MRtrix

MRtrix3 can be installed / run through multiple avenues:

Direct download through mechanisms tailored for different OS platforms;
Compiled from the source code in this repository, for which comprehensive instructions are provided in the online documentation;
Via containerisation technology using Docker or Singularity; see online documentation page for details.

Getting help

Instructions on software setup and use are provided in the online documentation. Support and general discussion is hosted on the MRtrix3 Community Forum. Please also look through the Frequently Asked Questions on the wiki section of the forum. You can address all MRtrix3-related queries there, using your 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 with full C++11 support (g++ 4.9 or later, clang++), Eigen (>=3.2.8), zlib, OpenGL (>=3.3), and Qt (>=4.8, or at least 5.1 on MacOSX).

Clone Git repository and compile:

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

Set the PATH:
- Bash shell:
  
  run the set_path script provided:
```
  $ ./set_path
```
  or edit the startup ~/.bashrc or /etc/bash.bashrc file manually by adding this line:
```
  $ export PATH=/<edit as appropriate>/mrtrix3/bin:$PATH
```
- C shell:
  
  edit the startup ~/.cshrc or /etc/csh.cshrc file manually by adding this line:
```
  $ setenv PATH /<edit as appropriate>/mrtrix3/bin:$PATH
```
Test installation:

Command-line:
```
 $ mrconvert
```
GUI:
```
 $ 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.

Building a specific release of MRtrix3

You can build a particular release of MRtrix3 by checking out the corresponding tag, and using the same procedure as above to build it:

git checkout 3.0_RC3
./configure
./build

Contributing