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nipreps / smriprep

Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)
https://nipreps.github.io/smriprep
Apache License 2.0
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RF: Remove much of the hardcoded `T1w` fields in favor of `anat` #433

Closed mgxd closed 3 months ago

mgxd commented 6 months ago

This is a supplemental PR to https://github.com/nipreps/nibabies/pull/360 - since nibabies also relies on smriprep, but may be processing in T2w space, this PR generalize many of the workflows/nodes/fields to account for other anatomical references.

mgxd commented 4 months ago

@effigies This should be ready for review. I've tried to limit any breaking changes, but regardless this will need to be included in a new minor release

codecov[bot] commented 3 months ago

Codecov Report

Attention: Patch coverage is 95.45455% with 2 lines in your changes missing coverage. Please review.

Project coverage is 66.45%. Comparing base (7852cba) to head (4a8a782).

Files Patch % Lines
smriprep/workflows/outputs.py 96.15% 1 Missing :warning:
smriprep/workflows/surfaces.py 90.90% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #433 +/- ## ========================================== + Coverage 66.37% 66.45% +0.08% ========================================== Files 30 30 Lines 2079 2087 +8 Branches 249 250 +1 ========================================== + Hits 1380 1387 +7 - Misses 698 699 +1 Partials 1 1 ```

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