A system and method for automatic detection of potential focal cortical dysplasias through magnetic resonance imaging. The method includes acquiring image data of a subject brain at a first resolution, analyzing the acquired image data to determine a thickness of cerebral gray matter, and matching the left cerebral hemisphere to the right cerebral hemisphere based on corresponding geometric features of the hemispheres. The method also includes generating a difference map comparing corresponding thicknesses of the hemispheres, identifying regions of abnormal differences in thickness as potential regions containing focal cortical dysplasias, and acquiring image data of the regions of abnormal differences in thickness at a second resolution. The method further includes generating images of the regions of abnormal differences in thickness from the acquired image data and displaying the images.
