An apparatus detects asymmetry in an object, such as a brain. The apparatus includes a processor programmed to fit a three-dimensional image of the object to a preselected shape, such as a standard brain atlas. The processor projects the three-dimensional image of the object to a two-dimensional surface image. The processor compares corresponding mirror image symmetric voxel pairs on the left and right sides of the surface image. The processor generates at least one of an asymmetry map and an asymmetry index based on the deviations in the pixel pairs. The processor can also mask, before the comparison, pixels of the surface image which are asymmetric in a normal brain.