Editing Scanco Administration (section)

==Extract Results==

===UPAT_LIST command===

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

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

:* there is no option for using group codes

:* there is no option for using evaluation types


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

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

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

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

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

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

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

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


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===Sometimes _UPAT_XT2_POST.PDF verses _UPAT_XT2.PDF===

The _UPAT_XT2.PDFs are generated by the standard XTII evaluation scripts (not cluster version) that process the UPAT part on the same node as the IPL part. All the scripts that use

 UE:UCT_EVALUATION_V6_UPAT_FILL_E5E6.COM

produce the above PDFs.

The _UPAT_XT2_POST.PDFs are generate by the cluster version of the XTII evaluation scripts that process the UPAT part on the same node for every evaluation and the IPL part on different nodes. All the scripts that use:

 UE:STARTER_UPAT_POSTPROCESS.COM

produce the _UPAT_XT2_POST.PDFs.

You can change the name of the PDF in the <code>UE:STARTER_UPAT_POSTPROCESS.COM</code> if you want (and have permission!).

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===Create XtremeCT II patient report manually===
These are instructions on how to create a PDF report for XtremeCT II. However, before you dive into this, please try using script 118 (Standard Radius/Tibia Patient Post Processing) as it does exactly the steps below, but is automated and much easier. If that still doesn't work, then follow these instructions.

The basic concept is that a template PS file has the trabecular results (Eval_Type 5) and the cortical results (Eval_Type 6) combined into a single PS file. That PS file is then converted to PDF.

These instructions are based on the script <code>UE:UCT_EVALUATION_V6_UPAT_PRINT_E5E6.COM</code>

We use patient number 2870 and measurement number 15313 as an example. The picture number is D0013335 and this is a RL scan. The participant is CABHS_0001_RL_M00.

We assume a TIF image of the bone was already created. Check to see if it exists:

 $ dir IDISK1:[XTREMECT2.DATA.UPAT_VIEWS]PAT00002870_MEAS00015315_3D_1.TIF

If it doesn't exist, you'll have to create it using the scripts defined in UE:UCT_EVALUATION_V6_CREATE_TIF.COM. See section below titled Create 3D image for XtremeCT II patient report manually.

We define this image as a logical:

 $ DEFINE TIF_FILELOGICAL IDISK1:[XTREMECT2.DATA.UPAT_VIEWS]PAT00002870_MEAS00015315_3D_1.TIF

We define any of the possible template report sheets we might use. Rarely we'd use anything
but the "baseline" version, but sometimes it might be helpful to have reports with follow-up.

 $ DEFINE UPAT_EVAL_E5_SHEET_BASELINE UU:UPAT_EVAL_E5E6_BASELINE_DYNAMIC_LETTER.PS
 $ DEFINE UPAT_EVAL_E5_SHEET05 UU:UPAT_EVAL_E5E6_FUP05_DYNAMIC_LETTER.PS
 $ DEFINE UPAT_EVAL_E5_SHEET10 UU:UPAT_EVAL_E5E6_FUP10_DYNAMIC_LETTER.PS
 $ DEFINE UPAT_EVAL_E5_SHEET15 UU:UPAT_EVAL_E5E6_FUP15_DYNAMIC_LETTER.PS
 $ DEFINE UPAT_EVAL_E5_SHEET20 UU:UPAT_EVAL_E5E6_FUP20_DYNAMIC_LETTER.PS

Since we fill out the template first with E5 (trabecular) results, we want to ensure we can
subsequently fill out the report with E6 (cortical) results. So, we need to avoid the place
holders in the report from being overwritting by setting this logical:

 $ DEF/USER PRS_KEEP_KEYWORDS TRUE

Now we run UPAT_LIST once for E5 and create a temporary output, then again for E6 for the 
final output:

<pre>
$ UPAT_LIST
  Program: upat_print_list V2.0
  Started:  1-JUN-2022 16:35:08.24
  Mode (1 = list, 2 = print, 3 = show) [1]: 2
  Mode:    Print mode
  Patient # (1-2900) [1]: 2870
  Site (found RL TR) [TR]: RL
  Evaluation type (1-6) [4]: 5
  Group Code [0]: 
  Maximum # of follow-ups (0-19) [19]: 
  Template file [default]: 
  Output filename [SYS$SCRATCH:UPAT_PAT_E5_2870_RL.PS]: SYS$SCRATCH:TEMP_D0013333_UPAT_XT2.PS
  # copies [1]: 0

$ UPAT_LIST
  Program: upat_print_list V2.0
  Started:  1-JUN-2022 16:36:12.49
  Mode (1 = list, 2 = print, 3 = show) [1]: 2
  Mode:    Print mode
  Patient # (1-2900) [1]: 2870
  Site (found RL TR) [TR]: RL
  Evaluation type (1-6) [4]: 6
  Group Code [0]: 
  Maximum # of follow-ups (0-19) [19]: 
  Template file [default]: SYS$SCRATCH:TEMP_D0013333_UPAT_XT2.PS
  Output filename [SYS$SCRATCH:UPAT_PAT_E6_2870_RL.PS]: SYS$SCRATCH:D0013333_UPAT_XT2.PS
  # copies [1]: 0
</pre>

We convert the PS to a PDF and clean up temporary files.

 $ @SCOM:PS_TO_PDF.COM DELETE SYS$SCRATCH:D0013333_UPAT_XT2.PS
 $ DELETE SYS$SCRATCH:TEMP_D0013333_UPAT_XT2.PS;*

Lastly, we rename the file appropriately

 $ rename D0013333_UPAT_XT2.PDF CABHS_0001_RL_M00_UPAT_XT2.PDF

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=== Create 3D image for XtremeCT II patient report manually ===

Here we create the 3D image used in XtremeCT II patient reports manually. You'll need to set an appropriate preset for the visualization first (i.e. based on skeletal site):
<pre>
$ SETUP_FILE = "UU:3D_PRESET_UPAT_RL_1.DAT"
$ SETUP_FILE = "UU:3D_PRESET_UPAT_RR_1.DAT"
$ SETUP_FILE = "UU:3D_PRESET_UPAT_TL_1.DAT"
$ SETUP_FILE = "UU:3D_PRESET_UPAT_TR_1.DAT"
</pre> 

Then we define which segmented aim file to use:
<pre>
$ EVAL_SEGAIM = "DISK2:[XTREMECT2.DATA.00002891.00015311]D0013333_SEG.AIM"
</pre>

Now define the name of the output file using the standardized format that has patient and measurement number:

<pre>
$ PRINT_FILE = "IDISK1:[XTREMECT2.DATA.UPAT_VIEWS]PAT00002870_MEAS00015315_3D_1.TIF"
</pre>

Then run UCT_3D_BATCH (as opposed to UCT_3D which does not take the setup file in the command line):

<pre>
$ UCT_3D_BATCH 'SETUP_FILE' 'EVAL_SEGAIM' 'PRINT_FILE'
</pre>

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


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

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

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

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

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


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===UCT_LIST Extract results===

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

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

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

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

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

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

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

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

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


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

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

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


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

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

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

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

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

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


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