1. An apparatus for automatically processing medical images of brain regions, comprising: (a) a medical imaging system configured for scanning a patient's brain in three dimensions to generate three dimensional (3D) medical brain image data; (b) at least one processor configured for automatically performing image processing on said 3D medical brain image data; (c) a memory storing instructions executable by said processor; and (d) a display device coupled to said computer processor, said display device configured for displaying 3D medical images; (e) said instructions when executed performing steps comprising: (i) determining brain structures in a brain extraction process which removes non-brain image elements; (ii) classifying brain tissue types; (iii) segmenting cerebrum imaging which determines which portions of the image information belong to specific physiological structures; (iv) anatomical refinement comprising ventricle filling in response to ventricle information extracted from the image, removal of dura mater, and correcting subcortical area; (v) reconstructing surfaces of the brain including both white and grey matter in response to generating a surface mesh and correcting mesh topology; (vi) wherein each of the above steps are performed in response to said programming without user interaction or intervention; and (vii) displaying a 3D brain image showing classification of brain tissues, segmentation of different brain portions and surface reconstructions, with ventricle filling on said display.