MRtrix 3.0.1 release

We are pleased to announce the immediate release of MRtrix 3.0.1.

This is primarily a bug fix release. We recommend users upgrade as soon as practical, using the instructions provided on our downloads pages (for precompiled packages), or the usual procedure for installations from source.

The full changelog is attached below. Noteworthy changes include:

All the best from the MRtrix3 team!



  • MSYS2: Alteration to how pre-compiled package is installed on Windows MSYS2. See updated instructions here.


General fixes

  • Documentation:

    • 404: Ensure that links to old documentation pages that have since moved / been removed now redirect to a more sensible information page.

    • Install from source: Updates to instructions.

    • mrgrid: Fix documentation referring to previous mrresize command rather than new mrgrid command (thanks to @TCsquared for report).

  • Progress bars: Fix intended appearance of progress bars when the stderr outputs of MRtrix3 commands are piped to a file.

  • Stats commands: Fixes issue when the subject filename list resides in the current working directory, and no template directory is defined (thanks to @nadluru for report).

  • write_mrtrix.m: Fix syntax of new code that was compatible with Octave but not MatLab (thanks to @julien for report).

Individual command changes

  • dwifslpreproc:

    • eddy: Provide error messages from both CUDA and OpenMP versions of eddy if both fail.

    • -eddyqc_*: Fix overwrite of existing output directory (thanks to @jfhartzell for report).

    • Gradient table: Retain eddy's modified diffusion gradient table, which incorporates motion estimates. Also fixes operation of -rpe_all (and -rpe_header if all volumes were acquired with reversed phase encoding). Thanks to @paul-triebkorn for report.

    • mrtransform error: Fix operation when the number of DWI volumes matches a plausible Spherical Harmonic (SH) series.

  • fixelfilter: Remove erroneous statement from help page that was relevant for a development version of the code but not the release version (thanks to @scottkolbe for report).

  • fixelfilter / fixelcfestats: Support fixel-fixel connectivity matrices with more than 2 billion connections (thanks to @Ana_Han for report).

  • labelconvert: Compatibility with FreeSurfer version 7 lookup table (thanks to @david_rs06 for report).

  • mrthreshold: Fix operation when no output image is specified (and the calculated threshold(s) is(/are) written to the terminal.

  • mrview:

    • Colour maps: Add viridis and inferno colour maps.

    • Tractography tool: Various fixes, including misalignment between streamlines and track scalar data (thanks to @julien for report).

  • mtnormalise: Warn if only one contrast is provided.

  • mrcolour: Fix PET colour map.

  • tckgen:

    • iFOD2: Fix iFOD2 sampling statistics reporting via -info.

    • DEBUG_TERMINATIONS: Fix for if variable DEBUG_TERMINATIONS is uncommented in code.