Name: high-resolution in vivo manual segmentation protocol for human hippocampal subfields using 3t magnetic resonance imaging
Uploaded: 2015-11-10T14:00:00
Description: Watch this Scientific Journal Video about High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging at JoVE.com

The authors would like to acknowledge support from the CAMH Foundation, thanks to Michael and Sonja Koerner, the Kimel Family, and the Paul E. Garfinkel New Investigator Catalyst Award. This project was funded by the Fonds de Recherches Sant&#233; Qu&#233;bec, the Canadian Institutes of Health Research (CIHR), the Natural Sciences and Engineering Research Council of Canada, the Weston Brain Institute, the Alzheimer&#39;s Society of Canada, and the Micheal J. Fox Foundation for Parkinson&#39;s Research (MMC), as well as CIHR, the Ontario Mental Health Foundation, NARSAD, and the National Institute of Mental Health (R01MH099167) (ANV). The authors would also like to thank Anusha Ravichandran for assistance acquiring the images.

Study Participants
The protocol in this manuscript was developed for five representative high-resolution images collected from healthy volunteers (3F, 2M; age 29-57, avg. 37) who were free of neurological and neuropsychiatric disorders and cases of severe head trauma. All subjects were recruited at the Centre for Addiction and Mental Health (CAMH). The study was approved by the CAMH Research Ethics Board and was conducted in keeping with the Declaration of Helsinki. All subjects provided written...

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Hippocampal subfield segmentation in MR images is well-represented in the literature. However, existing protocols exclude portions of the hippocampus20,23,33,35, apply only to fixed images37, or require ultra-high field scanners for image acquisition35,37. This manuscript offers a segmentation protocol that includes five major subdivisions (CA1, CA2/CA3, CA4/dentate gyrus, SR/SL/SM, and subiculum) of the hippocampus and spans the entire anterior-posterior length of the structure. The comp...

The hippocampus is a widely studied medial temporal lobe structure that is associated with episodic memory, spatial navigation, and other cognitive functions10,31. Its role in neurodegenerative and neuropsychiatric disorders such as Alzheimer&#8217;s disease, schizophrenia, and bipolar disorder is well-documented4,5,18,24,30. The goal of this manuscript is to provide additional detail to the manual segmentation protocol published previously34 for human hippocampal subfields on high-resolution magnetic resonance (MR) images acquired at 3T. Additionally, the video component accompanying this manuscript will provide further assistance to researchers who wish to implement the protocol on their own datasets.
The hippocampus can be divided into subfields based on cytoarchitectonic differences observed in histologically-prepared post-mortem specimens12,22. Such post-mortem specimens define the ground truth for the identification and study of hippocampal subfields; however preparations of this nature require specialized skills and equipment for staining, and are limited by the availability of fixed tissue, especially in diseased populations. In vivo imaging has the advantage of a much larger pool of subjects, and also presents the opportunity for follow-up studies and observing changes in populations. Although it has been shown that signal intensities in T2-weighted ex vivo MR images reflect cellular density13, it is still difficult to identify undisputed borders between subfields using solely MR signal intensities. As such, a number of different approaches for identifying histology-level detail on MR images have been developed.
Some groups have made efforts to reconstruct and digitize histological datasets and then use these reconstructions along with image registration techniques to localize hippocampal subfield neuroanatomy on in vivo MR1,2,8,9,14,15,17,32. Although this is an effective technique for mapping a version of the histological ground truth directly onto MR images, reconstructions of this nature are difficult to complete. 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 subfields35,37. Even at 7T-9.4T and with such a small voxel size, the cytoarchitectonic characteristics of hippocampal subfields are not visible. As such, manual segmentation protocols have been developed that approximate the known histological boundaries on MR images. These protocols determine subfield boundaries by interpreting local image contrast differences and defining geometric rules (such as straight lines and angles) relative to visible structures. Although images taken at a high field strength are able to offer detailed insight into hippocampal subfields, high-field scanners are not yet common in clinical or research settings, so 7T and 9.4T protocols currently have limited applicability. Similar protocols have been developed for images collected on 3T and 4T scanners11,20,21,23,24,25,28,33. Many of these protocols are based on images with sub-1mm voxels voxel dimensions in the coronal plane, but have large slice thicknesses (0.8-3 mm)11,20,21,23,25,28,33 or large inter-slice distances20,28, both of which result in a significant measurement bias in the estimation of volumes of the individual subfields. Additionally, many of the existing 3T protocols exclude subfields in all or part of the hippocampal head or tail20,23,25,33 or do not provide detailed segmentations of important substructures (i.e., combine the DG with CA2/CA3 or do not include the strata radiatum/lacunosum/moleculare of the CA)11,20,21,23,24,25,28,33. There is therefore a need in the field for a detailed description of a protocol that can reliably identify relevant subfields throughout the head, body, and tail of the hippocampus that is based on a scanner commonly available in clinical and research settings. Efforts are currently underway by the Hippocampal Subfields Group (www.hippocampalsubfields.com) to harmonize the hippocampal subfield segmentation process between laboratories, similar to an existing harmonization effort for whole hippocampal segmentation6, and an initial paper comparing 21 existing protocols was recently published38. The work from this group will further elucidate optimal segmentation procedures.
This manuscript provides detailed written and video instructions for reliably implementing the hippocampal subfield segmentation protocol described previously by Winterburn and colleagues34 on high-resolution 3T MR images. The protocol has been implemented on five images of healthy controls for the whole hippocampus and five hippocampal subfields (CA1, CA2/CA3, CA4/dentate gyrus, strata radiatum/lacunosum/moleculare, and subiculum). These segmented images are available to the public online (cobralab.ca/atlases/Hippocampus). The protocol and the segmented images will be useful for groups who wish to study detailed hippocampal neuroanatomy in MR images.

<table border="0">
	<tbody>
		<tr>
			<td>Discovery MR750 3T</td>
			<td>GE</td>
			<td>NA</td>
			<td>Or equivalent 3T scanner</td>
		</tr>
		<tr>
			<td>Minc Tool Kit</td>
			<td>McConnell Brain Imaging Center, Montreal Neurological Institute</td>
			<td>NA</td>
			<td>Open source: http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit</td>
		</tr>
	</tbody>
</table>

high-resolution in vivo manual segmentation protocol for human hippocampal subfields using 3t magnetic resonance imaging

The human hippocampus has been broadly studied in the context of memory and normal brain function and its role in different neuropsychiatric disorders has been heavily studied. While many imaging studies treat the hippocampus as a single unitary neuroanatomical structure, it is, in fact, composed of several subfields that have a complex three-dimensional geometry. As such, it is known that these subfields perform specialized functions and are differentially affected through the course of different disease states. Magnetic resonance (MR) imaging can be used as a powerful tool to interrogate the morphology of the hippocampus and its subfields. Many groups use advanced imaging software and hardware (&#62;3T) to image the subfields; however this type of technology may not be readily available in most research and clinical imaging centers. To address this need, this manuscript provides a detailed step-by-step protocol for segmenting the full anterior-posterior length of the hippocampus and its subfields: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus (DG), strata radiatum/lacunosum/moleculare (SR/SL/SM), and subiculum. This protocol has been applied to five subjects (3F, 2M; age 29-57, avg. 37). Protocol reliability is assessed by resegmenting either the right or left hippocampus of each subject and computing the overlap using the Dice&#39;s kappa metric. Mean Dice&#39;s kappa (range) across the five subjects are: whole hippocampus, 0.91 (0.90-0.92); CA1, 0.78 (0.77-0.79); CA2/CA3, 0.64 (0.56-0.73); CA4/dentate gyrus, 0.83 (0.81-0.85); strata radiatum/lacunosum/moleculare, 0.71 (0.68-0.73); and subiculum 0.75 (0.72-0.78). The segmentation protocol presented here provides other laboratories with a reliable method to study the hippocampus and hippocampal subfields in vivo using commonly available MR tools.

Results from the protocol reliability test are summarized in Table 2. For the whole bilateral hippocampus, mean spatial overlap as measured by Dice&#8217;s kappa is 0.91 and ranges from 0.90 - 0.92. Subfield kappa values range from 0.64 (CA2/CA3) to 0.83 (CA4/dentate gyrus). Mean volumes for all subfields and the whole hippocampus are reported in Table 3. Volumes for the whole hippocampus range from 2456.72-3325.02 mm3. The CA2/CA3 is the smallest subfield at 208.33 mm3</...

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

The goal of this manuscript is to study the hippocampus and hippocampal subfields using MRI. The manuscript describes a protocol for segmenting the hippocampus and five hippocampal substructures: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus, strata radiatum/lacunosum/moleculare, and subiculum.

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

The human hippocampus has been broadly studied in the context of memory and normal brain function and its role in different neuropsychiatric disorders has ...

Research

JoVE Journal

Neuroscience

Magnetic Resonance Spectroscopy of live Drosophila melanogaster using Magic Angle Spinning

Magnetic Resonance Spectroscopy of live Drosophila melanogaster using Magic Angle Spinning

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High-resolution Structural Magnetic Resonance Imaging of the Human Subcortex In Vivo and Postmortem

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