fmriprep

Find full documentation on https://fmriprep.org/en/stable/

Also see fMRI Preprocessing, Preprocess Functional (Hallquist pipeline)

Follow up fmriprep outputs (*_desc-preproc_bold.nii.gz) with xcpd.

Example usage:

• Hera/Projects/Habit/mr/fmriprep_habitstudy.bash

• fmriprep can reuse freesurfer when run before (otherwise will run minimal version internally).
• When in Docker or using accross users, specify a shared templateflow directory to reduce redownloading templates (every run in case of docker).
• log files are per subject. Rerunning overwrites. For iterative runs of on going longitudinal data collection, use a separate _ses-$SES for each session.