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FreeSurfer Numerical Recipies Replacement

Our objective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer.


Status: Completed.

  1. 12 numerical recipes replaced with open source alternatives, mainly using VXL.
  2. 14 unit tests run nightly.

  • Use case: 'Unit tests pass with all replacements.'
  • Difficulty: Medium-High
  • Impact: High
  1. Write test cases for each algorithm (Snyder, Jen): done
  2. Identify replacements (Snyder, Jen): done
  3. Integrate required libraries into FreeSurfer build process (Snyder, Jen): done
  4. Iteratively replace recipes with substitutes and run tests (Snyder, Jen): done