Thanks for your reply.
The same command works on a different computer, so I think it has to do with the way mrtrix was setup on this computer. Does the “not found” error message give any indication to the source of this problem? Example: “5ttgen: [DEBUG] run.versionMatch() (from run.py:373): Command fsl5.0-standard_space_roi not found in MRtrix3 bin/ directory”