MRtrix3Tissue v5.2.9

This temporary minor release improves compatibility with certain other software tools.

Backwards compatibility with all MRtrix3Tissue v5.x.x releases is retained.

MRtrix3Tissue v5.2.8

This release brings in an upstream MRtrix3 bug fix for dwi2mask when using the -fslgrad option.

Backwards compatibility with all MRtrix3Tissue v5.x.x releases is retained.

MRtrix3Tissue v5.2.7

This release brings in a series of upstream MRtrix3 bug fixes.

Backwards compatibility with all MRtrix3Tissue v5.x.x releases is retained, so updating should be safe (and easy)!

MRtrix3Tissue v5.2.0

This release brings in a few upstream MRtrix3 developments and bug fixes, including a few critical fixes to make SIFT2 work well with the comments that are now present in most text files (see also the release notes for MRtrix3Tissue v4.0.0).

The MRtrix3Tissue website at https://3Tissue.github.io is now more complete, including a basic single-subject pipeline at https://3Tissue.github.io/doc/single-subject.html (which also serves as a reliable tutorial) and more details and information about SS3T-CSD at https://3Tissue.github.io/doc/ss3t-csd.html .

MRtrix3Tissue v5.1.0

This release (finally!) adds the Single-Shell 3-Tissue CSD (SS3T-CSD) method for public (beta) release!

The method is currently available via the ss3t_csd_beta1 command. Take a look at its command line help page for the basic input and output arguments. By default, expect a run time of roughly 3x the length of a multi-tissue CSD run on a similarly sized dataset, as the algorithm progresses through its iterations (each taking about the equivalent time of 1 multi-tissue CSD run).

More information and tips will be added soon at https://3Tissue.github.io/doc/ss3t-csd.html .

MRtrix3Tissue v5.0.0

This release brings in a series of upstream MRtrix3 developments and bug fixes. The most critical bug fixes relate to population_template, which now works again as originally intended. The other most important updates and changes end users should be aware of include:

• dwipreproc has been renamed to dwifslpreproc
• it's now mandatory to specify to mrtransform whether to perform FOD reorientation (-reorient_fod yes) or not (-reorient_fod no)
• mrtransform has a new -modulate option to perform intensity or FOD modulation
• several changes and improvements to dwidenoise: new noise estimator, new edge voxel handling and a new default patch size based on the number of volumes; check the dwidenoise command line documentation for detailed information.
• several changes and improvements to mrthreshold, resulting in a new interface and options.
• more precise variance (and consequentially also standard deviation) calculation by mrmath and mrstats
• several changes to complex data handling by mrcalc
• a bug fix for foreach to avoid duplicated jobs when multi-threading

The dwi2response dhollander algorithm has been tested to continue working as before after the changes to mrthreshold.

The private SS3T-CSD beta implementation has been successfully rebased on this new release and compatibility has been validated. After about 1.5 months of private beta testing, feedback and improvements to the interface, default operation and overall robustness, we're now nearly ready to transition to a public (beta) release. A heartfelt thank-you to the private beta test users: your feedback has helped me to reach this goal. A great reminder that engaging with users is a good thing.

MRtrix3Tissue v4.1.7

This release brings in a few MRtrix3 bug fixes, including a critical bug fix for dwicat. (not to be confused with mrcat)

MRtrix3Tissue v4.1.3

This release brings in a couple of MRtrix3 developments related to the transformcalc command and a critical bug fix for population_template.

MRtrix3Tissue v4.0.0

This release brings in a series of upstream MRtrix3 developments, and updates dwi2response dhollander (and dholl_old) to match. The most important change end users should be aware of is that several commands that output text files, will now add comments (lines starting with #, followed by other text) in those text files to describe certain "header" information. For example, dwi2response dhollander will add 2 lines of comments at the start of each output response function text file: these document the full command that was run (by the user) to generate those outputs (and the version of the software), as well as the b-values of the response function.

The private SS3T-CSD beta will be rebased on this new release, so compatibility can be maintained and thoroughly checked.

Finally, note that with the release of MRtrix3Tissue v4.0.0, any v3.x.x numbering is indeed skipped: this is to avoid confusion with respect to MRtrix3 releases.

MRtrix3Tissue v2.2.0

Following feedback from the private SS3T-CSD beta test users, the default ODF rendering colour has been changed to a user-friendly shade of blue. This mainly helps with the use case of overlaying WM FODs on a basic TEC map, but it also seems to provide better 3D cues for glyph rendering in general (e.g. DWI signal profiles, response functions, etc...). Additionally, a few minor Pylint errors have been resolved.

Note the (private) SS3T-CSD beta implementation is not available yet at this stage in the public MRtrix3Tissue releases. The private beta is ongoing and growing, and will eventually transition into a public beta stage.