Longitudinal metrics workflow Fix #200#297
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Thanks @jpillai00 — reusing Closed as part of #301 Stage 0. |
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Implement rbc longitudinal metrics: resolve per-regressor regressed_bold/cleaned_bold + brain mask from space-longitudinal functional derivatives, read TR from NIfTI header, and call single_session_metrics unchanged. Reuse cross-sectional export_metrics for BIDS output naming. Co-authored-by: Janhavi Pillai <janhavipillai3@gmail.com>
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) * Add longitudinal metrics orchestration (port from #297) Resolve per-regressor regressed/cleaned BOLD and brain mask from space-longitudinal derivatives, read TR from NIfTI header, call single_session_metrics unchanged. Reuse cross-sectional export_metrics for BIDS naming. Co-authored-by: Janhavi Pillai <janhavipillai3@gmail.com> * Add longitudinal QC, all pipeline, and full_pipeline tests QC: Dice/Jaccard between anat and BOLD brain masks in longitudinal space, pass threshold Dice >= 0.85. Viz tracked in #303/#304. All pipeline: template -> anat -> func -> metrics -> qc. Template writes to disk cross-session; per-session stages hand off func outputs in-memory. process_anat/process_func now return workflow outputs. CLI: Add --regressor and --task to `rbc longitudinal all`. Tests: Tier-4 full_pipeline tests for metrics, QC, and all-vs-sequential equivalence under tests/full_pipeline/longitudinal/. * Fix anat groupby dropping mask rows in longitudinal resolve T1w suffix filter in run() excluded masks from the DataFrame passed to process_anat, so resolve_longitudinal_anat couldn't find them. Drop the filter. Pre-existing Stage 4 bug exposed by new tests. * Add --regressor to longitudinal metrics CLI Replace DataFrame-based discovery (queried a non-existent 'reg' column) with explicit --regressor, matching cross-sectional. * Fix longitudinal all test fixture missing --session-label Fixture ran cross-sectional func only for ses-test but invoked `rbc longitudinal all` without --session-label, so it iterated ses-retest (no func derivatives) and crashed on an empty BOLD DataFrame. * Apply only participant filter to template discovery in all pipeline Template needs all sessions to find multi-session subjects. Session/task filters apply only to per-session stages, not discover_template_inputs. * Clean up tech debt: TR validation, FS auth, QC load_table TR: Promote resolve_tr/warn_implausible_tr to public API. Replace _read_header_tr with _read_derivative_tr that pipes through resolve_tr for validation and plausibility warnings. Add --tr override to longitudinal metrics CLI. FS auth: Rename _setup_freesurfer_auth -> setup_freesurfer_auth, export from template.py, import at module level in all.py. QC: Replace manual concat of session.anat + session.func + tpl_df with load_table, matching cross-sectional qc.py. --------- Co-authored-by: Janhavi Pillai <janhavi.pillai@gmail.com>
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draft for now.. need to test this! & this is based off #282
Extends the longitudinal pipeline to compute derivative metrics (ALFF, fALFF, ReHo, smoothing, z-scoring, and atlas-based timeseries extraction) on longitudinal-space BOLD, mirroring the existing cross-sectional metrics workflow.
Key changes:
bids/longitudinal.pyLongitudinalMetricsInputsTypedDict,resolve_longitudinal_metrics(resolves per-regressor regressed/cleaned BOLD and brain mask from longitudinal derivatives), andexport_longitudinal_metrics(delegates to existing export_metrics)orchestration/longitudinal.pyprocess_metricswhich resolves inputs, reads TR from nifti header, runssingle_session_metrics, and exports outputs; added metrics andatlas_filesparameters torun()cli/longitudinal.py--metricsflag and--atlasargument (defaulting to schaefer_200); TR and FWHM are not exposed as CLI params and use hardcoded defaults (read from header and 6mm respectively) to match cross-sectional behaviorNo changes to
workflows/metrics.py- single_session_metrics already works generically for both cross-sectional and longitudinal space.