Registration

the CS Carpal Pipeline

1. Create the subject directory. It must have the format: E#####_scan; where # is substituted with a digit. Import files/folders from Bioengineering:
   • original_scans/ CT_Scans [scans of all wrist positions]
   • original_stacks/ [segmented neutral position of wrist]
   • crop_values.txt
2. Run batchGen.pl to create the master batch files.
   • Run it from the top level of the subject directory.
   • The first time you run it, run with the --crop option, so it imports the data from the crop_values.txt file.
   • The script batchGen.pl creates three files: regbatch.list, subsetbatch.list, unixbatch.sh, and batchgen.cfg.
   1. The script unixbatch.sh uses the other two files to dispatch commands in parallel to a processor farm.
   2. The subsetbatch.list has a set of commands invoking the subset program.
   3. The regbatch.list file contains a list of WristRegistration commands.
   4. The configuration file batchgen.cfg contains the parameters used for this run.

E06001_scan>  $G/install_linux/bin/wrist/batchGen.pl  --crop

1. Run unixbatch.sh from the top level of the subject directory.
   • This should go through and run all the major steps.
   • ./unixbatch.sh
2. After unixbatch.sh finishes, you need to validate the output of the registration steps
   • Use WristVis to check the registration
   • 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.
3. Folders collected_results and auto_registr_resuls contain the same registration results in different formats, whereas classified_scans contains the tissue classification results