SPM12 is a free matlab package that performs automatic extraction of gray matter, white matter, csf, skull, and scalp from T1 weighted MRI. SPM outputs probability-weighted tissue mask images, with the same dimensions as the input. This would be a good starting point to make/edit 3D models.
Papers: Ashburner J, Friston KJ. Unified segmentation. Neuroimage. 2005 Ashburner J. SPM: a history. Neuroimage. 2012
There are also various other automatic brain MRI segmentation tools, mostly running in Linux. E.g., FreeSurfer is a very powerful one that outputs brain surface maps as 3D vertex mesh data.