Hi Chris,
The command lscpu will give you detailed information about your CPU. One of the lines reports the number of cores (listed as CPU(s)), with a more detailed breakdown in terms of actual cores and threads per core (for hyper-threading systems). One thing to watch out for is that on a HPC system, you might end up running that command on the head node rather than one of the compute nodes, so you could get different results.
If you want to check exactly how many threads mrtrix is using, you can try running any command (e.g. mrconvert) with the -debug option. It’ll report how many threads are being launched at runtime.