In functional neurosurgery, there is a growing need for accurate localization of the functional targets. Since deep brain stimulation (DBS) of the Vim thalamic nucleus has been proposed for the treatment of Parkinson's disease, the target has evolved toward the globus pallidus and subthalamic nucleus (STN) and the therapeutic indications have enlarged to include psychiatric disorders such as Tourette syndrome or obsessive compulsive disorders. In these pathologies, the target has been restrained to smaller functional subterritories of the basal ganglia, requiring more refined techniques to localize smaller and smallerbrain regions, often invisible in routine clinical MRI. Different strategies have been developed to identify such deep brain targets. Direct methods can identify structures in the MRI itself, but only the larger ones. Indirect methods are based on the use of anatomical atlases. The present strategy comprised a 3D histological atlas and the MRI of the same brain specimen, and deformation methodology developped to fit the atlas toward the brain of any given patient. In this paper, this method is evaluated in the aim of being applied to further studies of anatomo-clinical correlation. The accuracy of the method is first discussed, followed by the study of short series of Parkinsonian patients treated by DBS, allowing to compare the deformed atlas with various per- and post-operative data.