Registration

the CS Carpal Pipeline

1. Create the subject directory [EXXXXX_scan] & import files/folders from Bioengineering:
   1. original_scans/ CT_Scans [scans of all wrist positions]
   2. original_stacks/ [segmented neutral position of wrist]
   3. crop_values.txt
2. Run batchGen.pl to create the master batch files
   1. should always be run from the top level of the subject directory
   2. the first time you run it, run with the --crop option, so it imports the data from the crop_values.txt file.
   3. batchGen.pl should create three files: regbatch, subsetbatch, & unixbatch. unixbatch is the master file that calls the other three
   4. /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. Use WristVis to check the registration
   2. 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.
5. Folders collected_results & auto_registr_resuls contain the same registration results in different formats, whereas classified_scans contains the tissue classification results