smriprep.workflows.base module

sMRIPrep base processing workflows.

smriprep.workflows.base.init_single_subject_wf(*, sloppy, debug, derivatives, freesurfer, hires, fs_no_resume, layout, longitudinal, low_mem, msm_sulc, name, omp_nthreads, output_dir, skull_strip_fixed_seed, skull_strip_mode, skull_strip_template, spaces, subject_id, bids_filters, cifti_output)[source]

Create a single subject workflow.

This workflow organizes the preprocessing pipeline for a single subject. It collects and reports information about the subject, and prepares sub-workflows to perform anatomical and functional preprocessing.

Anatomical preprocessing is performed in a single workflow, regardless of the number of sessions. Functional preprocessing is performed using a separate workflow for each individual BOLD series.

Workflow Graph: (Source code)

Parameters:

sloppy (bool) – Quick, impercise operations. Used to decrease workflow duration.
debug (bool) – Enable debugging outputs
derivatives (list of directories) – Fast-track the workflow by searching for existing derivatives.
freesurfer (bool) – Enable FreeSurfer surface reconstruction (may increase runtime)
hires (bool) – Enable sub-millimeter preprocessing in FreeSurfer
fs_no_resume (bool) – Adjust pipeline to reuse base template of an existing longitudinal freesurfer output
layout (BIDSLayout object) – BIDS dataset layout
longitudinal (bool) – Treat multiple sessions as longitudinal (may increase runtime) See sub-workflows for specific differences
low_mem (bool) – Write uncompressed .nii files in some cases to reduce memory usage
name (str) – Name of workflow
omp_nthreads (int) – Maximum number of threads an individual process may use
output_dir (str) – Directory in which to save derivatives
skull_strip_fixed_seed (bool) – Do not use a random seed for skull-stripping - will ensure run-to-run replicability when used with –omp-nthreads 1
skull_strip_mode (str) – Determiner for T1-weighted skull stripping (force ensures skull stripping, skip ignores skull stripping, and auto automatically ignores skull stripping if pre-stripped brains are detected).
skull_strip_template (Reference) – Spatial reference to use in atlas-based brain extraction.
spaces (SpatialReferences) – Object containing standard and nonstandard space specifications.
subject_id (str) – List of subject labels
bids_filters (dict) – Provides finer specification of the pipeline input files through pybids entities filters. A dict with the following structure {<suffix>:{<entity>:<filter>,…},…}

Inputs:

subjects_dir – FreeSurfer SUBJECTS_DIR

smriprep.workflows.base.init_smriprep_wf(*, sloppy, debug, derivatives, freesurfer, fs_subjects_dir, hires, fs_no_resume, layout, longitudinal, low_mem, msm_sulc, omp_nthreads, output_dir, run_uuid, skull_strip_mode, skull_strip_fixed_seed, skull_strip_template, spaces, subject_list, work_dir, bids_filters, cifti_output)[source]

Create the execution graph of sMRIPrep, 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: (Source code)

Parameters:

sloppy (bool) – Quick, impercise operations. Used to decrease workflow duration.
debug (bool) – Enable debugging outputs
derivatives (list of directories) – Fast-track the workflow by searching for existing derivatives.
freesurfer (bool) – Enable FreeSurfer surface reconstruction (may increase runtime)
fs_subjects_dir (os.PathLike or None) – Use existing FreeSurfer subjects directory if provided
hires (bool) – Enable sub-millimeter preprocessing in FreeSurfer
layout (BIDSLayout object) – BIDS dataset layout
longitudinal (bool) – Treat multiple sessions as longitudinal (may increase runtime) See sub-workflows for specific differences
low_mem (bool) – Write uncompressed .nii files in some cases to reduce memory usage
msm_sulc (bool) – Run Multimodal Surface Matching with sulcal depth maps
omp_nthreads (int) – Maximum number of threads an individual process may use
output_dir (str) – Directory in which to save derivatives
run_uuid (str) – Unique identifier for execution instance
skull_strip_fixed_seed (bool) – Do not use a random seed for skull-stripping - will ensure run-to-run replicability when used with –omp-nthreads 1
skull_strip_mode (str) – Determiner for T1-weighted skull stripping (force ensures skull stripping, skip ignores skull stripping, and auto automatically ignores skull stripping if pre-stripped brains are detected).
skull_strip_template (Reference) – Spatial reference to use in atlas-based brain extraction.
spaces (SpatialReferences) – Object containing standard and nonstandard space specifications.
subject_list (list) – List of subject labels
work_dir (str) – Directory in which to store workflow execution state and temporary files
bids_filters (dict) – Provides finer specification of the pipeline input files through pybids entities filters. A dict with the following structure {<suffix>:{<entity>:<filter>,…},…}