Wrist Pipeline Technical Details

1. Wrist scan (e.g., CT)
   multiple positions including “neutral pose”
   $G: N/A (done at Engineering)
   Output: volume image (multiple 2D slices forming stack)
2. For Neutral position, for each bone, for each slice, draw contour by hand
   $G: N/A (done at Engineering)
   Output: Point Cloud (i.e., a “.stack” file)
3. Classify/segmentation/registration
   INPUT: a) crop_values.txt, b) .iv files for point clouds w/ “mimcs”, c) original scan to MRI (uses stack files)
   scripts: project/wrist/pipeline/batchGen.py
   $G: project/wrist/program/registration/
   $G: project/wrist/program/visualizer/ [Windows program]
   Output: (files in “auto_registr_results/” directory)
4. Inter-bone distance fields
   INPUT: inertial results (w/ matlab code in Engineering -- .dat files)
   INPUT: a) .iv files, b) RT files, c) inertial files (.dat files)
   scripts: project/wrist/pipeline/joints_one_linux.sh
   scripts: project/wrist/pipeline/joints_one_linux.sh
   $G: project/wrist/program/distancefield/
   $G: project/wrist/program/jointViewer/
5. Growing cartilage
   $G: project/wrist/program/cartilage/
   $G: project/wrist/program/jointCartilageViewer/
6. Ligaments
   $G: project/wrist/program/ligament/
   For example, see project/wrist/program/ligament/Makefile and search for "test"