Hi Shandra,

I've never done what your looking for in rats, but I know freesurfer parcellates human brains. So, what if you change the MNI human atlas (which freesurfer uses) by a rat atlas, and then parcellate with freesurfer. This is the LONI rat atlas: 
http://www.loni.ucla.edu/Atlases/Atlas_D...

I hope it works for you.

Regards,