FIX: Write out Freesurfer-derived outputs #3512
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tsalo
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effigies
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #3512 +/- ##
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+ Coverage 73.56% 73.61% +0.05%
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Files 60 60
Lines 4600 4609 +9
Branches 585 586 +1
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+ Hits 3384 3393 +9
Misses 1087 1087
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effigies
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Aug 27, 2025
Co-authored-by: Chris Markiewicz <[email protected]>
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@effigies thanks for correcting the outputs. It looks like everything's working. This doesn't write out aseg and aparcaseg files to the func directory, so that might need to be addressed (maybe in a separate PR?). I also didn't try to collect precomputed derivatives. Not sure if that's a feature you had planned for these particular outputs though. |
If someone wants it, they can open a PR. LGTM. |
tsalo
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effigies
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25.2.0 (October 01, 2025) New feature release in the 25.2.x series. This release is an *fMRIPrep Long-Term Support (LTS)* release. The planned support window is 4 years, until October 2029. This release is an incremental improvement over 25.1.x, but includes some fixes and improvements that do not fit within our `bug-fix policy <https://www.nipreps.org/devs/releases/#bug-fix-releases>`__. Importantly, the change in interpolation in 25.1.0 introduced artifacts for some datasets. This release changes the default interpolation mode to ``grid-constant``, which resolves those problems while not reintroducing the issue the previous release sought to fix. This release also (finally) introduces per-session processing. The ``--session-label`` flag selects the sessions to process, and the ``--subject-anatomical-reference`` flag indicates whether and how to combine across sessions. Existing filters passed via ``--bids-filter-file`` may need to be updated or removed in favor of using these flags to achieve the desired behavior. We would like to thank the AMP-SCZ and ENIGMA consortia for testing out and providing feedback on this release. * FIX: Clean up output report language (#3529) * FIX: Default to grid-constant interpolation mode (#3516) * FIX: Adapt to transposed ndcoords in nitransforms (#3517) * FIX: Write out Freesurfer-derived outputs (#3512) * FIX: Add kwargs to _warnings.py (#3483) * ENH: Resample BOLD data to any surface template space using the Connectome Workbench (#3461) * ENH: Add boldref / sbref to source metadata (#3532) * ENH: Add dedicated session filtering, alternative anatomical template options (#3495) * ENH: Write out goodvoxels mask (#3513) * ENH: Add registration metadata to boldref-to-anat transforms (#3500) * ENH: Write out cortex mask GIFTIs (#3491) * ENH: Update transforms.py according to new transform chain of nitransforms (#3494) * RF/DOC: Improve and document command-line parser defaults (#3487) * DOC: Explain better SDC and B0FieldSource requirement (#2768) * DOC: Document `freesurfer` parameter in BOLD confound workflow init (#3504) * DOC: Add myself to contributor list (#3506) * DOC: Fix non-standard Input/Output docstring section management (#3505) * MNT: Split Dockerfile into base and pixi layers (#3521) * MNT: Replace conda with pixi and lock (#3503) * MNT: Update license metadata using SPDX expression (#3486) * MNT: no need to re-run `ruff check` after `ruff format` (#3480) * MNT: Update pre-commit ruff legacy alias (#3479)
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Closes #3511. I don't think I accounted for the versions of aseg and aparcaseg that get written out to the func directory, and I haven't thought about precomputed derivatives at all.
Changes proposed in this pull request
init_anat_preproc_wftoinit_single_subject_wf