dmriprep.workflows.base module

dMRIPrep base processing workflows.

dmriprep.workflows.base.init_dmriprep_wf()

Create the base workflow.

This workflow organizes the execution of dMRIPrep, with a sub-workflow for each subject. If FreeSurfer’s recon-all is to be run, a FreeSurfer derivatives folder is created and populated with any needed template subjects.

Workflow Graph
../_images/dmriprep-workflows-base-1.png

(Source code, png, svg, pdf)

dmriprep.workflows.base.init_single_subject_wf(subject_id)

Set-up the preprocessing pipeline for a single subject.

It collects and reports information about the subject, and prepares sub-workflows to perform anatomical and diffusion MRI preprocessing.

Anatomical preprocessing is performed in a single workflow, regardless of the number of sessions. Diffusion MRI preprocessing is performed using a separate workflow for a full DWI entity. A DWI entity may comprehend one or several runs (for instance, two opposed PE directions.

Workflow Graph
../_images/dmriprep-workflows-base-2.png

(Source code, png, svg, pdf)

Parameters

subject_id (str) – List of subject labels

Inputs

subjects_dir (os.pathlike) – FreeSurfer’s $SUBJECTS_DIR