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


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.

Download full-text


Available from: Stephen Pickup
  • Source
    • "The border of typical ProS with CA1 is usually located at the point where narrower py of CA1 switches to wider py of the ProS and/ or where the overall vertical orientation of CA1 (py) changes to the overall horizontal orientation of the subicular cortices. This point can be clearly appreciated in high-resolution MRI scans (see images in Fatterpekar et al., 2002; Shepherd et al., 2007; Fischl et al., 2009; Yushkevich et al., 2009; Augustinack et al., 2010; Henry et al., 2011; Wisse et al., 2012). In addition, the border between ProSu and CA1u can be easily identified on MRI slices because CA1u always occupies ID2 while ProS is located medial to CA1u and resides within ID3 (if it exits). "

    Full-text · Dataset · Oct 2015
    • "These inconsistent results may be due to the use of volumetric measurements focused on the whole hippocampus or anterior or posterior sections [Raz and Rodrigue, 2006; Shing et al., 2011; Van Petten , 2004]. In recent years, approaches indexing hippocampal subfield volume and shape have provided novel alternatives for characterization of hippocampal morphology in vivo [Winterburn et al., 2013; Yang et al., 2013; Yushkevich et al., 2009, 2010]. As the hippocampus is not a homogeneous structure , application of these new approaches may help to address the inconsistent findings from more conventional measurements of hippocampal structure [La Joie et al., 2010; Mueller and Weiner, 2009; Mueller et al., 2007; Yang et al., 2013]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Newer approaches to characterizing hippocampal morphology can provide novel insights regarding cognitive function across the lifespan. We comprehensively assessed the relationships among age, hippocampal morphology, and hippocampal-dependent cognitive function in 137 healthy individuals across the adult lifespan (18-86 years of age). They underwent MRI, cognitive assessments and genotyping for Apolipoprotein E status. We measured hippocampal subfield volumes using a new multiatlas segmentation tool (MAGeT-Brain) and assessed vertex-wise (inward and outward displacements) and global surface-based descriptions of hippocampus morphology. We examined the effects of age on hippocampal morphology, as well as the relationship among age, hippocampal morphology, and episodic and working memory performance. Age and volume were modestly correlated across hippocampal subfields. Significant patterns of inward and outward displacement in hippocampal head and tail were associated with age. The first principal shape component of the left hippocampus, characterized by a lengthening of the antero-posterior axis was prominently associated with working memory performance across the adult lifespan. In contrast, no significant relationships were found among subfield volumes and cognitive performance. Our findings demonstrate that hippocampal shape plays a unique and important role in hippocampal-dependent cognitive aging across the adult lifespan, meriting consideration as a biomarker in strategies targeting the delay of cognitive aging. Hum Brain Mapp, 2015. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.
    No preview · Article · May 2015 · Human Brain Mapping
  • Source
    • "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. "
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Feb 2015 · NeuroImage
Show more