Morphometric assessment of brain structures has been shown to be a reliable indicator of pathology. However, prior studies have been inconsistent or even contradictory due to partial volume effects and operator dependence. A preliminary system to automate the measurement process was developed for, and delivered to, Long Island Jewish Hospital. The operator's role is to choose the structure to be measured and to oversee the automatic extraction. A discrete Stokes theorem is used to compute the partial volumes. System accuracy of 2% has been demonstrated.