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.geolab_parcellation¶
- brainprep.interfaces.geolab_parcellation(tractogram_file, affine_file, invwarp_file, workspace_dir, output_dir, entities)[source]¶
Superficial white matter (SWM) parcellation.
Superficial white matter (SWM) parcellation was performed using GeoLab, a geometry-based tractography parcellation framework that segments hundreds of short-range bundles by combining streamline-geometry features with atlas-based registration.
- Parameters:
- tractogram_fileFile
Path to the tractogram file of one subject.
- affine_fileFile
Path to the MNI template to T1 affine transform.
- invwarp_fileFile
Path to the T1 to MNI template warp.
- 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]
mrtrix_warp_file : File - T1 to template MrTrix warp file.
labels_file : File - Text file containing atlas tractogram labels.
qc_file : File - TSV file containing the template overlap scores.