Hi Justin,
Multiple CPUs can be used when running 3dDeconvolve with
the -jobs option. However, that is perhaps the only place
where the software tries to take such advantage.
While it is easy for the user to break up a linear process
to take advantage of extra CPUs, I don't know of anyone that
actually bothers to do it, myself included.
Dual CPU systems work quite well, for single user systems.
- rick