Isosurface is incredibly expensive, you probably do not want to use it for densely sampled data like structural mri scans. I know because I tried exactly that method years ago when I was trying to develop 3D visualization techniques in matlab. Lucky for you there are matlab programs that could help.
Solution 1: Volumetric 3 is a full matlab application for visualizing layered 3D density matrices. It was designed to work with fmri and mri but it can handle arbitrary 3D arrays stored as .mat files.
Solution 2: A much simpler tool is Vol3D. But with a lot of programming on your end you can get it to do pretty much anything volumetric 3 does, in that they use highly similar (though distinct) techniques for generating visualizations.