Use MrTrix with vistasoft

This page describes how to use MRTrix with vistasoft.

MRtrix is a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibers, using constrained spherical deconvolution (CSD) and probabilistic streamlines. This page describes how to install and use this package with vistasoft. Elsewhere, we describe how to run MRtrix on local data. We often use MRtrix along with the Linear Fascicle Evaluation (LiFE) technology. We describe how to run LiFE on a separate page .

This page still assumes MRTrix version 2. Now MRTrix team developed the later version of the MRTrix, MRTrix version 3. The functions in vistasoft is only compatible with MRTrix version 2 now.

See [MRTrix Examples](MRTrix Examples) for a example usage with vistasoft.

Install MRtrix

If you are running Ubuntu, mrtrix is part of the neurodebian command set. You should check to see that [the neurodebian repo] (http://neuro.debian.net/#) is installed, and then use that to install the mrtrix package.

MRtrix can also be downloaded from [this site] (https://www.nitrc.org/projects/mrtrix/).

There is a github repository for [the developmental version] (https://github.com/jdtournier/mrtrix3).

** Write bashrc example in Ubuntu **

See Michael Perry about dockerization.

Build MRTrix

See the [MRtrix documentation] (http://jdtournier.github.io/mrtrix-0.2/install/unix.html) for information on building, required libraries.

Enable Multi-threading

By default MRtrix will read a configuration file for additional options. Among those options is Multi-Threading. The configuration file (.mrtrix.conf) should be stored in your home directory. Run the following command in your shell to enable the multi-threading option in MRtrix - you can adjust the number of threads as you like.

echo "NumberOfThreads: 4" > $HOME/.mrtrix.conf

Setting the number of threads to a large value (e.g., 130) will use all the available cores on the current machine without crashing. See the [MRtrix documentation] (http://jdtournier.github.io/mrtrix-0.2/install/unix.html) for more info.

Run MRTrix

To check that you can run MRtrix (ie that the install went ok) try:

mrview

If you get a window, relax, everything worked out just fine.