This is a quick run-down of how to make a 3D model in 3DSlicer or Slicer3.
So you don't actually have to do the structures and all. You can threshold and then click the 3D crystal looking thing and just make the model and rename it there to what you want and it will build as you work.
You can do the same thing with the brain atlas, but it may not be as good, especially if you're doing smoothing.
Brain atlases can be found at http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
