DTI-NODDI

Daisuke Matsuyoshi (National Institute for Radiological Sciences (QST-NIRS) and Araya, Inc.)

Implementation of diffusion tensor image based neurite orientation dispersion and density imaging (DTI-NODDI) written in Python.

Installation

Python

• Python3 (>=3.7)

Package dependencies

• argparse (>=1.4.0)
• numpy (>=1.16.5)
• scipy (>=1.3.1)
• nibabel (>=3.1.0)

Usage

Basic usage

dti_noddi_fit.py <b-value> --L1 <L1 file> --L2 <L2 file> --L3 <L3 file> [options]
dti_noddi_fit.py <b-value> --FA <FA file> --MD <MD file> [options]

Output

Output parameter maps in NIfTI-1 format (*.nii.gz), including:

1. Orientation dispersion index ( DTINODDI_ODI )
2. Intracellular volume fraction, aka neurite density index ( DTINODDI_ICVF )
3. Fractinoal anisotropy ( DTINODDI_FA ) Using standard DTI.
4. Mean diffusivity ( DTINODDI_MD ) Using standard DTI, but correct for b-value.

Examples

• Using eigenvalue files (if b-value is 2000 s/mm-2)
  • Will output DTINODDI_ODI, DTINODDI_ICVF, DTINODDI_FA, and DTINODDI_MD files.

$ python dti_noddi_fit.py 2000 --L1 L1.nii.gz --L2 L2.nii.gz --L3 L3.nii.gz

• Using FA and MD files (if b-value is 1000 s/mm-2)
  • Will output DTINODDI_ODI, and DTINODDI_ICVF files.

$ python dti_noddi_fit.py 1000 --FA FA.nii.gz --MD MD.nii.gz

• [options] --mask
  • Applying a binary mask image

$ python dti_noddi_fit.py 2000 --L1 L1.nii.gz --L2 L2.nii.gz --L3 L3.nii.gz --mask DWI_nodif_brain_mask.nii.gz

• [options] --MK
  • Heuristic correction for diffusional kurtosis (using mean kurtosis)

$ python dti_noddi_fit.py 2000 --L1 L1.nii.gz --L2 L2.nii.gz --L3 L3.nii.gz --MK MK.nii.gz

Reference

• Edwards LJ, Pine KJ, Ellerbrock I, Weiskopf N, Mohammadi S (2017) NODDI-DTI: Estimating neurite orientation and dispersion parameters from a diffusion tensor in healthy white matter. Front Neurosci 11:720.

License

The DTI-NODDI is free but copyright software, distributed under the terms of the GNU Affero General Public License v3.0.

Copyright (C) 2020 Daisuke Matsuyoshi

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see https://www.gnu.org/licenses/.