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.


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.