feat(cli): Create --force flag that accepts a list, replacing individual --force-* flags
#3442
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## master #3442 +/- ##
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+ Coverage 72.37% 72.96% +0.59%
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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)
* 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)
* RF: Upgrade nitransforms and remove workarounds (#3378)
* DOC: Fix xfm extension in the outputs docs (#3435)
* DOC: Mention fMRIPost-AROMA in parser documentation (#3356)
* MNT: Remove CLI flags with expired deprecation periods (#3445)
* MNT: Update pinned environment (#3440)
* MNT: Bump pins, update RTD config (#3425)
* MNT: Declare linux/amd64 platform during Docker build (#3422)
* MNT: Bump astral-sh/setup-uv from 4 to 5 (#3417)
* MNT: Test support for Python 3.13 (#3416)
* MNT: Install Workbench CLI via conda (#3410)
* MNT: Update minimum dependencies, test with tox-uv (#3412)
* MNT: Install c3d through conda (#3382)
* CI: Fetch tags and 200 commits to support describe (#3381)
* CI: Build docker images in GHA, store cache inline and push to GHCR (#3380)
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This is in preparation to allow
--force fmap-jacobian(see #3367). I want to first establish the--forceflag as a replacement for--force-bbr,--force-no-bbrand--force-syn.cc @mgxd @oesteban I'm not sure if we've talked about this before. I think it's an overall worthwhile cleanup.