Install and update

Installation

Below are some general quick installation instructions, mostly aimed at Unix-based systems (e.g. Linux or Apple macOS). While it’s technically possible to run MRtrix3Tissue on Windows, it’s not the most convenient or enjoyable experience. Since diffusion MRI preprocessing typically relies on FSL and/or ANTs, a Unix-based system is even more encouraged.

In addition to the below information, further OS-specific instructions are also available: Linux, macOS, Windows.

If you’ve used an older version of MRtrix3 before, such as the “release candidate 3 (RC3)”, you might want to read some release information first to inform yourself of the most critical changes in usage (e.g. name changes of certain commands).

Quick install

Install dependencies; these include: Python (>=2.7), a C++ compiler with full C++11 support (g++ 4.9 or later, clang++), Eigen (>=3.3), zlib, OpenGL (>=3.3) and Qt (>=4.8 or at least 5.1 on macOS). Refer to the OS-specific instructions for details: Linux, macOS, Windows.

Clone Git repository, configure and build:

git clone https://github.com/3Tissue/MRtrix3Tissue.git MRtrix3Tissue
   
cd MRtrix3Tissue
   
./configure
   
./build

Set the PATH (assuming you’re using the Bash shell):

Run the provided set_path script:
```
./set_path
```
This will automatically update the ~/.bashrc startup file (or ~/.bash_profile on macOS) for you. You can also instruct the set_path script to explicitly update a specific startup file, e.g.:
```
./set_path ~/.profile
```
You can also edit the appropriate startup file for your system manually and add this line at the end:
```
export PATH=/<edit as appropriate>/MRtrix3Tissue/bin:$PATH
```
Once you’ve run the set_path script or edited a startup file, you have to close and re-open a terminal for this startup file to (automatically) run and your PATH to be correctly set.
Test your installation:

Command line:
```
 mrinfo
```
GUI:
```
 mrview
```

Keep MRtrix3Tissue up to date

Update your installation by opening a terminal in the MRtrix3Tissue folder, and type:
```
git pull

./build
```
If ./build doesn’t work immediately, you may need to re-run the configure script:
```
./configure
```
and re-run ./build again. You don’t have to update or set your PATH again if it was also set before.

Build a specific version of MRtrix3Tissue

You can build a specific version of MRtrix3Tissue by checking out its so-called “tag”, and using the same procedure as above to build it:

git checkout 3Tissue_v5.1.0

./configure

./build

Optimising performance

By default, the configure script’s output instructs the build script to produce generic code suitable for any current CPU. However, you can also have this process produce code that’s more specifically tailored to the specific CPU in your computer. As this can improve performance of your MRtrix3Tissue installation, it’s worth considering if your installation will only run on your computer (and not be moved to another computer).

To achieve this, you need to set the ARCH environment variable to native right before running ./configure:

export ARCH=native

./configure

./build

Not installing the GUI

If you’re installing MRtrix3Tissue on a system where you don’t plan to use mrview and shview (e.g. a server, HPC system or cluster), you can avoid building these GUI tools. This also means Qt and OpenGL won’t be required.

To achieve this, you need to provide the -nogui option to ./configure:

./configure -nogui

./build

Problems

Problems typically call for feedback or support.

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