Do I need to set the -nthreads option manually in each command to trigger the parallel computing?
Yes, MRtrix3 will automatically execute commands in parallel. No, you do not need to set
-nthreads manually. By default, the no. threads is set to the number of processor cores on your system. You can also change this default in your configuration file.
@dchristiaens Got it! Thanks Daan.