Registration

the CS Carpal Pipeline

1. Upload all Files and create the subject directory (this is done)
2. Run batchGen.pl to create the master batch files- (you should start here)
   1. located for now at: /map/gfx0/data/wrist/batchfiles/linuxconvert/batchGen.pl
   2. should always be run from the top level of the subject directory
   3. the first time you run it, run with the --crop option, so it imports the data from the crop_values.txt file.
   4. batchGen.pl should create three files: regbatch, subsetbatch, & unixbatch. unixbatch is the master file that calls the other three
   5. /map/gfx0/data/wrist/batchfiles/linuxconvert/batchGen.pl --crop
3. Run unixbatch from the top level of the subject directory.
   1. This should go through and run all the major steps
   2. ./unixbatch
4. After unixbatch finishes, you need to validate the output of the registration steps
   1. 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.