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.tractseg.tractseg_parcellation

brainprep.interfaces.tractseg.tractseg_parcellation(fod_file, mrtrix_warp_file, scalar_map_files, scalar_map_names, workspace_dir, output_dir, entities)

White matter (WM) parcellation.

White-matter bundle segmentation was performed using TractSeg, a deep-learning-based framework that directly predicts tract-specific segmentations, orientations, and tractograms from diffusion-derived fiber-orientation peaks. This approach enables fast and anatomically consistent delineation of major white-matter pathways without requiring whole-brain tractography or atlas registration.

Parameters:

fod_fileFile

Path to the fiber orientation distributions (FOD) file of one subject.

mrtrix_warp_fileFile

T1 to MNI MrTrix warp file.

scalar_map_fileslist[File]

Scalar maps (i.e., FA, MD, …) used to derive tractometry data.

scalar_map_nameslist[str]

Names associated to scalar maps.

workspace_dir: Directory

Working directory with the workspace of the current processing.

output_dirDirectory

Directory where the reoriented image will be saved.

entitiesdict

A dictionary of parsed BIDS entities including modality.

Returns:

commandlist[list[str]]

Parcellation computation command-lines.

outputstuple[File]

• tractometry_files : list[File] - Generated tractometry data for each input scalar map.