Name: three-dimensional shape modeling and analysis of brain structures
Uploaded: 2019-11-14T10:00:00
Description: Watch this Scientific Journal Video about Three-Dimensional Shape Modeling and Analysis of Brain Structures at JoVE.com

这项工作由韩国国家研究基金会（JP作为PI）资助。JK由庆保国立大学研究基金资助;MCVH由罗福戈慈善信托基金和爱丁堡皇家学会资助。海马分割改编自英国爱丁堡临床脑科学中心的Karen Ferguson博士编写的内部指南。

脑MR图像是根据当地机构审查委员会和道德委员会批准的协议获得的。
注：形状建模和分析工具可从 NITRC 存储库<a href="https://www.nitrc.org/projects/dtmframework/" target="_blank">下载：https://www.nitrc.org/projects/dtmframework/</a>。GUI 软件 （DTMModeling.exe） 可在提取后执行。 <!--The publication list on the shape modeling tools can be found in the project webpage: <a href="http://cgv.kaist.ac.kr/brain" target="_blank"...

<ol>
	<li>Costafreda, S. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+hippocampal+shape+analysis+predicts+the+onset+of+dementia+in+mild+cognitive+impairment.">Automated hippocampal shape analysis predicts the onset of dementia in mild cognitive impairment.</a> NeuroImage. 56 (1), 212-219 (2011).</li><li>Platero, C., Lin, L., Tobar, M. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Longitudinal+Neuroimaging+Hippocampal+Markers+for+Diagnosing+Alzheimer's+Disease.">Longitudinal Neuroimaging Hippocampal Markers for Diagnosing Alzheimer's Disease.</a> Neuroinformatics. , 1-19 (2018).</li><li>Vald&#233;s Hern&#225;ndez, M. D. 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总之，我们描述了大脑结构形状分析的软件管道，包括（1）使用开放工具进行MR图像分割（2）使用可变形模板模型进行个体形状重建，以及（3）定量形状差异通过与模板模型的传递形状对应进行测量。在错误发现率（FDR）校正下进行统计分析，以调查与神经病理过程相关的大脑结构形态变化的意义。
我们的建模管道内部使用内部工具从主题图像构建模板模型。模板构造的步...

大脑结构的形状分析已成为研究其形态变化在病理过程中，如神经退行性疾病和老化1的首选工具。需要采用各种计算方法，1）从医学图像中准确划定目标结构的边界，2）以3D曲面网格的形式重建目标形状;3）通过形状参数化或曲面配准在单个形状模型中构建主体间对应关系，4）定量评估个人或群体之间的区域形状差异。在过去的几年中，许多方法已经引入神经成像研究，每个这些步骤。然而，尽管该领域取得了显著进展，但目前没有多少框架适用于研究。在本文中，我们使用自定义的形状建模工具和公开提供的图像分割工具描述大脑结构形状分析的每个步骤。
在这里，我们演示了大脑结构的形状分析框架，通过左右海马的形状分析使用成人对照和阿尔茨海默病患者的数据集。海马的萎缩被认为是神经退行性疾病2、3、4中的关键成像生物标志物。在我们的形状分析框架中，我们采用了目标结构的模板模型和形状建模过程中的模板到图像可变形的配准。模板模型对总体中目标结构的一般形状特征进行编码，并且它还提供了一个基线，用于通过各个模型与模板模型的传递关系量化各个模型之间的形状差异。在模板到图像的配准中，我们开发了一种拉普拉克表面变形方法，将模板模型与单个图像中的目标结构拟合，同时最大限度地减少模板模型5、6、7中点分布的失真。最近关于认知老化8、早期发现轻度认知障碍9的神经成像研究验证了该框架的可行性和鲁棒性，并探讨了大脑结构变化与皮质醇水平10之间的关联。这种方法将使得在进一步的神经成像研究中更容易使用形状建模和分析方法。

three-dimensional shape modeling and analysis of brain structures

大脑结构的统计形状分析被用来研究其结构变化与病理过程之间的关系。我们开发了一个软件包，用于准确和可靠的形状建模和基于组的分析。在这里，我们介绍了一个用于形状分析的管道，从单个三维形状建模到定量组形状分析。我们还使用开放式软件包描述了预处理和分段步骤。这个实用的指南将帮助研究人员在大脑结构的3D形状分析中节省时间和精力。

这里描述的形状建模过程已用于各种神经成像研究老化6，8，10和阿尔茨海默氏病5，9。特别是，这种形状建模方法在海马区654名受试者8人的形状分析中显示了其准确性和敏感性。对软件和公开可用的软件，ShapeWork，LDDMM-TI和SPHARM-PDM的定量分...

Watch this Scientific Journal Video about Three-Dimensional Shape Modeling and Analysis of Brain Structures at JoVE.com

Three-Dimensional Shape Modeling and Analysis of Brain Structures

我们引入了一种半自动方案，用于大脑结构的形状分析，包括使用开放软件进行图像分割，以及使用自动建模包进行进一步组式形状分析。在这里，我们演示了3D形状分析协议的每一步，其中海马分割从大脑MR图像。

脑结构三维形状建模与分析

Statistical shape analysis of brain structures has been used to investigate the association between their structural changes and pathological processes. ...

准确恢复形状特征对粗糙和嘈杂的分割是实现单个大脑形状模型之间的良好解剖对应的关键。我们的框架为单个形状建模、分组模板构造和形状畸形计算提供了各种工具。它已被用于人类大脑的大型数据集。演示这个程序将是JailKim博士，一个前研究生从我的实验室谁开发了大脑形状建模的软件。对于海马分段的手动编辑，打开T1重量磁共振图像和自动海马分段结果在图形用户界面软件。单击显示窗口中的图标以选择日冕视图并滚动浏览卷，直到找到取消的扇形。包括海马面膜中的未粘膜，使用加减函数在海马体退去后编辑海马体的掩码。继续编辑海马面膜，直到找到海马尾巴。当丘脑的脉动核比海马体更优退时，前核就会出现。完成编辑海马体的最后一个日冕切片，其中前半角的整个长度是可见的，但尚未与语料库的氦连续。然后，以 NifTI 格式保存左右海马的蒙版。若要构造组模板模型加载形状建模插件，然后单击"打开目录"以打开包含感兴趣研究总体的二进制掩码的目录。输入所需的顶点数，然后单击组模板构造的模板构造。然后检查均形状网格。对于单个形状重建，加载感兴趣的 T1 加权磁共振图像及其相应的分段掩码，并选择工作目录保存文件。为单个形状建模选择模板模型，并根据需要检查和修改形状建模插件中的建模参数。因此，我们的建模框架几乎是自动化的，但是，有些步骤需要用户确认。例如，如果海马区域的值不是一个用户必须更改强度参数。然后，在工具包工作台的 3D 视图中检查结果。要执行形状和变形测量，请在软件的数据管理器中选择感兴趣的主体的形状模型，然后单击"选择模板"以选择感兴趣的模板以获取测量。在这里，可以观察到海马模板模型的代表性变形，用于单个形状重建。该方法诱导模板模型的大到小比例变形，以最大限度地减少其点分布的失真，同时恢复单个形状特征。在此图中，显示了两个主题及其分割蒙版重建的形状模型。在这些图像中，可以观察到单个形状模型对齐的平均值模型和形状差向量与单个形状模型。这些数据表示投影到平均模型上的平均形状变形贴图。对于脑组织体积小的组，以及脑组织体积较大的组。两组的形状畸形图在相应区域呈现海马形状差异的相反模式。将分段掩码和单个或共享模型一起检查。如果模型未拟合图像边界，请调整建模参数以获得最佳结果。可以使用形状畸形进行统计分析，以调查组形，我们还在项目页面上为分析提供了 MATLAB 代码。这种稳健的方法已应用于许多临床研究，不仅涉及关键结构建模，如阿尔茨海默氏症或衰老研究，而且涉及需要分析复合骨骼的足骨疾病。

Research

JoVE Journal

Neuroscience

Dissection and Culture of Mouse Dopaminergic and Striatal Explants in Three-Dimensional Collagen Matrix Assays

小鼠多巴胺和三维胶原基质检测纹状体外植体的解剖和文化

Midbrain dopamine (mdDA) neurons project via the medial forebrain bundle towards several areas in the telencephalon, including the striatum1. ...

科研

神经科学

Three-dimensional Confocal Analysis of Microglia/macrophage Markers of Polarization in Experimental Brain Injury

偏振的实验性脑损伤小胶质细胞/巨噬细胞标志物的三维共聚焦分析

After brain stroke microglia/macrophages (M/M) undergo  rapid activation with dramatic morphological and phenotypic changes that  include expression of ...

Protocol for Three-dimensional Confocal Morphometric Analysis of Astrocytes

协议星形胶质细胞的三维共聚焦形态分析

As glial cells in the brain, astrocytes have diverse functional roles in the central nervous system. In the presence of harmful stimuli, astrocytes modify ...

Three-dimensional Imaging and Analysis of Mitochondria within Human Intraepidermal Nerve Fibers

人 Intraepidermal 神经纤维内线粒体三维成像及分析

The goal of this protocol is to study mitochondria within intraepidermal nerve fibers. Therefore, 3D imaging and analysis techniques were developed to ...

Peering at Brain Polysomes with Atomic Force Microscopy

在脑核糖凝视与原子力显微镜

The translational machinery, i.e., the polysome or polyribosome, is one of the biggest and most complex cytoplasmic machineries in cells. Polysomes, ...

Anatomically Inspired Three-dimensional Micro-tissue Engineered Neural Networks for Nervous System Reconstruction, Modulation, and Modeling

解剖学启发的三维微组织工程神经网络用于神经系统重建，调制和建模

Functional recovery rarely occurs&#160;following injury or disease-induced degeneration within the central nervous system (CNS)&#160;due to the inhibitory ...

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

小鼠大脑皮层细胞组织的大尺度三维成像

The mammalian neocortex is composed of many types of excitatory and inhibitory neurons, each with specific electrophysiological and biochemical ...

Chronic Implantation of Whole-cortical Electrocorticographic Array in the Common Marmoset

常见马莫塞的全皮质电皮质阵列的慢性植入

Electrocorticography (ECoG) allows the monitoring of electrical field potentials from the cerebral cortex with high spatiotemporal resolution. Recent ...

Focused Ultrasound Induced Blood-Brain Barrier Opening for Targeting Brain Structures and Evaluating Chemogenetic Neuromodulation

聚焦超声诱导血脑屏障打开，用于靶向大脑结构和评估化学遗传神经调控

Acoustically Targeted Chemogenetics (ATAC) allows for the noninvasive control of specific neural circuits. ATAC achieves such control through a ...

Three-Dimensional Motor Nerve Organoid Generation

三维运动神经器官生成

A fascicle of axons is one of the major structural motifs observed in the nervous system. Disruption of axon fascicles could cause developmental and ...