Releases: nipreps/fmriprep
25.2.5 LTS
Release notes
Bug-fix release in the 25.2.x series.
This release restores compatibility with the treatment of multi-session data with older versions of fMRIPrep by providing the --no-track-sessions flag. Future versions of fMRIPrep may have different default behaviors for multi-session data, so please report any issues you encounter with either setting of this flag or multi-session data in general.
Changes
- FIX: Reuse fewer config options when using
--config-file(#3625) - FIX: Missing logger (#3624)
- FIX: Avoid overwriting codecarbon output (#3623)
- FIX: Sanitize plus signs in from entities in workflow names (#3604)
- ENH: add
--[no-]track-sessionsflag to lessen session label strictness (#3614)
Full Changelog: 25.2.4...25.2.5
25.2.4 LTS
Release Notes
Bug-fix release in the 25.2.x series.
This release addresses some errors in multi-echo and multi-session processing.
Changes
- FIX: Set source_file in ds_report* nodes at resampling level (#3590)
- FIX: Ravel multi-echo data for BIDSSourceFile with precomputed smriprep (#3583)
- FIX: Ensure multi-echo processing and slice timing correction text is in boilerplate (#3577)
- FIX: Pass session_id to fieldmap finder (#3573)
- FIX: Import LinAlgError from a stable location (#3572)
- ENH: Raise error if two-echo data are provided (#3570)
- MNT: Prune Ubuntu environment before building docker images (#3571)
Full Changelog: 25.2.3...25.2.4
25.2.3 LTS
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
25.2.2 LTS
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 (#3547)
Full Changelog: 25.2.1...25.2.2
25.2.1 LTS
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 (#3545)
- DOC: Include template metadata information when resampling BOLD to surface (#3544)
Full Changelog: 25.2.0...25.2.1
25.2.0 LTS
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 (#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
freesurferparameter 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 checkafterruff format(#3480) - MNT: Update pre-commit ruff legacy alias (#3479)
New Contributors
- @miltoncamacho made their first contribution in #3483
- @AxelCouturierCIBM made their first contribution in #3494
- @jhlegarreta made their first contribution in #3505
- @toomanycats made their first contribution in #2768
Full Changelog: 25.1.4...25.2.0
Contributors
Assets 2
25.1.4
25.1.3
Release notes
Patch release in the 25.1.x series.
This resolves a bug introduced in a dependency between 25.1.1 and 25.1.2.
Full Changelog: 25.1.2...25.1.3
25.1.2
25.1.1
Release Notes
Patch release in the 25.1.x series.
This includes small fixes for working with precomputed fieldmaps, including adding fieldmap correction sections to the reports, which were previously omitted if the fieldmap was not calculated during the fMRIPrep run.