Magnetic resonance images provide a comprehensiveness of analysis of the human brain and levels of resolution never achieved by other modes of pathoanatomic analysis. We review a strategy and technology of MRI-based image analysis which extracts independent measures of brain volumes, shape and position. These parameters are readily correlated with behavioral as well as physiological measures derived from PET and the emerging technology of MRI-based in vivo spectroscopy. A coordinate program which draws upon these methods will have wide applications in human brain science and the study of dynamic properties of human brain disease.