Editing Scanco Administration (section)

===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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