Characterization of hippocampal subfields using ex vivo MRI and histology data: Lessons for in vivo segmentation

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Hippocampal subfield segmentation on in vivo MRI is of great interest for cognition, aging, and disease research. Extant subfield segmentation protocols have been based on neuroanatomical references, but these references often give limited information on anatomical variability. Moreover, there is generally a mismatch between the orientation of the histological sections and the often anisotropic coronal sections on in vivo MRI. To address these issues, we provide a detailed description of hippocampal anatomy using a postmortem dataset containing nine specimens of subjects with and without dementia, which underwent a 9.4 T MRI and histological processing. Postmortem MRI matched the typical orientation of in vivo images and segmentations were generated in MRI space, based on the registered annotated histological sections. We focus on the following topics: the order of appearance of subfields, the location of subfields relative to macroanatomical features, the location of subfields in the uncus and tail and the composition of the dark band, a hypointense layer visible in T2-weighted MRI. Our main findings are that: (a) there is a consistent order of appearance of subfields in the hippocampal head, (b) the composition of subfields is not consistent in the anterior uncus, but more consistent in the posterior uncus, (c) the dark band consists only of the CA-stratum lacunosum moleculare, not the strata moleculare of the dentate gyrus, (d) the subiculum/CA1 border is located at the middle of the width of the hippocampus in the body in coronal plane, but moves in a medial direction from anterior to posterior, and (e) the variable location and composition of subfields in the hippocampal tail can be brought back to a body-like appearance when reslicing the MRI scan following the curvature of the tail. Our findings and this publicly available dataset will hopefully improve anatomical accuracy of future hippocampal subfield segmentation protocols.


  • Robin de Flores
  • David Berron
  • Song Lin Ding
  • Ranjit Ittyerah
  • John B. Pluta
  • Long Xie
  • Daniel H. Adler
  • John L. Robinson
  • Theresa Schuck
  • John Q. Trojanowski
  • Murray Grossman
  • Weixia Liu
  • Stephen Pickup
  • Sandhitsu R. Das
  • David A. Wolk
  • Paul A. Yushkevich
  • Laura E.M. Wisse
Enheter & grupper
Externa organisationer
  • University of Pennsylvania
  • Allen Institute for Brain Science
  • Guangzhou Medical University

Ämnesklassifikation (UKÄ) – OBLIGATORISK

  • Medicinsk bildbehandling
  • Radiologi och bildbehandling


StatusE-pub ahead of print - 2019 nov 1
Peer review utfördJa