Editing Scanco Administration (section)

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


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

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


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

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


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

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

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

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


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

====Error: Writing to UPAT database fails====

Sometimes when performing a morphological evaluation we get an error when writing to the UPAT database. This is entirely preventable. The error may look like this snippet from the LOG file:

<pre>
...snip...
Reading AIM file 6
DK0:[XTREMECT2.DATA.00002783.00016788]D0014390_TRAB_1N.AIM...
!> Reading AimVersion020
!> Image size after D1charCmp (run-length) uncompression will be:
!> Type of data               Char       1 byte/voxel
!> Total memory size          82.7       Mbyte
Trabecular Analysis (5)
starting calculations
Scanner-ID: 3401
Updating old record 16788
getting new eval record...
New Eval record:       58416
getting new slice records...
TIME:  8-MAR-2024 10:41:00.63
ERROR:
Writing indexed record (upat slice)
MESSAGE: %FOR-W-INCKEYCHG, inconsistent key change or duplicate key!
STATUS:            2
CODE:           50
FACILITY: FORTRAN
--------------
UPAT_FILL_DB V2.0-1
   Eval-Type: [5]:    Group-Code: [0]: Evaluation Type 6 Cortical
Analysis
    ISQ-File: [isqfile.ISQ]:      Aim-File: [aimfile1.AIM]:
Ct.Mask-File: [aimfile7.AIM]:       Ct-File: [aimfile8.AIM]:
...snip...
</pre>

The problem is because when running several jobs at once on the cluster there could be parallel attempts to write to the database. The solution is to ensure that all jobs that write 
to the database are run on the exact same queue. However, to leverage the cluster performance and running parallel jobs, we can split a typical morphological evaluation into two parts.
The first part is spread across all available queues, and the second part directs the final writing to database to a single queue (e.g., <code>SCEVAL_FAST</code>).

In <code>UCT_EVALUATION</code> or any <code>HIJACK</code>scripts, we need to replace:

<pre>
$ PAR1 = "EVAL:UE:UCT_EVALUATION_V6.COM|UE:IPLV6_UPAT_REDO_E5E6_XT2.COM|UE:UCT_EVALUATION_V6_UPAT_FILL_E5E6.COM|UE:UCT_EVALUATION_V6_CREATE_TIF.COM|UE:UCT_EVALUATION_V6_UPAT_PRINT_E5E6_NM.COM|"
</pre>

with 
<pre>
$ PAR1 = "EVAL:UE:UCT_EVALUATION_V6.COM|UE:IPLV6_UPAT_REDO_E5E6_XT2.COM|UE:STARTER_UPAT_POSTPROCESS_NM.COM|"
</pre>

The script <code>UE:STARTER_UPAT_POSTPROCESS.COM</code>, or in this case the version that does no matching (<code>UE:STARTER_UPAT_POSTPROCESS_NM.COM</code>) replaces the following three scripts:

 UE:UCT_EVALUATION_V6_UPAT_FILL_E5E6.COM
 UE:UCT_EVALUATION_V6_CREATE_TIF.COM
 UE:UCT_EVALUATION_V6_UPAT_PRINT_E5E6_NM.COM

We still can call <code>UE:IPLV6_UPAT_REDO_E5E6_XT2.COM</code> if we need to re-run the morphological analysis, but the other three scripts are specifically sent to <code>SCEVAL_FAST</code> to avoid any conflicts writing to the database.

If this doesn't fix the problem then also double-check that the sample/measurement number of the scan embedded in the ISQ is correct. There are occasions when that's been mistaken. See other FAQ entry about adjusting file header

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

====UCT_EVALUATION customization====

When you start <code>UCT_EVALUATION</code> and select <code>Scripts</code> from the top menu, and then <code>Modify</code>, select a script. You can choose the radio button for <code>Basic</code> or <code>Advanced</code>. In the <code>Basic</code> you'll see something like this:

 Project: UPAT_XT2
 Eval-Script: UE:UCT_EVALUATION_V6.COM
 IPL-Script: UE:IPLV6_UPAT_E5E6_XT2.COM
 User-Script: UE:STARTER_UPAT_POSTPROCESS.COM

Make sure that IPL-Script always has a script named IPLV6_... and that User-Script always has names like EVAL_...

Switch into <code>Advanced</code> mode and you'll see all the variables explicitly set. For example, a typical <code>P1</code> value is:

 EVAL --> UE:UCT_EVALUATION_V6.COM|UE:IPLV6_UPAT_REDO_E5E6_XT2.COM|UE:STARTER_UPAT_POSTPROCESS.COM

If you select <code>EVAL</code> you will see the window at the bottom explain what each parameter is. For example for <code>EVAL</code> it says:

 EVAL: evalfile | iplfile | userfile0 | userfile1 [| userfileN ...] (Nmax = 5)

So, that means <code>Eval-Script</code> is <code>UE:UCT_EVALUATION_V6.COM</code>, <code>IPL-Script</code> is <code>UE:IPLV6_UPAT_REDO_E5E6_XT2.COM</code> and <code>User-Script</code> is <code>UE:STARTER_UPAT_POSTPROCESS.COM</code>.

When you run an evaluation with this script it will create a file in the measurement directory called something like <code>E0000684_EVAL_UPAT_XT2.COM</code>, which will contain:

 <--snip-->
 $ IPL_CALC2   :== 
 $ IPL_CALC3   :== 
 $ IPL_CALC4   :== 
 $ IPL_CALC5   :== 
 $ IPL_CALC6   :== 
 $ IPL_CALC7   :== 
 $!
 $! Defining entry point for IPL Loops:
 $!
 $ UCT_EVALUATION_CUSTOM_TARGET:
 $!
 $!
 $! Starting IPL
 $!
 $ @UE:IPLV6_UPAT_E5E6_XT2.COM
 $!
 $! User Procedure 0:
 $ SET NOON 
 $ @UE:UCT_EVALUATION_V6.COM -
 "EVAL:UE:UCT_EVALUATION_V6.COM||UE:UCT_EVALUATION_V6_UPAT_FILL_E5E6.COM|UE:UCT_EVALUATION_V6_CREATE_TIF.COM|UE:UCT_EVALUATION_V6_UPAT_PRINT_E5E6.COM" -
 <--snip-->

The <code>UCT_EVALUATION_V6.COM</code> does the parsing of all variables passed by the GUI and then writes a script that is executed, beginning with all definitions of all the symbols. It then calls the IPL-script, which is written to the output file (command procedure to be executed as a batch job) as

 write outfile "$ @UE:''iplfile'"

Your User-Script(s) are then <b>EXECUTED</b> during the parsing, so they need to add (write) content to the script rather than do something. So these scripts need to <b>WRITE</b> the <b>COMMANDS</b> of what has to be done later, not contain the commands itself. For example, rather than

 $ delete 'ipl_file'

It needs to be 

 $ write outfile "$ delete ''ipl_file'"

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

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

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

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

Known bugs:

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

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

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

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

Will correct that of course in the next version.


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

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


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

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

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


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]