Magnetic Resonance (MR) imaging allows volumetric quantification of a variety of neuroanatomical structures using two dimensional (2D) images as well as three-dimensional (3D) reconstruction of the brain and any of its constituent parts. Three-dimensional analysis permits integration of the neuroanatomical changes which occur in pathologic states, with the cognitive and behavioral changes elucidated through neuropsychological assessment. This paper describes uniform methods for 3D neuroanatomical isolation of the neocortex, ventricular system, and hippocampus in both normal and pathologic states. The 3D methods are described in detail using two different software programs, ANALYZE and IMAGE. Three-dimensional neuroanatomical reconstructions were carried out on a patient who sustained a very severe traumatic brain injury. The 3D image analysis in the patient with traumatic brain injury, revealed structural changes in frontal and temporal cortex, ventricular dilation, and hippocampal atropy. The neuropsychological impairments in this patient, were consistent with the observed neuroanatomical changes revealed on 3D image reconstruction. This technology permits precise determinations of the extent and severity of the neuroanatomical changes which follow neurological injury disease.