1. A method comprising: storing in memory pre-operative brain atlas data that defines a plurality of nuclei of an atlas space; intra-operatively obtaining neurophysiological data for a plurality of known sites in a brain of a given patient to provide corresponding intra-operative neurophysiological data for at least a portion of the sites; performing, by a computer processor, a constrained optimization to fit the preoperative brain atlas data based at least in part on the intra-operative neurophysiological data; wherein the constrained optimization includes maximizing a number of the at least the portion of the sites that are correctly fitted to the atlas space on a nucleus by nucleus basis with respect to the nuclei defined in the pre-operative brain atlas data, and generating an enhanced brain atlas based on a transformation derived from the constrained optimization; and adjusting the transformation relative to at least one axis of stereotactic coordinate system for the given patient.