Maastricht Diffusion Toolbox
Project description
The Maastricht Diffusion Toolbox, MDT, is a framework and library for parallelized (GPU and multi-core CPU) diffusion Magnetic Resonance Imaging (MRI) modeling. MDT’s object oriented and modular design allows arbitrary user specification and combination of: biophysical MRI compartment models, diffusion- and T1, T2, T2* based microstructure models, likelihood functions and optimization algorithms. MDT was designed with compatibility in mind and adheres to input, output and variable names conventions used by other related software tools. Many diffusion and relaxometry microstructure models are included, and new models can be added simply by adding Python script files. MDT can be extended to other modalities and other parametric models estimated from data volumes varying along controlled parameters (such as b-values, diffusion times, TE, TM, flip angle, etc). The parallelized accelerated computations allow for tens to hundred times faster model fitting, even on standard GPU hardware, which makes MDT ideal for large group studies or population studies.
Summary
Free software: LGPL v3 license
Python and OpenCL based
GUI, command line and python interface
Scriptable modeling: write new compartment equations and combine compartments into models
Full documentation: http://maastrichtdiffusiontoolbox.readthedocs.io
Project home: https://github.com/cbclab/MDT
Uses the GitLab workflow
Tags: diffusion, dMRI, MRI, optimization, parallel, opencl, python
Quick installation guide
The basic requirements for MDT are:
Python 3.x (recommended) or Python 2.7
OpenCL 1.2 (or higher) support in GPU driver or CPU runtime
Linux
For Ubuntu >= 16 you can use:
sudo add-apt-repository ppa:robbert-harms/cbclab
sudo apt-get update
sudo apt-get install python3-mdt
For Debian users and Ubuntu < 16 users, install MDT with:
sudo apt-get install python3 python3-pip python3-pyopencl python3-numpy python3-nibabel python3-pyqt5 python3-matplotlib python3-six python3-yaml python3-argcomplete libpng-dev libfreetype6-dev libxft-dev
sudo pip3 install mdt
Note that python3-nibabel may need NeuroDebian to be available on your machine. An alternative is to use pip3 install nibabel instead.
Windows
The installation on Windows is a little bit more complex and the following is only a quick reference guide. For complete instructions please view the complete documentation.
Install Anaconda Python 3.5
Install MOT using the guide at https://mot.readthedocs.io
Open a Anaconda shell and type: pip install mdt
For more information and installation instructions, please see: https://maastrichtdiffusiontoolbox.readthedocs.org
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