MR/CT head registration

I have just started using 3D slicer. I would like to register 3D head CT with head MR. I have data for the whole body CT and just the head of the MR. Is there a way to remove the body slices of the CT before registration with the head MR? What registration method would you recommend?

you can crop the CT volume by cropVolume module.

I have been using BRAINS general registration to register MR and CT volumes. I am using MMI as the cost metric. How can I display the MMI result before and after registration?