Editing Scanco Administration (section)

===Standard Reconstruction===
Scans are automatically submitted for reconstruction, so manual submission is usually only necessary if there was a problem during reconstruction (e.g., a power failure).

*To reconstruct all slices from the RSQ, first delete or rename the old ISQ. 
*To reconstruct a selection of slices, a valid ISQ must exist. There is an offset of 1 slice when designating slice selection.
'''General Usage for Interactive Reconstruction''':
<pre>
$ uct_reconstruction P1 P2 P3

P1: RSQ Filename
P2: Slice number (A – all, start:finish)
P3: Log file of batch job
</pre>
'''General Usage for Non-interactive Reconstruction''':
  $ submit/noprint/que=sys$slow um:uct_reconstruction.com/params=(<b>DISK2:[MICROCT.DATA.00000610.00002449]C000####.RSQ </b>, a)
*Normally jobs are submitted to sys$slow queue instead of running them interactively.


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====Reconstruct a selection of slices====
Here are examples of how to reconstruct a single RSQ file: C0007655.RSQ, sample 4111 and measurement 9899. <br>
To reconstruct slices 101 to 201 and submit the job to the sys$slow queue:
<pre>
$ submit/noprint/que=sys$slow um:uct_reconstruction.com /log=sys$scratch:reco4111.log/para=(dk0:[microct.data.00004111.00009899]C0007655.rsq, 100:200, sys$scratch:reco4111.log)
</pre>
*The command must be all on one line (or use hyphen), and it wants the 3 parameters: filename, slices, and log.file name
 

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====Reconstruct all slices====
To reconstruct all slices, use “a” for all slices and submit the job to the sys$slow queue:
<pre>
$ delete C0007655.ISQ;*
$ submit/noprint/que=sys$slow um:uct_reconstruction.com/log=sys$scratch:reco4111.log/para=(dk0:[microct.data.00004111.00009899]C0007655.rsq, a, sys$scratch:reco4111.log)
</pre>
*The .log filename is up to you, as long as it's the same at both places. 
*Give full pathname for RSQ file.


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====Reconstruct multiple files====
For multiple files, create a script and submit the job to the sys$slow queue. For example,
<pre>
$ cd sys$scratch
$ eve reco_all.com   
</pre>
Or open editor (command 'Edit'), put the following lines in the file and save it as .e.g sys$scratch:reco_all.com:
<pre>
$ uct_reconstruction dk0:[microct.data.00004111.00009899]C0007655.rsq a
$ uct_reconstruction dk0:[microct.data.00004111.00009900]C0007656.rsq a
$ uct_reconstruction dk0:[microct.data.00004111.00009001]C0007657.rsq a
$ exit
</pre>
Save the script and exit the text editor, then submit the job (e.g. to sys$slow):
<pre>
$ submit/noprint/que=sys$slow/log=sys$scratch:reco4111.log sys$scratch:reco_all.com
</pre>
All the files will be reconstructed as a single job, with one log file.


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====Batch reconstruction ====
The reconstruction software available for the XT2 & microCT systems supports the /batch syntax that replaces reco_all.com. 
You can split a manual reconstruction into several jobs using

 $ uct_reconstruction DK0:[XTREMECT2.DATA.00001234.00005678]D0123456.RSQ a/batch=16


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====Update to uct_reconstruction V6.2-5, March 2019====

As of March 2019, we should only use uct_reconstruction v6.2-5 on xtremect2. 
For studies with baseline and follow-up scans overlapping this time, the old version (V6.2-2) can still be accessed using
<pre>
$ uct_old_recon
</pre>
Changing reconstruction versions can lead to small systematic differences in the result parameters of a trabecular bone analysis. The old version should only be accessed by those who absolutely need to use it. (Scanco recommends re-reconstructing all measurements of a study with version 6.2-5 instead).


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