Systems and methods for clinical neuronavigation in accordance with embodiments of the invention are illustrated. One embodiment includes a method for generating a brain stimulation target, including obtaining functional magnetic resonance imaging (fMRI) image data of a patient's brain, where brain imaging data describes neuronal activations within the patient's brain, determining a brain stimulation target by mapping at least one region of interest to the patient's brain, locating functional subregions within the at least one region of interest based on the fMRI image data, determining functional relationships between at least two brain regions of interest, generating parameters for each functional subregion, generating a target quality score for each functional subregion based on the parameters and selecting a brain stimulation target based on its target quality score and the patient's neurological condition.