Note

This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the user guide for the big picture.

brainprep.interfaces.fmriprep.fmriprep_wf

brainprep.interfaces.fmriprep.fmriprep_wf(t1_file, func_files, dataset_description_file, freesurfer_dir, workspace_dir, output_dir, entities)[source]

Compute fMRI prep-processing using fMRIPrep.

Parameters:
t1_fileFile

Path to the input T1w image file.

func_fileslist[File]

Path to the input functional image files of one subject.

dataset_description_fileFile

Path to the BIDS dataset description file.

freesurfer_dirDirectory

Path to an existing FreeSurfer subjects directory where the reconall command has already been performed.

workspace_dir: Directory

Working directory with the workspace of the current processing, and where subject specific data are symlinked.

output_dirDirectory

Directory where the prep-processing related outputs will be saved

entitiesdict

A dictionary of parsed BIDS entities including modality.

Returns:
commandlist[str]

Pre-processing command-line.

outputstuple[File | list[File]]

  • mask_files : File - Brain masks in template spaces.

  • fmri_image_files : list[File] - Pre-processed rfMRI volumes: T1w and MNI152NLin2009cAsym.

  • fmri_surf_files: File - Pre-processed rfMRI surfaces: fsnative and fsLR23k.

  • confounds_file : File - File with calculated confounds.

  • qc_file : File - Visual report.

Raises:
ValueError

If the ‘FREESURFER_HOME’ environment variable is not defined.

Notes

  • Creates BIDS subject specific working directory using copy in ‘rawdata’ folder.

  • Create FreeSurfer subject directory using copy in ‘freesurfer’ folder.

  • To avoid paths that are too long and not allowed by FreeSurfer, use the ‘/tmp’ directory. To prevent data leakage, please bind ‘/tmp’ to a secure location.

  • Store intermediate pre-processing outputs in ‘work’.

  • Use as many CPUs as available.