Editing Scanco User Instructions (section)

===Extract Results from XtremeCT Database using UPAT_LIST===
*Run <code>$ UPAT_LIST</code> to take in a range of samples and extract the standard patient results, which may include scans from other projects.
**Run <code>$ UPAT_LIST -h</code> to print out help for all parameters. 
**For standard analysis on XtremeCT2, the default Evaluation Type 4=XT1 is not applicable. To get results for XtremeCT2, you need to run upat_list twice.  Once for evaluation 5 and once for 6.
<pre>   Evaluation type (1-6) [4]:   Type code of evaluation (4=XT1, 5=trabecular, 6=cortical, default=4) </pre>


*Run <code>$ @com:EXTRACT_UPAT_LIST</code> to take in a list of sample numbers and extract the standard patient results with follow-ups and append them to a result file.  
<pre>
$ @COM:EXTRACT_UPAT_LIST P1 P2 P3 P4 P5

    P1 = Sample List
    P2 = Site (RR, RL, TR, TL, R*, T*, *)
    P3 = Number of Follow-Ups (max 19)
    P4 = Results Output File
    P5 = Eval type (4=XT1, 5=Trab, 6=Cort)
</pre>

:An example to extract all sites:
<pre>
$ @com:EXTRACT_UPAT_LIST mysamples.txt * 19 myresults.txt 5
</pre>


*Run <code>$ @com:EXTRACT_UPAT_LIST_NOMATCH</code> to take in a list of sample numbers and extract the standard patient results without matching follow-ups and append them to a result file.  
<pre>
$ @com:EXTRACT_UPAT_LIST_NOMATCH P1 P2 P3 P4 P5

    P1 = Sample List
    P2 = Site (RR, RL, TR, TL, R*, T*, *)
    P3 = Number of Follow-Ups (max 19)
    P4 = Results Output File
    P5 = Eval type (4=XT1, 5=Trab, 6=Cort)
</pre>

:An example to extract all sites:
<pre>
$ @com:EXTRACT_UPAT_LIST_NOMATCH mysamples.txt * 19 myresults.txt 5
</pre>


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