Methods and apparatus for verifying operability of a neurophysiological-based control system include generating a test stimulus that will result in a predetermined neurophysiological response in a user. Neurophysiological brain activity signals obtained from the user in response to the test stimulus are processed to generate a test neurophysiological response. The test neurophysiological response and a predetermined neurophysiological response are compared to determine if the neurophysiological-based control system is operating properly.