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| 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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| #Upload all Files and create the subject directory (this is done) | | [[Registration of Bones Across Positions#Technical Notes|Use instructions here]] |
| #Run batchGen.pl to create the master batch files- (you should start here)
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| **located for now at: /map/gfx0/data/wrist/batchfiles/linuxconvert/batchGen.pl
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| ##should always be run from the top level of the subject directory
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| ##the first time you run it, run with the --crop option, so it imports the data from the crop_values.txt file.
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| ##batchGen.pl should create three files: regbatch, subsetbatch, & unixbatch. unixbatch is the master file that calls the other three
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| ##/map/gfx0/data/wrist/batchfiles/linuxconvert/batchGen.pl --crop
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| #Run unixbatch 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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| ##./unixbatch
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| #After unixbatch finishes, you need to validate the output of the registration steps
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| ##If there are errors, re-run batchGen.pl, without the --crop option, and choose NOT to re-run all parts. Then let it hopefully help you through the process.
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