A high-resolution computational atlas of the human hippocampus from postmortem magnetic resonance imaging at 9.4 T

Abstract

This paper describes the construction of a computational anatomical atlas of the human hippocampus. The atlas is derived from high-resolution 9.4 Tesla MRI of postmortem samples. The main subfields of the hippocampus (cornu Ammonis fields CA1, CA2/3; the dentate gyrus; and the vestigial hippocampal sulcus) are labeled in the images manually using a combination of distinguishable image features and geometrical features. A synthetic average image is derived from the MRI of the samples using shape and intensity averaging in the diffeomorphic non-linear registration framework, and a consensus labeling of the template is generated. The agreement of the consensus labeling with manual labeling of each sample is measured, and the effect of aiding registration with landmarks and manually generated mask images is evaluated. The atlas is provided as an online resource with the aim of supporting subfield segmentation in emerging hippocampus imaging and image analysis techniques. An example application examining subfield-level hippocampal atrophy in temporal lobe epilepsy demonstrates the application of the atlas to in vivo studies.

Hippocampal Subregions are Differentially Affected in the Progression to Alzheimer's Disease

“…Imaging studies have used methods for identifying these hippocampal subfields through unfolding methods in high resolution functional MRI (Zeineh et al, 2000(Zeineh et al, , 2001Ekstrom et al, 2009) and high resolution in vivo (Mueller et al, 2007;Theysohn et al, 2009;Van Leemput et al, 2009) and ex vivo (Yushkevich et al, 2009) structural MRI mapping. These subfields are independent of subregional definitions of the hippocampus along its longitudinal axis (head, body, and tail) that are more readily evaluated in lower resolution imaging studies.…”

High-resolution <em>In Vivo</em> Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging

“…3. Slice B: Hippocampal Head 1: Label the low-intensity area in the middle of the hippocampal formation as SR/SL/SM 13,37 . When the bend along the inferior edge of the hippocampus becomes clear, use this landmark as the lateral border separating the subiculum from the CA1 12,22 .…”

“…When the bend along the inferior edge of the hippocampus becomes clear, use this landmark as the lateral border separating the subiculum from the CA1 12,22 . Continue to follow the longest axis of the hippocampus to draw the CA1-subiculum border on the supero-medial tip 37 .…”

“…Projects such as these are limited by the availability of intact medial temporal lobe specimens, histological techniques, data loss during histological processing, and the fundamental morphological inconsistencies between fixed and in vivo brains. Other groups have used high-field scanners (7T or 9.4T) in an effort to acquire in vivo or ex vivo images with a small enough (0.20-0.35 mm isotropic) voxel size to visualize spatially localized differences in image contrast that are used to infer boundaries between subfields 35,37 . Even at 7T-9.4T and with such a small voxel size, the cytoarchitectonic characteristics of hippocampal subfields are not visible.…”

Seven-Tesla MRI and neuroimaging biomarkers for Alzheimer’s disease

“…2, 57,63,97,100 Due to the plethora of labeling protocols and guidelines in the literature, there have been attempts to compare different protocols and standardize across guidelines to produce a unified segmentation protocol.…”