====== fmriprep ======

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

Also see [[:tools:fmri_preproc]], [[:tools:preprocessfunctional]]

Follow up ''fmriprep'' outputs (''*_desc-preproc_bold.nii.gz'') with [[:tools:xcpd]].

Example usage:
  * ''Hera/Projects/Habit/mr/fmriprep_habitstudy.bash''

===== Considerations =====

  * fmriprep can reuse freesurfer when run before (otherwise will run minimal version internally).
  * When in [[:tools: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.