The third ventricle is surrounded by the structures of the diencephalon of the brain. The diencephalon is part of the central processing unit or motherboard of the brain. It connects and coordinates the lobes of the brain on its rostral (top) end, to the brainstem, cerebellum and spinal cord on its caudal (lower) end.he posterior perforated substance is the area of the floor of the third ventricle that is penetrated by many blood vessels. The subthalamus portion of the floor of the third ventricle is located beneath the thalamus toward the rear and flanks of the hypothalamus.