title: A three-dimensional, histological and deformable atlas of the human basal ganglia. I. Atlas construction based on immunohistochemical and MRI data.
abstract: This paper describes the construction of an atlas of the human basal ganglia. The successive steps of the construction were as follows. First a postmortem specimen was subjected to a MRI acquisition prior to extraction of the brain from the skull. The brain was then cryosectioned (70 microm thickness). One section out of ten (80 sections) was Nissl-stained with cresyl violet, another series of 80 sections was immunostained for the calcium binding protein calbindin. Contours of basal ganglia nuclei including their calbindin-stained functional subdivisions, fiber bundles and ventricles (n=80 structures) were traced from histological sections and digitized. A novelty of this atlas is the MRI acquisition, which represents the core data element of the study. MRI was used for the coregistration of the atlas data and permitted, through multimodal (Nissl, calbindin, images of cryosectioning, T1 and T2 MRI) and 3D optimization, the production of anatomically and geometrically consistent 3D surfaces, which can be sliced through any desired orientation. The atlas MRI is also used for its deformation to provide accurate conformation to the MRI of living patients, thus adding information at the histological level to the patient's MRI volume. This latter aspect will be presented in a forthcoming paper.
authors.affiliation: INSERM U679, Neurologie et Thérapeutique Expérimentale, Hôpital de la Salpêtrière, Université Pierre et Marie Curie, Faculté de Médecine, Paris, France. yelnik@ccr.jussieu.fr
authors.forename: Jérôme
authors.initials: J
authors.lastname: Yelnik
authors.forename: Eric
authors.initials: E
authors.lastname: Bardinet
authors.forename: Didier
authors.initials: D
authors.lastname: Dormont
authors.forename: Grégoire
authors.initials: G
authors.lastname: Malandain
authors.forename: Sébastien
authors.initials: S
authors.lastname: Ourselin
authors.forename: Dominique
authors.initials: D
authors.lastname: Tandé
authors.forename: Carine
authors.initials: C
authors.lastname: Karachi
authors.forename: Nicholas
authors.initials: N
authors.lastname: Ayache
authors.forename: Philippe
authors.initials: P
authors.lastname: Cornu
authors.forename: Yves
authors.initials: Y
authors.lastname: Agid
mesh_terms: D001479:Basal Ganglia / Q000033:anatomy & histology* / Q000378:metabolism; D001931:Brain Mapping / Q000379:methods*; D064026:Calbindins; D016208:Databases, Factual; D006801:Humans; D021621:Imaging, Three-Dimensional / Q000379:methods*; D007150:Immunohistochemistry; D008279:Magnetic Resonance Imaging; D008297:Male; D008875:Middle Aged; D064030:S100 Calcium Binding Protein G / Q000378:metabolism; D012984:Software
chemical_list: D064026:Calbindins; D064030:S100 Calcium Binding Protein G