The basal ganglia is always fun to render. I've done it for the macaque brain. Take a look at this previous post for how you might do it.
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afni.nimh.nih.gov]
Each region can be made into a separate surface. Transparency/opacity is controllable for each surface. Besides the object controller, you can also right-click select in each object and then ctrl-o to change opacity of just that object and ctrl-p to change between points/mesh/fill/hide modes for that surface. It's a very interactive way of navigating through the objects in the surface.