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A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex

The neocortex is the largest component of the mammalian cerebral cortex. It integrates sensory inputs with experiences and memory to produce sophisticated responses to an organism's internal and external environment. While areal patterning of the mouse neocortex has been mapped using histological te... Full description

Journal Title: NeuroImage September 2013, Vol.78, pp.196-203
Main Author: Ullmann, Jeremy F.P.
Other Authors: Watson, Charles , Janke, Andrew L. , Kurniawan, Nyoman D. , Reutens, David C.
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: ISSN: 1053-8119 ; DOI: 10.1016/j.neuroimage.2013.04.008
Link: http://dx.doi.org/10.1016/j.neuroimage.2013.04.008
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recordid: sciversesciencedirect_elsevierS1053-8119(13)00335-2
title: A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex
format: Article
creator:
  • Ullmann, Jeremy F.P.
  • Watson, Charles
  • Janke, Andrew L.
  • Kurniawan, Nyoman D.
  • Reutens, David C.
subjects:
  • Atlas
  • Cortex
  • Isocortex
  • Magnetic Resonance Imaging
  • Segmentation
ispartof: NeuroImage, September 2013, Vol.78, pp.196-203
description: The neocortex is the largest component of the mammalian cerebral cortex. It integrates sensory inputs with experiences and memory to produce sophisticated responses to an organism's internal and external environment. While areal patterning of the mouse neocortex has been mapped using histological techniques, the neocortex has not been comprehensively segmented in magnetic resonance images. This study presents a method for systematic segmentation of the C57BL/6J mouse neocortex. We created a minimum deformation atlas, which was hierarchically segmented into 74 neocortical and cortical-related regions, making it the most detailed atlas of the mouse neocortex currently available. In addition, we provide mean volumes and relative intensities for each structure as well as a nomenclature comparison between the two most cited histological atlases of the mouse brain. This MR atlas is available for download, and it should enable researchers to perform automated segmentation in genetic models of cortical disorders. •We present a methodology for delineation of the C57BL/6J mouse neocortex in MRI.•We successfully delineated 74 neocortical and cortical-related regions.•We calculated mean volumes and contrast intensities for each structure.
language: eng
source:
identifier: ISSN: 1053-8119 ; DOI: 10.1016/j.neuroimage.2013.04.008
fulltext: fulltext
issn:
  • 10538119
  • 1053-8119
url: Link


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titleA segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex
creatorUllmann, Jeremy F.P. ; Watson, Charles ; Janke, Andrew L. ; Kurniawan, Nyoman D. ; Reutens, David C.
ispartofNeuroImage, September 2013, Vol.78, pp.196-203
identifierISSN: 1053-8119 ; DOI: 10.1016/j.neuroimage.2013.04.008
subjectAtlas ; Cortex ; Isocortex ; Magnetic Resonance Imaging ; Segmentation
descriptionThe neocortex is the largest component of the mammalian cerebral cortex. It integrates sensory inputs with experiences and memory to produce sophisticated responses to an organism's internal and external environment. While areal patterning of the mouse neocortex has been mapped using histological techniques, the neocortex has not been comprehensively segmented in magnetic resonance images. This study presents a method for systematic segmentation of the C57BL/6J mouse neocortex. We created a minimum deformation atlas, which was hierarchically segmented into 74 neocortical and cortical-related regions, making it the most detailed atlas of the mouse neocortex currently available. In addition, we provide mean volumes and relative intensities for each structure as well as a nomenclature comparison between the two most cited histological atlases of the mouse brain. This MR atlas is available for download, and it should enable researchers to perform automated segmentation in genetic models of cortical disorders. •We present a methodology for delineation of the C57BL/6J mouse neocortex in MRI.•We successfully delineated 74 neocortical and cortical-related regions.•We calculated mean volumes and contrast intensities for each structure.
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abstractThe neocortex is the largest component of the mammalian cerebral cortex. It integrates sensory inputs with experiences and memory to produce sophisticated responses to an organism's internal and external environment. While areal patterning of the mouse neocortex has been mapped using histological techniques, the neocortex has not been comprehensively segmented in magnetic resonance images. This study presents a method for systematic segmentation of the C57BL/6J mouse neocortex. We created a minimum deformation atlas, which was hierarchically segmented into 74 neocortical and cortical-related regions, making it the most detailed atlas of the mouse neocortex currently available. In addition, we provide mean volumes and relative intensities for each structure as well as a nomenclature comparison between the two most cited histological atlases of the mouse brain. This MR atlas is available for download, and it should enable researchers to perform automated segmentation in genetic models of cortical disorders. •We present a methodology for delineation of the C57BL/6J mouse neocortex in MRI.•We successfully delineated 74 neocortical and cortical-related regions.•We calculated mean volumes and contrast intensities for each structure.
pubElsevier Inc.
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date2013-09