A method and apparatus for evaluating motivational and emotional circuitry in the brain during paradigms focused on specific motivational functions, to directly determine which components and how much the motivational and emotional brain circuitry responds. This circuitry response answers questions focused on normal and abnormal behavior, along with questions regarding the normal and abnormal function of the circuitry. The results of interrogating the motivational and emotional circuitry can be used for objectively measuring, in individual humans or animals, their preferences or responses to motivationally salient stimuli including but not limited to stimuli which are internal or external, conscious or non-conscious, pharmacological or non-pharmacological therapies, diseased based processes or not, financial or non-financial, etc. This method and apparatus for measuring brain activity during motivational and emotional functions can further be used to predict individual choices, preferences and planned behaviors, plus interpret internal experiences without recourse to the subjects participation or their voluntary description of these choices, preferences, planned behaviors, or internal experiences.