http://mipav.cit.nih.gov/ will do this too, but some kind of framebuffer is still needed for this particular utility (say xvfb, not all MIPAV components have this requirement).  Utilities->3d Slice Tools->Remove slice.  Then save as yourFavoriteSlice.png. It's scriptable as well.

If you create a script in mipav and you want to see if it'll work without the xvfb buffer, use -headless and see if the script completes.