A system and method identifies different components of the pain experience (nociceptive (tissue damage), neuropathic (nerve damage) and psychological) and their relative contributions by the use of magnetic resonance spectroscopy (MRS) to measure absolute and relative concentrations of metabolites in specific brain regions in the central nervous system or brain. The system and method can be used as a diagnostic tool for the assessment of the relative contribution of different aspects of the pain experience as well as monitoring of response to interventions directed at modifying these components.