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.
- Python3 (>=3.7)
- argparse (>=1.4.0)
- numpy (>=1.16.5)
- scipy (>=1.3.1)
- nibabel (>=3.1.0)
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 parameter maps in NIfTI-1 format (*.nii.gz
), including:
- Orientation dispersion index (
DTINODDI_ODI
) - Intracellular volume fraction, aka neurite density index (
DTINODDI_ICVF
) - Fractinoal anisotropy (
DTINODDI_FA
) Using standard DTI. - Mean diffusivity (
DTINODDI_MD
) Using standard DTI, but correct for b-value.
- 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
- 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.
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/.