25.2 (LTS)

[effigies]

25.2.0 (October 01, 2025)

Release Notes

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.

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.

Changes

• FIX: Clean up output report language (FIX: Clean up output report language #3529)
• FIX: Default to grid-constant interpolation mode (fix: Default to grid-constant interpolation mode #3516)
• FIX: Adapt to transposed ndcoords in nitransforms (fix: Adapt to transposed ndcoords in nitransforms #3517)
• FIX: Write out Freesurfer-derived outputs (FIX: Write out Freesurfer-derived outputs #3512)
• FIX: Add kwargs to _warnings.py (add kwargs to _warnings.py #3483)
• ENH: Resample BOLD data to any surface template space using the Connectome Workbench (ENH: Resample BOLD data to any surface template space using the Connectome Workbench #3461)
• ENH: Add boldref / sbref to source metadata (enh: add boldref / sbref to source metadata #3532)
• ENH: Add dedicated session filtering, alternative anatomical template options (ENH: Add dedicated session filtering, alternative anatomical template options #3495)
• ENH: Write out goodvoxels mask (ENH: Write out goodvoxels mask #3513)
• ENH: Add registration metadata to boldref-to-anat transforms (feat: Add registration metadata to boldref-to-anat transforms #3500)
• ENH: Write out cortex mask GIFTIs (ENH: Write out cortex mask GIFTIs #3491)
• ENH: Update transforms.py according to new transform chain of nitransforms (Update transforms.py according to new tranform chain of nitransforms #3494)
• RF/DOC: Improve and document command-line parser defaults (RF/DOC: Parser defaults #3487)
• DOC: Explain better SDC and B0FieldSource requirement (Explain better SDC and B0FieldSource requirement. #2768)
• DOC: Document freesurfer parameter in BOLD confound workflow init (DOC: Document freesurfer parameter in BOLD confound workflow init #3504)
• DOC: Add myself to contributor list (DOC: Add myself to contributor list #3506)
• DOC: Fix non-standard Input/Output docstring section management (DOC: Fix non-standard Input/Output docstring section management #3505)
• MNT: Split Dockerfile into base and pixi layers (chore: Split Dockerfile into base and pixi layers #3521)
• MNT: Replace conda with pixi and lock (chore: Replace conda with pixi and lock #3503)
• MNT: Update license metadata using SPDX expression (MNT: PEP 639 compliance #3486)
• MNT: no need to re-run ruff check after ruff format (MNT: no need to re-run ruff check after ruff format #3480)
• MNT: Update pre-commit ruff legacy alias (MNT: Update pre-commit ruff legacy alias #3479)

New Contributors

• @miltoncamacho made their first contribution in add kwargs to _warnings.py #3483
• @AxelCouturierCIBM made their first contribution in Update transforms.py according to new tranform chain of nitransforms #3494
• @jhlegarreta made their first contribution in DOC: Fix non-standard Input/Output docstring section management #3505
• @toomanycats made their first contribution in Explain better SDC and B0FieldSource requirement. #2768

Full Changelog: 25.1.4...25.2.0

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This discussion was created from the release 25.2.0.

[effigies]

25.2.1 (October 03, 2025)

Release Notes

Bug-fix release in the 25.2.x series.

This fix addresses an issue seen when in datasets with multiple anatomical sessions that do not perform per-session processing. It also updates the citation boilerplate when resampling to non-FreeSurfer, non-fsLR surface templates.

Changes

• FIX: Pass actual T1w files to summary interface (fix: pass actual t1w files to summary interface #3545)
• DOC: Include template metadata information when resampling BOLD to surface (DOC: Include template metadata information when resampling BOLD to surface #3544)

Full Changelog: 25.2.0...25.2.1

[effigies]

25.2.2 (October 06, 2025)

Release Notes

Bug-fix release in the 25.2.x series.

This fix addresses an issue in the Docker containers.
FreeSurfer's recon-all depends on a full Perl installation being available in the environment.

Changes

• FIX: Ensure perl is installed in container (fix(docker): Ensure perl is installed in container #3547)

Full Changelog: 25.2.1...25.2.2

[effigies]

25.2.3 (October 17, 2025)

Release notes

Bug-fix release in the 25.2.x series.

This fix addresses an incompatibility between the PyBIDS and universal-pathlib dependencies. The only change is reverting universal-pathlib to a compatible version in the lock file, which will also fix the container.

Full Changelog: 25.2.2...25.2.3