In functional stereotactic neurosurgery, one of the cornerstones upon which the success and the operating time depends is an accurate targeting. The subthalamic nucleus (STN) is the usual target involved when applying Deep Brain Stimulation (DBS) for the Parkinson’s disease (PD). Unfortunately, STN is usually not clearly visible in common medical imaging modalities, which justifies the use of atlas-based segmentation techniques to infer the STN location. We propose a scheme that allows both, to perform a comparison between different non-rigid atlas registration algorithms and to evaluate their usability to locate the STN automatically. Using our validation evaluation scheme and accurate registration algorithms we demonstrate that automatic STN localization is possible and accurate.