Workflows (Preprocessing → Longitudinal Statistics)

This repo is built around two workflows:

Preprocessing: run CAT12 standalone on a BIDS dataset and produce BIDS-derivatives outputs.
Statistics: run a longitudinal group model (VBM or surface modalities) on CAT12 outputs, screen contrasts, and optionally run TFCE correction.

Workflow A — Preprocessing (BIDS App style)

Entry point: ./cat12_prepro

Inputs:

BIDS dataset (bids_dir)
Output derivatives directory (output_dir)

Outputs (typical):

output_dir/dataset_description.json
output_dir/sub-*/ses-*/mri/… (VBM volumes like mwp1*, optionally smoothed)
output_dir/sub-*/ses-*/surf/… (thickness etc., optionally resampled/smoothed)
output_dir/quality_measures_*.csv, TIV.txt (if enabled)

Longitudinal behavior:

If a subject has 2+ sessions, the processor selects the CAT12 longitudinal batch template.
If a subject has 1 session, it runs the cross-sectional template.

Workflow B — Longitudinal statistics

Entry point: ./cat12_stats

Inputs (standard mode):

--cat12-dir: the preprocessing output directory
--participants: a BIDS participants.tsv

Outputs (typical):

results/<modality>/<analysis_name>/
- SPM.mat, contrast images, screening summary
- TFCE outputs (when enabled)
- report.html
- logs/pipeline.log

TFCE behavior:

The pipeline supports a two-stage (probe → full) strategy by default to detect permutation instability and adjust nuisance handling.

Recommended end-to-end pattern

# 1) Preprocess into derivatives
./cat12_prepro /data/bids /data/derivatives/cat12 participant --preproc --qa --tiv

# 2) Run longitudinal group analysis
./cat12_stats --cat12-dir /data/derivatives/cat12 --participants /data/bids/participants.tsv --modality vbm