MRtrix3Tissue v2.1.1

This release brings in a new MRtrix3 bug fix for mrview volume navigation (in certain scenarios, mrview could crash when navigating between volumes). Additionally, the "View options" tool in mrview now allows navigation of any (number of) dimension(s) in images.

Due to the mrview bug fix, users are highly recommended to update their MRtrix3Tissue v2.0.0 installation to v2.1.1.

MRtrix3Tissue v2.0.0

This release updates the 2019 version of dwi2response dhollander with a minor improvement to robustness, while now relying less on the tensor fit (now only for the initial FA map and threshold).
The old (2016) version of the algorithm is temporarily added as dholl_old, mostly for reference, but is definitely deprecated and will be removed again in a future version.

Additionally, this release brings in a hotfix for the cross-correlation metric in mrmetric and an mrview bug fix for volume group navigation.

MRtrix3Tissue v1.5.2

This release mainly updates the testing framework to make use of the new forked test data repository 3Tissue/MRtrix3Tissue_TestData. This test data repository collects all relevant test data on its master branch, so MRtrix3Tissue users can easily test their installation. The relevant documentation has also been simplified, targeting mostly end users.

Additionally, this release incorporates 2 small hotfixes as well as a change to simplify importing libraries in Python scripts.

MRtrix3Tissue v1.0.0

This is the first MRtrix3Tissue production release. This release introduces the new 2019 version of the dwi2response dhollander algorithm, but also brings in a very large amount (~ 1 year) of MRtrix3 developments. Several major changes end users should be aware of include:

• the dwi2response dhollander algorithm has been improved (new 2019 version), mostly impacting the single-fibre WM response function estimation. This should generally allow for a better subsequent dwi2fod multi-tissue (2-tissue, 3-tissue) fit, for both multi-shell as well as single-shell data. The new algorithm is also faster than the old one.
• average_response has been renamed to responsemean, with different default behaviour
• the old dwinormalise and dwiintensitynorm for intensity normalisation in single-tissue pipelines have been recombined into dwinormalise (with algorithm selection). Note that dwinormalise is only recommended still for single-tissue pipelines. For multi-tissue (2-tissue, 3-tissue) pipelines, mtnormalise is recommended instead, to be performed immediately following dwi2fod.
• dwi2tensor changed its default fitting strategy from ordinary least-squares (OLS) followed by iterative weighted least-squares (IWLS), to weighted least-squares (WLS) followed by IWLS
• mrresize, mrpad and mrcrop have been removed and recombined into the new mrgrid
• foreach shows progress differently, and has several new options; though basic usage remains the same (i.e. backward compatible)

Due to the amount and impact of the changes (which go beyond the aforementioned list), it's generally not recommended to switch between older versions of MRtrix3Tissue or MRtrix3 and this new version during your ongoing projects (experiments, studies, ...); i.e. either stick with your current version to finish up ongoing projects, or alternatively re-run most processing consistently using a "clean" installation of this new version.

MRtrix3Tissue v0.1.0

This pre-release updates README.md, build, configure, set_path and package_mrtrix for a better MRtrix3Tissue user experience during installation. It doesn't change the functionality of these scripts, but changes the naming to MRtrix3Tissue in some places, and clarifies the link between MRtrix3Tissue and MRtrix3 at key points. The intention is to avoid confusion for users and provide as much clarity as possible.

MRtrix3Tissue v0.0.48

This pre-release is identical to MRtrix3's master branch on 8th May 2019: it includes MRtrix 3.0, Release Candidate 3 (3.0_RC3) and 48 hotfixes, added over about 1 year.

MRtrix3Tissue v0.0.0

This pre-release is identical to MRtrix 3.0, Release Candidate 3 (3.0_RC3), which was originally released on 11th May 2018.