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]), 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.

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.