Welcome to the MRtrix user documentation!ΒΆ

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 (Tournier et al.. 2004; Tournier et al., 2007; Jeurissen et al., 2014), a probabilisitic streamlines algorithm for fibre tractography of white matter (Tournier et al., 2012), fixel-based analysis of apparent fibre density and fibre cross-section (Raffelt et al., 2012; Raffelt et al., 2015; Raffelt et al., 2016), quantitative structural connectivity analysis (Smith et al., 2012; Smith et al., 2013; Smith et al., 2015; Christiaens et al., 2015), and non-linear spatial registration of fibre orientation distribution images (Raffelt et al., 2011).

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

Quantitative Structural Connectivity

Fixel-Based Analysis

Spatial Normalisation

Concepts

Tips and Tricks

Troubleshooting

Reference