OK, you’re running within a WM, using the open-source mesa drivers, which provide software rendering (as far as I know). It’s a recent version though, so it ought to work relatively well. But until recently, I didn’t think it was possible to do what you’re doing at all… There’s a chance this might be down to an issue with the OpenGL drivers on your VM – although it still sounds like a strange issue to be having… Is there any chance you could try installing MRtrix in Windows directly, see if the issue persists?
There’s nothing particularly exotic with your data either, and it’s isotropic, so difficult to see why coronal would be affected in particular. I’ll try creating an image with those parameters and see if that triggers anything on my system…