An apparatus and method for performing automatic 3D image segmentation and reconstruction of organ structures, which is particularly well-suited for use on cortical surfaces is presented. A brain extraction process removes non-brain image elements, then classifies brain tissue as to type in preparation for a cerebrum segmentation process that determines which portions of the image information belong to specific physiological structures. Ventricle filling is performed on the image data based on information from a ventricle extraction process. A reconstruction process follows in which specific surfaces, such as white matter (WM) and grey matter (GM), are reconstructed.