# Welcome to the MRtrix3 user documentation!¶

MRtrix3 provides a large suite of tools for image processing, analysis and visualisation, with a focus on the analysis of white matter using diffusion-weighted MRI ([Tournier2019]). Features include the estimation of fibre orientation distributions using constrained spherical deconvolution ([Tournier2004]; [Tournier2007]; [Jeurissen2014]), a probabilisitic streamlines algorithm for fibre tractography of white matter ([Tournier2012]), fixel-based analysis of apparent fibre density and fibre cross-section ([Raffelt2012]; [Raffelt2015]; [Raffelt2017]), quantitative structural connectivity analysis ([Smith2012]; [Smith2013]; [Smith2015]; [Christiaens2015]), and non-linear spatial registration of fibre orientation distribution images ([Raffelt2011]). MRtrix3 also offers comprehensive visualisation tools in mrview.

These applications have been written from scratch in C++, using the functionality provided by Eigen, and Qt. The software is currently capable of handling DICOM, NIfTI and AnalyseAVW image formats, amongst others. The source code is distributed under the Mozilla Public License.

Use of the MRtrix3 software package in published works should be accompanied by the following citation:

J.-D. Tournier, R. E. Smith, D. Raffelt, R. Tabbara, T. Dhollander, M. Pietsch, D. Christiaens, B. Jeurissen, C.-H. Yeh, and A. Connelly. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 202 (2019), pp. 116–37.

Tip

Make sure to use the version of this documentation that matches your version of this software. You can select the version on the lower left of this page.

## Getting help¶

There are a variety of sources of help and information to bring you up to speed with MRtrix3. These include:

## Key features¶

While MRtrix3 is primarily intended to be used for the analysis of diffusion MRI data, at its fundamental level it is designed as a general-purpose library for the analysis of any type of MRI data. As such, it provides a back-end to simplify a large number of operations, many of which will be invisible to the end-user. Specifically, MRtrix3 features:

• a consistent command-line interface, with inline documentation for each command;
• universal import/export capabilities when accessing image data across all MRtrix3 applications;
• Multi-file numbered image support to load multiple images as a single multi-dimensional dataset;
• efficient use of Unix Pipelines for complex workflows;
• high performance on modern multi-core systems, with multi-threading used extensively throughout MRtrix3;
• available on all common modern operating systems (GNU/Linux, MacOSX, Windows);
• a consistent Coordinate system with most operations performed in scanner/world coordinates where possible.

## Installation¶

MRtrix3 runs on GNU/Linux, macOS, Microsoft Windows platforms, and other Unix platforms. For most users, the simplest way to install MRtrix3 is to use one of the pre-compiled packages. For details, please refer the main MRtrix website.

If the precompiled packages are not available, we provide specific instructions for building the software from source. This is normally a simple process, but does require more compute resources and expertise. See the relevant pages for details.

## Commands¶

The MRtrix3 software package includes a suite of tools for image analysis and visualisation. With the exception of mrview and shview, all MRtrix3 executables are designed to be run via a terminal using a consistent command-line interface. While many of the tools and features are discussed within tutorials found in this documentation, a comprehensive List of MRtrix3 commands can be found in the reference section. These lists provide links to the help page (manual) for each executable, which can also be accessed by typing the -help option after the executable name on the terminal.

Tip

Some proficiency with the Unix command-line is required to make the best use of this software. There are many resources online to help you get started if you are not already familiar with it. We also recommend our own Introduction to the Unix command-line, which was written with a particular focus on the types of use that are common when using MRtrix3.