We are pleased to announce the immediate release of MRtrix 3.0.4.
This is a bug fix release – this should not affect ongoing studies, other than in exceptionally rare circumstances. 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.
See the full changelog below for details.
All the best from the MRtrix3 team!
configure: ignore CFLAGS & LDFLAGS from qmake
Prevent the LTO options introduced with Qt 5.15 from causing non-trivial conflicts with clang++.
Eigen 3.4 compatibility
Fixes compilation from source on macOS, since homebrew now ships with Eigen 3.4.
Fix MIME & icon handling on linux
On Linux, the ./install_mime_types.sh command should now produce a working launcher for mrview, with recognised mime types that launch correctly and show up with the MRtrix icon.
build: Fix build progress
Prevents the different lines on the build progress feedback from claiming that there are different numbers of total compilation tasks.
Multiple changes (2):
fslsplit when running dwifslpreproc with -eddy_options " ... --cnr_maps ..."
mrview appearance in Singularity when built based on the Docker container.mrview CONTRIBUTING.md: General revisions (2)
Based on interactions with both internal and external contributors, revise and clarify documentation page that provides guidance for generation of novel MRtrix3 contributions.
Fix link to advanced debugging help page
Replace dead hyperlink with one to relevant wiki page on community forum.
Fixels (and Dixels): Double negative typo
Tiny fix affecting Fixel docs page
README.md: Add Twitter reference
Thanks to BIDS Specification for the idea.
connectomestats:
Output paths
Change output paths for some files to be consistent with other statistical inference commands.
Fix GLM mode selection
Improve execution speed in case where design matrix is identical per edge, and fix operation in case where design matrix changes per edge.
dwicat: Support 3D images
Fixes processing when an input image to dwicat is a 3D image containing a single b=0 volume.
dwifslpreproc:
Strip DW encoding from padding slice
Prevents an error regarding absence of a diffusion gradient table following the applytopup step.
Refine slspec modification Corrects use case where slice encoding direction is negative, slice-to-volume correction is used, the number of slices is odd, and EddyQC is invoked.
dwi2response manual: avoid unnecessary brain mask calculation
This algorithm is based entirely on manual selection of voxels, and therefore execution of a brain masking algorithm is superfluous. This step is now appropriately skipped.
mrconvert: Fix gradient table export
Export external gradient table files in the specific use case where only a linear transform is applied.
mrclusterstats: Fix for multiple variance groups
Where multiple variance groups are used, command was erroneously trying to write the standard deviation map for all variance groups to a single image path.
mrtransform: DWI grad export
Where it is requested that the DWI gradient table be exported to an external file, such export erroneously did not occur if only a linear transform was applied.
mrview:
Fix -tractography.tsf_colourmap option
Fixes handling in cases of erroneous usage.
Connectome tool: fix display of empty nodes
Permits use of tool for parcellations that have not been converted in order to increment sequentially from 1.
Thanks for report @adsouza.
population_template: Correct transformation of mask data
Where initial alignment was explicitly disabled by the user, mrtransform was erroneously applied to the last contrast instead of the mask.
tckconvert:
Capability to write binary .vtk files
New command-line option -binary, which applies only to the .vtk format.
PLY output: Fix incorrect face orientation
The cap placed on the end of each streamline was previously incorrectly oriented, resulting in erroneous interpretation in 3D printing software.
tcksift2: Fix fixel masking
Fixels that are only traversed by a solitary streamline will now be excluded from the optimisation as originally intended.
tensor2metric: avoid crash when supplying input with wrong size
Check if the input image consists of 6 volumes, and thus can be interpreted as tensor data.
population_template: Fix incorrect handling of masks when using -initial_alignment none
When no initial alignment was requested, the last available contrast was transformed as opposed to the mask. This would lead to unwanted behaviour (in case of a scalar contrast) or an exception (in case of an ODF). Only affected outcome of population_template when initial alignment was explicitly turned off, so most studies are probably not affected.
mrclusterstats: Fix incorrect writing of standard deviation maps when using multiple variance blocks
When multiple variance blocks were specified with the -variance option, all of the output standard deviation maps were written to the same file instead of a different file per variance block.
Various Philips data handling updates:
MRTRIX_PRESERVE_PHILIPS_ISO can be set to override the MRtrix3 default behaviour of ignoring the pre-generated trace-weighted image. Import additional Siemens enhanced fields
Fixes absent fields SliceTiming, EchoTime, MultibandAccelerationFactor & SliceEncodingDirection for some data.
Fix XA10A data parsing
Thanks to @neurolabusc for contributions to resolving these issues.
Fix GE data gradient table import
Thanks to @blezek for reporting, @neurolabusc for assistance in diagnosis and rectification, and Jaemin Shin for testing, providing test data, and providing insights from GE.
Export: Exception on too few axes Avoid invalid memory access when ROI is malformed in tck header.tck file header contains an entry for the ROI that doesn’t have the expected 2 fields, this leads to a segfault when using e.g. tckinfo or tck2fixel. The change here consists simply of making sure that if only one token is parsed, a second empty string is added as the second, which then avoids the invalid memory access, and permits these headers to be used (the alternative is simply to ignore them, but I’m not sure that’s the best thing to do here). Multiline key-value metadatafprintf doesn’t take cell array arguments. mrtrix3.run: Fix default MRTRIX_LOGLEVEL
Default value for environment variable MRTRIX_LOGLEVEL was being erroneously written as an integer type rather than a string. In some environments, the subprocess module attempts to check whether environment variables correspond to filesystem paths, and this results in a TypeError due to this specific envvar not being a string.
mrtrix3.utils.RunList
Pass kwargs to run.command().
Fix help page generation
Handle upstream changes in ArgParse, whereby the name for the default option group has now been changed from ‘optional arguments’ to the (arguably more sensible) ‘options’.