For color volume printing, you may want to look at SlicerFab and this post.
For color surface printing (e.g. FreeSurfer), I would look at ShapeWays support for color VRML files. The image below shows their matte sandstone (which I prefer to their glossy sandstone). The sandstone has a nice mass, and printing just one hemisphere provides a flat side that is nice for a paperweight.
You can create VRML format meshes with Surfice, which you can get from NITRC or GitHub. The model I show below was created by selecting the Scripting/Python/basic_paint_surface menu item and then choosing the Advanced/SaveMesh menu item. You can also create this type of mesh from the graphical interface. Finally, for an example of FreeSurfer brain regions (e.g. annot files), you can use File/Open to open the “/fs/lh.curv” mesh and select Overlays/AddOverlays to select the “/fs/boggle.annot”, which will create the mesh below with the MindBoggle map.
