A three-dimensional, histological and deformable atlas of the human basal ganglia. I. Atlas construction based on immunohistochemical and MRI data

Neuroimage. 2007 Jan 15;34(2):618-38. doi: 10.1016/j.neuroimage.2006.09.026. Epub 2006 Nov 15.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Basal Ganglia / anatomy & histology*
  • Basal Ganglia / metabolism
  • Brain Mapping / methods*
  • Calbindins
  • Databases, Factual
  • Humans
  • Imaging, Three-Dimensional / methods*
  • Immunohistochemistry
  • Magnetic Resonance Imaging
  • Male
  • Middle Aged
  • S100 Calcium Binding Protein G / metabolism
  • Software


  • Calbindins
  • S100 Calcium Binding Protein G