1. A system for carrying out functional magnetic resonance imaging (fMRI) in an individual, the system comprising: a) an apparatus for delivering a nucleic acid comprising a nucleotide sequence encoding a light-responsive polypeptide to a target neural cell population in the individual, wherein the light-responsive opsin polypeptide is a light-responsive ion channel or a light-responsive ion pump; b) a light source for delivering a light pulse to a target neural cell population expressing the light-responsive polypeptide, thereby stimulating the target neural cell population, wherein the target neural cell population is in a first region of the brain in the individual; and c) a functional magnetic resonance imaging device that is configured to scan multiple regions of the brain to allow for observation of a neural reaction in response to the stimulation in at least one of the multiple regions of the brain and, in response, determine whether neural projections in a second region of the brain are connected to at least some of the cells of the modified target cell population in the first region of the brain.