i think its a novel comparison. As sheep, swine and monkey brains have been nuroanatomically characterized independently.

Sure, anyone with the know-how and resources can do just about anything.  First, decide what types of neuroanatomical analyses you'd like to do, and then process your tissue in a consistent manner conducive to those analyses.  A Nissl stain is probably a good place to start, you can calculate volumes, do cell counts and look at cell morphology to a certain extent; you could also look at gyrification, cerebellar foliation etc..  If you keep multiple series from the sectioned brains you can also do immunohistochemistry to label any number of things (e.g., nonapeptides, apoptosis, calcium binding proteins) throughout the brain.  The statistical analyses of those measurements will also be relatively simple but given the closer evolutionary ties between ungulates v. primates I would run phylogenetically corrected tests.  If you plan to look at circuitry make sure one test does not interfere with another, perhaps block your brains.