Welcome to the MRtrix user documentation!

MRtrix 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. Features include the estimation of fibre orientation distributions using constrained spherical deconvolution ([Tournier2004]; [Tournier2007]; [Jeurissen2014]), visualisation of these via directionally-encoded colour maps ([Dhollander2015a]) and panchromatic sharpening ([Dhollander2015b]), 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]).

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.

Install

Getting started

DWI Pre-processing

Constrained Spherical Deconvolution

Fixel-Based Analysis

Quantitative Structural Connectivity

Spatial Normalisation

Concepts

Tips and Tricks

Troubleshooting

Reference