Deploying MRtrix3

The installation instructions provided in the preceding pages produce a working install for the current user only. There are many advantages to this:

  • no need for admin privileges, either for the initial install (beyond installation of dependencies), or any subsequent updates;
  • users are in control of the precise version of MRtrix3 they are using for their specific projects - no system updates will interfere with their study.

However, system administrators and software distributors will want to install MRtrix3 in a system-wide location to make it accessible to all users; and/or to deploy it to other systems without requiring a full rebuild. While MRtrix3 does not provide an explicit command to do this, it is a trivial process:

  • build the code
  • copy the bin/, lib/ and share/ folders together to the desired target location
  • set the PATH to point to the bin/ folder.

This can be done any number of ways. The only requirement is that these 3 folders are co-located alongside each other, so that the executables can find the MRtrix3 shared library, and the scripts can find the requisite python modules.

Note also that this structure is broadly compatible with the Linux Filesystem Hierarchy Standard. It should be perfectly possible to merge the MRtrix3 bin/, lib/ and share/ folders with the system’s existing equivalent locations in /usr/ or /usr/local/ if desired, in which case there would be no need to explicitly set the PATH (assuming /usr/bin or /usr/local/bin/ are already in the PATH). However, there is no requirement that it be installed anywhere in particular, and we expect most sysadmins will prefer to place them in a separate location to minimise any chance of conflict.

Below we provide step-by-step instructions for creating a single tar file that can then be copied to other systems and extracted in the desired folder:

  1. Obtain, configure and build the desired version of MRtrix3:

    $ git checkout
    $ cd mrtrix3
    $ ./configure
    $ ./build
  2. Collate the relevant folders and their contents into a single archive file:

    $ tar cvfz mrtrix3.tgz bin/ lib/ share/
  3. Copy the resulting mrtrix3.tgz file over to the target system, into a suitable location., for example (as root):

    # mkdir /usr/local/mrtrix3
    # cp mrtrix3.tgz /usr/local/mrtrix3/
  4. Extract the archive in this location (as root):

    # cd /usr/local/mrtrix3/
    # tar xvfz mrtrix3.tgz

    Assuming no errors were generated, you can safely remove the mrtrix3.tgz file at this point.

  5. Add the newly-extracted bin/ folder to the PATH, e.g.:

    $ export PATH=/usr/local/mrtrix3/bin:"$PATH"

    At which point MRtrix3 command should be available to the corresponding user.

    Note that the above command will only add MRtrix3 to the PATH for the current shell session. You would need to add the equivalent line to your users’ startup scripts, using whichever mechanism is appropriate for your system.