A system and method is useful for treating amblyopia and other conditions by visual stimulation of the brain. Automatic discrimination between a pair or more of similar body organs, such as the eyes is accomplished for improved safety and efficacy of a treatment. Automatic measurement of a physiological parameter or state in response to a stimulation treatment (responsiveness) over time is also accomplished. Measurements are done over time, within the same treatment session, or between the same treatment session to allow for adapting the visual stimulation used for test and assessment purposes, visual stimulation used for treatment, or a combination of testing and treatment.
