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| [https://wiki.brown.edu/confluence/display/orthobio/Compiling+the+CS+Carpal+Pipeline|Compiling the CS Carpal Pipeline] | | [https://wiki.brown.edu/confluence/display/orthobio/Compiling+the+CS+Carpal+Pipeline|Compiling the CS Carpal Pipeline] |
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| #Create the subject directory. It must have the format: E#####_scan; where # is substituted with a digit. Import files/folders from Bioengineering:
| | [[Registration of Bones Across Positions#Technical Notes|Use instructions here]] |
| #* <code>original_scans/</code> CT_Scans [scans of all wrist positions]
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| #* <code>original_stacks/</code> [segmented neutral position of wrist]
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| #* <code>crop_values.txt</code>
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| #Run <code>batchGen.pl</code> to create the master batch files.
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| #* Run it from the top level of the subject directory.
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| #* The first time you run it, run with the <code>--crop</code> option, so it imports the data from the crop_values.txt file.
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| #* <code>batchGen.pl</code> should create three files: <code>regbatch</code>, <code>subsetbatch</code>, and <code>unixbatch</code>. <code>unixbatch</code> is the master file that calls the other three
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| <pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre>
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| #Run <code>unixbatch</code> from the top level of the subject directory.
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| #* This should go through and run all the major steps.
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| #* <code>./unixbatch</code>
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| #After <code>unixbatch</code> finishes, you need to validate the output of the registration steps
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| #* Use <code>WristVis</code> to check the registration | |
| #* If there are errors, re-run <code>batchGen.pl</code>, without the <code>--crop</code> option, and choose NOT to re-run all parts. Then let it hopefully help you through the process.
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| #Folders <code>collected_results</cdoe> and <code>auto_registr_resuls</code> contain the same registration results in different formats, whereas <code>classified_scans</code> contains the tissue classification results
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