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MRtrix3 provides a large suite of tools for image processing, analysis andvisualisation, with a focus on the analysis of white matter usingdiffusion-weighted MRI ([Tournier2019]). Features include the estimation offibre orientation distributions using constrained spherical deconvolution([Tournier2004]; [Tournier2007]; [Jeurissen2014]), a probabilisiticstreamlines algorithm for fibre tractography of white matter ([Tournier2012]),fixel-based analysis of apparent fibre density and fibre cross-section([Raffelt2012]; [Raffelt2015]; [Raffelt2017]), quantitative structuralconnectivity analysis ([Smith2012]; [Smith2013]; [Smith2015];[Christiaens2015]), and non-linear spatial registration of fibre orientationdistribution images ([Raffelt2011]). MRtrix3 also offers comprehensivevisualisation tools in mrview.

These applications have been written from scratch in C++, using thefunctionality provided by Eigen, and Qt. The software is currentlycapable of handling DICOM, NIfTI and AnalyseAVW image formats, amongst others.The source code is distributed under the Mozilla Public License.

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Use of the MRtrix3 software package in published works should be accompaniedby the following citation:

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Tip

Wirecast pro 12 2 0 download free. Make sure to use the version of this documentation that matches your versionof this software. You can select the version on the lower left of this page.

Getting help¶

There are a variety of sources of help and information to bring you up to speedwith MRtrix3. These include:

• the main MRtrix3 documentation (thesepages);
• our Introduction to the Unix command-lineif you're unfamiliar with the terminal (though you'll readily find plenty ofexcellent tutorials online);
• our Community Forum for support and generaldiscussion about the use of MRtrix3 – you can address allMRtrix3-related queries there, using your GitHub or Google login to postquestions.
• our Frequently Asked Questions, hostedas a user-editable wiki category within our forum.

Key features¶

While MRtrix3 is primarily intended to be used for the analysis ofdiffusion MRI data, at its fundamental level it is designed as ageneral-purpose library for the analysis of any type of MRI data. As such,it provides a back-end to simplify a large number of operations, many ofwhich will be invisible to the end-user. Specifically, MRtrix3 features:

• a consistent command-line interface, withinline documentation for each command;
• universal import/export capabilities whenaccessing image data across all MRtrix3 applications;
• Multi-file numbered image support to load multiple images as asingle multi-dimensional dataset;
• efficient use of Unix Pipelines for complex workflows;
• high performance on modern multi-core systems, with multi-threadingused extensively throughout MRtrix3;
• available on all common modern operating systems (GNU/Linux,MacOSX, Windows);
• a consistent Coordinate system with mostoperations performed in scanner/world coordinates where possible.

Installation¶

MRtrix3 runs on GNU/Linux, macOS, Microsoft Windows platforms, and other Unixplatforms. For most users, the simplest way to install MRtrix3 is to use oneof the pre-compiled packages. For details, please refer the main MRtrixwebsite.

If the precompiled packages are not available, we provide specific instructionsfor building the software from source. This is normally a simple process, butdoes require more compute resources and expertise. See the relevant pages for details.

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Commands¶

The MRtrix3 software package includes a suite of tools for image analysis andvisualisation. With the exception of mrview and shview, allMRtrix3 executables are designed to be run via a terminal using a consistentcommand-line interface. While many of the toolsand features are discussed within tutorials found in this documentation, acomprehensive List of MRtrix3 commands can be found in the referencesection. These lists provide links to the help page (manual) for eachexecutable, which can also be accessed by typing the -help option afterthe executable name on the terminal.

Tip

Some proficiency with the Unix command-line is required to make the best useof this software. There are many resources online to help you getstarted if you are not already familiar with it. We also recommend our ownIntroduction to the Unix command-line, which was written with aparticular focus on the types of use that are common when using MRtrix3.

Install

Getting started

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DWI Pre-processing

Constrained Spherical Deconvolution

Fixel-Based Analysis

Quantitative Structural Connectivity

Concepts

Tips and Tricks

Reference