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feat: Add --fs-legacy-id flag#3606

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effigies wants to merge 3 commits intonipreps:maint/25.2.xfrom
effigies:fs-legacy-id
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feat: Add --fs-legacy-id flag#3606
effigies wants to merge 3 commits intonipreps:maint/25.2.xfrom
effigies:fs-legacy-id

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Changes proposed in this pull request

This adds a --fs-legacy-id flag to disable adding _ses-<label> to FreeSurfer subject IDs. This can't be turned on by default for backwards compatibility reasons. Separately, we need to discuss what the best way forward is in general.

I think this is related to #3581, but that appears not to be limited to FreeSurfer. Need to think more there, as well.

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codecov bot commented Feb 10, 2026

Codecov Report

❌ Patch coverage is 30.00000% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.18%. Comparing base (16a8b29) to head (4280633).

Files with missing lines Patch % Lines
fmriprep/workflows/base.py 0.00% 6 Missing and 1 partial ⚠️
Additional details and impacted files
@@               Coverage Diff                @@
##           maint/25.2.x    #3606      +/-   ##
================================================
- Coverage         73.27%   73.18%   -0.09%     
================================================
  Files                60       60              
  Lines              4856     4866      +10     
  Branches            630      632       +2     
================================================
+ Hits               3558     3561       +3     
- Misses             1156     1162       +6     
- Partials            142      143       +1     

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I think this is the best solution with minimal friction for the 25.2.X series - I've opened up #3607 to discuss changes for the 26.0.x series

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Are there other impacts on derivative reuse besides FS?

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