We are pleased to announce the immediate release of MRtrix3.0.8.
This is a bug fix release, fixing some long-standing issues with MRView on macOS, as well as a couple of issues that have become apparent since the release of the previous version. 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.
Apologies all for the delay in putting together a more curated changelog.
Full changelog
Bug fixes
tckglobal: Restore operation
The tckglobal command was inoperational from versions 3.0.5 through 3.0.7 due to API changes and an absence of adequate testing.
Further, race conditions were identified when running the command using multi-threading that resulted in undefined behaviour. These have affected the command since its first inclusion in MRtrix3. It is difficult to predict exactly how deleterious such behaviour may have been to the quality of reconstructed tractograms, though given the stochastic nature of the process it may have been of relatively low consequence. These are now rectified with only a small performance penalty.
Thanks for reporting John Kruper!
Fix race condition in ThreadedLoop
Another race condition that could potentially affect any operation that loops over an image in a multi-threaded manner.
tcksift2: Minor fixes to diagnosis data
Reporting the number of excluded fixels, and scatterplot generated by the -output_debug option, now appropriately omit an empty fixel that is used internally by the code but is not a member of the fixel dataset.
Thanks for report @phipru!
Fix phase encoding handling on 3.0.7
The automated handling of phase encoding information has turned out to be a complete nightmare, as evidenced by the size of the validation project. With 3.0.7 some fixes were issued but testing was not adequately exhaustive. Hopefully with these additional tests ongoing issues with running dwifslpreproc will be resolved…
MRView
Fix tractography rendering performance on macOS
This PR fixes the longstanding performance issues in the viewer on macOS when visualising tractography streamlines (using pseudotubes). Note: This fix has introduced problems in scenarios where tractography data are visualised in conjunction with other tools, and may affect all platforms, not only MacOS. A future 3.0.9 patch will rectify this. If users encounter mrview crashes with version 3.0.8, reverting to the 3.0.7 version of mrview, or compiling the master branch from source following the merge of #3233, should work.
mrcalc: Docs: Combining mag&phase into complex data
Added to the Example Usages for mrcalc how to combine magnitude and phase data from Siemens scanners into an image with complex datatype to facilitate complex data denoising.
I am personally trying to get into the habit of ensuring that any effort I invest in assisting community members in done in a scalable way, by putting it in the right location and form for many people to benefit from it, saving myself from repeating the same answer multiple times. This is also a way in which community members can contribute to the documentation that does not require programming proficiency: if there is some description that would have saved you a lot of time and effort in understanding a command or concept, or an example usage of a command that you think might be of benefit to others to be aware of, please do make suggestions (or add them yourself!).
