# MRtrix 3.0\_RC3 -\> 3.0.0 changelog **URL:** \ **Category:** Uncategorized\ **Created:** [April 22, 2020, 1:58pm UTC](https://community.mrtrix.org/t/mrtrix-3-0-rc3-3-0-0-changelog/3552 "2020-04-22T13:58:26Z")\ **Posts on this page:** 1\ **Showing post:** 3
**Author:** ![rsmith](https://community.mrtrix.org/user_avatar/community.mrtrix.org/rsmith/32/2672_2.png) [@rsmith](https://community.mrtrix.org/u/rsmith)\ **Post date:** [April 22, 2020, 1:59pm UTC](https://community.mrtrix.org/t/mrtrix-3-0-rc3-3-0-0-changelog/3552/3 "2020-04-22T13:59:46Z")
# 2. Major software changes #### Documentation - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [_MRtrix3_ reference](https://github.com/MRtrix3/mrtrix3/pull/1734): Include reference to the _MRtrix3_ manuscript in all commands. - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [Wiki](https://github.com/MRtrix3/mrtrix3/pull/1622): Some _MRtrix3_-related documentation has been moved from the online software documentation into the [“`wiki`” section of the community forum](https://community.mrtrix.org/c/wiki/12). This will enable more dynamic updates of documentation when recommendations change, and also permit user contributions. #### Package management Binary installers/packages are now available at [https://www.mrtrix.org/download](https://www.mrtrix.org/download) for multiple platforms: - [![](https://github.com/bjeurissen.png?size=24)](https://github.com/bjeurissen) [standalone installer for macos](https://www.mrtrix.org/download/macos-standalone) : this will fetch and install the binaries for the latest MRtrix3 release. It includes `mrview` and `shview` as macos application bundles, enabling tight system integration (e.g. exposing `mrview` as a proper macos application, enabling file icons for supported images and double clicking in Finder, …). - [![](https://github.com/jdtournier.png?size=24)](https://github.com/jdtournier) [![](https://github.com/clebreto.png?size=24)](https://github.com/clebreto) [anaconda packages](https://github.com/MRtrix3/mrtrix3/pull/1824) for both [Linux](https://www.mrtrix.org/download/linux-anaconda) and [macos](https://www.mrtrix.org/download/macos-anaconda) : enable easy installation for [anaconda](https://www.anaconda.com/) or [miniconda](https://docs.conda.io/en/latest/miniconda.html) users. - [![](https://github.com/jdtournier.png?size=24)](https://github.com/jdtournier) [msys2 package for Windows](https://www.mrtrix.org/download/windows-msys2) : enables easy installation for [msys2](https://www.msys2.org/) users. #### Python scripts - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [API](https://github.com/MRtrix3/mrtrix3/pull/1449): Considerable changes to the _MRtrix3_ Python API. These will mostly be irrelevant for most users (`-tempdir` renamed to `-scratch` is the only interface change), but will affect anyone writing their own scripts to run against the API. #### Registration - [![](https://github.com/maxpietsch.png?size=24)](https://github.com/maxpietsch) [registration](https://github.com/MRtrix3/mrtrix3/pull/1798) Added support for multi-contrast registration in `mrregister` and `population_template`. `mrregister` results will differ [slightly](https://github.com/MRtrix3/mrtrix3/pull/1798#issuecomment-569521433) from previous results due to changes to the midway-space calculation. This and changes to the population template grid and masking will also affect `population_template` results. #### Statistical inference - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [CFE](https://github.com/MRtrix3/mrtrix3/pull/1543): `fixelcfestats` defaults to an intrinsically normalised version of the CFE equation, which provides an effect comparable to non-stationarity correction but without computational penalty. The former behaviour can be accessed using the `-cfe_legacy` option. - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [F-tests](https://github.com/MRtrix3/mrtrix3/pull/1543): Ability to perform F-tests (`-ftests` option). - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [FBA](https://github.com/MRtrix3/mrtrix3/pull/1543): Calculations previously performed internally within `fixelcfestats` are now spread across multiple commands. See new commands `fixelconnectivity` and `fixelfilter`. - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [Fixel matrix format](https://github.com/MRtrix3/mrtrix3/pull/1693): A new format for storing the sparse fixel-fixel connectivity matrix on the fileysstem has been produced. This is generated by new command `fixelconnectivity`, and utilised as input by new command `fixelfilter` as well as `fixelcfestats`. Interested developers can use this format for direct, easy-to-read access to these data for their own projects. - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [Heteroscedasticity](https://github.com/MRtrix3/mrtrix3/pull/1662): Ability to define variance groups (`-variance` option). Also fun to say. 🙃 - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [Limited shuffles](https://github.com/MRtrix3/mrtrix3/pull/1662): Better handling of use cases where the maximal number of possible shuffles is small. - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [Model errors](https://github.com/MRtrix3/mrtrix3/pull/1543): Model errors can be treated as exchangeable (randomly permuted), independent & symmetric (randomly negated), or both (`-errors` option). - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [Multiple hypotheses](https://github.com/MRtrix3/mrtrix3/pull/1543): Multiple hypotheses can be tested in a single command invocation (and not just the “inverse contrast”). Achieved by providing a contrast _matrix_ rather than a _vector_. Note that this also means that the `-negative` command-line option is no longer present; equivalent functionality is achieved by providing a contrast matrix with two rows, where the values in the second row are negated relative to the first. - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [Per-element design matrices](https://github.com/MRtrix3/mrtrix3/pull/1543): Design matrix can vary between individual elements (e.g. fixels) tested; due to regressors (of interest or of no interest) where the value is unique for each fixel / voxel / connectome edge tested (`-column` option), and/or data exclusion on a per-element basis (non-finite input data values). Useful for dealing with inconsistent brain cropping due to incomplete coverage or subject motion ([documentation page](https://mrtrix.readthedocs.io/en/latest/fixel_based_analysis/mitigating_brain_cropping.html)). - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [Restricted exchangeability](https://github.com/MRtrix3/mrtrix3/pull/1662): Ability to define (non-hierarchical) restricted exchangeability (`-exchange_within` and `-exchange_whole` options). - [![](https://github.com/Lestropie.png?size=24)](https://github.com/Lestropie) [Z-statistic](https://github.com/MRtrix3/mrtrix3/pull/1639): Statistical enhancement algorithms are applied to the corresponding Z-statistics for each hypothesis. This makes empirical statistical enhancement behaviour more consistent across studies of different sizes, between _t_-tests and _F_-tests, and reduces non-stationarity when excluding data on a per-element basis. #### `dwi2response dhollander` - [![](https://github.com/thijsdhollander.png?size=24)](https://github.com/thijsdhollander) [New single-fibre selection](https://github.com/MRtrix3/mrtrix3/pull/1545): New built-in algorithm for selecting exemplar single-fibre WM voxels. #### `dwidenoise` - [![](https://github.com/dchristiaens.png?size=24)](https://github.com/dchristiaens) [Complex data](https://github.com/MRtrix3/mrtrix3/pull/1525): Command can now operate natively on complex data. This facilitates denoising datasets that contain both magnitude and phase images, provided the latter have also been exported. A key advantage of denoising in the complex domain is that it offers a means to reduce Rician bias. ##### `population_template` - [![](https://github.com/maxpietsch.png?size=24)](https://github.com/maxpietsch) [leave-one-out-registration](https://github.com/MRtrix3/mrtrix3/pull/1798): registers each image to the current template that was created without this image in the intensity aggregation. - [![](https://github.com/maxpietsch.png?size=24)](https://github.com/maxpietsch) [robust initialisation](https://github.com/MRtrix3/mrtrix3/pull/1798): allows more robust template initialisation of images with extreme intensity values. - [![](https://github.com/maxpietsch.png?size=24)](https://github.com/maxpietsch) [aggregation](https://github.com/MRtrix3/mrtrix3/pull/1798): Added options for intensity value aggregation across images in `population_template`. It now supports mean, median, and weighted average aggregation. - [![](https://github.com/maxpietsch.png?size=24)](https://github.com/maxpietsch) [NaN-masking](https://github.com/MRtrix3/mrtrix3/pull/1798): The template does not contain contributions from areas outside the original field-of-view of input images. Previously these counted as zero in the averaging, biasing the template towards zero if input images were cropped. Added a NaN-masking option to also exclude areas outside the masks from contributing to the template intensity. --- _[View the full topic](https://community.mrtrix.org/t/mrtrix-3-0-rc3-3-0-0-changelog/3552)._