Quantifying inter-individual anatomical variability in the subcortex using 7 T structural MRI

Neuroimage. 2014 Jul 1;94:40-46. doi: 10.1016/j.neuroimage.2014.03.032. Epub 2014 Mar 17.


Functional magnetic resonance imaging (MRI) data are usually registered into standard anatomical space. However, standard atlases, such as LPBA40, the Harvard-Oxford atlas, FreeSurfer, and the Jülich cytoarchitectonic maps all lack important detailed information about small subcortical structures like the substantia nigra and subthalamic nucleus. Here we introduce a new subcortical probabilistic atlas based on ultra-high resolution in-vivo anatomical imaging from 7 T MRI. The atlas includes six important but elusive subcortical nuclei: the striatum, the globus pallidus internal and external segment (GPi/e), the subthalamic nucleus, the substantia nigra, and the red nucleus. With a sample of 30 young subjects and carefully cross-validated delineation protocols, our atlas is able to capture the anatomical variability within healthy populations for each of the included structures at an unprecedented level of detail. All the generated probabilistic atlases are registered to MNI standard space and are publicly available.

Keywords: Anatomical atlas; Basal ganglia; Red nucleus; Substantia nigra; Subthalamic nucleus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Brain / anatomy & histology*
  • Computer Simulation
  • Female
  • Humans
  • Image Enhancement / methods
  • Image Interpretation, Computer-Assisted / methods*
  • Imaging, Three-Dimensional / methods*
  • Information Storage and Retrieval / methods*
  • Magnetic Resonance Imaging / methods*
  • Male
  • Models, Anatomic*
  • Models, Biological
  • Models, Statistical*
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Young Adult