Ubuntu / Debian Linux

Using the package manager, installation in Ubuntu and Debian is relatively straightforward.

For Ubuntu >= 16 the MOT package can be installed from our Personal Package Archive (PPA) using:

$ sudo add-apt-repository ppa:robbert-harms/cbclab
$ sudo apt-get update
$ sudo apt-get install python3-mdt python3-pip
$ sudo pip3 install tatsu

By using a PPA your Ubuntu system can update MDT automatically whenever a new version is out. Unfortunately there is no debian package for the Tatsu requirement yet, as such, we need to install it manually.

For Debian, and Ubuntu < 16, using a PPA is not possible (because of missing dependent packages) and we need a more manual installation. Please install the dependencies first:

$ sudo apt install python3 python3-pip python3-pyopencl \
    python3-numpy python3-nibabel python3-pyqt5 \
    python3-matplotlib python3-yaml python3-argcomplete \
    libpng-dev libfreetype6-dev libxft-dev

Note that python3-nibabel may need NeuroDebian to be available on your machine. An alternative is to use pip3 install nibabel instead.

Next, install MDT with:

$ sudo pip3 install mdt

This might recompile a few packages to use the latest versions.

Alternatively, you could try the Singularity recipe at , kindly made available by an user of MDT.

A docker installation is also available. If you do, a tip from an MDT user is that “when you use Docker it is mandatory to mount the directory in the ~/.mdt/<latest version>/ inside container in order to work.”

After installation please continue with the section Initialization below.


MDT uses the Microstructure Optimization Toolbox (MOT) for all analysis computations. Please install MOT first ( Afterwards this installation should be fairly straightforward.

Note that MDT depends on PyQt5 so make sure you do not attempt to run it in an environment with PyQt4 or earlier. If you followed the MOT install guide and installed the Anaconda version 4.2 or higher with Python3.x, you should be fine. Again, see for details.

Having followed the MOT install guide we can now install MDT. Open an Anaconda console and use:

$ pip install mdt

If that went well please continue with the Initialization below.


Installation on Mac is pretty easy using the Anaconda 4.2 or higher Python distribution. Please download and install the Python3.x 64 bit distribution, version 4.2 or higher which includes PyQt5, from Anaconda and install it with the default settings.

Afterwards, open a terminal and type:

$ pip install mdt

To install MDT to your system. If that went well please continue with the Initialization below.

Please note that Mac support is experimental due to the unstable nature of the OpenCL drivers in Mac. Users running Running MDT with the GPU as selected device may experience crashes. Running MDT in the CPU seems to work though.


After installation we need to initialize the MDT components folder in your home folder. Use:

$ mdt-init-user-settings

in your bash or Anaconda console to install the MDT model library to your home folder.

Test the installation

If all went well and MDT is installed and initialized, we can now perform some basic tests to see if everything works well. The first command to try is:

$ mdt-list-devices

which should print to the console a list of available CL devices. If this crashes or if there are no devices returned, please check to see if your OpenCL drivers are correctly installed. If it works but no devices can be found then please refer to the section No OpenCL device found.

Next, one could try starting the graphical interface using:

$ mdt-gui

or, equivalently,


This should start the GUI. If there are problems in this stage it is most likely related to Qt problems. Please check if you have installed the Qt5 package and not the Qt4 package.