Hi @zzcpage,
All MRtrix commands are already multi-threaded, this should already be using all available cores – assuming this hasn’t been over-ridden by command-line arguments (via the -nthread option), the MRTRIX_NTHREADS environment variable, or the NumberOfThreads config file variable. You can verify how many threads are actually being used with the -debug option, which should report something like this (along with a lot of other information):
mrconvert: [DEBUG] launching 32 threads "loop threads"...
Assuming this isn’t the issue, this wiki article may be relevant?
All the best,
Donald.