Methods and systems for controlling a prosthesis using a brain imager that images a localized portion of the brain are provided according to one embodiment of the invention. The brain imager provides motor cortex activation data by illuminating the motor cortex with near infrared light (NIR) and detecting the spectral changes of the NIR light as passes through the brain. These spectral changes can be correlated with brain activity related to limbic control and may be provided to a neural network, for example, a fuzzy neural network that maps brain activity data to limbic control data. The limbic control data may then be used to control a prosthetic limb. Other embodiments of the invention include fiber optics that provide light to and receive light from the surface of the scalp through hair.