Editing Scanco Administration (section)

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


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


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


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


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

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

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

<pre>
$ @com:import_manual.com

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

So:

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

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

<b>IMPORTANT: BE VERY SURE NOT TO MIX UP MEASUREMENT AND SAMPLE NUMBER !!!</b>

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

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

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

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

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

<b>Autosubmit</b>

<pre>$ import_autosubmit.com</pre>

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

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

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

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

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

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

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

then you can just start it with

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

And I also recommend to put into login.com:

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

(yes, with all these double-quotes)

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


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===Scan FAQ===
====Unlock a locked controlfile====
In November 2023, Stephan Weiss suggested you can use:

  mcr ut:UCT_UPD_EVALSCR_MISC.EXE

and set locked to 0. For example, to change script #61:

  $ mcr ut:UCT_UPD_EVALSCR_MISC.EXE
  UCT_UPD_EVALSCR_MISC V1.0
  
  V IDX escript/Rec. Description
      1      1/1    XtremeCT Standard Patient Evaluation (RL,RR,TL,TR,CU)
      2      1/7    XtremeCT Standard Patient Evaluation (RL,RR,TL,TR,CU)
  *   3      1/9    XtremeCT Standard Patient Evaluation (RL,RR,TL,TR,CU)
      4      2/2    QC1 Trabecular Morphometry
      5      2/8    QC1 Trabecular Morphometry
      6      2/384  QC1 Trabecular Morphometry
  *   7      2/401  QC1 Trabecular Morphometry
      8      3/3    QC2
      9      3/6    QC2
     10      3/385  QC2
  *  11      3/402  QC2
  *  12      4/4    3D Segmentation of VOI, 1 solid objectAIM
  *  13      5/5    3D Seg. of 2 VOIs: solid dense in transparent low dens obj obj
    <snip>
    356     60/283  TEST - STEP2 SCSRV1_FAST
  * 357     60/290  Can be reused, irrelevant content
    358     61/284  TEST - STEP2 SCSRV1_FAST
  * 359     61/291  Can be reused, irrelevant content
    360     62/296  MCP Meta auto contour
  <snip>
    559    127/558  (ML) Knee Segmentation
  * 560    127/559  (ML) Knee Segmentation
  Choose evalscript Record (IDX): [560]: 359
  Description [Can be reused, irrelevant content]: 
  Valid [1]: 
  Locked [1]: 
  Favourite [0]: 
  Category [32]: 
  
  Save Record ? [Y]: Y
  Rewriting DB Idx          291
  Record saved successfully
  End of program

Also see the instructions about setting VALID and LOCKED in another part of the wiki under the heading "Valid and Locked Settings for an eval script"

But my old instructions are:

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

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

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

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


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


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


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


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

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


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


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

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

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

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


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====Error: High resolution 30 µm scans and avoiding buffer overrun error====
If you get an error of a Buffer Overrun when scanning at high resolution on the XtremeCT II, use this command prior to open the measurement software from the very same terminal:

<pre>
$ DEFINE UCT_MEASUREMENT_SHARED_FRAMES 1
$ uct_measurement
</pre>
This could be set permanently, but it may then also delay the patient scan saving.

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


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


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

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