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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.

Description

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