func_processing.resources.fmriprep package
Submodules
func_processing.resources.fmriprep.preprocess module
Functions for running fMRIprep.
Run FreeSurfer and fMRIprep.
- func_processing.resources.fmriprep.preprocess.run_fmriprep(subj, scratch_deriv, scratch_dset, sing_img, tplflow_dir, fs_license)
Run fMRIprep.
Utilize singularity image of nipreps/fmriprep. The spaces is currently hardcoded for the EMU project. Also references the FreeSurfer priors that should have previously been generated.
- Parameters
subj (str) – BIDS subject string
scratch_deriv (str) – path to /scratch/foo/derivatives
scratch_dset (str) – path to /scratch/foo/dset
sing_img (str) – path to fmriprep singularity image
tplflow_dir (str) – path to templateflow directory
fs_license (str) – path to FreeSurfer license
- func_processing.resources.fmriprep.preprocess.run_freesurfer(subj, subj_t1, freesurfer_dir, work_dir)
Run FreeSurfer.
Convert the subject’s T1w file into mgz format and place in required location. Then run FreeSurfer.
While 4 cpus is default for -parallel, -openmp supplied for ease of increasing resources. Make sure to update submit.submit_hpc_sbatch usage as well.
- Parameters
subj (str) – BIDS subject string
subj_t1 (str) – path to subject’s T1w file
freesurfer_dir (str) – path to derivatives/freesurfer
work_dir (str) – path to working/scratch/fmriprep/subj