25.0.0

[effigies]

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 (fix: Detect and apply precomputed fieldmaps #3439)
• FIX: Calculate bold mask and dummy scans in transform-only runs (fix: Calculate bold mask and dummy scans in transform-only runs #3428)
• FIX: Use consistent skull-stripping pre- and post- SDC (fix: Use consistent skull-stripping pre- and post- SDC #3415)
• FIX: Use removeprefix instead of lstrip or ternary operator (fix: Use removeprefix instead of lstrip or ternary operator #3409)
• FIX: Listify sessions when generating reports (fix: Listify sessions when generating reports #3408)
• FIX: Ensure fieldmap is resampled correctly in report (FIX: Ensure fieldmap is resampled correctly in report #3387)
• FIX: Stop excluding FS minc_modify_header used during fallback registration (FIX: Stop excluding FS minc_modify_header used during fallback registration #3372)
• FIX: Repair and test query for precalculated baseline/boldref files (Fix: Repair and test query for precalculated baseline/boldref files #3370)
• FIX: Repair search for precomputed transforms (FIX: Repair search for precomputed transforms #3369)
• ENH: Enable Jacobians only for PEPOLAR by default, allow forcing (feat: Enable Jacobians only for PEPOLAR by default, allow forcing #3443)
• ENH: Create --force flag that accepts a list, replacing individual --force-* flags (feat(cli): Create --force flag that accepts a list, replacing individual --force-* flags #3442)
• ENH: Output fsLR meshes on subject surfaces (feat: Output fsLR meshes on subject surfaces #3411)
• ENH: Flexibilize "sophisticated" pepolar to allow monomodal execution (ENH: Flexibilize "sophisticated" pepolar to allow monomodal execution #3393)
• ENH: Update FSL packages for reported bug fixes (ENH: update fsl packages for reported bug fixes #3374)
• RF: Calculate RMSD from motion transforms (rf: Calculate RMSD from motion transforms #3427)
• RF: Reconstruct motion confounds from minimal derivatives (rf: Reconstruct motion confounds from minimal derivatives #3424)
• RF: Replace deprecated pkgutil.find_loader (rf(py314): Replace deprecated pkgutil.find_loader #3384)
• RF: Upgrade nitransforms and remove workarounds (RF: Upgrade nitransforms and remove workarounds #3378)
• DOC: Fix xfm extension in the outputs docs ([DOC] fix xfm extension in the outputs docs #3435)
• DOC: Mention fMRIPost-AROMA in parser documentation (Mention fMRIPost-AROMA in parser documentation #3356)
• MNT: Remove CLI flags with expired deprecation periods (feat(cli): Remove CLI flags with expired deprecation periods #3445)
• MNT: Update pinned environment (chore(deps): Update pinned environment #3440)
• MNT: Bump pins, update RTD config (chore: Bump pins, update RTD config #3425)
• MNT: Declare linux/amd64 platform during Docker build (chore(docker): Declare linux/amd64 platform during build #3422)
• MNT: Bump astral-sh/setup-uv from 4 to 5 (Chore(deps): Bump astral-sh/setup-uv from 4 to 5 #3417)
• MNT: Test support for Python 3.13 (chore: Test support for Python 3.13 #3416)
• MNT: Install Workbench CLI via conda (chore(build): Install Workbench CLI via conda #3410)
• MNT: Update minimum dependencies, test with tox-uv (chore: Update minimum dependencies, test with tox-uv #3412)
• MNT: Install c3d through conda (Install c3d through conda #3382)
• CI: Fetch tags and 200 commits to support describe (CI: Fetch tags and 200 commits to support describe #3381)
• CI: Build docker images in GHA, store cache inline and push to GHCR (CI: Build docker images in GHA, store cache inline and push to GHCR #3380)

New Contributors

• @psadil made their first contribution in FIX: Repair search for precomputed transforms #3369

Full Changelog: 24.1.1...25.0.0

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This discussion was created from the release 25.0.0.