A new stereotaxic multiarchitectonic atlas of the human thalamus in a 3D MRI navigation system Klaus Niemann 1 , Dagmar Noelchen 1 , Daniel Jeanmonod 2 , Anne Morel 2 1 Department of Neuroanatomy, University of Technology (RWTH), D-52057 Aachen, Germany and 2 Laboratory for Functional Neurosurgery, Neurosurgical Clinic, University Hospital, CH-8091 Zürich, Switzerland Email: niemann@cajal.medizin.rwth-aachen.de, amorel@nch.unizh.ch Summary. In the context of MRI-guided stereotaxy a new stereotaxic atlas of the human thalamus was developed in order to improve anatomical definition and precision in the prediction of the exact location of thalamic targets. It is based on multiarchitectonic parcellation (Nissl, myelin, calcium-binding proteins). Sagittal atlas data were digitized and registered together with 3D MRI data sets. In a coarse to fine strategy the atlas-to-patient transformation matrix is refined. Thus the atlas is tailored to the individual anatomy of the patient. The effects of the rigid transformation are directly monitored on the computer screen using visible anatomical landmarks as control. Keywords: Brain atlas, calcium-binding proteins, magnetic resonance imaging, 3D navigation, stereotaxy, thalamus 1 Introduction 1.1 Stereotaxic atlases of the thalamus Stereotaxic histological atlases provide information concerning the location of brain structures in a Cartesian coordinate system based on anatomical landmarks related to the ventricular system. The atlases date back to an era when CT and MR imaging of the brain were not yet available and the exact 3D location of intracerebral targets could only be inferred from their position relative to the intracerebral fluid spaces. In stereotaxic interventions for the treatment of chronical functional disorders such as neurogenic pain and Parkinson’s disesase [1], the tip of a probe is advanced through a burrhole in the skull along a precalculated trajectory towards a target situated in deep diencephalic areas of the brain. Microelectrode recordings on the fly as well as electrical stimulation serve as control for the trajectory and the correct target site. At the target site, coagulation of the target or implantation of depth electrodes is performed. Although thalamic contours are partly discernible in MR imaging, intrathalamic targets cannot be visually identified in pre-operative low-field MR images. This is due to the fact that signal intensities within the thalamus are