A protocol for manual segmentation of medial temporal lobe subregions in 7 Tesla MRI

Neuroimage Clin. 2017 May 26:15:466-482. doi: 10.1016/j.nicl.2017.05.022. eCollection 2017.


Recent advances in MRI and increasing knowledge on the characterization and anatomical variability of medial temporal lobe (MTL) anatomy have paved the way for more specific subdivisions of the MTL in humans. In addition, recent studies suggest that early changes in many neurodegenerative and neuropsychiatric diseases are better detected in smaller subregions of the MTL rather than with whole structure analyses. Here, we developed a new protocol using 7 Tesla (T) MRI incorporating novel anatomical findings for the manual segmentation of entorhinal cortex (ErC), perirhinal cortex (PrC; divided into area 35 and 36), parahippocampal cortex (PhC), and hippocampus; which includes the subfields subiculum (Sub), CA1, CA2, as well as CA3 and dentate gyrus (DG) which are separated by the endfolial pathway covering most of the long axis of the hippocampus. We provide detailed instructions alongside slice-by-slice segmentations to ease learning for the untrained but also more experienced raters. Twenty-two subjects were scanned (19-32 yrs, mean age = 26 years, 12 females) with a turbo spin echo (TSE) T2-weighted MRI sequence with high-resolution oblique coronal slices oriented orthogonal to the long axis of the hippocampus (in-plane resolution 0.44 × 0.44 mm2) and 1.0 mm slice thickness. The scans were manually delineated by two experienced raters, to assess intra- and inter-rater reliability. The Dice Similarity Index (DSI) was above 0.78 for all regions and the Intraclass Correlation Coefficients (ICC) were between 0.76 to 0.99 both for intra- and inter-rater reliability. In conclusion, this study presents a fine-grained and comprehensive segmentation protocol for MTL structures at 7 T MRI that closely follows recent knowledge from anatomical studies. More specific subdivisions (e.g. area 35 and 36 in PrC, and the separation of DG and CA3) may pave the way for more precise delineations thereby enabling the detection of early volumetric changes in dementia and neuropsychiatric diseases.

Keywords: AG, Ambient Gyrus; CA1, Cornu Ammonis 1; CA2, Cornu Ammonis 2; CA3, Cornu Ammonis 3; CS, Collateral Sulcus; CSF, Cerebrospinal Fluid; CSa, anterior; CSp, posterior; CaS, Calcarine sulcus; DG, Dentate Gyrus; ErC, Entorhinal Cortex; FG, Fusiform Gyrus; HB, Hippocampal Body; HH, Hippocampal Head; HT, Hippocampal Tail; MTL, Medial Temporal Lobe; OTS, Occipito-temporal Sulcus; PhC, Parahippocampal Cortex; PhG, Parahippocampal Gyrus; PrC, Perirhinal Cortex; SRLM, Stratum radiatum lacunosum-moleculare; SaS, Semiannular Sulcus; Sub, Subiculum.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Brain Mapping / methods*
  • Brain Mapping / standards
  • Dentate Gyrus / diagnostic imaging
  • Dentate Gyrus / physiology
  • Female
  • Hippocampus / diagnostic imaging*
  • Hippocampus / physiology
  • Humans
  • Magnetic Resonance Imaging / methods*
  • Magnetic Resonance Imaging / standards
  • Male
  • Temporal Lobe / diagnostic imaging*
  • Temporal Lobe / physiology
  • Young Adult