dmriprep.workflows.base module

dMRIPrep base processing workflows.

dmriprep.workflows.base.clean_datasinks(workflow)View on GitHub
dmriprep.workflows.base.get_estimator(layout, fname)View on GitHub
dmriprep.workflows.base.init_dmriprep_wf()View on GitHub

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, session_id=None, name=None)View on GitHub

Organize 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

  • session_id – Session label(s) for this workflow.

  • name – Name of the workflow. If not provided, will be set to sub_{subject_id}_ses_{session_id}_wf.

Inputs:

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

dmriprep.workflows.base.map_fieldmap_estimation(layout, subject_id, dwi_data, ignore_fieldmaps, use_syn, force_syn, filters)View on GitHub