MRtrix 3.0.1 release

Announcements
2

Changelog

Installation

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

Compilation

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.