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.mrtrix3.dwi_preproc

brainprep.interfaces.mrtrix3.dwi_preproc(t1_file, dwi_files, workspace_dir, output_dir, entities)[source]

Preprocessed BIDS-compliant diffusion weighted image (DWI) using MrTrix3 mrtrix3_connectome pipeline.

The operations performed by the preproc step:

  • DWI: Denoising; Gibbs ringing removal; motion, eddy current and EPI distortion correction and outlier detection & replacement; brain masking, bias field correction and intensity normalization; rigid-body registration & transformation to T1-weighted image.

  • T1-weighted image: bias field correction; brain masking.

And the the participant step:

  • DWI: Response function estimation; FOD estimation.

  • T1-weighted image: Tissue segmentation; gray matter parcellation.

  • Combined: Whole-brain streamlines tractography; SIFT2; connectome construction.

Parameters:
t1_fileFile

Path to the input T1w image file.

dwi_fileslist[File]

Path to the input diffusion weighted image files of one subject.

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:
commandslist[list[str]]

DWI preprocessing command-lines.

outputstuple[File]

  • dwi_preproc_file : File - The preprocessed DWI image file.

  • wm_fod_file : File - The WM fiber orientation distributions file.

  • tractogram_file : File - The tractogram file.

  • mask_file : File - The brain mask file.

  • connectome_file : File - The structural connectome file.

  • affine_file : File - Path to the MNI template to T1 affine transform.

  • warp_file : File - Path to the MNI template to T1 warp.

  • invwarp_file : File - Path to the T1 to MNI template warp.