I am trying to perform FBA using single-tissue CSD following the instructions on the MRtrix3 documentation. However, when I try to run the fixelconnectivity command, I get “command not found”. I am running MRtrix over a cluster, and am not sure if it is because I am running an earlier version. The module is listed as “MRtrix3/060419/gcc.7.1.0”. Does anyone know how I could either update MRtrix through a cluster or if there is another command I can use to get around this step?
It sounds like you’re running an earlier version. That command was introduced to the codebase a while ago, but was first released officially as part of version 3.0.0 (23 April 2020). You can check the exact version you’re running by invoking any MRtrix3 command with the -version option (e.g. mrinfo -version).
If you want to update your installation, there should be nothing stopping you from doing so within your own home folder and running it on the cluster, using the instructions for building from source. You don’t need administrative privileges to do this, as long as the required dependencies are already installed. You may need to load some modules to get access to those dependencies, including a sufficiently recent compiler, but that’ll depend on how the cluster is set up.
Alternatively, if anaconda is available on the cluster, you may be able to install our precompiled anaconda package in your home folder as well. I’m not that familiar with anaconda though, but there should be plenty of online resources to help with that.