Subthalamic nucleus (STN) deep brain stimulation (DBS) has been demonstrated as an efficient surgical treatment in patients with Parkinson's disease suffering from severe disabilities in their motor symptoms (tremor, akinesia, rigidity) [1]. Sometimes, patients with STN DBS have secondary neuropsychological and/or psychiatric effects because the STN has a small size and a functional subdivision into motor, associative and limbic parts [8]. Therefore, targeting is an important step of the neurosurgical procedure as the DBS could induce undesirable side-effects. To improve targeting, many authors created either anatomical atlases [2,4] or multimodal databases [5-7]. They demonstrated that multimodal databases improved targeting accuracy over anatomical atlases. We presented a validation automatic segmentation of the basal ganglia based on a manual segmentation of these structures completed on a 3T MRI-template. This is the first step to increase accuracy of the targeting of DBS in order to improve the clinical outcome of DBS procedures.