Windows installation

This page provides information for installing MRtrix3Tissue on Windows systems. This information is provided in addition to the general installation instructions.

Note that, 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 instead. You might want to consider a virtual machine or similar if you’re stuck on a Windows system.

Requirements

These are the basic requirements to install and run all command line tools:

C++11 compliant compiler
Python version >= 2.7
zlib compression library
Eigen version >= 3.3

These are additional requirements to install and run the GUI (mrview and shview):

Qt version >= 4.8
an OpenGL 3.3 compliant graphics card and corresponding software driver

These are optional dependencies:

libTIFF version >= 4.0 (for TIFF support)
FFTW version >= 3.0 (for improved performance in certain applications)
libpng (for PNG support)

All these dependencies are installed below by the MSYS2 package manager.

Installing dependencies

Download and install the most recent 64-bit MSYS2 installer from http://msys2.github.io (msys2-x86_64-*.exe), and follow the installation instructions from the MSYS2 wiki.
Run the program “MinGW-w64 Win64 Shell” from the start menu.
Update the system packages, by following the instructions:
```
pacman -Syuu
```
Close the terminal, start a new “MinGW-w64 Win64 Shell”, and repeat as necessary until no further packages are updated.

It was reported that this MSYS2 system update gives a number of instructions, including: terminating the terminal when the update is completed, and modifying the shortcuts for executing the shell(s). Although these instructions are not as prominent as they could be, it is absolutely vital that they are followed strictly correctly!
From the “MinGW-w64 Win64 Shell” run:
```
pacman -S git python pkg-config mingw-w64-x86_64-gcc mingw-w64-x86_64-eigen3 mingw-w64-x86_64-qt5 mingw-w64-x86_64-fftw mingw-w64-x86_64-libtiff mingw-w64-x86_64-libpng
```
Sometimes pacman may fail to find a particular package from any of the available mirrors. If this occurs, you can download the relevant package from SourceForge: place both the package file and corresponding .sig file into the /var/cache/pacman/pkg directory, and repeat the pacman call above.

Sometimes pacman may refuse to install a particular package, claiming e.g.:
```
error: failed to commit transaction (conflicting files)
mingw-w64-x86_64-eigen3: /mingw64 exists in filesystem
Errors occurred, no packages were upgraded.
```
Firstly, if the offending existing target is something trivial that can be deleted, this is all that should be required. Otherwise, it is possible that MSYS2 may mistake a file existing on the filesystem as a pre-existing directory; a good example is that quoted above, where pacman claims that directory /mingw64 exists, but it is in fact the two files /mingw64.exe and /mingw64.ini that cause the issue. Temporarily renaming these two files, then changing their names back after pacman has completed the installation, should solve the problem.

Installing MRtrix3Tissue

Once the required dependencies are present and installed, you can refer to the general installation instructions to install MRtrix3Tissue.

Problems

Problems typically call for feedback or support.

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