Bring ASLPrep in line with fMRIPrep 25.0.0

[tsalo]

Closes #502. The trick I used was to create branches from 24.0.0 and 25.0.0 on my fMRIPrep fork and then squash and merge 25.0.0 into 24.0.0 to see the final set of changes in the commit's diff.

Changes proposed in this pull request

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[tsalo]

The current changes make the GE results look terrible. I don't think the M0 scan is being selected as the reference image.

[tsalo]

I fixed it, but the coregistration still doesn't look good.

[Copilot]

Pull Request Overview

This PR updates ASLPrep to align with fMRIPrep 25.0.0, introducing a unified --force CLI option, enhanced fieldmap precomputation, and propagation of Jacobian correction flags across workflows.

• Replace separate --force-ge, --force-syn, etc., with a single --force list and deprecate old flags
• Add caching for BIDSLayout, adjust collect_derivatives to include precomputed transforms, and buffer precomputed fieldmaps in init_single_subject_wf
• Introduce jacobian parameter throughout ASL workflows and update reporting interfaces

Reviewed Changes

Copilot reviewed 23 out of 23 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
aslprep/workflows/base.py	Fieldmap caching and buffer setup for precomputed maps
aslprep/workflows/asl/fit.py	Added jacobian flag propagation and replaced movpar/rmsd outputs
aslprep/cli/parser.py	Unified deprecated flags into new --force option
aslprep/utils/bids.py	Cached BIDSLayout and refined collect_derivatives queries
aslprep/data/reports-spec.yml	Updated caption to reference the new --force syntax

Comments suppressed due to low confidence (1)

tests/test_cli.py:239

• The new '--force' options (e.g., 'fmap-jacobian', 'ge', 'no-ge') lack dedicated tests. Add unit tests to verify these flags correctly influence workflow behavior, including Jacobian propagation.

--force

[Copilot]

Pull Request Overview

This pull request updates ASLPrep to align with fMRIPrep 25.0.0 by incorporating revised fieldmap estimation logic, improving workflow connections, and updating command‐line flags and configurations.

• Revised key workflows (base, fit, outputs, etc.) to integrate new fieldmap handling and logging.
• Changed variable names and flag syntax (e.g., renaming sbref_file to sbref_files and using the new --force flag patterns).
• Updated tests and configuration files for consistency with the new code changes.

Reviewed Changes

Copilot reviewed 23 out of 23 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
aslprep/workflows/base.py	Added logging for precomputed T1w and updated fieldmap estimation.
aslprep/workflows/asl/outputs.py	Included ‘asl_mask’ in outputs and updated node connections.
aslprep/workflows/asl/fit.py	Renamed sbref variable to sbref_files and updated transform nodes.
aslprep/cli/parser.py	Updated deprecated flag handling with DeprecatedAction.
aslprep/tests/*	Adjusted expected outputs and CLI flags to match new changes.
aslprep/config.toml and others	Modified configuration parameters to reflect fMRIPrep 25.0.0 updates.

[tsalo]

The coregistration looks comparable between the old and new versions, so I'm going to merge.