ENH: Add dedicated session filtering, alternative anatomical template options #3495
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| processing_groups = None | ||
| """List of tuples (participant, session(s)) that will be preprocessed.""" |
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This is derived from participant_label, session_label and subject_anatomical_reference. Might be handy for reporting, but it does mean that the config object state can be inconsistent.
IMO it would be better just to calculate the groups when needed with a well-isolated function rather than deal with (de)serialization and consistency.
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i also considered omitting, but decided to include it since having that provenance is nice. session_label is only populated if --session-label is used, otherwise all sessions pertaining to that subject are queried from the layout (and that information is not currently being stored). the config object should never be changed, just the dict representation of it (and when dumping to toml).
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Co-authored-by: Taylor Salo <[email protected]>
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| if not sessions: | ||
| raise RuntimeError( | ||
| '`--subject-anatomical-reference sessionwise` was requested, but no sessions ' | ||
| f'found for subject {subject}.' | ||
| ) |
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This seems like it shouldn't be an error. No sessions is the same as a single session, so I would expect it to work the same. I think changing this to:
if subject_anatomical_reference == 'sessionwise' and sessions:
subject_session_list.extend((subject, session) for session in sessions)
else:
subject_session_list.append((subject, sessions))should cover your use cases... That said, this isn't tested, so it's hard to figure out what's happening.
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was maintaining the logic first implemented in smriprep, but i agree that raising an error is a bit too strict - imo, a warning would suffice.
Co-authored-by: Chris Markiewicz <[email protected]>
25.2.0 (October 01, 2025) New feature release in the 25.2.x series. This release is an *fMRIPrep Long-Term Support (LTS)* release. The planned support window is 4 years, until October 2029. This release is an incremental improvement over 25.1.x, but includes some fixes and improvements that do not fit within our `bug-fix policy <https://www.nipreps.org/devs/releases/#bug-fix-releases>`__. Importantly, the change in interpolation in 25.1.0 introduced artifacts for some datasets. This release changes the default interpolation mode to ``grid-constant``, which resolves those problems while not reintroducing the issue the previous release sought to fix. This release also (finally) introduces per-session processing. The ``--session-label`` flag selects the sessions to process, and the ``--subject-anatomical-reference`` flag indicates whether and how to combine across sessions. Existing filters passed via ``--bids-filter-file`` may need to be updated or removed in favor of using these flags to achieve the desired behavior. We would like to thank the AMP-SCZ and ENIGMA consortia for testing out and providing feedback on this release. * FIX: Clean up output report language (#3529) * FIX: Default to grid-constant interpolation mode (#3516) * FIX: Adapt to transposed ndcoords in nitransforms (#3517) * FIX: Write out Freesurfer-derived outputs (#3512) * FIX: Add kwargs to _warnings.py (#3483) * ENH: Resample BOLD data to any surface template space using the Connectome Workbench (#3461) * ENH: Add boldref / sbref to source metadata (#3532) * ENH: Add dedicated session filtering, alternative anatomical template options (#3495) * ENH: Write out goodvoxels mask (#3513) * ENH: Add registration metadata to boldref-to-anat transforms (#3500) * ENH: Write out cortex mask GIFTIs (#3491) * ENH: Update transforms.py according to new transform chain of nitransforms (#3494) * RF/DOC: Improve and document command-line parser defaults (#3487) * DOC: Explain better SDC and B0FieldSource requirement (#2768) * DOC: Document `freesurfer` parameter in BOLD confound workflow init (#3504) * DOC: Add myself to contributor list (#3506) * DOC: Fix non-standard Input/Output docstring section management (#3505) * MNT: Split Dockerfile into base and pixi layers (#3521) * MNT: Replace conda with pixi and lock (#3503) * MNT: Update license metadata using SPDX expression (#3486) * MNT: no need to re-run `ruff check` after `ruff format` (#3480) * MNT: Update pre-commit ruff legacy alias (#3479)
3 participants
Builds off nipreps/smriprep#480
Adds new arguments:
--session-labelfor a more streamlined way to filter sessions--subject-anatomical-referenceto determine how the reference anatomical should be constructed.