Surface-based deformation markers obtained from diffeomorphic mapping of the amygdala are used to study specific atrophy patterns in a combined mild cognitively impaired and demented cohort compared with cognitively normal aging subjects. Statistical analysis demonstrates with high significance in a small sample of legacy data that deformation-based morphometry provides sensitive markers for locating atrophy in the amygdala. With respect to a high-field amygdala atlas, significant atrophy was found in the basomedial and lateral nucleus subregions.