Add BIDS entrypoint, smoke tests, and routing fixes#841
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karl-koschutnig wants to merge 2 commits into
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Add BIDS entrypoint, smoke tests, and routing fixes#841karl-koschutnig wants to merge 2 commits into
karl-koschutnig wants to merge 2 commits into
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- Introduced run_fastsurfer_bids.py as a BIDS-App entrypoint for FastSurfer. - Added BIDS dataset discovery and processing logic. - Updated README.md to include usage instructions for BIDS. - Created BIDS.md documentation for detailed BIDS entrypoint information. - Added integration tests for BIDS functionality and fetching OpenNeuro dataset. - Included necessary dependencies in pyproject.toml for BIDS support.
- Added a developer-oriented smoke test for the BIDS add-on. - Updated `test_bids_openneuro.sh` to include new usage options. - Introduced `_requires_cross_sectional_passthrough` function to handle passthrough flags. - Added tests for the new passthrough functionality. - Improved documentation in BIDS.md and README.md for clarity on new options.
Member
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Hi , thanks, we will take a look. One thing up front, fixes should not be mixed into feature PRs . Can you do a separate PR for the CC numpy 2 fix (and @ClePol can check that). After merging it, we can rebase this one. |
Author
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Thanks, Martin, for your prompt response. |
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Description
This PR adds initial BIDS support to FastSurfer via a new run_fastsurfer_bids.py entrypoint.
Scope
Tests / developer workflow
Routing fix
During testing, --seg_only exposed an invalid path where multi-session BIDS subjects were still being sent to long_fastsurfer.sh, which does not support --seg_only / --surf_only.
This PR fixes that by forcing cross-sectional routing when those passthrough flags are present.
Additional fix included
While validating cross-sectional runs, the Corpus Callosum pipeline failed under NumPy 2.x because it used np.cross() on 2D vectors. This PR replaces those calls with an explicit signed 2D cross-product and adds a regression test.
Validated
Out of scope / missing