afni.nimh.nih.gov

I'm surprised that you are using a thick-slice dataset as your anatomical reference. In my experience, this is quite difficult. Why don't you gather a high-resolution 3D dataset (pulse sequence names: GE=SPGR, Siemens=MPRAGE, ???) with about 1 mm resolution in all directions? This looks much nicer and is easier to use.

bob cox