This repository owns the project-specific harmonization of RF1 Shared Reward with OpenNeuro ds003745 version 2.1.1 plus the documented sub-144 event repair. It does not replace either source dataset and does not copy RF1 FEAT trees.
Start with CURRENT_STATUS.md and the Cooper handoff. The task-ready inventory is 744 runs / 393 subject-sessions before final imaging QC. Pooled full-trial activation and provisional VS-PPI L1/L2 processing and computational verification are complete. The separate canonical RF1 phase-resolved activation run is also complete: 655 runs / 346 subject-sessions (309 fixed-effects L2, 37 L1 passthroughs). All processing was performed on Linux2. Source-review resolutions and the current behavioral policy are documented in the status/handoff, not pending blanket recovery work.
Use the current contrast crosswalk for Cooper's input selection: full-trial punishment contrasts 27/28 map to RF1 phase-resolved 31/32. Do not mix these model families. The proposed pooled phase-resolved analysis still requires validated SRNDNA phase-resolved outputs.
There are two intentional models: rf1-sra-sharedreward fits RF1-only
phase-resolved activation (14 EVs/34 contrasts); this repository fits both
datasets with the pooled full-trial contract (28 activation contrasts; PPI
28 interactions + physiology COPE29). Shared grid/smoothed-BOLD resources do not
make those FEAT COPEs interchangeable.
ds003745 source BIDS RF1 canonical Linux2 BIDS/derivatives
fMRIPrep -> wsinc5 RF1 grid preprocessed RF1-grid BOLD
| |
+---- approved AFNI total-6-mm BOLD ----+
|
source events -> harmonized full-trial EVs |
| |
+--------- input QC / task gate -------+
|
sharedreward-aging pooled L1 / L2
(fit BOTH datasets here)
|
output audit + scientific exclusions -> L3
The experiments are not temporally identical. ds003745 was organized as 2 runs × 9 partner/valence blocks × 8 trials. Its published event_<partner>_<feedback> rows describe recoverable full-trial epochs (usually about 3.5 seconds), accompanied by block rows. Although decision and outcome displays were conceptually distinct, their exact phase boundaries are not assumed recoverable from the published files.
RF1 retains its richer canonical decision/outcome events. Cross-dataset harmonization happens only in this repository as a model-specific derivative:
- ds003745: retain published
event_<partner>_<feedback>onset/duration; - RF1: derive a full-trial epoch from validated decision onset through the matching outcome offset;
- harmonization never rewrites source BIDS; approved source corrections such as sub-144 are separately guarded and documented upstream;
- never manufacture phase-resolved ds003745 timing.
A block-level ds003745 model is scientifically legitimate as a sensitivity analysis, but is not automatically a pooled model because RF1 did not use the same historical block design.
Phase 0 approved a 6-mm total classic-FWHM target on 2026-08-23 after complete cross-dataset characterization. The original 765-run audit remains the smoothing-decision evidence; subsequent runs use the same fixed procedure and require the same achieved-smoothness QC. Pooled L3 remains out of scope at this stage.
The ds003745 cohort is resampled with a frozen run-level manifest, identity-grid AFNI wsinc5 interpolation for continuous BOLD, nearest-neighbor interpolation for masks, per-run grid checks, and an independent cohort audit. The sharper wsinc5 interpolant is used to minimize interpolation-induced smoothness while moving already-normalized MNI data onto the RF1 grid. Generated imaging remains under ignored derivatives/harmonized; only compact run records and QC tables belong in Git.
Baseline smoothness is measured from the exact RF1 analysis inputs and from paired ds003745 inputs before and after RF1-grid resampling. RF1 confounds are referenced from the authoritative rf1-sra-linux2/derivatives/fsl/confounds_tedana outputs rather than duplicated here. Both classic Gaussian FWHM and ACF parameters are retained. Matched preprocessing uses classic combined FWHM as the explicit 3dBlurToFWHM stopping criterion; ACF remains a diagnostic here and should be estimated from first-level residuals when it is used for cluster-based inference. The 6-mm target is total achieved smoothness, not an added 6-mm kernel. MRIQC may be added as complementary acquisition QC, but it does not replace analysis-input smoothness, tSNR, motion, or coverage characterization. Coverage preserves the historical inferior cerebellum/posterior-brainstem exemption through a provenance-tracked TemplateFlow-minus-exemption mask; this mask is distinct from the full TemplateFlow tSNR reference.
The complete 765-run preprocessing control confirmed that FEAT-equivalent nominal 6-mm SUSAN would yield materially greater total smoothness (mean 8.260 mm in ds003745 and 7.919 mm in RF1) than the approved AFNI total target (5.775 and 5.852 mm). Production therefore retains the AFNI-smoothed files and keeps FEAT smoothing at zero. The reproducible numerical summary and mean ± SEM figure are under qc/.
The current authoritative inventory contains 667 RF1 session-01 Shared Reward runs plus 100 ds003745 runs. Both sub-12032 runs completed incremental smoothing and input QC on September 2. The catch-up smoothing wrapper's nonzero exit concerned the already-approved sub-10657 exception; its skipped consolidated audit still needs an evidence-only closure, not another smoothing run. Five additional RF1 runs regained event timing through upstream source repair; the September 15 event audit and cohort rebuild incorporate the recovered sources. See the current status index for exact records.
Production L1 uses RF1's authoritative headerless TedanaPlusConfounds.tsv matrices. Single-echo ds003745 receives a provenance-tracked headerless matrix with the same fMRIPrep base columns, cosine regressors, and non-steady-state regressors; rejected TEDANA ICA components are RF1-only by design. Use --parallel-types to run activation and seed PPI together inside each bounded run-level worker (up to twice --jobs FEAT processes); the wrapper also retains a sequential default. Two eligible runs are combined with fixed effects; a one-run subject uses the L1 cope directly rather than a fictitious fixed-effects model.
See code/HARMONIZATION_AUDIT.md, docs/EXCLUSION_POLICY.md, and code/README.md. Run static/synthetic checks with make test.