A system for fitting of a three-dimensional pre-operative anatomical brain atlas based on neurophysiological data of a patient comprising: means for providing three-dimensional pre-operative anatomical brain atlas data for a region of interest of a given patient relative to a three-dimensional coordinate system; and means for intra-operatively obtaining neurophysiological data for a plurality of sites in the region of interest for the given patient and for providing corresponding intra-operative neurophysiological data for at least a portion of the sites; characterized in that: the three-dimensional pre-operative anatomical brain atlas data defines nuclei, i.e. anatomical structures, in the region of interest; and the system further comprises: means for classifying said at least a portion of the sites into respective nuclei classifications based on the intra-operative neurophysiological data; and means for fitting the three-dimensional pre-operative anatomical brain atlas data to the corresponding intra-operative neurophysiological data by performing a constrained optimization that optimizes a consistency between said at least a portion of the sites and said nuclei defined by the three-dimensional pre-operative anatomical brain atlas data, wherein the optimization applies different weights to different ones of said at least a portion of the sites depending on the respective nuclei into which the respective sites have been classified. means for providing three-dimensional pre-operative anatomical brain atlas data for a region of interest of a given patient relative to a three-dimensional coordinate system; and means for intra-operatively obtaining neurophysiological data for a plurality of sites in the region of interest for the given patient and for providing corresponding intra-operative neurophysiological data for at least a portion of the sites; characterized in that: the three-dimensional pre-operative anatomical brain atlas data defines nuclei, i.e. anatomical structures, in the region of interest; and the system further comprises: means for classifying said at least a portion of the sites into respective nuclei classifications based on the intra-operative neurophysiological data; and means for fitting the three-dimensional pre-operative anatomical brain atlas data to the corresponding intra-operative neurophysiological data by performing a constrained optimization that optimizes a consistency between said at least a portion of the sites and said nuclei defined by the three-dimensional pre-operative anatomical brain atlas data, wherein the optimization applies different weights to different ones of said at least a portion of the sites depending on the respective nuclei into which the respective sites have been classified. the three-dimensional pre-operative anatomical brain atlas data defines nuclei, i.e. anatomical structures, in the region of interest; and the system further comprises: means for classifying said at least a portion of the sites into respective nuclei classifications based on the intra-operative neurophysiological data; and means for fitting the three-dimensional pre-operative anatomical brain atlas data to the corresponding intra-operative neurophysiological data by performing a constrained optimization that optimizes a consistency between said at least a portion of the sites and said nuclei defined by the three-dimensional pre-operative anatomical brain atlas data, wherein the optimization applies different weights to different ones of said at least a portion of the sites depending on the respective nuclei into which the respective sites have been classified. means for classifying said at least a portion of the sites into respective nuclei classifications based on the intra-operative neurophysiological data; and means for fitting the three-dimensional pre-operative anatomical brain atlas data to the corresponding intra-operative neurophysiological data by performing a constrained optimization that optimizes a consistency between said at least a portion of the sites and said nuclei defined by the three-dimensional pre-operative anatomical brain atlas data, wherein the optimization applies different weights to different ones of said at least a portion of the sites depending on the respective nuclei into which the respective sites have been classified.