$ IF F$SEARCH(“seg_file�?) .EQS. ““

$ THEN

$ ipl_scanco_prog

/db_scanco_activate false

! read, then gauss filter aim

/read org org_file

/gauss_lp org gau

-sigma 1.2

-support 2

/del org

! cutout with gobj

/gobj_maskaimpeel_ow

-input_output gau

-gobj_filename gobj_file

-peel_iter 0

! threshold

/threshold

-input gau

-output seg

-lower_in_perm 250

-upper_in_perm 1000

-value_in_range 127

/write

-name gau

-filename gau_file

-compress false

/del gau

/write

-name seg

-filename seg_file

-compress bin

..

$ ON ERROR THEN CONTINUE

$ ENDIF

$!------------------------------------------------------------------------------

$!Morphological and anisotropic analysis

$!------------------------------------------------------------------------------

$ipl_scanco_prog

/db_scanco_activate false

/read seg seg_file

/tri

-input seg

-output tri

-gobj_filename gobj_file

-peel_iter -1

-ip_sigma 2.000000

-ip_support 0

-ip_threshold 64

-interpolate true

-nr_ave_iter 0

-t_dir_radius 2

-epsilon 1.200000

-size_image 512 512

-scale_image 0.700000

-edges false

-nr_views 0

..

$ ON ERROR THEN CONTINUE

$ipl_scanco_prog

/db_scanco_activate false

/read seg seg_file

/dt_object_param

-input seg

-output out

-gobj_filename gobj_file

-roi_radius_factor 10000.000000

-ridge_epsilon 0.900000 

-assign_epsilon 1.800000

-histofile_or_screen none

..

$ ON ERROR THEN CONTINUE

$ipl_scanco_prog

/db_scanco_activate false

/read seg seg_file

/dt_background_param

-input seg

-output out

-gobj_filename gobj_file

-roi_radius_factor 10000.000000

-ridge_epsilon 0.900000

-assign_epsilon 1.800000

-histofile_or_screen none

..

$ ON ERROR THEN CONTINUE

$ipl_scanco_prog

/db_scanco_activate false

/read seg seg_file

/dt_mat_param

-input seg

-output out

-gobj_filename gobj_file

-roi_radius_factor 10000.000000

-ridge_epsilon 0.900000

-assign_epsilon 1.800000

-histofile_or_screen none

..

$ ON ERROR THEN CONTINUE

$ipl_scanco_prog

HowTo: Example submit_all_ipl.com


$ com := UT:IPL_SUBMIT_USER.COM

$ dir = F 
$ENVIRONMENT(“DEFAULT�?) - “.COM]�?

$ proc_maskxy := ‘dir.COM]IPL_MASKXY_SUBMIT_ALL.COM

$ proc_maskxz := ‘dir.COM]IPL_MASKXZ_SUBMIT_ALL.COM

$ proc_trabtop := ‘dir.COM]IPL_TRABTOP_SUBMIT_ALL.COM

$!------------------------------------------------------------------------------

$ IF P1 .EQS ““

$ THEN

$ SAY “Usage: SAI [ALL,MASKXY,MASKXZ,TRABTOP]

$ EXIT

$ ENDIF

$!------------------------------------------------------------------------------

$ IF P1 .NES “ALL�? THEN GOTO ‘P1’

$!------------------------------------------------------------------------------

$ MASKXY:

$ FDA @’com’ ‘dir’.MODELS]*’p2’*_INNER_XY.GOBJ [] USER:MASKXY BLUND_EVAL ‘dir’.LOG]
‘proc_maskxy’

$ IF P1 .NES “ALL�? THEN GOTO ENDCOM

$!------------------------------------------------------------------------------

$ MASKXZ:

$ FDA @’com’ ‘dir’.MODELS]*’p2’*_UPPER_XZ.GOBJ [] USER:MASKXZ BLUND_EVAL ‘dir’.LOG]
‘proc_maskxz’

$ IF P1 .NES “ALL�? THEN GOTO ENDCOM

$!------------------------------------------------------------------------------

$ TRABTOP:

$ FDA @’com’ ‘dir’.MODELS]*’p2’*_MASK_XZ.AIM [] USER:TRABTOP BLUND_EVAL ‘dir’.LOG]
‘proc_trabtop’

$ IF P1 .NES “ALL�? THEN GOTO ENDCOM

$!------------------------------------------------------------------------------

$ ENDCOM:

$ EXIT

$!------------------------------------------------------------------------------

HowTo: Example ipl_maskxy_submit_all.com


$!

$! _/_/_/ _/_/_/ _/

$! _/ _/ _/ _/ Image Processing Language

$! _/ _/_/_/ _/

$! _/ _/ _/ (c) Andres Laib, IBT/ETH Zürich

$! _/_/_/ _/ _/_/_/_/

$!

$!

$!

$! IPL Batch Scanco

$!

$! Calculation of morphometric properties in the TRAB region.

$!

$!

$ p2 = p2 - “_INNER_XY�?

$!

$ define log_file ‘p1’

$ define sum_file ‘p2’_MASK_XZ.AIM

$ define seg_file ‘p2’_MSK_INNER.AIM

$ define xzaim_file ‘p2’_INNER_XZ.AIM

$ define gobj_1_file ‘p2’_INNER_XY.GOBJ

$ define gobj_2_file ‘p2’_TOPER_XZ.GOBJ

$!

$ show log log_file

$ show log sum_file

$ show log seg_file

$ show log xzaim_file

$ show log gobj_1_file

$ show log gobj_2_file

$!

$!

$ ipl_scanco_prog :=  
$um:ipl_scanco_m64.exe

$!

$ ON ERROR THEN CONTINUE

$!

$!------------------------------------------------------------------------------

$!Create an AIM with INNER_XY.GOBJ, write XZ version.

$! (Send pos info to log files)

$!------------------------------------------------------------------------------

$ IF F 
$SEARCH(“xzaim_file�?) .EQS. ““

$ THEN

$ ipl_scanco_prog
/db_scanco_activate false
! read xy inner gobj
/gobj_to_aim
-gobj_filename gobj_1_file
-output gob
-peel_iter 0
/examine gob
-item geometry
/flip_aim gob flip
-new_xydir xz
/examine flip
-item geometry
/write flip xzaim_file
..

$ ON ERROR THEN CONTINUE

$ GOTO ENDCOM

$ ENDIF

$! Before proceeding to this next part, the “pos�? of the INNER_XZ.AIM files

$! created above must be reset from 0 to the proper values based on aims

$! before and after flipping. The change in the AIM is done with a

$! script that calls program “aimod�?.

$!

$!------------------------------------------------------------------------------

$!Create an AIM mask AIM with INNER_XZ.AIM and TOPER_XZ.GOBJ

$!------------------------------------------------------------------------------

$ IF F 
$SEARCH(“sum_file�?) .EQS. ““

$ THEN

$ ipl_scanco_prog
/db_scanco_activate false
/read in xzaim_file
/gauss_lp in gau
-sigma 3.0
-support 3
/del in
/threshold gau seg
-lower_in_perm 450
-upper_in_perm 1000
-value_in_range 63
/del gau
/write seg seg_file
-compress bin
/del seg
! read xz toper gobj
/read seg seg_file
/gobj_mask seg
-gobj_filename gobj_2_file
-peel_iter 0
/read bot seg_file
/set_value bot
-value_object 64
-value_background 0
/concat bot seg sum
-common_region_only false
-add_not_overlay true
/del seg
/del gob
! write the final aim
/write sum sum_file
-compress bin
..

$! 
$ DELETE/LOG ‘’seg_file’;

$ GOTO ENDCOM

$ ENDIF

$ ON ERROR THEN CONTINUE

$!------------------------------------------------------------------------------

$ ENDCOM:

$ EXIT

HowTo: Example flip_xz.com


$!-----------------------------------------------------------------------------

$! RENAME SAMPLES

$!-----------------------------------------------------------------------------

$ project = “HERZOG�?

$ dir = “DISK40:[DATA.UCT.PROJECTS�?

$ IF F 
$SEARCH(“‘’dir’.’’project’]*.*�?) .NES. ““

$ THEN

$ dir = “‘’dir’.’’project’�?

$ ELSE

$ SAY ““

$ SAY “Directory ‘’dir’.’’project’] is empty.�?

$ SAY ““

$ EXIT

$ ENDIF

$!-----------------------------------------------------------------------------

$! 
$ @UT:IPL_FLIP.COM ‘dir’.MODELS]HERZOG_CAT_00WK-01-NORMAL_GFILT.AIM -

$! ‘dir’.MODELS]HERZOG_CAT_00WK-01-NORMAL_GFILT_XZ.AIM XZ

$!

$ @UT:IPL_FLIP.COM ‘dir’.MODELS]HERZOG_CAT_70MO-1B-CLAT-R_GFILT.AIM -
‘dir’.MODELS]HERZOG_CAT_70MO-1B-CLAT-R_GFILT_XZ.AIM XZ

$ @UT:IPL_FLIP.COM ‘dir’.MODELS]HERZOG_CAT_74MO-1D-ACLT-L_GFILT.AIM -
‘dir’.MODELS]HERZOG_CAT_74MO-1D-ACLT-L_GFILT_XZ.AIM XZ

$ @UT:IPL_FLIP.COM ‘dir’.MODELS]HERZOG_CAT_74MO-1D-CLAT-R_GFILT.AIM -
‘dir’.MODELS]HERZOG_CAT_74MO-1D-CLAT-R_GFILT_XZ.AIM XZ

$!-----------------------------------------------------------------------------

$ EXIT

$!-----------------------------------------------------------------------------

HowTo: Example eval.com


$!------------------------------------------------------------------------------

$!EVAL.COM

$!------------------------------------------------------------------------------

$IF P1 .EQS. ““

$THEN

$ SAY ““

$ SAY “Usage:�?

$ SAY “ 
$ @EVAL.COM RESDIR [ADPGSE] SAMPLE_ID [MEAS_ID] [PAR5-8]�?

$ SAY ““

$ SAY “ A: All�?

$ SAY “ D: Set Measurement Directory�?

$ SAY “ G: Generate AIM interactively�?

$ SAY “ S: Startup SAP�?

$ SAY “ E: Evaluating AIM�?

$ SAY ““

$ EXIT

$ENDIF

$!------------------------------------------------------------------------------

$ON CONTROL_C THEN GOTO ENDCOM

$ON CONTROL_Y THEN GOTO ENDCOM

$IF P2 .EQS. ““ THEN P2 = “D�?

$IF F 
$INTEGER(P2) .NES. 0

$THEN

$ P4 = P3

$ P3 = P2

$ P2 = “A�?

$ENDIF

$!------------------------------------------------------------------------------

$!CHECK DIRECTORY SYNTAX

$!------------------------------------------------------------------------------

$olddir = F 
$PARSE(F 
$DIRECTORY()) - “.;�?

$IF P3 .NES. ““

$THEN

$ IF P4 .NES. ““

$ THEN

$ CDN UD *’P3’ *’P4’

$ ELSE

$ CDN UD *’P3’ 0 
$!------------------------------------------------------------------------------

$!EVAL.COM

$!------------------------------------------------------------------------------

$IF P1 .EQS. ““

$THEN

$ SAY ““

$ SAY “Usage:�?

$ SAY “ 
$ @EVAL.COM RESDIR [ADPGSE] SAMPLE_ID [MEAS_ID] [PAR5-8]�?

$ SAY ““

$ SAY “ A: All�?

$ SAY “ D: Set Measurement Directory�?

$ SAY “ G: Generate AIM interactively�?

$ SAY “ S: Startup SAP�?

$ SAY “ E: Evaluating AIM�?

$ SAY ““

$ EXIT

$ENDIF

$!------------------------------------------------------------------------------

$ON CONTROL_C THEN GOTO ENDCOM

$ON CONTROL_Y THEN GOTO ENDCOM

$IF P2 .EQS. ““ THEN P2 = “D�?

$IF F 
$INTEGER(P2) .NES. 0

$THEN

$ P4 = P3

$ P3 = P2

$ P2 = “A�?

$ENDIF

$!------------------------------------------------------------------------------

$!CHECK DIRECTORY SYNTAX

$!------------------------------------------------------------------------------

$olddir = F 
$PARSE(F 
$DIREC

$ ENDIF

$ENDIF

$dir = F 
$PARSE(F 
$DIRECTORY()) - “.;�?

$length = F 
$LENGTH(dir)

$id = F 
$EXTRACT(length-18,18,dir)

$IF (F 
$EXTRACT(0,2,id) .NES. “00�?) .OR. (F 
$EXTRACT(9,2,id) .NES. “00�?)

$THEN

$ SAY “ “

$ SAY “ THIS IS NOT A MEAUSUREMENT DIRECTORY:�?

$ SAY “ ‘’dir’�?

$ SAY “ “

$ EXIT

$ENDIF

$SET DEF UCT-DATA-M:[‘id’

$isqdata = F 
$SEARCH(“*.ISQ�?)

$isqdata = isqdata - F 
$PARSE(isqdata,,,�?VERSION�?)

$aimdata = F 
$SEARCH(“*.AIM�?) - “_TRAB�? - “_CORT�?

$aimdata = F 
$SEARCH(“‘’aimdata’�?)

$aimdata = aimdata - F 
$PARSE(aimdata,,,�?VERSION�?)

$IF (P2 .NES. “D�?) .AND. (isqdata .EQS. ““) .AND. (aimdata .EQS. ““)

$THEN

$ SAY “ “

$ SAY “ NO IMAGE DATA IN THIS DIRECTORY:�?

$ SAY “ ‘’dir’�?

$ SAY “ “

$ EXIT

$ENDIF

$IF F 
$SEARCH(“*.COM�?) .NES. ““

$THEN

$ SAY ““

$ SAY “THERE SEEM TO BE STILL UNRECONSTRUCTED SLICES IN THIS DIRECTORY:�?

$ DIRECTORY *.COM

$ EXIT

$ENDIF

$!------------------------------------------------------------------------------

$!PROCESSING

$!------------------------------------------------------------------------------

$IF P2 .EQS. “D�? THEN GOTO ENDCOM

$!------------------------------------------------------------------------------

$IF F 
$LOCATE(“A�?,P2) .NE. F 
$LENGTH(P2)

$THEN

$! SAP IS INVOKED

$ IF isqdata .NES. ““ THEN P2 = “GSE�?

$ IF isqdata .EQS. ““ THEN P2 = “SE�?

$! SAP IS NOT INVOKED

$! IF isqdata .NES. ““ THEN P2 = “GE�?

$! IF isqdata .EQS. ““ THEN P2 = “E�?

$ENDIF

$SAY ““

$!------------------------------------------------------------------------------

$IF F 
$LOCATE(“G�?,P2) .NE. F 
$LENGTH(P2)

$THEN

$ IF (isqdata .NES. ““) .AND. ((aimdata .EQS. ““) .OR. (P2 .EQS. “G�?))

$ THEN

$ SAY “- Evaluate ‘’isqdata’�?

$ DEFINL UCT_DEFAULT_ISQ ‘isqdata’

$ DEFINL UCT_EVALUATION UCT-DATA-R:[‘P1’.COM]UCT_EVALUATION.COM

$ UCT_EVALUATION

$ DEASSIGN UCT_DEFAULT_ISQ

$ DEASSIGN UCT_EVALUATION

$ IF P2 .NES. “G�?

$ THEN

$ SAY “- Waiting for evaluation job to complete ...�?

$ counter = 1

$ loop:

$ WAIT 00:00:10

$ elapsed_time = counter * 10

$ IF counter .eq. 1

$ THEN

$ SAY “ - job has been runing for ‘’F 
$STRING(elapsed_time)’ seconds�?

$ ELSE

$ SAY “[2K[1A - job has been runing for ‘’F 
$STRING(elapsed_time)’ seconds�?

$ ENDIF

$ ctx = ““

$ temp = F 
$CONTEXT (“PROCESS�?,ctx,�?JOBTYPE�?,�?BATCH�?,�?EQL�?)

$ loop_pid:

$ pid = F 
$PID(ctx)

$ IF pid .NES. ““

$ THEN

$ image = F 
$GETJPI(pid,�?IMAGNAME�?)

$ aimdata = F 
$SEARCH(“*.AIM�?)

$ IF (F 
$LOCATE(“ISQ_TO_AIM�?,image) .NES. F 
$LENGTH(image)) - .OR. (aimdata .EQS. ““)

$ THEN

$ counter = counter + 1

$ GOTO loop

$ ELSE

$ GOTO loop_pid

$ ENDIF

$ ENDIF

$ aimdata = F 
$SEARCH(“*.AIM�?)

$ aimdata = aimdata - F 
$PARSE(aimdata,,,�?VERSION�?)

$ ENDIF

$ ENDIF

$ENDIF

$!------------------------------------------------------------------------------

$IF F 
$LOCATE(“S�?,P2) .NE. F 
$LENGTH(P2)

$THEN

$ IF F 
$SEARCH(aimdata) .NES. ““

$ THEN

$ show sym aimdata

$ SAY “- Startup SAP ‘’aimdata’...�?

$ SAPXZ -s ‘aimdata’

$ ELSE

$ SAY ““

$ SAY “No aimdata found in directory.�?

$ SAY “Program exits right now.�?

$ GOTO ENDCOM

$ ENDIF

$ENDIF

$!------------------------------------------------------------------------------

$IF F 
$LOCATE(“E�?,P2) .NE. F 
$LENGTH(P2)

$THEN

$ id_dir = F 
$EXTRACT(0,8,id) + “]�? + F 
$EXTRACT(9,8,id) + “.DIR�?

$ IF F 
$SEARCH(“UCT-DATA-R:[‘’P1’.’’id_dir’�?) .EQS. ““

$ THEN

$ SAY “- Create Result Directory ...�?

$ CREATE/DIR/LOG UCT-DATA-R:[‘P1’.’id’

$ ENDIF

$ IF aimdata .NES. ““

$ THEN

$ aimname = F 
$PARSE(aimdata,,,�?NAME�?)

$ aimnum = F 
$EXTRACT(0,8,id)

$ aimfull = “UCT-DATA-R:[‘’P1’.’’id’’’aimname’�?

$ comfile = “UCT-DATA-R:[‘’P1’.COM]IPL_SCANCO_V64.COM�?

$ logfile = “UCT-DATA-R:[‘’P1’.LOG]IPL_PRE_’’aimnum’_’’aimname’.LOG�?

$! SHOW SYMBOL aimname

$! SHOW SYMBOL aimnum

$! SHOW SYMBOL aimfull

$! SHOW SYMBOL comfile

$! SHOW SYMBOL logfile

$ !-------------------------------------------------------------------

$ IF F 
$SEARCH(“‘’aimfull’_GFILT.AIM�?) .EQS. ““

$ THEN

$! CP ‘aimdata’ ‘aimfull’.AIM

$ IF F 
$SEARCH(aimdata) .NES. ““ THEN 
IF F 
$SEARCH(isqdata) .NES. ““ THEN DELETE/NOCONFIRM ‘isqdata’;*

$ SUBDATA ‘comfile’ ‘logfile’ -
‘aimdata’ ‘aimfull’!/QUEUE=BLUND_EVAL

$ ENDIF

$ ENDIF

$ENDIF

$!------------------------------------------------------------------------------

$ ENDCOM:

$IF F 
$SEARCH(“UCT-DATA-M:[‘’id’*.*�?) .NES. ““

$THEN

$ DIRECTORY/NOTRAILER UCT-DATA-M:[‘id’

$ELSE

$ dir1 = F 
$EXTRACT(0,8,id)

$ dir2 = F 
$EXTRACT(9,8,id)

$ DELETE UCT-DATA-M:[‘dir1’]’dir2’.DIR;,UCT-DATA-M:[000000]’dir1’.DIR;

$ENDIF

$IF F 
$SEARCH(“UCT-DATA-R:[‘’P1’.’’id’*.*�?) .NES. ““ THEN -
DIRECTORY/NOTRAILER UCT-DATA-R:[‘P1’.’id’

$SAY ““

$SET DEF ‘olddir’

$EXIT

$!------------------------------------------------------------------------------

HowTo: Example eval_all.com


$ eval_herzog e 245

$ eval_herzog e 246

$ eval_herzog e 247

$ eval_herzog e 248

$ eval_herzog e 249

$ eval_herzog e 250

How To Section 3 - Software Installation and SetupInstall Packages from Source CDPrograms:

CMake 1.66: A program that generates VC++ Workspace and UNIX Makefiles automatically to facilitate platform independence. 

http://www.cmake.org
VTK 4.2: Visualization Toolkit is a package containing various visualization algorithms.
http://public.kitware.com/VTK/
ITK 1.2: Insight Segmentation and Registration Toolkit is a package similarly designed to VTK and well integrated with VTK. It contains image processing algorithms.
http://www.itk.org
FLTK 1.1.2: Fast Light Toolkit for GUI development in C++.
http://www.fltk.org/
Qt: A professional toolkit for GUI development.
http://www.trolltech.com/
vtkMy: The personal developed code by Dr. Steven Boyd that integrates into VTK for micro-CT (or MR) imaging. 

http://www.ucalgary.ca/~skboyd/
Registration Application: An interesting registration tool developed by researchers at University of North Carolina.
http://caddlab.rad.unc.edu/
WinZip: A utility to unzip source files.
WinCVS: Version control software.

Step-by-Step:

Install CMake. See the file README IMPORTANT.txt in that directory regarding installing the latest version of FindFLTK.cmake.
Install VTK with the following CMake options:
BUILD EXAMPLES
SHARED LIB:  on
DATAROOT: points to where sample data is located.
USE_HYBRID, USE_PATENTED, USE_RENDERING: on
WRAP_JAVA: off
BUILD_SHARED_LIBRARIES: on
USE_ANSI_STDLIB: on
Install FLTK 1.2 (doesn’t require CMake)
Install ITK with the following CMake options:
EXAMPLES: on
TESTING: on
SYSTEM_STDLIB: on
(When installing the documentation, use the .zip version on the PC.)
Install ITK applications (not required, but has some interesting examples).
Install vtkMy project using CMake
WRAP_JAVA: off
BUILD_SHARED_LIBRARIES: on

Suggested directory structure

Use CMake whenever a new project is to be developed. ALWAYS use CMake. Look at the VTK or ITK packages for examples on its use, or use the PDF manual for CMake available on this CD.

Directory structures


D:\pack\fltk-1.1.2	FLTK


D:\pack\vtk42\html	VTK documentation	

D:\pack\vtk42\VTK-4.2.1	VTK source

D:\pack\vtk42\VTKData-release-4-2	VTK data

D:\pack\vtk42\bin	Built VTK project (CMake points here for binaries).


D:\code\vtkMy\src	SBoyd’s source code

D:\code\vtkMy\inc	Include files required to build vtkMy

D:\code\vtkMy\bin	Built vtkMy project (CMake points here).


D:\pack\itk12\InsightApplications-1.2.0	ITK sample applications

D:\pack\itk12\InsightToolkit-1.2.0	ITK source

D:\pack\itk12\InsightToolkit-1.2.0-doxygen	ITK documentation

D:\pack\itk12\itk	Built ITK project (CMake points here for binaries)

D:\pack\itk12\itkapps	Built ITK sample applications (CMake points here)

Add a project to vtkMy

Add a new project directory in the vtkMy/src/Applications directory.
Update the CMakeLists.txt file in /src/Applications to include the new directory in the SUBDIRS() list.
Copy the CMakeLists.txt and source code files from an existing project such as AppMohr and put them into the new directory. These files can be edited for your new project.
Edit the copied CMakeList.txt file and the change the name of the .cxx to the name of the new project.
Run CMake, taking the source code from vtkMy/src and building the binaries in vtkMy/bin.
Open the Visual C++ workspace and edit the source code (since at the moment it will be a duplicate of whatever project you copied in step 3).
Compile your new code. Usually, all the development should be done in the “Debug�? mode (rather than “Release�?, etc.).
If, to run your application, you need to include command line arguments, go to the menu item [Project][Settings], and on the ‘debug’ tab set the Program Arguments as shown.



File:VtkMy Project Settings.jpg

Install a package on the Sun

Go to directory /local/stow and create a new directory for your package:
/stow/faim/bin (binaries)
/stow/faim/lib (libraries)
/stow/faim/share (documentation)

From /local/stow, run umask 022, and then stow faim.
Done.

Setting up WinCVS to use PuTTY to connect to vtkMy

Setting up WinCVS to use PuTTY is fairly straghtforward, but does require a few configuration settints in addition to installing the software. You can do it with the following steps.

Install PuTTY (http://www.chiark.greenend.org.uk/~sgtatham/putty/).
Install wincvs (http://www.wincvs.org/)
Make a key:
Follow menus: Start/Programs/PuTTY/PuTTYgen From the PuTTY Manual: 

...press the "Generate" button and PuTTYgen will begin the process of actually generating the key.
First, a progress bar will appear and PuTTYgen will ask you to move the mouse around to generate randomness. Wave the mouse in circles over the blank area in the PuTTYgen window, and the progress bar will gradually fill up as PuTTYgen collects enough randomness. You don't need to wave the mouse in particularly imaginative patterns (although it can't hurt); PuTTYgen will collect enough randomness just from the fine detail of exactly how far the mouse has moved each time Windows samples its position.
When the progress bar reaches the end, PuTTYgen will begin creating the key. The progress bar will reset to the start, and gradually move up again to track the progress of the key generation. It will not move evenly, and may occasionally slow down to a stop; this is unfortunately unavoidable, because key generation is a random process and it is impossible to reliably predict how long it will take.
When the key generation is complete, a new set of controls will appear in the window to indicate this.
Set the key comment and password. Set the key comment to your email address by typing it into the "Key Comment" box. Set the password by entering it twice, once in the "Key passphrase" box and once in the "Confirm Passphrase" box.
Save the keys:
 save the public key on your desktop as identity.pub and the private one as identity.ppk
Email the identity.pub file as an attachment to skboyd@ucalgary.ca and ask for it to be added to the .ssh/authorized_keys file for your cvs repository. Please specify which repository you are requesting access to in the e-mail (i.e., vtkMy).
Setup environment variables
Choose Menus:
Start/Settings/Control Panel
Double click on the "System" Control Panel
Pick the "Advanced" tab and pick "Environment Varibles..."
Add User environement variables
-	Add PLINK_PROTOCOL value "ssh"
- Add CVS_RSH value "plink"
-	Edit or Add PATH appending value ";C:\Program Files\PuTTY"
In WinCVS, bring up the "Preferences" dialogue box from the Admin menu
In the "General" tab put in your CVSROOT value, (i.e. :ext:myusername@m177.enme.ucalgary.ca:/localhost/cvsroot)
File:Wincvs general.jpg
Switch to the "Ports" tab.
Tick the box there labelled "Check for an alternate rsh name" and in the text entry field to the right enter "plink". 
File:Wincvs ports tab.jpg
Select "OK" on teh "Preferences" dialogue box.
Once you've heard back from the administrator (skboyd) that your ssh keys have been added, test your putty key configuration:
Double click on "identity.ppk" on your desktop. If this doesn’t start pagaent.exe automatically, then manually start the program from the directory you installed putty.exe.
If your identity file isn't already loaded, you will be prompted for the password you entered in step 4.
The Pageant icon (a little PC with a hat) should appear in the bottom right menu bar.



You should now be able to use WinCVS to access the repository, with a secure connection whenever Pageant is running. You can start Pageant by double-clicking on your identity.ppk file.

Setting up CVS access from Linux/UnixTo understand the codes for a CVS update, see page 121 of CVS users guide, section A.16.2.

Valuable resource for understanding ssh:
http://www-106.ibm.com/developerworks/library/l-keyc.html
http://www-106.ibm.com/developerworks/library/l-keyc2/
Setting up SSH access from "localbox" to "remotebox": 
 Localbox:
ssh-keygen -t rsa [use a passphrase]
NOTE: Put the "id_rsa" (private file) in ~/.ssh.  There should only be one of these on a 	machine account.
NOTE: Put the “id_rsa.pub�? (public file) in ~/.ssh as “authorized_keys�? on remote machines; see “Remotebox�? below.
scp identity.pub skboyd@remotebox: [don't forget the last colon]
in ~/.bashrc:
export CVS_RSH=ssh
export CVSROOT=:ext:skboyd@m177.enme.ucalgary.ca:/localhost/cvsroot
eval `ssh-agent` {use the funny back single quotes}


Remotebox:

cat identity.pub >> ~/.ssh/authorized_keys
To avoid writing your passphrase every time you log on, run:
ssh-add
Should work if ssh-agent is already running (eval `ssh-agent`  in the .bashrc file).
Do the following to limit access to cvs for the users:
edit the public key installed in the .ssh/authorized_keys file with the following at the beginning of the public key line:
command="/usr/bin/ssh server"

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.

Using CVS from a command line

To find a difference:
 $ cvs diff mylocalfile.cxx 
To add a new file:
 $ cvs add mynewfile.cxx 
 $ cvs commit mynewfile.cxx 
To update local file:
 $ cvs update -dCP 
or
 $ cvs update -dCP myfile.cxx 
To check if a more recent version is available:
 $ cvs diff myfile.cxx 
or
 $ cvs update 
To update CVS repository:
 $ cvs commit mylocalfile.cxx

FTP Instructions for ENME

The server ftp.enme.ucalgary.ca can be logged into as an anonymous user.

Command Line Instructions: Windows or Unix

Start the FTP program. In windows, go to the [start button] and select [run] and type cmd to start a command window. In Unix, open a terminal window. Type at the ‘>’ prompt:
 > ftp ftp.enme.ucalgary.ca
Log in as an anonymous user and send your email (e.g., me@ucalgary.ca) as password.
Change directories to the hidden directory /incoming/skboyd:
 > cd /incoming/skboyd
Set transfer mode to binary or ascii, depending on your needs. For example, an MSWord document should be sent in binary mode. Type one of the following:
 > binary
 > ascii
Transfer the documents with the put statement.
 > put mydocument.doc
When finished, log off the FTP server:
 > bye


 Sample Windows FTP Session
File:Windows ftp.jpg
Sample Linux FTP Session
File:Linux ftp.jpg

Windows Instructions: WinFTP

If there is an FTP application available such as WinFTP then take care to make the settings as shown in these snapshots:


File:Ftp one.jpg
File:Ftp two.jpg

Sun Blade 2500 in CCITDetailsTechnical support 1-800-872-4786

S/N: FE34720093
P/N: 380-0855-01
Contract # NK10013125
Case ID number 6398-3799 (Why must we run fsck on /space repeatedly?)
Resolved.
Case ID number 6413-1564 (Screen saver locks keyboard and mouse)
Not resolved. Swasti (303-272-6510) will send an e-mail describing the solution.
Case ID number 6419-0306 (Files are invisible when typing ‘ls’)
Resolved by replacin ‘ls’ with a working binary from another 5.8 Sun (Byron provided the file).
Contacts at Sun in Calgary:
Dale (261-6557, 510-7350),
Denis (680-9804),
Chris (515-2890).
Contacts at UCalgary:
Bryan Gooding (220-8443),
Khee Teck Wong (220-3349)
Other Contacts:
Witold Owoc (Witold.Owoc@ccsicompucom.com)
Case ID number 6404-0086 (Non responsive?)
Case ID number 6460-0193 (regarding upgrade to Solaris 10 with [raid?] array configuration problem)

Technical information

IP: 136.159.118.224
Gateway: 136.159.118.1
DNS servers: 136.159.1.21 (ucnet.ucalgary.ca) 136.159.34.201 (itnet.ucalgary.ca)
Configuration
Internal hard disk 35 GB mirrored (‘/’ and ‘/space’)
Disk array (250 GB) (‘/data’) set up with RAID 5 software

Configuration August 17, 2005

Witold.Owoc@ccsicompucom.com
Completed items:

- SB2500 firmware updated to the current level
- Solaris 10 3/05 installed
- internal disks mirrored
- current (as of 2005/08/19) Solaris patches installed
  (exluding problematic 119107-03)
- 5 external disks made into RAID-5 for /data
  (perfomed extensive testing to determine RAID
  and filesystems parameters that deliver acceptable
  level of performance)
- system login enabled for sftp, ssh and console only
- network services disabled or restricted
- enabled and configured Network Time Protocol (NTP)) client
- installed from Solaris 10 Software Companion CD
  the following packages (into /opt/sfw/bin):
   SFWcvs   cvs 1.11.17 - Concurrent Versions System
   SFWgcmn  gcmn - Common GNU package
   SFWgfile fileutils 4.1 - GNU file management utilities
   SFWncur  ncurses 5.2 - new curses library
   SFWqt    qt 3.1.1 - C++ GUI framework
   SFWrpm   rpm 4.1 - Red Hat Package Manager
   SFWrsync rsync 2.6.3.1 - flexible replacement for rcp
   SFWscrn  screen 4.0.2 - A full-screen window manager
- perfomed (automated) Sun VTS system testing

Not completed:

- firewall filter - access for 136.159 network only.

It turned out to be not easy to perform that task
remotely. May be I will just give exact step by
step instructions, then anybody can copy&paste.

Set up

Set up of DNS service. Modified the following files:
		/etc/nsswitch.conf  (refer to SunSolve document ID 11975)
		/etc/resolve.conf 
		/etc/defaultrouter  (refer to SunSolve document ID 17947)
Installed Forte Update 2 compilers.
Disabled telnet
edit  /etc/inet/inetd.conf  & comment out the "telnet" line
kill -HUP the inetd process
Add openssh
Added user accounts: useradd –u 1002 –g 1000 –d /space/home/swiss –s “/bin/bash�? swiss
Note: set user id 1002 based on next available number in /etc/passwd
As root: passwd swiss (to set user password)
As root: Make directory /space/home/swiss
Copy of .bashrc and .bash_profile from another account in ~swiss
Chown swiss:research ~swiss (to set the owner and groups properly)
Note: common settings for paths are located in:
 	/local/share/userconf/bashrc 
			/local/share/userconf/bash_profile
Programs installed under /local/stow
stow
cmake, ssh, cvs, vtkMy, itk, vtk, qt
Always run ‘umask 022’ then ‘stow package-name’

Trouble Shooting

System freezes: ‘stop-A’ and then ‘init 6’ to reboot machine cleanly. Check the /var/adm logs to see what problems occurred.

System Administration

‘init 6’ to reboot machine cleanly (as opposed to ‘reboot –n’)
‘init 5’ to shut down machine cleanly
/etc/passwd (gives user definitions such as default shell and home directory location)
/etc/group (gives group definitions)
chmod a+trwx /data (makes /data sticky so all users can write to the disk)
For disk quota setting see ‘man edquota’
To fix a disk run: ‘fsck –y /dev/md/rdsk/d3 (for /space; -y option could be substituted)
Run ‘metastat’ to get the status of mirrored drives
See /var/adm/message* if there are system problems
See ‘dmsg’ also about possible problems.

Patches

Adding patches: www.sunsolve.sun.com
‘patchadd /var/spool/patch 108528-17’ to install a single patch, or
‘patchadd –M /var/spool/patch 108528-17 108940-06’ to install multiple patches.

Bash files/localhost/share/userconf/bashrc

# bashrc - System-wide initialization for everybody's ~/.bashrc
  
# Directories to consider as ``local improvements to the operating system.
prefix=/localhost/usr
exec_prefix=${prefix}
x_prefix=/usr/openwin 
    
# First, add the local directories into the paths.
export INFOPATH=${prefix}/info
export MANPATH=${prefix}/share/man:${prefix}/man
export PATH=${exec_prefix}/bin:/localhost/bin
export LD_LIBRARY_PATH="${exec_prefix}/lib"
export PRINTER=101@ps
export MOZILLA_HOME=/local/lib/communicator 
  
# Add in the the /usr/local directory for host-specific binaries.
if [ -d "/usr/local" ]; then
  case "$MANPATH" in
  */usr/local/man*) ;;
  *) MANPATH="$MANPATH:/usr/local/man" ;;
  esac
 
  case "$PATH" in
  */usr/local/bin*) ;;
  *) PATH="$PATH:/usr/local/bin" ;;
  esac
  
  case "$LD_LIBRARY_PATH" in
  */usr/local/lib*) ;;
  *) LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib" ;;
  esac
fi

# Add in system-specific directories.
case "$OSTYPE" in
[lL]inux | [lL]inux-*)
  export INFOPATH="$INFOPATH:/usr/info"
  export MANPATH="$MANPATH:/usr/man:/usr/X11R6/man"
  export PATH="$PATH:/bin:/usr/bin:/usr/local/bin:/usr/X11R6/bin:/opt/kde/bin"
  export PRINTER=325@ps
  alias idraw="LD_LIBRARY_PATH=/local/lib/LINUX /local/bin/idraw"
  ;;
SunOS | solaris2.[5-9] | solaris2.10 | solaris)

export MANPATH="$MANPATH:/usr/man:/opt/SUNWspro/man:/opt/SUNWste/license_tools/man"

  export MANPATH="$MANPATH:/usr/man:/opt/sfw/man:/opt/SUNWste/license_tools/man"

export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib:/usr/openwin/lib:/usr/ucblib"

  export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/openwin/lib:/usr/ucblib"

export PATH="$PATH:/opt/SUNWspro/bin:/usr/ccs/bin:/usr/bin:/usr/ucb:/usr/lib/nis"

  export PATH="$PATH:/opt/SUNWvts/bin:/opt/sfw/bin:/usr/ccs/bin:/usr/bin:/usr/ucb:/usr/lib/nis"
  export INFOPATH="$INFOPATH"
  alias mail='/usr/ucb/mail'
  ;;
SunOS4)
  export OPENWINHOME=${x_prefix}
  export MANPATH="$MANPATH:/apps/man:/usr/man:/usr/lang/man:${OPENWINHOME}/man"
  export PATH="/apps/bin:/usr/local/bin:/usr/ucb:/usr/bin:/usr/lang"
  export INFOPATH=/apps/info
  ;;
[iI]rix6 | [iI]rix6.3 | [iI]rix6.5)
  export INFOPATH="$INFOPATH:/usr/share/info"
  export MANPATH="$MANPATH:/usr/share/catman"
  #$PATH contains ~/bin:/local/bin:/usr/local/bin" as bash default
  export PATH="$PATH:/usr/bsd:/usr/bin:/usr/bin/X11:/usr/freeware/bin:/usr/sbin:/sbin:/usr/etc"
  ;;
*)
  echo "bashrc: no defaults for OSTYPE=\"$OSTYPE\"" 1>&2
  MANPATH="$MANPATH:/usr/man"
  PATH="$PATH:/bin:/usr/bin"
  ;;
esac

# Add in X11 directories.
if [ -n "$x_prefix" ] && [ -d $x_prefix ]; then
  case "$MANPATH" in
  *$x_prefix/man*) ;;
  *) MANPATH="$MANPATH:$x_prefix/man" ;;
  esac

 case "$PATH" in
  *$x_prefix/bin*) ;;
  *) PATH="$PATH:$x_prefix/bin" ;;
  esac
fi

# Make sure files are created with the correct permissions.
# NOTE: The umask command takes an argument that specifies the permission
# bits that you do *not* want turned on by default.
# Read the chmod(1) manual page for more information.
#
# Thus, 077 means: g-rwx,o-rwx, which is maximum protection.
umask 022 

# Don't set aliases if the shell is non-interactive.
if [ -n "$PS1" ]; then
  set -o noclobber    # Don't allow redirection to overwrite existing files.
  set -o notify       # Report job exit status immediately.
  set -o ignoreeof    # Don't allow ^D to terminate the shell.  

  # Set the prompt string to the hostname and working directory.
  if [ -z "$TERMREC_ON" ]
  then
      # usual prompt
      export PS1='\h:\W \$ '
  else
      # termrec prompt
      export PS1='\h:\W (termrec)\$ '
  fi

  # Set up common aliases to use for interactive sessions.
  alias j='jobs -l'      # Check the current jobs with 
  alias lsa='ls -F'
  alias ll='ls -alF'
  alias dir='ll'
  alias which='type -a'
fi

/local/share/userconf/bash_profile

# bash_profile - System-wide initialization for ~/.bash_profile

# mail check interval and location
export MAIL=$HOME/Maildir
export MAILCHECK=300

export XAPPLRESDIR=$XAPPLRESDIR:/local/share/X11/app-defaults 

# limit core file size to 0
ulimit -c 0

if [ "$TERM" = "iris-ansi-net" -o "$TERM" = "xterm-color" ] ; 
then 
	eval `/usr/ucb/tset -s -Q xterm`
	fi

echo "This terminal type is $TERM."
# general terminal characteristics
# stty erase '^H' -parenb cs8

# Add commands below this comment, if you would like them to be run
# automatically when you log in via rlogin or telnet.
# The `date' command is given as an example.
#date
if [ -f ~/.profile ] ; then
	. ~/.profile
fi

/space/home/skboyd/.bashrc

# .bashrc - Initialization file for the Bourne-Again SHell (BASH)
#
# This file is executed at the beginning of every interactive bash shell
# invocation.  It is also read by your .xsession and .bash_profile, so
# don't put any commands in here that require user intervention.
#
# If you want applications or other interactive programs to start
# automatically when you begin a session with the X Window System,
# add code to your .xsession file.
#
# If you want commands to be run automatically when you login via
# rlogin or telnet, add code to your .bash_profile file. 

# Fetch system-specific initialization.
source /localhost/share/userconf/bashrc

# This line sets your program search path.
export PATH=~/bin:$PATH:.

# Add your own personal aliases, functions, variable settings, etc.,
# below this comment ...
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/localhost/usr/lib:/usr/ucblib

export CVSROOT=:ext:skboyd@m177.enme.ucalgary.ca:/localhost/cvsroot
export CVS_RSH=ssh

# 
# Qt
# 

#QTDIR=/localhost/stow/qt-x11-free-3.2.1
#PATH=$PATH:$QTDIR/bin
#MANPATH=$QTDIR/doc/man:$MANPATH
#LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$QTDIR/lib
#export QTDIR PATH MANPATH LD_LIBRARY_PATH

/space/home/skboyd/.bash_profile

# .bash_profile - Login startup file for the Bourne-Again SHell (BASH)
#
# This file is executed at the beginning of every non-X login session.
# DO NOT EDIT ANY PART OF THIS FILE, except for the list of commands
# at the very bottom of the file.
#
# Generally, you should only edit your .xsession to start up applications
# automatically when you start a session with the X Window System.
#
# Edit your .bashrc if you want to set aliases and environment variables.

# Always read in the ~/.bashrc, to get our default environment.
if [ -r ~/.bashrc ]; then
  source ~/.bashrc
fi

# Get the terminal characteristics.
source /localhost/share/userconf/bash_profile

Access iCentre using Thin ClientIP: 136.159.119.226, can use ssh, or Thin Client.

The following is the procedure to have your Window PC ready to
connect to SGI and run graphical applications.
1. Download & install interface login program from
ThinAnyWhere:http://www.thinanywhere.com/downloads.php4   Select
Client-side Software,
2.login detail:

 After you launcher ThinAnyWhere, enter User name: ****  Passwd: ****
 Remote IP: 136.159.119.227  Port: 27500(default)  Session ID: 0  (default)
 Server Code: 2109771   Bandwidth: Medium (default or your choice)
 Display 1024 x 768   8bit-pseudo (default or your Choice)

3.Launch Xterm on the SGI:

 After you have loged in, click the SGIXterm, type your SGI password, you

will have a xterm,

 in the xterm window, you could run your application.

An account has to be created on the PC server, you can use our SGI by remotely logging in the SGI.
Contact: Tingge Wang <tinwang@ucalgary.ca>

Use UAlberta Westgrid (Finite element analysis)

Get at account:

Dear Steve:

I have a summer student that I'd like to run some FE models on the
UAlberta Westgrid (nexus.westgrid.ca).  Should I get her to sign up for
an account, or is this something I should/can do for her?

She should sign up herself, using the web page at
<https://rsg.nic.ualberta.ca>, joining your existing WestGrid project,
number 500018.

Login: ssh skboyd@nexus.westgrid.ca 
Password: pword: std#1 plus first four letters of std#1
Useful links:
http://www.ualberta.ca/CNS/RESEARCH/WestGrid/
http://www.ualberta.ca/CNS/RESEARCH/PBS/index.westgrid.html

On nexus, there are two directories:
HOME: /site/home/skboyd
WORK: /scratch/skboyd

Transfer your AIM to nexus:

Use ftp from nexus to the CCIT SUN (136.159.118.224) to transfer one or two AIMs to the 'work' directory on aurora.
Use ebe_mesh on nexus to generate the mesh with the required options (i.e., -v?).
Change back to the HOME directory and modify 'josh01.pbs' to reflect the name of the new mesh.  You'll have to use VI to modify the file.  Instructions on use of 'vi' are in the UNIX book that is sitting on the shelf (or ask Stephan or Michael perhaps?).
Submit the job: 'qsub josh01.pbs'
Check the status of the job: qstat (see http://www.ualberta.ca/CNS/RESEARCH/PBD/index.html)
Copy the 'e' and 'o' files to HOME/eo
Transfer the .dat file with ftp back to your PC (delete the .inp file).

DONE! (after repeating a whole PILE of times!)

HowTo: Install faimLinux

Installing faim on linux requires a fortran 95 compiler to be installed.
Go to http://www.g95.org/ and download the linux x86 binary and install
Modify the faim make file in faim/src so it points to the f95 compiler and then type make in the command line. It should now be installed.

Installing faim on westgrid is the same as in linux except that there is a list of installed fortran compilers on the westgrid website and gmake must be used instead of make.)

Windows

Installing faim on windows requires 'make' software to be installed.
Go to http://www.cygwin.com/ and install with the development option set to install.
A fortran compiler for windows can be obtained from
http://www.g95.org.
Go to command line and cd to faim/src and type make.
(faim should now be installed. )
Set the path in environment variables under system, advanced settings in the control panel to point to where it is installed.

MiscellaneousHowTo: Set-up and use X-WIN 32

X-win 32 is an X-server that allows a Windows-based operating system display a virtual screen of another operating system, such as Linux or OpenVMS. This HowTO has been tailored specifically for connecting to the VMS system at the University of Calgary, Foothills Medical Center 3D Morphometrics Lab from a Windows XP operating system.

To use X-Win 32, please ensure that you have a registered program installed on your system. If you do not have a registered version but would like to download a trial version that is useable for 60 days, please visit http://www.starnet.com/products/ and select the “Download X-win 32�? on the left column. You will need to fill out some personal information including a valid email address to which they will send you the product information and download instructions. Once you have completed this, you can proceed with the following steps.

Run X-win 32 from the start menu or desktop shortcut. A small blue “X�? should appear in the lower left hand corner of your start-bar.          File:Xwin32 1.png
If you have never configured X-win 32 before, a screen will automatically pop-up asking you to create an account. If this is the case, just jump to step 2.
Otherwise, double-click on this icon to open the X-win 32 configuration panel.
If in the X-win 32 config panel, and are wanting to create a new account, select the “Wizard�? button on the menu. This will lead you to another panel asking you to select a connection method. This will be the screen you will see if you are installing X-Win 32 for the first time. Ensure that you choose “StarNetSSH�? and then click next.      File:Xwin32 2.png
On the next screen, the hostname you need to type in will be “sceval.ucalgary.ca�?. Click next.
Enter in the username and password for the system at this host.
Next, it will ask you for the host command. On the options there, scroll down and choose “VMS�?. Click next.
Now enter in a descriptive name of the system you are connecting to. Click finish.
You should now be back at the X-win 32 configuration panel. If not, double-click on the blue X on the lower left corner of your start bar. You should see the session you just created listed in the menu. Highlight your selection by clicking on it. On the panels above, there is a “Color�? panel. Click this panel and you will be brought to a screen with various color options. On the lower left corner there are two checkboxes, ensure that only the “PseudoColor Mode�? option has a checkbox in it. Click the “apply�? button.         File:Xwin32 3.png
You have successfully created a X-server with to the remote system. Click the “OK�? button on the X-win 32 configuration panel.
Next, a SecureSSH client must be configured that will bridge the X-server session to your computer. To do this, “Putty�? is a common and effective tool.
In the Start menu, locate your X-Win 32 6.1 drop down menu. In there, select “Putty�?.
Once in the Putty menu, you will see a screen asking you for your Host Name and there will be a bunch of Saved Sessions nearer to the bottom. Click in the “Saved Sessions�? field and type in “sceval.ucalgary.ca�?. Now click in the “Host Name�? field and type in “sceval.ucalgary.ca�?. Do not anything else quite yet.          File:Xwin32 4.png
On the left hand side of the Putty panel, there will be a long menu. Close to the bottom there will be an “SSH�? menu with “Tunnels�? underneath it. Click “Tunnels�?.
In the Tunnels menu, the very first field is called “Enable X11 Forwarding�?. Ensure this is checked.   File:Xwin32 5.png
Back on the left-hand side menu at the top, click the “Sessions�? option. You will back at the original Putty screen.  On the left beside the “Saved Sessions�? menu, there will be a “Save�? button, click it.
You have successfully configured an SSH bridge to the VMS system in the hospital. Click the “Open�? button to open a connection to the VMS system.
Note: In the future, to open a connection to the VMS system, you need to ensure you have opened the X-win 32 program first. Then go to your start menu and open the Putty program. You will see your session “sceval.ucalgary.ca�? in your Saved Sessions menu. You just need to double-click this option and it will automatically connect you with the VMS system.
A login screen will pop-up asking you for your username and password. Once you have provided this information you will be logged into the VMS system. All of the typical VMS commands will work from this prompt. However, when accessing remotely it is sometimes beneficial to open several terminals. To do this, type in “dec�? at the prompt and hit enter. This will open up a more familiar looking command window. The same command can be used again to create more terminals.

Note: You must be aware of the command line shortcuts to access the terminals. Some of the common commands are:
evalc – opens up the UCT Evaluation program
sap – opens up the Structure Analysis Program
uct_3d – open up the 3D graphic viewer

If further programs need to be opened, please refer to the Micro-CT Scanner user’s manualHowTo: Have multiple UCT-Tool users

Trying to have more than one person run the main UCT tool, during a session on sceval.ucalgary.ca, at the same time (ie. one locally and one from a remote terminal)...

The problem is color allocation. The controlbox already grabs color for meas. and normal eval tool.?????? I assume this means the answer is no then?

UCT Reading Data TroublesHowTo: fix the UCT_EVALUATION, if given an error message regarding failure to read data.

Note: This problem is specifically refering to using the "VOI" logical to  run the evaluation. In this case, pressing "Evaluation 3D" should simply extract a normal and segmented AIM.

An example log file of this: DISK1:[MICROCT.SCRATCH]UCT_EVALUATION_VOI.LOG;56It was actually version 55; that crashed. It tried to read 261 slices, but the ISQ only contains 260 slices.-Check what the eval (or voi) program shows for that scan ?-Did you start the voi with normal pushing, or did you start it 'by hand' and gave -1 for dimension ?

-The 'missing last slice' problem is known, but the VOI should not crash if you do not select that slice in the white box.

?????????? what does this mean, the missing last slice prob is known??HowTo: Restart the SCEVAL_FAST queue

How to: Restart the SCEVAL_FAST queue, if somehow stopped, on our sceval.ucalgary.ca workstation.  Do I need to be user "calibration" to do this?

As any user, you may restart it. Use the following command:$ start sceval_fastHowever, it should be started every time you reboot, so difficult to say why it was stopped...

HowTo: Select multiple samples quicklyHold the Shift and/or Ctrl key.

How to: Search for a particular samplenameYou can use the samplename filter field on top, to display only the names containing the filter string.

HowTo: Start the move/copyBby clicking on 'Start...'Note: The 'Script...' button is for advanced users.

HowTo: Use the 'Script' buttonThis will this will generate a script: sys$scratch:archive.comYou you may submit this in 'batch mode' later (e.g. over night) by typing: $ scanco_submit_command sys$scratch:archive.com/after=23:59

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.

/que=sceval_fastInsert a tape, but do NOT mount the tape in the normal program.Note: If necessary: if it's a new tape, initialize it as usual.The batch job will be started one minute before midnight in the example above.The following will show you that it is holding until then: $ show entry

For more help on this, try the following help commands: $ help submit /after$ help dcl_tips date_time example

HowTo: Do Weekly and Full System BackUps

It is possible under some circumstances that the hard disk may crash.  Therefore a regular copy should be made of the UCT database for data security.
In other words, a backup should be performed each week of the system’s data for that week and each month a full backup of the system should be made.  The following describes the process to do this.

There are two special backup tapes that are used alternately for both weekly and full backups, labeled BCKP0A and BCKP0B.
The BCKP stands for backup and the A and B are the tape identifiers.
The reason for using two tapes is to ensure that older data is not overwritten.



File:UCT Disk2.jpg

To perform weekly backup:
On Friday afternoon, insert into the tape device, the special backup tape opposite from the one used the previous week (ie. use Tape A, if Tape B was used the week before).  To determine this, check on the Weekly Backup schedule sheet.
Open up the UCT_BACKUP tool, shown in the Figure above.:*•	Under the heading “Disk Information�? and “Tape:�? click on Mount.
When “Tape: mounted as BCKP0_�? appears under “Disk Information�?, click on Weekly Backup at the bottom of the window.  A message will appear inquiring if the special tape for backup is inserted in the device, and click on Yes.

HowTo: Continue writting when a tape is fullWhen the tape is full, there should be a message displayed about continuing on another tape.

Hit ctrl+C to interrupt the program, take a fresh tape, initialize it, and then select the remaining scans to archive again.

Then hit 'start'.



Important Reminders:

While the tape is running and being written to, 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.

WE STRONGLY URGE YOU TO DO THE WEEKLY BACKUP (SAFETY BACKUP OF USER DISK1 WITH YOUR DATABASES ON IT).

2 users DID experience disk crashes last year, and without the weekly backup, you may still have all scans on the data disk (e.g. disk2). But without the databases, you cannot tell which scans belong the which sample!

HowTo: Install vtkMy with Qt on Linux

qt-devel must be downloaded and installed from any rpm website and then cmake must be run with the following setting for qt:

QT_INCLUDE_DIR                   /usr/lib/qt-3.3/include
QT_MOC_EXECUTABLE                /usr/bin/moc
QT_QASSISTANTCLIENT_LIBRARY      /usr/lib/qt-3.3/lib/libqassistantclient.a
QT_QT_LIBRARY                    /usr/lib/qt-3.3/lib/libqt-mt.so
QT_UIC_EXECUTABLE                /usr/bin/uic

HowTo: Avoid errors due to a one-off reading ISQ problem

The last slice in the ISQ cannot be read on occasion during the evaluation process - i.e., creating the AIM.
(Scanco is aware of this problem.)
The interm solution is to make sure that the last slice in the ISQ is not selected when you start the evaluation.
When using the white box to set your ROI, make sure that the box does not include the last slice of the ISQ.

HowTo: Tabulate evaluation data directly from LOG filesThis also applies for data from the 3D database.

If the sample was properly imported into our database ($uct_import) and if the database was activated in the ipl, all the results go into our 3D database, and you can just get them out with the usual
$ uct_list

Otherwise, the command to 'tabulate' .log files:$ search xxxx.log "ov "

Or, whatever you want to search for,
$ search/output=sys$scratch:ov.txt xxxx.log "ov "
to put the results into a .txt file.

HowTo: Searching multiple log filesTo search more than one log file, and get output into one single file:$ fda/output=xxx.txt search *.log "ov "The fda means 'file do all' and is a script of ours 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.

SAP realtedFix SAP colours when green

(using the standard gray colourmap), if changing color maps doesn't help.

Menu point 'Norm, Default is Bone = 16000.Take max for 32000, or 'Adapt slice'.Note: Do NOT take 'adapt vol' - it will be extremely slow! Every single mouse-click it re-calculates whole volume...Run SAP from the command line

$ sap -s FILENAME.aim

Use SAP with XV to create tiff images

Sample images of captured images can be found in DISK3:[MICROCT.PROJECTS.RA.IMAGES] 

1. Open SAP

$ sap -s FILENAME.AIM

2. Find desired image/plane/zoom etc. that you want to capture 

3. Open XV by typing xv in the command line

$ xv

4. Make sure SAP frames the desired images correctly on the screen 

5. In XV, click grab 

6. When it is finished capturing the image, make sure you click SAVE!

Use SAP, CoreLUT or XV with XWin32 or Hummingbird Exceed

You need two things on your computer: (1) an X windows server (e.g., XWin32 or Hummingbird Exceed), and (2) an SSH client to run your X applications (e.g., Putty or SSH Secure Client).
For SAP, CoreLUT or XV to work with XWin32, the visual display must be set to 8-bit. The evaluation tool evalc can be used in place of uct_evaluation via the 8-bit display.
XWin32
In the XWin Configuration, choose the "Windows" tab, check the box for "Legacy PseudoColor Support".  It may be necessary to restart Putty and Xwin32 before the settings take effect.  If you want to switch back to 24-bit display, uncheck the "Legacy PseudoColor Support" and restart the programs.
Hummingbird Exceed
Under server settings, be sure to select "pseudocolor" display.
SSH Client
Make sure the X-tunneling is turned on so that X applications can be used with these SSH clients.  Two SSH clients are recommended:

putty
SSH Secure Shell v3.2.9 http://www.ssh.com

@@ Line 30: / Line 30: @@
 #*Set beam hardening and ring artifact reduction on the minimum settings that are visibly necessary.
 #*Set smoothing to minimum or off.
-#*Set the “cross-section to ? upper limit just a little above the top end of the grey spectrum of the sample to optimise contrast in the reconstructed images. I usually put the lower limit halfway down the upper slope of the peak of background - some background will facilitate dataset thresholding (see next comment).
+#*Set the “cross-section to image�? upper limit just a little above the top end of the grey spectrum of the sample to optimise contrast in the reconstructed images. I usually put the lower limit halfway down the upper slope of the peak of background - some background will facilitate dataset thresholding (see next comment).
 # You can use the threshold module in the program 3d-calculator to get the optimum thresholding to binary images.
 #: Download this from [http://www.eur.nl/fgg/orthopaedics/Downloads.html| here] if you don’t have it yet.
@@ Line 710: / Line 710: @@
 :* Type: <code>r2m 404 421</code> (these are the measurement numbers). Makes a file called REN2MODELS.COM.
 :* if you want to rename also GOBJ + THRES + FILT aims, type <code>r2m ALL (+meas #)</code>
-:*Edit the COM file. Change xx.yy to MICHIGAN (capitals). Change ? to ? and ? to ? so that all files are the same length.
+:*Edit the COM file. Change xx.yy to MICHIGAN (capitals). Change “right�? to “r�? and “left�? to “l�? so that all files are the same length.
 :* @REN2MODELS.COM (moves the files to the MODELS directory).
 :* Test that the AIMs were properly moved to the MODELS directory by typing: <code>dh0</code> (tests no files in 000... from projects directory).
@@ Line 723: / Line 723: @@
 :*Start <code>sap</code> and <code>pwindows</code>.
 :<i>Option 2: Automatic</i>
-:* Generate an SAP.COM file using <code>@ut:create_sap-pw.com </code>or “<code>csp</code>?
+:* Generate an SAP.COM file using <code>@ut:create_sap-pw.com </code>or “<code>csp</code>�?
 :* Edit SAP.COM. Then start with <code>@SAP.COM XY</code>.
 :* Make XY, YZ and XZ 2d images, and some detail images. Always close <code>pwindows</code> before <code>sap</code>. The next AIM will be automatically loaded.
@@ Line 1,134: / Line 1,134: @@
   <br>$!Gauss filter, cutout with GOBJ, and threshold
   <br>$!------------------------------------------------------------------------------
-  <br>$ IF F$SEARCH(?) .EQS. ““
+  <br>$ IF F$SEARCH(“seg_file�?) .EQS. ““
   <br>$ THEN
   <br>$ ipl_scanco_prog
@@ Line 1,236: / Line 1,236: @@
 ===HowTo: Example submit_all_ipl.com===
   <br>$ com := UT:IPL_SUBMIT_USER.COM
-  <br>$ dir = F <br>$ENVIRONMENT(?) - “.COM]?
+  <br>$ dir = F <br>$ENVIRONMENT(“DEFAULT�?) - “.COM]�?
   <br>$ proc_maskxy := ‘dir.COM]IPL_MASKXY_SUBMIT_ALL.COM
   <br>$ proc_maskxz := ‘dir.COM]IPL_MASKXZ_SUBMIT_ALL.COM
@@ Line 1,247: / Line 1,247: @@
   <br>$ ENDIF
   <br>$!------------------------------------------------------------------------------
-  <br>$ IF P1 .NES ? THEN GOTO ‘P1’
+  <br>$ IF P1 .NES “ALL�? THEN GOTO ‘P1’
   <br>$!------------------------------------------------------------------------------
   <br>$ MASKXY:
   <br>$ FDA @’com’ ‘dir’.MODELS]*’p2’*_INNER_XY.GOBJ [] USER:MASKXY BLUND_EVAL ‘dir’.LOG]
   ‘proc_maskxy’
-  <br>$ IF P1 .NES ? THEN GOTO ENDCOM
+  <br>$ IF P1 .NES “ALL�? THEN GOTO ENDCOM
   <br>$!------------------------------------------------------------------------------
   <br>$ MASKXZ:
   <br>$ FDA @’com’ ‘dir’.MODELS]*’p2’*_UPPER_XZ.GOBJ [] USER:MASKXZ BLUND_EVAL ‘dir’.LOG]
   ‘proc_maskxz’
-  <br>$ IF P1 .NES ? THEN GOTO ENDCOM
+  <br>$ IF P1 .NES “ALL�? THEN GOTO ENDCOM
   <br>$!------------------------------------------------------------------------------
   <br>$ TRABTOP:
   <br>$ FDA @’com’ ‘dir’.MODELS]*’p2’*_MASK_XZ.AIM [] USER:TRABTOP BLUND_EVAL ‘dir’.LOG]
   ‘proc_trabtop’
-  <br>$ IF P1 .NES ? THEN GOTO ENDCOM
+  <br>$ IF P1 .NES “ALL�? THEN GOTO ENDCOM
   <br>$!------------------------------------------------------------------------------
   <br>$ ENDCOM:
@@ Line 1,284: / Line 1,284: @@
   <br>$!
   <br>$!
-  <br>$ p2 = p2 - ?
+  <br>$ p2 = p2 - “_INNER_XY�?
   <br>$!
   <br>$ define log_file ‘p1’
@@ Line 1,309: / Line 1,309: @@
   <br>$! (Send pos info to log files)
   <br>$!------------------------------------------------------------------------------
-  <br>$ IF F <br>$SEARCH(?) .EQS. ““
+  <br>$ IF F <br>$SEARCH(“xzaim_file�?) .EQS. ““
   <br>$ THEN
   <br>$ ipl_scanco_prog
@@ Line 1,329: / Line 1,329: @@
   <br>$ GOTO ENDCOM
   <br>$ ENDIF
-  <br>$! Before proceeding to this next part, the ? of the INNER_XZ.AIM files
+  <br>$! Before proceeding to this next part, the “pos�? of the INNER_XZ.AIM files
   <br>$! created above must be reset from 0 to the proper values based on aims
   <br>$! before and after flipping. The change in the AIM is done with a
-  <br>$! script that calls program ?.
+  <br>$! script that calls program “aimod�?.
   <br>$!
   <br>$!------------------------------------------------------------------------------
   <br>$!Create an AIM mask AIM with INNER_XZ.AIM and TOPER_XZ.GOBJ
   <br>$!------------------------------------------------------------------------------
-  <br>$ IF F <br>$SEARCH(?) .EQS. ““
+  <br>$ IF F <br>$SEARCH(“sum_file�?) .EQS. ““
   <br>$ THEN
   <br>$ ipl_scanco_prog
@@ Line 1,385: / Line 1,385: @@
   <br>$! RENAME SAMPLES
   <br>$!-----------------------------------------------------------------------------
-  <br>$ project = ?
+  <br>$ project = “HERZOG�?
-  <br>$ dir = “DISK40:[DATA.UCT.?
+  <br>$ dir = “DISK40:[DATA.UCT.PROJECTS�?
-  <br>$ IF F <br>$SEARCH(“‘’dir’.’’project’]*.*?) .NES. ““
+  <br>$ IF F <br>$SEARCH(“‘’dir’.’’project’]*.*�?) .NES. ““
   <br>$ THEN
-  <br>$ dir = “‘’dir’.?
+  <br>$ dir = “‘’dir’.’’project’�?
   <br>$ ELSE
   <br>$ SAY ““
-  <br>$ SAY “Directory ‘’dir’.’’project’] is empty.?
+  <br>$ SAY “Directory ‘’dir’.’’project’] is empty.�?
   <br>$ SAY ““
   <br>$ EXIT
@@ Line 1,418: / Line 1,418: @@
   <br>$THEN
   <br>$ SAY ““
-  <br>$ SAY “Usage:?
+  <br>$ SAY “Usage:�?
-  <br>$ SAY “ <br>$ @EVAL.COM RESDIR [ADPGSE] SAMPLE_ID [MEAS_ID] [PAR5-8]?
+  <br>$ SAY “ <br>$ @EVAL.COM RESDIR [ADPGSE] SAMPLE_ID [MEAS_ID] [PAR5-8]�?
   <br>$ SAY ““
-  <br>$ SAY “ A: ?
+  <br>$ SAY “ A: All�?
-  <br>$ SAY “ D: Set Measurement ?
+  <br>$ SAY “ D: Set Measurement Directory�?
-  <br>$ SAY “ G: Generate AIM ?
+  <br>$ SAY “ G: Generate AIM interactively�?
-  <br>$ SAY “ S: Startup ?
+  <br>$ SAY “ S: Startup SAP�?
-  <br>$ SAY “ E: Evaluating ?
+  <br>$ SAY “ E: Evaluating AIM�?
   <br>$ SAY ““
   <br>$ EXIT
@@ Line 1,432: / Line 1,432: @@
   <br>$ON CONTROL_C THEN GOTO ENDCOM
   <br>$ON CONTROL_Y THEN GOTO ENDCOM
-  <br>$IF P2 .EQS. ““ THEN P2 = ?
+  <br>$IF P2 .EQS. ““ THEN P2 = “D�?
   <br>$IF F <br>$INTEGER(P2) .NES. 0
   <br>$THEN
   <br>$ P4 = P3
   <br>$ P3 = P2
-  <br>$ P2 = ?
+  <br>$ P2 = “A�?
   <br>$ENDIF
   <br>$!------------------------------------------------------------------------------
   <br>$!CHECK DIRECTORY SYNTAX
   <br>$!------------------------------------------------------------------------------
-  <br>$olddir = F <br>$PARSE(F <br>$DIRECTORY()) - “.;?
+  <br>$olddir = F <br>$PARSE(F <br>$DIRECTORY()) - “.;�?
   <br>$IF P3 .NES. ““
   <br>$THEN
@@ Line 1,455: / Line 1,455: @@
   <br>$THEN
   <br>$ SAY ““
-  <br>$ SAY “Usage:?
+  <br>$ SAY “Usage:�?
-  <br>$ SAY “ <br>$ @EVAL.COM RESDIR [ADPGSE] SAMPLE_ID [MEAS_ID] [PAR5-8]?
+  <br>$ SAY “ <br>$ @EVAL.COM RESDIR [ADPGSE] SAMPLE_ID [MEAS_ID] [PAR5-8]�?
   <br>$ SAY ““
-  <br>$ SAY “ A: ?
+  <br>$ SAY “ A: All�?
-  <br>$ SAY “ D: Set Measurement ?
+  <br>$ SAY “ D: Set Measurement Directory�?
-  <br>$ SAY “ G: Generate AIM ?
+  <br>$ SAY “ G: Generate AIM interactively�?
-  <br>$ SAY “ S: Startup ?
+  <br>$ SAY “ S: Startup SAP�?
-  <br>$ SAY “ E: Evaluating ?
+  <br>$ SAY “ E: Evaluating AIM�?
   <br>$ SAY ““
   <br>$ EXIT
@@ Line 1,469: / Line 1,469: @@
   <br>$ON CONTROL_C THEN GOTO ENDCOM
   <br>$ON CONTROL_Y THEN GOTO ENDCOM
-  <br>$IF P2 .EQS. ““ THEN P2 = ?
+  <br>$IF P2 .EQS. ““ THEN P2 = “D�?
   <br>$IF F <br>$INTEGER(P2) .NES. 0
   <br>$THEN
   <br>$ P4 = P3
   <br>$ P3 = P2
-  <br>$ P2 = ?
+  <br>$ P2 = “A�?
   <br>$ENDIF
   <br>$!------------------------------------------------------------------------------
@@ Line 1,482: / Line 1,482: @@
   <br>$ ENDIF
   <br>$ENDIF
-  <br>$dir = F <br>$PARSE(F <br>$DIRECTORY()) - “.;?
+  <br>$dir = F <br>$PARSE(F <br>$DIRECTORY()) - “.;�?
   <br>$length = F <br>$LENGTH(dir)
   <br>$id = F <br>$EXTRACT(length-18,18,dir)
-  <br>$IF (F <br>$EXTRACT(0,2,id) .NES. ?) .OR. (F <br>$EXTRACT(9,2,id) .NES. ?)
+  <br>$IF (F <br>$EXTRACT(0,2,id) .NES. “00�?) .OR. (F <br>$EXTRACT(9,2,id) .NES. “00�?)
   <br>$THEN
   <br>$ SAY “ “
-  <br>$ SAY “ THIS IS NOT A MEAUSUREMENT DIRECTORY:?
+  <br>$ SAY “ THIS IS NOT A MEAUSUREMENT DIRECTORY:�?
-  <br>$ SAY “ ?
+  <br>$ SAY “ ‘’dir’�?
   <br>$ SAY “ “
   <br>$ EXIT
   <br>$ENDIF
   <br>$SET DEF UCT-DATA-M:[‘id’
-  <br>$isqdata = F <br>$SEARCH(“*.?)
+  <br>$isqdata = F <br>$SEARCH(“*.ISQ�?)
-  <br>$isqdata = isqdata - F <br>$PARSE(isqdata,,,??)
+  <br>$isqdata = isqdata - F <br>$PARSE(isqdata,,,�?VERSION�?)
-  <br>$aimdata = F <br>$SEARCH(“*.?) - ? - ?
+  <br>$aimdata = F <br>$SEARCH(“*.AIM�?) - “_TRAB�? - “_CORT�?
-  <br>$aimdata = F <br>$SEARCH(?)
+  <br>$aimdata = F <br>$SEARCH(“‘’aimdata’�?)
-  <br>$aimdata = aimdata - F <br>$PARSE(aimdata,,,??)
+  <br>$aimdata = aimdata - F <br>$PARSE(aimdata,,,�?VERSION�?)
-  <br>$IF (P2 .NES. ?) .AND. (isqdata .EQS. ““) .AND. (aimdata .EQS. ““)
+  <br>$IF (P2 .NES. “D�?) .AND. (isqdata .EQS. ““) .AND. (aimdata .EQS. ““)
   <br>$THEN
   <br>$ SAY “ “
-  <br>$ SAY “ NO IMAGE DATA IN THIS DIRECTORY:?
+  <br>$ SAY “ NO IMAGE DATA IN THIS DIRECTORY:�?
-  <br>$ SAY “ ?
+  <br>$ SAY “ ‘’dir’�?
   <br>$ SAY “ “
   <br>$ EXIT
   <br>$ENDIF
-  <br>$IF F <br>$SEARCH(“*.?) .NES. ““
+  <br>$IF F <br>$SEARCH(“*.COM�?) .NES. ““
   <br>$THEN
   <br>$ SAY ““
-  <br>$ SAY “THERE SEEM TO BE STILL UNRECONSTRUCTED SLICES IN THIS DIRECTORY:?
+  <br>$ SAY “THERE SEEM TO BE STILL UNRECONSTRUCTED SLICES IN THIS DIRECTORY:�?
   <br>$ DIRECTORY *.COM
   <br>$ EXIT
@@ Line 1,517: / Line 1,517: @@
   <br>$!PROCESSING
   <br>$!------------------------------------------------------------------------------
-  <br>$IF P2 .EQS. ? THEN GOTO ENDCOM
+  <br>$IF P2 .EQS. “D�? THEN GOTO ENDCOM
   <br>$!------------------------------------------------------------------------------
-  <br>$IF F <br>$LOCATE(?,P2) .NE. F <br>$LENGTH(P2)
+  <br>$IF F <br>$LOCATE(“A�?,P2) .NE. F <br>$LENGTH(P2)
   <br>$THEN
   <br>$! SAP IS INVOKED
-  <br>$ IF isqdata .NES. ““ THEN P2 = ?
+  <br>$ IF isqdata .NES. ““ THEN P2 = “GSE�?
-  <br>$ IF isqdata .EQS. ““ THEN P2 = ?
+  <br>$ IF isqdata .EQS. ““ THEN P2 = “SE�?
   <br>$! SAP IS NOT INVOKED
-  <br>$! IF isqdata .NES. ““ THEN P2 = ?
+  <br>$! IF isqdata .NES. ““ THEN P2 = “GE�?
-  <br>$! IF isqdata .EQS. ““ THEN P2 = ?
+  <br>$! IF isqdata .EQS. ““ THEN P2 = “E�?
   <br>$ENDIF
   <br>$SAY ““
   <br>$!------------------------------------------------------------------------------
-  <br>$IF F <br>$LOCATE(?,P2) .NE. F <br>$LENGTH(P2)
+  <br>$IF F <br>$LOCATE(“G�?,P2) .NE. F <br>$LENGTH(P2)
   <br>$THEN
-  <br>$ IF (isqdata .NES. ““) .AND. ((aimdata .EQS. ““) .OR. (P2 .EQS. ?))
+  <br>$ IF (isqdata .NES. ““) .AND. ((aimdata .EQS. ““) .OR. (P2 .EQS. “G�?))
   <br>$ THEN
-  <br>$ SAY “- Evaluate ?
+  <br>$ SAY “- Evaluate ‘’isqdata’�?
   <br>$ DEFINL UCT_DEFAULT_ISQ ‘isqdata’
   <br>$ DEFINL UCT_EVALUATION UCT-DATA-R:[‘P1’.COM]UCT_EVALUATION.COM
@@ Line 1,540: / Line 1,540: @@
   <br>$ DEASSIGN UCT_DEFAULT_ISQ
   <br>$ DEASSIGN UCT_EVALUATION
-  <br>$ IF P2 .NES. ?
+  <br>$ IF P2 .NES. “G�?
   <br>$ THEN
-  <br>$ SAY “- Waiting for evaluation job to complete ...?
+  <br>$ SAY “- Waiting for evaluation job to complete ...�?
   <br>$ counter = 1
   <br>$ loop:
@@ Line 1,549: / Line 1,549: @@
   <br>$ IF counter .eq. 1
   <br>$ THEN
-  <br>$ SAY “ - job has been runing for ‘’F <br>$STRING(elapsed_time)’ ?
+  <br>$ SAY “ - job has been runing for ‘’F <br>$STRING(elapsed_time)’ seconds�?
   <br>$ ELSE
-  <br>$ SAY “[2K[1A - job has been runing for ‘’F <br>$STRING(elapsed_time)’ ?
+  <br>$ SAY “[2K[1A - job has been runing for ‘’F <br>$STRING(elapsed_time)’ seconds�?
   <br>$ ENDIF
   <br>$ ctx = ““
-  <br>$ temp = F <br>$CONTEXT (?,ctx,??,??,??)
+  <br>$ temp = F <br>$CONTEXT (“PROCESS�?,ctx,�?JOBTYPE�?,�?BATCH�?,�?EQL�?)
   <br>$ loop_pid:
   <br>$ pid = F <br>$PID(ctx)
   <br>$ IF pid .NES. ““
   <br>$ THEN
-  <br>$ image = F <br>$GETJPI(pid,??)
+  <br>$ image = F <br>$GETJPI(pid,�?IMAGNAME�?)
-  <br>$ aimdata = F <br>$SEARCH(“*.?)
+  <br>$ aimdata = F <br>$SEARCH(“*.AIM�?)
-  <br>$ IF (F <br>$LOCATE(?,image) .NES. F <br>$LENGTH(image)) - .OR. (aimdata .EQS. ““)
+  <br>$ IF (F <br>$LOCATE(“ISQ_TO_AIM�?,image) .NES. F <br>$LENGTH(image)) - .OR. (aimdata .EQS. ““)
   <br>$ THEN
   <br>$ counter = counter + 1
@@ Line 1,569: / Line 1,569: @@
   <br>$ ENDIF
   <br>$ ENDIF
-  <br>$ aimdata = F <br>$SEARCH(“*.?)
+  <br>$ aimdata = F <br>$SEARCH(“*.AIM�?)
-  <br>$ aimdata = aimdata - F <br>$PARSE(aimdata,,,??)
+  <br>$ aimdata = aimdata - F <br>$PARSE(aimdata,,,�?VERSION�?)
   <br>$ ENDIF
   <br>$ ENDIF
   <br>$ENDIF
   <br>$!------------------------------------------------------------------------------
-  <br>$IF F <br>$LOCATE(?,P2) .NE. F <br>$LENGTH(P2)
+  <br>$IF F <br>$LOCATE(“S�?,P2) .NE. F <br>$LENGTH(P2)
   <br>$THEN
   <br>$ IF F <br>$SEARCH(aimdata) .NES. ““
   <br>$ THEN
   <br>$ show sym aimdata
-  <br>$ SAY “- Startup SAP ‘’aimdata’...?
+  <br>$ SAY “- Startup SAP ‘’aimdata’...�?
   <br>$ SAPXZ -s ‘aimdata’
   <br>$ ELSE
   <br>$ SAY ““
-  <br>$ SAY “No aimdata found in directory.?
+  <br>$ SAY “No aimdata found in directory.�?
-  <br>$ SAY “Program exits right now.?
+  <br>$ SAY “Program exits right now.�?
   <br>$ GOTO ENDCOM
   <br>$ ENDIF
   <br>$ENDIF
   <br>$!------------------------------------------------------------------------------
-  <br>$IF F <br>$LOCATE(?,P2) .NE. F <br>$LENGTH(P2)
+  <br>$IF F <br>$LOCATE(“E�?,P2) .NE. F <br>$LENGTH(P2)
   <br>$THEN
-  <br>$ id_dir = F <br>$EXTRACT(0,8,id) + “]? + F <br>$EXTRACT(9,8,id) + “.?
+  <br>$ id_dir = F <br>$EXTRACT(0,8,id) + “]�? + F <br>$EXTRACT(9,8,id) + “.DIR�?
-  <br>$ IF F <br>$SEARCH(“UCT-DATA-R:[‘’P1’.?) .EQS. ““
+  <br>$ IF F <br>$SEARCH(“UCT-DATA-R:[‘’P1’.’’id_dir’�?) .EQS. ““
   <br>$ THEN
-  <br>$ SAY “- Create Result Directory ...?
+  <br>$ SAY “- Create Result Directory ...�?
   <br>$ CREATE/DIR/LOG UCT-DATA-R:[‘P1’.’id’
   <br>$ ENDIF
   <br>$ IF aimdata .NES. ““
   <br>$ THEN
-  <br>$ aimname = F <br>$PARSE(aimdata,,,??)
+  <br>$ aimname = F <br>$PARSE(aimdata,,,�?NAME�?)
   <br>$ aimnum = F <br>$EXTRACT(0,8,id)
-  <br>$ aimfull = “UCT-DATA-R:[‘’P1’.?
+  <br>$ aimfull = “UCT-DATA-R:[‘’P1’.’’id’’’aimname’�?
-  <br>$ comfile = “UCT-DATA-R:[‘’P1’.COM]IPL_SCANCO_V64.?
+  <br>$ comfile = “UCT-DATA-R:[‘’P1’.COM]IPL_SCANCO_V64.COM�?
-  <br>$ logfile = “UCT-DATA-R:[‘’P1’.LOG]IPL_PRE_’’aimnum’_’’aimname’.?
+  <br>$ logfile = “UCT-DATA-R:[‘’P1’.LOG]IPL_PRE_’’aimnum’_’’aimname’.LOG�?
   <br>$! SHOW SYMBOL aimname
   <br>$! SHOW SYMBOL aimnum
@@ Line 1,611: / Line 1,611: @@
   <br>$! SHOW SYMBOL logfile
   <br>$ !-------------------------------------------------------------------
-  <br>$ IF F <br>$SEARCH(“‘’aimfull’_GFILT.?) .EQS. ““
+  <br>$ IF F <br>$SEARCH(“‘’aimfull’_GFILT.AIM�?) .EQS. ““
   <br>$ THEN
   <br>$! CP ‘aimdata’ ‘aimfull’.AIM
@@ Line 1,623: / Line 1,623: @@
   <br>$!------------------------------------------------------------------------------
   <br>$ ENDCOM:
-  <br>$IF F <br>$SEARCH(“UCT-DATA-M:[‘’id’*.*?) .NES. ““
+  <br>$IF F <br>$SEARCH(“UCT-DATA-M:[‘’id’*.*�?) .NES. ““
   <br>$THEN
   <br>$ DIRECTORY/NOTRAILER UCT-DATA-M:[‘id’
@@ Line 1,631: / Line 1,631: @@
   <br>$ DELETE UCT-DATA-M:[‘dir1’]’dir2’.DIR;,UCT-DATA-M:[000000]’dir1’.DIR;
   <br>$ENDIF
-  <br>$IF F <br>$SEARCH(“UCT-DATA-R:[‘’P1’.’’id’*.*?) .NES. ““ THEN -
+  <br>$IF F <br>$SEARCH(“UCT-DATA-R:[‘’P1’.’’id’*.*�?) .NES. ““ THEN -
   DIRECTORY/NOTRAILER UCT-DATA-R:[‘P1’.’id’
   <br>$SAY ““
@@ Line 1,784: / Line 1,784: @@
 #*	ssh-keygen -t rsa [use a passphrase]
 #:	NOTE: Put the "id_rsa" (private file) in ~/.ssh.  There should only be one of these on a 	machine account.
-#:	NOTE: Put the “id_rsa.? (public file) in ~/.ssh as ? on remote machines; see ? below.
+#:	NOTE: Put the “id_rsa.pub�? (public file) in ~/.ssh as “authorized_keys�? on remote machines; see “Remotebox�? below.
 #*	scp identity.pub skboyd@remotebox: [don't forget the last colon]
 #*	in ~/.bashrc:
@@ Line 1,938: / Line 1,938: @@
 ::		kill -HUP the inetd process
 :*	Add openssh
-:*	Added user accounts: <code>useradd –u 1002 –g 1000 –d /space/home/swiss –s “/bin/? swiss</code>
+:*	Added user accounts: <code>useradd –u 1002 –g 1000 –d /space/home/swiss –s “/bin/bash�? swiss</code>
 ::		Note: set user id 1002 based on next available number in /etc/passwd
 ::		As root: passwd swiss (to set user password)
@@ Line 2,273: / Line 2,273: @@
 *X-win 32 is an X-server that allows a Windows-based operating system display a virtual screen of another operating system, such as Linux or OpenVMS. This HowTO has been tailored specifically for connecting to the VMS system at the University of Calgary, Foothills Medical Center 3D Morphometrics Lab from a Windows XP operating system.
-*To use X-Win 32, please ensure that you have a registered program installed on your system. If you do not have a registered version but would like to download a trial version that is useable for 60 days, please visit http://www.starnet.com/products/ and select the “Download X-win ? on the left column. You will need to fill out some personal information including a valid email address to which they will send you the product information and download instructions. Once you have completed this, you can proceed with the following steps.
+*To use X-Win 32, please ensure that you have a registered program installed on your system. If you do not have a registered version but would like to download a trial version that is useable for 60 days, please visit http://www.starnet.com/products/ and select the “Download X-win 32�? on the left column. You will need to fill out some personal information including a valid email address to which they will send you the product information and download instructions. Once you have completed this, you can proceed with the following steps.
-#	Run X-win 32 from the start menu or desktop shortcut. A small blue ? should appear in the lower left hand corner of your start-bar.          [[Image:Xwin32_1.png|center]]
+#	Run X-win 32 from the start menu or desktop shortcut. A small blue “X�? should appear in the lower left hand corner of your start-bar.          [[Image:Xwin32_1.png|center]]
 #:If you have never configured X-win 32 before, a screen will automatically pop-up asking you to create an account. If this is the case, just jump to step 2.
 #:Otherwise, double-click on this icon to open the X-win 32 configuration panel.
-#	If in the X-win 32 config panel, and are wanting to create a new account, select the ? button on the menu. This will lead you to another panel asking you to select a connection method. This will be the screen you will see if you are installing X-Win 32 for the first time. Ensure that you choose ? and then click next.      [[Image:Xwin32_2.png|center]]
+#	If in the X-win 32 config panel, and are wanting to create a new account, select the “Wizard�? button on the menu. This will lead you to another panel asking you to select a connection method. This will be the screen you will see if you are installing X-Win 32 for the first time. Ensure that you choose “StarNetSSH�? and then click next.      [[Image:Xwin32_2.png|center]]
-#	On the next screen, the hostname you need to type in will be “sceval.ucalgary.?. Click next.
+#	On the next screen, the hostname you need to type in will be “sceval.ucalgary.ca�?. Click next.
 #	Enter in the username and password for the system at this host.
-#	Next, it will ask you for the host command. On the options there, scroll down and choose ?. Click next.
+#	Next, it will ask you for the host command. On the options there, scroll down and choose “VMS�?. Click next.
 #	Now enter in a descriptive name of the system you are connecting to. Click finish.
-#	You should now be back at the X-win 32 configuration panel. If not, double-click on the blue X on the lower left corner of your start bar. You should see the session you just created listed in the menu. Highlight your selection by clicking on it. On the panels above, there is a ? panel. Click this panel and you will be brought to a screen with various color options. On the lower left corner there are two checkboxes, ensure that only the “PseudoColor ? option has a checkbox in it. Click the ? button.         [[Image:Xwin32_3.png|center]]
+#	You should now be back at the X-win 32 configuration panel. If not, double-click on the blue X on the lower left corner of your start bar. You should see the session you just created listed in the menu. Highlight your selection by clicking on it. On the panels above, there is a “Color�? panel. Click this panel and you will be brought to a screen with various color options. On the lower left corner there are two checkboxes, ensure that only the “PseudoColor Mode�? option has a checkbox in it. Click the “apply�? button.         [[Image:Xwin32_3.png|center]]
-#	You have successfully created a X-server with to the remote system. Click the ? button on the X-win 32 configuration panel.
+#	You have successfully created a X-server with to the remote system. Click the “OK�? button on the X-win 32 configuration panel.
-#:Next, a SecureSSH client must be configured that will bridge the X-server session to your computer. To do this, ? is a common and effective tool.
+#:Next, a SecureSSH client must be configured that will bridge the X-server session to your computer. To do this, “Putty�? is a common and effective tool.
-#	In the Start menu, locate your X-Win 32 6.1 drop down menu. In there, select ?.
+#	In the Start menu, locate your X-Win 32 6.1 drop down menu. In there, select “Putty�?.
-#	Once in the Putty menu, you will see a screen asking you for your Host Name and there will be a bunch of Saved Sessions nearer to the bottom. Click in the “Saved ? field and type in “sceval.ucalgary.?. Now click in the “Host ? field and type in “sceval.ucalgary.?. Do not anything else quite yet.          [[Image:Xwin32_4.png|center]]
+#	Once in the Putty menu, you will see a screen asking you for your Host Name and there will be a bunch of Saved Sessions nearer to the bottom. Click in the “Saved Sessions�? field and type in “sceval.ucalgary.ca�?. Now click in the “Host Name�? field and type in “sceval.ucalgary.ca�?. Do not anything else quite yet.          [[Image:Xwin32_4.png|center]]
-#	On the left hand side of the Putty panel, there will be a long menu. Close to the bottom there will be an ? menu with ? underneath it. Click ?.
+#	On the left hand side of the Putty panel, there will be a long menu. Close to the bottom there will be an “SSH�? menu with “Tunnels�? underneath it. Click “Tunnels�?.
-#	 In the Tunnels menu, the very first field is called “Enable X11 ?. Ensure this is checked.   [[Image:Xwin32_5.png|center]]
+#	 In the Tunnels menu, the very first field is called “Enable X11 Forwarding�?. Ensure this is checked.   [[Image:Xwin32_5.png|center]]
-#	Back on the left-hand side menu at the top, click the ? option. You will back at the original Putty screen.  On the left beside the “Saved ? menu, there will be a ? button, click it.
+#	Back on the left-hand side menu at the top, click the “Sessions�? option. You will back at the original Putty screen.  On the left beside the “Saved Sessions�? menu, there will be a “Save�? button, click it.
-#	You have successfully configured an SSH bridge to the VMS system in the hospital. Click the ? button to open a connection to the VMS system.
+#	You have successfully configured an SSH bridge to the VMS system in the hospital. Click the “Open�? button to open a connection to the VMS system.
-#:Note: In the future, to open a connection to the VMS system, you need to ensure you have opened the X-win 32 program first. Then go to your start menu and open the Putty program. You will see your session “sceval.ucalgary.? in your Saved Sessions menu. You just need to double-click this option and it will automatically connect you with the VMS system.
+#:Note: In the future, to open a connection to the VMS system, you need to ensure you have opened the X-win 32 program first. Then go to your start menu and open the Putty program. You will see your session “sceval.ucalgary.ca�? in your Saved Sessions menu. You just need to double-click this option and it will automatically connect you with the VMS system.
-#	A login screen will pop-up asking you for your username and password. Once you have provided this information you will be logged into the VMS system. All of the typical VMS commands will work from this prompt. However, when accessing remotely it is sometimes beneficial to open several terminals. To do this, type in ? at the prompt and hit enter. This will open up a more familiar looking command window. The same command can be used again to create more terminals.
+#	A login screen will pop-up asking you for your username and password. Once you have provided this information you will be logged into the VMS system. All of the typical VMS commands will work from this prompt. However, when accessing remotely it is sometimes beneficial to open several terminals. To do this, type in “dec�? at the prompt and hit enter. This will open up a more familiar looking command window. The same command can be used again to create more terminals.
@@ Line 2,407: / Line 2,407: @@
 :To perform weekly backup:
 :*	On Friday afternoon, insert into the tape device, the special backup tape opposite from the one used the previous week (ie. use Tape A, if Tape B was used the week before).  To determine this, check on the Weekly Backup schedule sheet.
-:*	Open up the UCT_BACKUP tool, shown in the Figure above.:*•	Under the heading “Disk ? and “Tape:? click on Mount.
+:*	Open up the UCT_BACKUP tool, shown in the Figure above.:*•	Under the heading “Disk Information�? and “Tape:�? click on Mount.
-:*	When “Tape: mounted as ? appears under “Disk ?, click on Weekly Backup at the bottom of the window.  A message will appear inquiring if the special tape for backup is inserted in the device, and click on Yes.
+:*	When “Tape: mounted as BCKP0_�? appears under “Disk Information�?, click on Weekly Backup at the bottom of the window.  A message will appear inquiring if the special tape for backup is inserted in the device, and click on Yes.
@@ Line 2,473: / Line 2,473: @@
 :*Then put all the ov.txt, tv.txt, name.txt etc. files into excel.
+=SAP realted=
+==Fix SAP colours when green==
+(using the standard gray colourmap), if changing color maps doesn't help.
+:*Menu point 'Norm, Default is Bone = 16000.
+:*Take max for 32000, or 'Adapt slice'.
+::Note: Do NOT take 'adapt vol' - it will be extremely slow!  Every single mouse-click it re-calculates whole volume...
+==Run SAP from the command line==
+ $ sap -s <b>FILENAME</b>.aim
+==Use SAP with XV to create tiff images==
+Sample images of captured images can be found in DISK3:[MICROCT.PROJECTS.RA.IMAGES] <br>
+. Open SAP <br>
+ $ sap -s <b>FILENAME</b>.AIM
+. Find desired image/plane/zoom etc. that you want to capture <br>
+. Open XV by typing xv in the command line <br>
+ $ xv
+. Make sure SAP frames the desired images correctly on the screen <br>
+. In XV, click grab <br>
+. When it is finished capturing the image, make sure you click '''SAVE'''!
+==Use SAP, CoreLUT or XV with XWin32 or Hummingbird Exceed==
+You need two things on your computer: (1) an X windows server (e.g., XWin32 or Hummingbird Exceed), and (2) an SSH client to run your X applications (e.g., Putty or SSH Secure Client).
+For SAP, CoreLUT or XV to work with XWin32, the visual display must be set to 8-bit. The evaluation tool <code>evalc</code> can be used in place of <code>uct_evaluation</code> via the 8-bit display.
+<b>XWin32</b>
+In the XWin Configuration, choose the "Windows" tab, check the box for "Legacy PseudoColor Support".  It may be necessary to restart Putty and Xwin32 before the settings take effect.  If you want to switch back to 24-bit display, uncheck the "Legacy PseudoColor Support" and restart the programs.
+<b>Hummingbird Exceed</b>
+Under server settings, be sure to select "pseudocolor" display.
+<b>SSH Client</b>
+Make sure the X-tunneling is turned on so that X applications can be used with these SSH clients.  Two SSH clients are recommended:
+:* putty
+:* SSH Secure Shell v3.2.9 http://www.ssh.com

Sample Windows FTP Session	File:Windows ftp.jpg
Sample Linux FTP Session	File:Linux ftp.jpg

Archive: Difference between revisions

Yingzhu (talk | contribs)

Revision as of 19:39, 22 December 2020

How To Section 1 - Micro-CT Scanning

Micro-CT Scanning

Scanco Setting Possibilites

Settings Suggestions for SkyScan bone scanning

Corrections for Ring Artifacts and Filter Use

Specimen Holders

How To Section 2 - VMS Commands

Tables

Table 1 - Login and Software

Table 2 - Commands and Aliases

Table 3 - File Definitions

Table 4 - Reconstruction and Batch Jobs

Table 5 - Directory and File Organization

Table 6 - AIO Procedures

Table 7 - EVE Editor Commands

Project How To's

How To: Set up a new project

How To: Process a project

How To: Evaluate a project (PRE)

How To: Evaluate a project (POST)

How To: Measure reconstruction angle and align an image axially

How To: Rename the AIMs from the data base and move to MODELS

How To: Create 2D or 3D images

How To: Compile LOG files from IPL evaluation

Tape

How To: Tape is allocated to another user

How To: Deal with a full backup tape

How To: Initialize a new backup tape

How To: Archive (RSQ and AIM) files with a batch job

How To: Archive the RSQ (and AIM) files with the uct_backup tool

HowTo: Delete a measurement

HowTo: Archive a project

How To: Restore a project

Process

HowTo: Convert an AIM to a stack of TIFFs

HowTo: Reduce resolution of an AIM

HowTo: Switch the XY axis of an AIM

HowTo: Filter the AIM data

HowTo: Use the 64-bit procedures

HowTo: Use SAP effectively

HowTo: Select a threshold

HowTo: Run IPL in interactive mode

HowTo: Extract part of amask

Trouble-Shooting

HowTo: Get the correct colour map to display

HowTo: Add a new command

HowTo: Kill a string of processes

HowTo: Log in as XUCT in a terminal window

HowTo: Move files to other systems

HowTo: View TIFFS or GIFS

HowTo: Generate a text file

HowTo: Subselect a minimal AIM

HowTo: Set logicals and symbols on OpenVMS

Records

HowTo: Michigan project sheet

Sample COM Files

Scanco AIM File Format

Sample COM Files

HowTo: Example ipl_scanco_v64.com pre-processing

HowTo: Example ipl_scanco_v64.com post-processing

HowTo: Example submit_all_ipl.com

HowTo: Example ipl_maskxy_submit_all.com

HowTo: Example flip_xz.com

HowTo: Example eval.com

HowTo: Example eval_all.com

How To Section 3 - Software Installation and Setup

Install Packages from Source CD

Programs:

Step-by-Step:

Suggested directory structure

Directory structures

Add a project to vtkMy

Install a package on the Sun

Setting up WinCVS to use PuTTY to connect to vtkMy

Setting up CVS access from Linux/Unix

Using CVS from a command line

FTP Instructions for ENME