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MRtrix provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density

License: Mozilla Public License 2.0

Python 4.54% Shell 0.33% C++ 94.27% C 0.23% MATLAB 0.17% HTML 0.03% CSS 0.43%

mrtrix3's Introduction

MRtrix

Please visit the official website for MRtrix to access the documentation for MRtrix3, including detailed installation instructions.

Getting help

Support and general discussion is hosted on the MRtrix3 Community Forum. Please address all MRtrix3-related queries there. You can use you GitHub or Google login to post questions.

Quick install

Install dependencies by whichever means your system uses. These include: Python (>=2.6), a C++ compiler, POSIX threads, Eigen (>=3), zlib, OpenGL (>=3), and Qt (>=4.8 - >=5.1 on MacOSX).

Clone Git repository and compile:

 $ git clone https://github.com/MRtrix3/mrtrix3.git
 $ cd mrtrix3/
 $ ./configure 
 $ ./build

Set appropriate environment variables:

Bash shell:

  $ export PATH=/<edit as appropriate>/mrtrix3/release/bin:$PATH

C shell:

  $ setenv PATH /<edit as appropriate>/mrtrix3/release/bin:$PATH

Test installation:
```
 $ mrview
```

Keeping MRtrix3 up to date

You can update your installation at any time by opening a terminal in the mrtrix3 folder, and typing:
```
 git pull
 ./build
```
If this doesn't work immediately, it may be that you need to re-run the configure script:
```
 ./configure
```
and re-run step 1 again.

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