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@effigies effigies commented Sep 5, 2025

nipy/nitransforms#271 transposed image coordinate arrays. In the case of fMRIPrep, this was something we were transposing around, so this fix slightly simplifies things.

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codecov bot commented Sep 5, 2025

Codecov Report

❌ Patch coverage is 0% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 73.63%. Comparing base (ab58dc9) to head (7b7ad0a).
⚠️ Report is 4 commits behind head on master.

Files with missing lines Patch % Lines
fmriprep/interfaces/resampling.py 0.00% 1 Missing ⚠️
Additional details and impacted files
@@           Coverage Diff           @@
##           master    #3517   +/-   ##
=======================================
  Coverage   73.63%   73.63%           
=======================================
  Files          60       60           
  Lines        4612     4612           
  Branches      586      586           
=======================================
  Hits         3396     3396           
  Misses       1087     1087           
  Partials      129      129           

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@effigies effigies merged commit 50131fa into nipreps:master Sep 5, 2025
20 of 21 checks passed
effigies added a commit that referenced this pull request Oct 1, 2025
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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