A data acquisition system for use in conducting functional magnetic resonance imaging studies. fMRI studies can provide clues to the neurobiological basis of CNS disorders and reliable and quantifiable data relating to their symptoms. The data acquisition system includes a control station, a patient stimulus and response system and fMRI data acquisition software for controlling the operation of the system in response to operator input and acquiring fMRI data comprising MR images and associated behavioral response data. The stimulus and response system presents visual or auditory or other stimuli to the patient under direction of the control station while functional MRI scanning takes place. The MRI image data is collected from the MRI scanner and combined with the behavioral data generated as the patient responds to the stimuli and archived for later analysis and use. The system includes quality control measures for properly setting up the equipment and preparing and training the patient and for verifying data quality during the different steps in the process.