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.workflow.dmriprep.brainprep_dmriprep

brainprep.workflow.dmriprep.brainprep_dmriprep(t1_file, dwi_files, output_dir, keep_intermediate=False, **kwargs)[source]

Subject level diffusion MRI pre-processing.

Applies the following steps:

  1. Preprocessed diffusion weighted image (DWI) using MrTrix3 mrtrix3_connectome pipeline, preproc and participants steps.

  2. Compute diffusion tensor imaging (DTI) metrics using FSL dtifit

  3. Compute diffusion NODDI microstructural maps using AMICO (performed with default parameters).

The ROI-based structural connectivity is derived using the Brainnetome 246 (BNA246) ROI atlas. This atlas is composed of 210 cortical and 36 subcortical ROIs defined using structural connectivity, functional connectivity, and cytoarchitectonics.

Parameters:
t1_fileFile

Path to the input T1w image file.

dwi_fileslist[File]

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

output_dirDirectory

Directory where the prep-processing related outputs will be saved (i.e., the root of your dataset).

keep_intermediatebool

If True, retains intermediate results (i.e., the workspace); useful for debugging. Default False.

**kwargsdict
entities: dict

Dictionary of parsed BIDS entities.

Returns:
Bunch

A dictionary-like object containing:

  • dwi_preproc_file: File - pre-processed diffusion weighted image.

  • tractogram_file: File - the tractogram data.

  • mask_file: File - brain image file.

  • connectome_file: File - structural connectome data generated using the ‘craddock200’ atlas.

  • fa_file: File - DTI Fractional Anisotropy map.

  • md_file: File - DTI Mean Diffusivity map.

  • ndi_file: File - NODDI Neurite Density Index map.

  • fwf_file: File - NODDI Free Water Fraction map.

  • odi_file: File - NODDI Orientation Dispersion Index map.

  • geolab_labels_files: list[File] - text file containing geolab atlas tractogram labels.

  • tractseg_tractometry_files: list[File] - TractSeg tabular CSV tractometry data.

Raises:
ValueError

If the input T1w file is not BIDS-compliant.

Notes

This workflow assumes the T1w image is organized in BIDS.

References

Examples

TODO