Editing Scanco Administration (section)

==Evaluation FAQ==

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


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

/db_clear_eval
-input        "IPL_AIM

..
</pre>

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


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

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


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


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===Create your own IPL script===

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

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

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

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

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

Logicals are preferred in scripts to make them more universal.


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===Valid and Locked Settings for an eval script===

Each evaluation when running <code>UCT_EVALUATION</code> can be made <code>VALID</code> and <code>LOCKED</code>.

:<code>VALID</code>: The evaluation script shows up as an option to execute when running <code>UCT_EVALUATION</code>. When you notice script numbers missing in the list, it is because they have had <code>VALID=0</code>

:<code>LOCKED</code>: The evaluation script can be used, but the user cannot make changes to the script settings in <code>UCT_EVALUATION</code>. This is to protect from somebody causing an error in the script settings that affect all users.

It is not possible to delete a script, and it is not possible to add a script at an arbitrary script number. So, any newly added script gets the next monotonically increased script number. This can lead to scripts that have similar purposes being spread throughout the list of scripts, which is annoying.

It is possible to organize the scripts, although it is a fair amount of work and easy to make a mistake. As a normal user (e.g., 'xtremect2') run the script. If you are a different user you may need to set  the correct evalscript database first.

The most simple executable to run is

<pre>
run ut:UCT_UPD_EVALSCR_MISC.EXE

 <...snip...>
 * 578    127/563  (ML) Knee Segmentation
  579    128/569  NO PRINT - Patient Analysis 61µm, After manual corr. on GOBJ,NM
  580    128/570  NO PRINT - Patient Analysis 61µm, After manual corr. on GOBJ,NM
* 581    128/580  NO PRINT - Patient Analysis 61µm, After manual corr. on GOBJ,NM
  582    129/572  XtremeCT II - Standard Radius/Tibia Patient Post-processing,NM
  583    129/573  XtremeCT II - Standard Radius/Tibia Patient Post-processing,NM
* 584    129/574  XtremeCT II - Standard Radius/Tibia Patient Post-processing,NM
Choose evalscript Record (IDX): [584]: 337
Description [XtremeCT II - Standard Radius Patient Analysis 61µm]: 
Valid [1]: 
Locked [1]: 
Favourite [0]: 
Category [32]: 

Save Record ? [Y]: 
</pre>

A more comprehensive executable that allows the user to edit parameters in the script is:

<pre>
run UT:UCT_UPDATE_EVALSCRIPT.EXE

<...snip...>
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
*  14      6/10   Bone Trab. Morphometry (3D Seg, 3D Calc, Print Sheet)et)eet)
*  15      7/11   Convert to DICOM
   16      8/12   RESOLUTION, Standard Pat Eval, copy to UR, submit AutoCont
   17      8/13   RESOLUTION, Standard Pat Eval, copy to UR, submit AutoCont
   18      8/14   RESOLUTION, Standard Pat Eval, copy to UR, submit AutoCont
   19      8/15   RESOLUTION, Standard Pat Eval, copy to UR, submit AutoCont
   20      8/16   RESOLUTION, Standard Pat Eval, copy to UR, submit AutoCont
   21      8/17   RESOLUTION, Mimic, Std Pat Eval, copy to UR, submit AutoCont
   22      8/18   RESOLUTION, Standard Pat Eval, copy to UR, submit AutoCont
   23      8/23   RESOLUTION, Mimic, Std Pat Eval, copy to UR, submit AutoCont
   24      8/24   RESOLUTION, Mimic, Std Pat Eval, copy to UR, submit AutoCont
   25      8/33   RESOLUTION, Mimic, Std Pat Eval, copy to UR, submit AutoCont
   26      8/57   RESOLUTION, Mimic, Std Pat Eval, copy to UR, submit AutoCont
   27      8/58   RESOLUTION, Mimic, Std Pat Eval, copy to UR, submit AutoCont
   28      8/71   RESOLUTION, Mimic, Std Pat Eval, copy to UR, submit AutoCont
   29      8/72   RESOLUTION, Mimic, Std Pat Eval, copy to UR, submit AutoCont
   30      8/79   RESOLUTION, Mimic, Std Pat Eval, copy to UR, submit AutoCont
   31      9/19   RESOLUTION, Standard Pat Eval, copy to UR, submit AutoCont
   32      9/20   RESOLUTION, Standard Pat Eval, copy to UR, submit AutoCont
   33      9/21   RESOLUTION, Standard Pat Eval, copy to UR, submit AutoCont
   34      9/22   RESOLUTION, XCT2STD, Std Pat Eval, copy to UR, submit AutoCont
 <snip>
  572    127/559  (ML) Knee Segmentation
  573    127/561  (ML) Knee Segmentation
* 574    127/563  (ML) Knee Segmentation
  575    128/569  NO PRINT - Patient Analysis 61µm, After manual corr. on GOBJ,NM
* 576    128/570  NO PRINT - Patient Analysis 61µm, After manual corr. on GOBJ,NM
  577    129/572  XtremeCT II - Standard Radius/Tibia Patient Post-processing,NM
  578    129/573  XtremeCT II - Standard Radius/Tibia Patient Post-processing,NM
* 579    129/574  XtremeCT II - Standard Radius/Tibia Patient Post-processing,NM
  580    130/0    New Record
Choose evalscript Record (IDX,*=Valid): [579]: 
</pre>

Press Enter many times until you are prompted with <code>Save [Y]</code>

The <code>*</code> indicates which scripts are active. You can see there are multiple versions of the same script in many cases. If you want to activate or deactivate a script you must use the IDX number (not the script number). For example, if you want to edit script 128, you select the active IDX, which is 576.

Copying script information from one IDX entry to another is a manual process you can do in <code>UCT_EVALUATION</code>. Be careful!

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===Exporting evaluation script parameters to text===

Nik at Scanco installed a program onto our system, but it is only to be used VERY carefully. <b>Never</b> use the <code>import</code> function, only the <code>export</code> function.

It's reading the evalscript database defined by the logical <code>UCT_EVALSCRIPT_DATABASE</code>. The file is usually located at <code>UCTD:UCT_EVALSCRIPTS_*.DAT</code> and is part of the weekly database backup.

  $ run ut:uct_impexp_evalscripts

It will output an interactive session as following:

<pre>
UCT_IMPEXP_EVALSCRIPTS V1.0

Export (0) or Import (1) [0]:                                                       ! 0 for export
EXPORT File [SYS$SCRATCH:EVALSCRIPTS.TXT]:                                          ! output file
V No  IDX/INDEX  Description                                                        ! list of scripts
   1      1/2489 3D Segmentation of VOI, 1 solid object
   2      3/862  3D Segmentation of 3 VOIs, concatenation of all 3ionenation of
   3      4/608  3D Segmentation of 4 VOIs, concatenation of all 4ionicatenati
   4      5/2711 Bone Trab. Morphometry (3D Seg, 3D Calc, Print Sheet)
....
 342    460/2945 XtremeCT II - Standard Radius Patient Evaluation 61µm
 343    461/2946 XtremeCT II - Autocontour Largest bone (Radius or Tibia)
 344    463/2965 NK frequency table, histogram
 345    464/2968 Convert to DICOM
Export evalscript Record (IDX): [1]:                            ! enter the number of the eval script to export

</pre>

To export all scripts, just press <code>Enter</code> through the whole list. To stop, enter number 0. Afterwards check the output file <code>SYS$SCRATCH:EVALSCRIPTS.TXT</code>.

Please give it a try and let me know if you have any questions.

<b>Interpretation of output</b>

There will be records for each entry. Currently there are 76 entries:

<pre>
!
! Script           23
!
         594
          34
NO PRINT - Patient Analysis 61µm, After manual corr. on GOBJ    
  1357462144
    11358111
  1513331376
    12153769
           1
           0
           0
!!! Installed on request only !!! �Starts the standard patient analysis (segmentation and evaluation), �after manual correction on _TRAB.GOBJ ; _CORT.GOBJ will be corrected accordingly.�Same script for Radius and Tibia analyses�Send postprocessing to SCSRV1_FAST. No results sent to printer.                                                                                                                                                                                                                 
           0
           0
           0
           0
           0
                
           0
           0
          10UE:UCT_EVALUATION_V6.COM|UE:IPLV6_UPAT_REDO_E5E6_XT2.COM|UE:STARTER_UPAT_POSTPROCESS_NOPRINT.COM                                                                                                                                                                
           1?|?|+.ISQ|+.AIM|+_SEG.AIM|+_CORT_MASK.GOBJ|+_TRAB_MASK.GOBJ|+_CORT_MASK.AIM|+_TRAB_MASK.AIM|+_CORT_SEG.AIM|+_TRAB_SEG.AIM|+_PORE.AIM|+_TRAB_TH.AIM|+_TRAB_SP.AIM|+_TRAB_1N.AIM|+_CORT_TH.AIM|+_CORT_SP.AIM                                                      
           26|+.GOBJ|0|+_CORT_MASK.GOBJ|0|+_TRAB_MASK.GOBJ                                                                                                                                                                                                                  
           0                                                                                                                                                                                                                                                                
           8UPAT_XT2|?|?|?|?|SYS$SCRATCH:|+.LOG|SYS$FAST                                                                                                                                                                                                                    
           40.8|1|450|3000|2|0.8|1|320|3000|2                                                                                                                                                                                                                               
           6AUTO_UPAT_SHEET|0|SYS$PRINT|PS,PDF|1024                                                                                                                                                                                                                         
           0                                                                                                                                                                                                                                                                
           0                                                                                                                                                                                                                                                                
           0                                                                                                                                                                                                                                                                
           0                                                                                                                                                                                                                                                                
           0                                                                                                                                                                                                                                                                
           0                                                                                                                                                                                                                                                                
           0                                                                                                                                                                                                                                                                
                                                                                                                                
                                                                                                                                
                                                                                                                                
                                                                                                                                
   538976288
   538976288
     2105376
      0.0000000
      5.0000000
                
           0
           0
           3
      0.0000000
      0.0000000
                
           0
           0
           3
      0.0000000
      0.0000000
                
           0
           0
           3
      0.0000000
      0.0000000
                
!
!
</pre>

The first number after the line <code>! Script           23</code>, in this case <code>594</code> is the IDX number. The next number <code>34</code> is the position of the script in the list.

In the output file, each row is marked with a number. You have to be careful to not interpret the line incorrectly. The single-digit number that precedes the script value has a meaning:
 26|+.GOBJ|0|+_CORT_MASK.GOBJ|0|+_TRAB_MASK.GOBJ
means type <code>2</code> with script info: <code>6|+.GOBJ|0|+_CORT_MASK.GOBJ|0|+_TRAB_MASK.GOBJ</code>

 40.8|1|450|3000|2|0.8|1|320|3000|2
means type <code>4</code> with script info: <code>0.8|1|450|3000|2|0.8|1|320|3000|2</code>

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

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


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

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


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

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


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