These folders have the scripts for running the fMRI analysis pipeline, written in python and bash:
- Converting from raw DICOMS to run-separated data in BIDS specification
- Preprocessing using fMRIPrep
- The data are first run through the anatomical-only workflow using freesurfer within fMRIPrep because some participants only have structural data
- The data are then run through the rest of the fMRIPrep workflow including:
- Separating brain from skull, calculating brain tissue segmentation, spatial normalization
- Confound estimation
- Motion estimation for data exclusion
- First-level modeling
- Second-level modeling
See the Wiki page for more detailed information about running each step of the pipeline.