A system for optical imaging of intrinsic signals and visualization of functional maps overlaid with the 3D reconstruction of the cortex is presented. Optical imaging of intrinsic signals is an advantageous method for monitoring functional representation of eloquent areas of the cortex. The non-invasive method works free of contact and generates a map of cortical activation with a spatial resolution of less than 1 mm based on the changes in optical parameters of brain tissue during cortical activation. A system containing an illumination device, a surgical microscope, and a camera is described. Computation of the cortical activation map is done by comparison of recordings during rest and stimulation. 3D reconstruction of the cortex and overlay with the optical recording is achieved using the 3D visualization software AMIRA. Optical imaging of intrinsic signals can increase the identification of eloquent regions of the brain. The 3D visualization is beneficial for identifying the region and for inter-individual comparison of the cortical representation of eloquent areas.