A controller-based apparatus for diagnosis and treatment of a subject with acquired brain injury and dysfunction. Various embodiments of the invention described herein recognize that different body postures affect the autonomic nervous system differently, and therefore various external stimuli may have different therapeutic efficacies when a patient or subject is in each body posture. Postures, such as walking, sitting, standing, prone and supine, have different effects on the autonomic nervous system, and therefore some stimuli have different physiological efficacies while a patient or subject is in a given body posture. Disclosed embodiments of the present invention leverage this relationship to provide a controller-based apparatus that determines a combination of posture and stimulus that has optimal therapeutic effect, while minimizing health practitioner involvement. The controller based apparatus provides a treatment that stimulates the nervous system through a combination of noninvasive therapies that stimulate brain cells to increase their efficiency—this promotes the formation of pathways that help transfer information throughout the brain in such a way that in the end, the affected area of the brain and overall brain function are improved without medication or surgery.