# MRtrix 3.0 (release candidate 3) **URL:** \ **Category:** Announcements\ **Created:** [May 11, 2018, 2:02pm UTC](https://community.mrtrix.org/t/mrtrix-3-0-release-candidate-3/1624 "2018-05-11T14:02:33Z")\ **Posts on this page:** 1\ **Showing post:** 2
**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:** [May 11, 2018, 2:06pm UTC](https://community.mrtrix.org/t/mrtrix-3-0-release-candidate-3/1624/2 "2018-05-11T14:06:45Z")
# Interface changes - [![](https://community.mrtrix.org/uploads/default/original/2X/a/a09e72b3edfe021d17410605b97cacfc46b646bb.jpg)](https://github.com/thijsdhollander) [_`dwi2noise`_](https://github.com/MRtrix3/mrtrix3/pull/1211): Removed from the repository in favour of `-noise` option in `dwidenoise`. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/lestropie) [_`dwipreproc`_](https://github.com/MRtrix3/mrtrix3/pull/1297): `-cuda` option removed. The script will instead automatically detect the presence of a CUDA version of `eddy`; if this is run but fails, the script will then instead run the OpenMP version of `eddy` (if present). - [![](https://community.mrtrix.org/uploads/default/original/2X/a/a09e72b3edfe021d17410605b97cacfc46b646bb.jpg)](https://github.com/thijsdhollander) [_`fod2dec`_](https://github.com/MRtrix3/mrtrix3/pull/1211): Option `-outputmap` renamed to `-contrast`. - [![](https://community.mrtrix.org/uploads/default/original/2X/a/a09e72b3edfe021d17410605b97cacfc46b646bb.jpg)](https://github.com/thijsdhollander) [_`mesh2pve`_](https://github.com/MRtrix3/mrtrix3/pull/1211): Renamed to `mesh2voxel`, for consistency with other command names e.g. `fixel2voxel`, `voxel2fixel`, `voxel2mesh` (formerly `mrmesh`). - [![](https://community.mrtrix.org/uploads/default/original/2X/a/a09e72b3edfe021d17410605b97cacfc46b646bb.jpg)](https://github.com/thijsdhollander) [_`mrinfo`_](https://github.com/MRtrix3/mrtrix3/pull/1211): Options `-shells` and `-shellcounts` renamed to `-shell_bvalues` and `-shell_counts` to avoid ambiguity with renaming of `-shell` to `-shells` in other commands. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/lestropie) [_`mrmesh`_](https://github.com/MRtrix3/mrtrix3/pull/1313): Renamed to `voxel2mesh` for consistency with other command names, e.g. `fixel2voxel`, `voxel2fixel`, `mesh2voxel` (formerly `mesh2pve`). - [![](https://community.mrtrix.org/uploads/default/original/2X/a/a09e72b3edfe021d17410605b97cacfc46b646bb.jpg)](https://github.com/thijsdhollander) [_`mtbin`_](https://github.com/MRtrix3/mrtrix3/pull/1211): Removed from the repository in favour of `mtnormalise`. - [![](https://community.mrtrix.org/uploads/default/original/2X/a/a09e72b3edfe021d17410605b97cacfc46b646bb.jpg)](https://github.com/thijsdhollander) [_`tcknormalise`_](https://github.com/MRtrix3/mrtrix3/pull/1211): Renamed to `tcktransform`, for consistency with other command names related to spatial transformation & separation from other command names related to intensity normalisation. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/lestropie) [_`warpconvert`_](https://github.com/MRtrix3/mrtrix3/pull/1159): Change conversion type from a command-line option to a compulsory argument. - _Multiple commands_: * * * # Enhancements - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`5ttcheck`_](https://github.com/MRtrix3/mrtrix3/pull/1049): Better reporting of number and severity of issues detected in 5TT format compliance. - [![](https://community.mrtrix.org/uploads/default/original/2X/f/fc0336cb284b0f400cf1e2b1621b58f209608373.jpg)](https://github.com/matteomancini) [_`5ttgen gif`_](https://github.com/MRtrix3/mrtrix3/pull/1249): New `5ttgen` algorithm. Converts the results of the Geodesic Information Flow (GIF) algorithm into the 5TT format. - [![](https://community.mrtrix.org/uploads/default/original/2X/3/36a22d9497a23259c4aa9b8625e5511dea4fb11c.jpg)](https://github.com/jdtournier) [_`dirstat`_](https://github.com/MRtrix3/mrtrix3/pull/1157): - _`dwibiascorrect -ants`_: - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) _`dwipreproc`_: - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`fod2fixel`_](https://github.com/MRtrix3/mrtrix3/pull/1166): New option `-maxnum`, to specify maximum number of fixels per voxel. - _`labelconvert`_: - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`mrcalc`_](https://github.com/MRtrix3/mrtrix3/pull/1049): New option `-replace`, to replace all instances of some value with some other value. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`mrcat`_](https://github.com/MRtrix3/mrtrix3/pull/1145): Operates using native type required to support input images (including complex types). - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`mrdegibbs`_](https://github.com/MRtrix3/mrtrix3/pull/1175): Automatic detection of slice encoding direction where applicable. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`mrhistmatch`_](https://github.com/MRtrix3/mrtrix3/pull/1327): New algorithms for matching contrast between images that are linear rather than non-linear. This is for matching images that are of the same modality and comparable contrast, but raw intensities are not identical. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`mrtransform`_](https://github.com/MRtrix3/mrtrix3/pull/1291): New option `-strides`. - _`mrview`_: - [![](https://community.mrtrix.org/uploads/default/original/2X/3/36a22d9497a23259c4aa9b8625e5511dea4fb11c.jpg)](https://github.com/jdtournier) [_`sh2peaks`_](https://github.com/MRtrix3/mrtrix3/pull/1206): New option `-fast`; uses SH precomputer rather than SH transformation matrix. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`tckdfc`_](https://github.com/MRtrix3/mrtrix3/pull/1013): New command. Provides the Track-Weighted Dynamic Functional Connectivity (TW-dFC) method. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`tckmap`_](https://github.com/MRtrix3/mrtrix3/pull/1013): New option `-backtrack`. Does something _similar_ to back-tracking in Anatomically-Constrained Tractography (ACT): If seeking to sample underlying image values at streamline endpoints, but no valid image information appears underneath the streamline endpoint, back-track along the streamline until valid image data are found. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`tckstats`_](https://github.com/MRtrix3/mrtrix3/pull/1185): New option `-explicit`. Explicitly calculate the length of each streamline based on the distance between every pair of vertices, rather than relying on the step size information stored in the header. This should be used whenever the step size information is known to be untrustworthy, or a non-rigid transformation has been applied to the streamlines data. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`tsfvalidate`_](https://github.com/MRtrix3/mrtrix3/pull/1214): New command. Performs a comprehensive validation of a Track Scalar File (`.tsf`) against the corresponding track file (`.tck`), to ensure that not only do the relevant header entries match, but also that the number of tracks and number of vertices / values within each track match exactly. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`warpinvert`_](https://github.com/MRtrix3/mrtrix3/pull/1159): New command. Calculates the inverse of a non-linear warp field. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) _Continuous Integration Testing_: - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) _DICOM import_: - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_JSON import/export_](https://github.com/MRtrix3/mrtrix3/pull/1049): Better support of non-trivial data, e.g. arrays / matrices. - _Multiple commands_: - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_Multi-threading_](https://github.com/MRtrix3/mrtrix3/pull/1108): Distinguish between implicit and explicit multi-threading concurrency requests, for rare cases where this alters how many threads _MRtrix3_ should in fact spawn. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_Python scripts_](https://github.com/MRtrix3/mrtrix3/pull/1049): * * * # Fixes - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`5tt2gmwmi`_](https://github.com/MRtrix3/mrtrix3/pull/1219): Fix operation of `-mask_in` option. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`5ttgen fsl`_](https://github.com/MRtrix3/mrtrix3/pull/1066): Fix use of `-mask` option when mask does not match share voxel grid with T1 image. - [![](https://community.mrtrix.org/uploads/default/original/2X/7/7184ee7bec262090559e1bf4605f1e0645ac64ef.jpg)](https://github.com/bjeurissen) [_`configure`_](https://github.com/MRtrix3/mrtrix3/pull/1090): Better detection of FFTW3 libraries (for `mrdegibbs`) using `pkg-config`. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`dwi2mask`_](https://github.com/MRtrix3/mrtrix3/pull/1083): Fix command operation when image intensities are all below 1.0. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`dwigradcheck`_](https://github.com/MRtrix3/mrtrix3/pull/1168): Fix operation when no brain mask is provided, and gradient table is provided via `-grad` or `-fslgrad` options rather than the input image header. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`fixel2tsf`_](https://github.com/MRtrix3/mrtrix3/pull/1214): Prevent issues in correspondence between Track Scalar Files (`.tsf`) and track files (`.tck`) where underlying fixels contain non-finite values. - [![](https://community.mrtrix.org/uploads/default/original/2X/3/36a22d9497a23259c4aa9b8625e5511dea4fb11c.jpg)](https://github.com/jdtournier) [_`fixelcfestats`_](https://github.com/MRtrix3/mrtrix3/pull/1125): Fix subject file import issue arising from empty lines in text file. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`label2colour`_](https://github.com/MRtrix3/mrtrix3/pull/1126): Fix for when the command is used without an explicit lookup table (i.e. randomised node colouring). - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`mrtransform`_](https://github.com/MRtrix3/mrtrix3/pull/1134): Fix application of a non-linear warp field that does not lie on the same voxel grid as the template image. - _`mrview`_: - _`population_template`_: - [![](https://community.mrtrix.org/uploads/default/original/2X/3/36a22d9497a23259c4aa9b8625e5511dea4fb11c.jpg)](https://github.com/jdtournier) [_`set_path`_](https://github.com/MRtrix3/mrtrix3/pull/1172): Fix automatic detection of binaries location on Windows. - [![](https://community.mrtrix.org/uploads/default/original/2X/b/b8faf881c0c98868cf777bf8a367cfd542a888ed.png)](https://github.com/blezek) [_`tckconvert`_](https://github.com/MRtrix3/mrtrix3/pull/1088): - _`tckgen`_: - [![](https://community.mrtrix.org/uploads/default/original/2X/3/36a22d9497a23259c4aa9b8625e5511dea4fb11c.jpg)](https://github.com/jdtournier) [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`tckmap`_](https://github.com/MRtrix3/mrtrix3/pull/1288): Fix combined usage of `-dec` and `-stat_vox mean` options. - [![](https://community.mrtrix.org/uploads/default/original/2X/3/36a22d9497a23259c4aa9b8625e5511dea4fb11c.jpg)](https://github.com/jdtournier) [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`tcknormalise`_](https://github.com/MRtrix3/mrtrix3/pull/1154) (Note: now `tcktransform`): Proper handling of streamline vertices (or indeed entire streamlines) that lie outside the valid non-linear warp field data, with the output track file preserving the total number of streamlines in the input file (even if some of those streamlines now have zero vertices). - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) _`tckresample`_: - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`tckstats`_](https://github.com/MRtrix3/mrtrix3/pull/1326): Prevent command crash when input track file is empty. - [![](https://community.mrtrix.org/uploads/default/original/2X/3/36a22d9497a23259c4aa9b8625e5511dea4fb11c.jpg)](https://github.com/jdtournier) [_`warpinit`_](https://github.com/MRtrix3/mrtrix3/pull/1260): Make output warp field use the same axis strides as the input template image. - _DICOM import_: - _Multiple commands_: - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) _Python libraries_: - [![](https://community.mrtrix.org/uploads/default/original/2X/3/36a22d9497a23259c4aa9b8625e5511dea4fb11c.jpg)](https://github.com/jdtournier) [_Signal handling_](https://github.com/MRtrix3/mrtrix3/pull/1186): Fix setup of signal handler and its interaction with command initialisation / display of help pages. - [![](https://community.mrtrix.org/uploads/default/original/2X/3/36a22d9497a23259c4aa9b8625e5511dea4fb11c.jpg)](https://github.com/jdtournier) [_Windows_](https://github.com/MRtrix3/mrtrix3/pull/1176): Improve consistency of / support for the different Python versions provided in MSYS2. * * * # Other changes - [![](https://community.mrtrix.org/uploads/default/original/2X/3/36a22d9497a23259c4aa9b8625e5511dea4fb11c.jpg)](https://github.com/jdtournier) [_`build`_](https://github.com/MRtrix3/mrtrix3/pull/1295): New option `-persistent` to enhance Continuous Integration testing. - [![](https://community.mrtrix.org/uploads/default/original/2X/3/36a22d9497a23259c4aa9b8625e5511dea4fb11c.jpg)](https://github.com/jdtournier) [_`configure`_](https://github.com/MRtrix3/mrtrix3/pull/1177): New option `-nooptim` (no optimisation) to enhance Continuous Integration testing. - [![](https://community.mrtrix.org/uploads/default/original/2X/a/a09e72b3edfe021d17410605b97cacfc46b646bb.jpg)](https://github.com/thijsdhollander) [_`dwibiascorrect`_](https://github.com/MRtrix3/mrtrix3/pull/1148): Altered N4 bias field estimation parameters to reduce subsequent brain masking issues. - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_`mrconvert`_](https://github.com/MRtrix3/mrtrix3/pull/1049): More comprehensive description of command-line options in help page. - [![](https://community.mrtrix.org/uploads/default/original/2X/3/36a22d9497a23259c4aa9b8625e5511dea4fb11c.jpg)](https://github.com/jdtournier) [_Compressed image formats_](https://github.com/MRtrix3/mrtrix3/pull/1194): More expressive messages to indicate when errors occur in handling GZ files specifically. - [![](https://community.mrtrix.org/uploads/default/original/2X/a/a09e72b3edfe021d17410605b97cacfc46b646bb.jpg)](https://github.com/thijsdhollander) [_Config file_](https://github.com/MRtrix3/mrtrix3/pull/1211): Various fields renamed for consistency in overall name formatting of config file entries. - _Documentation_: - _Multiple commands_: - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) _Python libraries_: - Spherical Harmonic basis: - [![](https://community.mrtrix.org/uploads/default/original/2X/1/1a60609bdfe98a4b23889d0792b01b3f2076fef7.png)](https://github.com/Lestropie) [_Tractography code_](https://github.com/MRtrix3/mrtrix3/pull/1235): Modifications to improve external utilisation of this code (polymorphism). --- _[View the full topic](https://community.mrtrix.org/t/mrtrix-3-0-release-candidate-3/1624)._