To help surgeons to pre-operatively select the target location for DBS electrodes, functional atlases based on intra-operatively acquired data have been created in the past. Recently, many groups have reported on the occurrence of brain shift in stereotactic surgery and its impact on the procedure but not on the creation of such atlases. Due to brain shift, the pre- and intra-operative coordinates of anatomic structures are different. When building large population atlases, which rely on pre-operative images for normalization purposes, it is thus necessary to correct for this difference. In this paper, we propose a method to achieve this. We show evidence that electrophysiological maps built using corrected and uncorrected data are different and that the maps created using shift-corrected data correlate better than those created using uncorrected data with the final position of the implant. These findings suggest that brain-shift correction of intra-operatively recorded data is feasible for the construction of accurate shift-corrected electrophysiological atlases.