Running MRtrix in a Singularity container

MRtrix3 provides a large suite of tools for image processing, analysis and visualization, with a focus on the analysis of white matter using diffusion-weighted MRI. It requires several dependencies that make it easier to run as a container. However, as noted in the documentation, to run the GUI components of MRtrix3 (mrview & shview), an OpenGL 3.3 compliant graphics card is required as well as the corresponding software driver. This implies you cannot run the GUI components over a remote X11 connection, since it can’t support OpenGL 3.3+ rendering. Most of the other commands will run with the container. You can follow the tutorial and the following set of commands work on Ginsburg. mredit and voxel2mesh are two examples:

ml singularity
singularity build MRtrix3.sif docker://mrtrix3/mrtrix3:latest
export SINGULARITYENV_DISPLAY=$DISPLAY
export SINGULARITYENV_XDG_RUNTIME_DIR=$XDG_RUNTIME_DIR
singularity run --cleanenv -B /run MRtrix3.sif /opt/mrtrix3/bin/voxel2mesh
MRtrix 3.0.4                       voxel2mesh                        Dec 14 2022

     voxel2mesh: part of the MRtrix3 package
     
singularity run --cleanenv -B /run ../MRtrix3.sif /opt/mrtrix3/bin/mredit
MRtrix 3.0.4                         mredit                          Dec 14 2022

     mredit: part of the MRtrix3 package