Summary: The hippocampus is composed of distinct anatomical subregions that participate in multiple cognitive processes and are differentially affected in prevalent neurological and psychiatric conditions. Advances in high-field MRI allow for the non-invasive identification of hippocampal substructure. These approaches, however, demand time-consuming manual segmentation that relies heavily on anatomical expertise. Here, we share manual labels and associated high-resolution MRI data (MNI-HISUB25; submillimetric T1- and T2-weighted images, detailed sequence information, and stereotaxic probabilistic anatomical maps) based on 25 healthy subjects. Data were acquired on a widely available 3-Tesla MRI system using a 32 phased-array head coil. The protocol divided the hippocampal formation into three subregions: subicular complex, Cornu Ammonis 1, 2 and 3 (CA1-3), and CA4-dentate gyrus (CA4-DG). Segmentation was guided by consistent intensity and morphology characteristics of the densely myelinated molecular layer together with few geometry-based boundaries flexible to overall mesiotemporal anatomy, and achieved excellent intra-/inter-rater reliability (Dice index ≥90/87%). The dataset can inform neuroimaging assessments of the mesiotemporal lobe and help to develop segmentation algorithms relevant for basic and clinical neurosciences.

MRI data were acquired on a 3-Tesla Siemens TimTrio scanner using a 32-channel head coil. We obtained two sets of T1w images: a 3D magnetization-prepared rapid-acquisition gradient echo (MPRAGE) with millimetric resolution (repetition time (TR)=2300 ms; echo time (TE)=2.98 ms; inversion time (TI)=900 ms; flip angle=9°; matrix size=256×256; field-of-view (FOV)=256×256 mm2; 176 sagittal slices with 1 mm slice thickness resulting in 1×1×1 mm3 voxels; iPAT=2, acquisition time=5.30 min), and a submillimetric 3D MPRAGE (TR=3000 ms; TE=4.32 ms; TI=1500 ms; flip angle=7°; matrix size=336×384; FOV=201×229 mm2; 240 axial slices with 0.6 mm slice thickness resulting in 0.6×0.6×0.6 mm3 voxels; acquisition time=16.48 min; to increase the signal-to-noise ratio, two identical scans were acquired, motion corrected, and averaged into a single volume). T2w images were obtained using a 2D turbo spin-echo sequence (TR=10810 ms; TE=81 ms; flip angle=119°; matrix size=512×512; FOV=203×203 mm2, 60 coronal slices angled perpendicular to the hippocampal long axis, slice thickness=2mm, resulting in 0.4×0.4×2.0 mm3 voxels; acquisition time=5.47 min).

This dataset includes:

Authors:

  • Jessie Kulaga-Yoskovitz MSc
  • Boris C. Bernhardt PhD
  • Seok-Jun Hong MSc
  • Tommaso Mansi PhD
  • Kevin E. Liang MSc
  • Andre J.W. van der Kouwe PhD
  • Jonathan Smallwood PhD,
  • Andrea Bernasconi MD (PI)
  • Neda Bernasconi MD PhD (PI)

    • USAGE AGREEMENT
    Creative Commons License: Attribution - Non-Commercial

    Funding
    This work and BCB were supported by the Canadian Institutes of Health Research (CIHR MOP-57840 and CIHR MOP-123520).

     

    Data Release Table

    Imaging_Data

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    Publications:
    J. Kulaga-Yoskovitz, B.C. Bernhardt, S. Hong, T. Mansi, K. Liang, A. van der Kouve, J. Smallwood, A. Bernasconi, N. Bernasconi (2015) Multi-contrast and submillimetric 3T hippocampal subfield segmentation protocol and dataset. Scientific data, in press.