Update fmriprep requirement from <=24.1.1,>=24.1.0 to >=24.1.0,<=25.0.0

[dependabot]

Updates the requirements on fmriprep to permit the latest version.

Release notes

Sourced from fmriprep's releases.

25.0.0

Release notes

New feature release in the 25.0.x series.

This release substantially improves support for pre-computed derivatives. Previous releases would miss some derivatives and rerun the computations. Note that derivatives from previous versions will be accepted, so it should not be necessary to recompute derivatives from previous versions. The recommended command line is:

fmriprep BIDS_DIR OUT_DIR participant --derivatives fmriprep=PRECOMP_DIR

Note that multiple derivatives can be specified, for example:

fmriprep BIDS_DIR OUT_DIR participant \
  anat=PRECOMPUTED_ANATOMICAL_DIR \
  func=PRECOMPUTED_FUNCTIONAL_DIR

When the same file is found in multiple derivatives, the last one found takes precedence.

Additionally, --force-* flags have been consolidated into a single --force flag that can take multiple, space-separated arguments.

Structural processing changes

We now output white, pial and midthickness fsLR meshes on the subject surface. Look for sub-<subject>_hemi-<L|R>_space-fsLR_*_<surf>.surf.gii files.

Brain extraction has been modified slightly to more closely match the antsBrainExtraction.sh workflow distributed by ANTs. The impact should be minimal, but in rare cases this fixes a crash.

Fieldmap processing changes

SyN-SDC fieldmap filtering is now single-level, following the improvements for gradient-echo fieldmaps in 24.1.

Jacobian-weighting during fieldmap unwarping is now on by default only for PEPolar fieldmaps. To enable for other fieldmap types, use --force fieldmap-jacobian.

Changes

• FIX: Detect and apply precomputed fieldmaps (#3439)
• FIX: Calculate bold mask and dummy scans in transform-only runs (#3428)
• FIX: Use consistent skull-stripping pre- and post- SDC (#3415)
• FIX: Use removeprefix instead of lstrip or ternary operator (#3409)
• FIX: Listify sessions when generating reports (#3408)
• FIX: Ensure fieldmap is resampled correctly in report (#3387)
• FIX: Stop excluding FS minc_modify_header used during fallback registration (#3372)
• FIX: Repair and test query for precalculated baseline/boldref files (#3370)
• FIX: Repair search for precomputed transforms (#3369)
• ENH: Enable Jacobians only for PEPOLAR by default, allow forcing (#3443)
• ENH: Create --force flag that accepts a list, replacing individual --force-* flags (#3442)
• ENH: Output fsLR meshes on subject surfaces (#3411)
• ENH: Flexibilize "sophisticated" pepolar to allow monomodal execution (#3393)
• ENH: Update FSL packages for reported bug fixes (#3374)
• RF: Calculate RMSD from motion transforms (#3427)
• RF: Reconstruct motion confounds from minimal derivatives (#3424)
• RF: Replace deprecated pkgutil.find_loader (#3384)

... (truncated)

Changelog

Sourced from fmriprep's changelog.

25.0.0 (March 25, 2025)

New feature release in the 25.0.x series.

This release substantially improves support for pre-computed derivatives. Previous releases would miss some derivatives and rerun the computations. Note that derivatives from previous versions will be accepted, so it should not be necessary to recompute derivatives from previous versions. The recommended command line is::

fmriprep BIDS_DIR OUT_DIR participant --derivatives fmriprep=PRECOMP_DIR

Note that multiple derivatives can be specified, for example::

fmriprep BIDS_DIR OUT_DIR participant \
  anat=PRECOMPUTED_ANATOMICAL_DIR \
  func=PRECOMPUTED_FUNCTIONAL_DIR

When the same file is found in multiple derivatives, the last one found takes precedence.

Additionally, --force-* flags have been consolidated into a single --force flag that can take multiple, space-separated arguments.

Structural processing changes

We now output white, pial and midthickness fsLR meshes on the subject surface. Look for sub-<subject>_hemi-<L|R>_space-fsLR_*_<surf>.surf.gii files.

Brain extraction has been modified slightly to more closely match the antsBrainExtraction.sh workflow distributed by ANTs. The impact should be minimal, but in rare cases this fixes a crash.

Fieldmap processing changes

SyN-SDC fieldmap filtering is now single-level, following the improvements for gradient-echo fieldmaps in 24.1.

Jacobian-weighting during fieldmap unwarping is now on by default only for PEPolar fieldmaps. To enable for other fieldmap types, use --force fieldmap-jacobian.

All merged pull requests

• FIX: Detect and apply precomputed fieldmaps (#3439)
• FIX: Calculate bold mask and dummy scans in transform-only runs (#3428)
• FIX: Use consistent skull-stripping pre- and post- SDC (#3415)
• FIX: Use removeprefix instead of lstrip or ternary operator (#3409)
• FIX: Listify sessions when generating reports (#3408)
• FIX: Ensure fieldmap is resampled correctly in report (#3387)

... (truncated)

Commits

• 724db89 doc: Add missing contributor [skip ci]
• 77ae798 doc: Add missing contributors
• e1d4345 chore: Update zenodo ordering
• 1144dde chore: Add inline dependencies for update_zenodo.py
• ef7c4aa doc: 25.0.0 release notes
• b4edde2 feat(cli): Remove CLI flags with expired deprecation periods (#3445)
• 04febd2 feat: Enable Jacobians only for PEPOLAR by default, allow forcing (#3443)
• 3da2842 feat(cli): Remove CLI flags with expired deprecation periods
• 039963e feat(cli): Disable Jacobians by default except PEPOLAR, allow forcing
• 5566157 feat(cli): Create --force flag that accepts a list, replacing individual `-...
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[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.79%. Comparing base (a07b357) to head (451888f).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #499   +/-   ##
=======================================
  Coverage   83.79%   83.79%           
=======================================
  Files          38       38           
  Lines        4017     4017           
=======================================
  Hits         3366     3366           
  Misses        651      651           

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