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WMA: fiber clustering pipeline documentation

Key Investigators

Project Description

Software for data-driven white matter parcellation


  1. Improve user documentation and results checking documentation based on user feedback.
  2. Investigate alternatives for documentation.
  3. Create batch script to run entire pipeline.
  4. Update all versions of documentation; remove unused.
  5. http://dmri.slicer.org/whitematteranalysis/
  6. https://projects.iq.harvard.edu/whitematteranalysis/publications

Approach and Plan

  1. Batch script for running the fiber clustering pipeline.
  2. Give details about each processing step and the expected outputs.
  3. Have users from technical and clinical fields tested.

Progress and Next Steps

  1. Batch script for running the fiber clustering pipeline is done.
  2. Tested by mutltiple collaborators.
  3. Documentation of step-by-step instructions is done. It currently in a Google Doc and needs to be released donline soon.


Batch script: wm_apply_ORG_atlas_to_subject.sh Documentation:

Background and References

  1. Zhang, F., Wu, Y., Norton, I., Rathi, Y., Makris, N., O’Donnell, LJ. An anatomically curated fiber clustering white matter atlas for consistent white matter tract parcellation across the lifespan. NeuroImage, 2018 (179): 429-447

  2. O’Donnell, LJ., Wells III WM., Golby AJ., Westin CF. Unbiased groupwise registration of white matter tractography, in: International Conference on Medical Image Computing and Computer-Assisted Intervention, 2012 (pp. 123-130).

  3. O’Donnell, LJ., and Westin, C-F. Automatic tractography segmentation using a high-dimensional white matter atlas. Medical Imaging, IEEE Transactions on 2007 (26.11): 1562-1575.