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

Penn Image Computing and Science Laboratory (PICSL), Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA.
NeuroImage (Impact Factor: 6.36). 10/2008; 44(2):385-98. DOI: 10.1016/j.neuroimage.2008.08.042
Source: PubMed

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.

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Available from: Stephen Pickup, Aug 25, 2015
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    • "The final reconstructed and aligned bSSFP volumes were visualized using ITK-SNAP ( Segmentation of hippocampal subregions was performed manually according to anatomic atlases and our prior work (Duvernoy, 2005; Insausti and Amaral, 2008; Yushkevich et al., 2009; Zeineh et al., 2012). Detailed hippocampal subfield segmentation was performed of the hippocampal body only, not the tail or head. "
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    ABSTRACT: The hippocampus is a very important structure in memory formation and retrieval, as well as in various neurological disorders such as Alzheimer's disease, epilepsy and depression. It is composed of many intricate subregions making it difficult to study the anatomical changes that take place during disease. The hippocampal hilus may have unique neuroanatomy in humans compared to monkeys and rodents, with field CA3h greatly enlarged in humans compared to rodents, and a white-matter pathway, called the endfolial pathway, possibly only present in humans. In this study we have used newly developed 7.0T whole brain imaging, balanced steady-state free precession (bSSFP) that can achieve 0.4mm isotropic images to study, in vivo, the anatomy of the hippocampal hilus. A detailed hippocampal subregional segmentation was performed according to anatomic atlases segmenting the following regions: CA4, CA3, CA2, CA1, SRLM (stratum radiatum lacunosum moleculare), alveus, fornix, and subiculum along with its molecular layer. We also segmented a hypointense structure centrally within the hilus that resembled the endfolial pathway. To validate that this hypointense signal represented the endfolial pathway, we acquired 0.1mm isotropic 8-phase cycle bSSFP on an excised specimen, and then sectioned and stained the specimen for myelin using an anti-myelin basic protein antibody (SMI 94). A structure tensor analysis was calculated on the myelin-stained section to show directionality of the underlying fibers. The endfolial pathway was consistently visualized within the hippocampal body in vivo in all subjects. It is a central pathway in the hippocampus, with unknown relevance in neurodegenerative disorders, but now that it can be visualized noninvasively, we can study its function and alterations in neurodegeneration. Copyright © 2015. Published by Elsevier Inc.
    NeuroImage 02/2015; 112. DOI:10.1016/j.neuroimage.2015.02.029 · 6.36 Impact Factor
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    • "Subject Age Gender Weight (lb) Subject Age Gender Weight (lb) 1 23 M 155 11 21 F 126 2 31 F 150 12 25 M 150 3 24 F 100 13 22 M 130 4 57 F 170 14 43 M 180 5 43 F 217 15 26 M 240 6 35 M 210 16 42 F 180 7 45 F 180 17 52 M 156 8 27 F 180 18 39 M 210 9 22 F 160 19 50 F 260 10 44 M 155 20 27 M 175 Note: M, male; F, female. Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization 49 similarity metric (Avants et al. 2008; Yushkevich et al. 2009; Shi et al. 2011; Woo et al. 2012 "
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    ABSTRACT: Magnetic resonance imaging (MRI) is an essential tool in the study of muscle anatomy and functional activity in the tongue. Objective assessment of similarities and differences in tongue structure and function has been performed using unnormalised data, but this is biased by the differences in size, shape and orientation of the structures. To remedy this, we propose a methodology to build a 3D vocal tract atlas based on structural MRI volumes from 20 normal subjects. We first constructed high-resolution volumes from three orthogonal stacks. We then removed extraneous data so that all 3D volumes contained the same anatomy. We used an unbiased diffeomorphic groupwise registration using a cross-correlation similarity metric. Principal component analysis was applied to the deformation fields to create a statistical model from the atlas. Various evaluations and applications were carried out to show the behaviour and utility of the atlas.
    01/2015; 3(1). DOI:10.1080/21681163.2014.933679
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    • "Integration of data from myelin-stained (Geyer et al., 2011) sections of postmortem hippocampus into probabilistic atlases may greatly improve the reliability of hippocampal subregional boundary determinations. Future studies may benefit from the combination of computational unfolding, ROI analysis, MVPA (Bonnici et al., 2012), histology guided segmentation approaches (Adler et al., 2014), cytoarchitectural postmortem atlases (Yushkevich et al., 2009), high-field structural imaging (Mueller et al., 2007; Zeineh et al., 2014), and automated segmentation procedures (Van Leemput et al., 2009, Yushkevich et al., 2010, 2014) in order to provide a complete, accurate, and fast analysis of structural and functional imaging studies of human hippocampal subfields during normal memory and disorders such as Alzheimer's disease or temporal-lobe epilepsy. Our results summarize our recent improvements in high-resolution imaging and computational unfolding methods of the human hippocampus in vivo. "
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    ABSTRACT: Examining the function of individual human hippocampal subfields remains challenging because of their small sizes and convoluted structures. Previous human fMRI studies at 3 T have successfully detected differences in activation between hippocampal cornu ammonis (CA) field CA1, combined CA2, CA3, and dentate gyrus (DG) region (CA23DG), and the subiculum during associative memory tasks. In this study, we investigated hippocampal subfield activity in healthy participants using an associative memory paradigm during high-resolution fMRI scanning at 7 T. We were able to localize fMRI activity to anterior CA2 and CA3 during learning and to the posterior CA2 field, the CA1, and the posterior subiculum during retrieval of novel associations. These results provide insight into more specific human hippocampal subfield functions underlying learning and memory and a unique opportunity for future investigations of hippocampal subregion function in healthy individuals as well as those suffering from neurodegenerative diseases.
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