Quantitative mouse brain phenotyping based on single and multispectral MR protocols.
Quantitative mouse brain phenotyping based on single and multispectral MR protocols.
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DOI：
10.1016/j.neuroimage.2012.07.021
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发表时间：
2012-11-15
期刊：
影响因子：
5.7
通讯作者：
Johnson, G. Allan
中科院分区：
文献类型：
--
作者：
Badea, Alexandra;Gewalt, Sally;Avants, Brian B.;Cook, James J.;Johnson, G. Allan
关键词：
已经为人脑开发了复杂的图像分析方法，但这些工具仍然需要进行调整和优化，以用于定量小动物成像。我们提出了一个框架，在小鼠模型的神经和精神疾病的定量解剖表型。该框架包括一个图集空间，图像采集协议和软件工具，以注册图像到这个空间。我们表明，一套分割工具设计的人类神经成像可以纳入一个管道，用于分割小鼠脑图像采集多光谱磁共振成像（MR）协议。我们提出了一种灵活的方法来分割这种超图像，优化配准，并确定特定结构的图像通道的最佳组合。采用T1、T2* 和T2对比度的脑成像对海马和尾壳核（Hc和CPu）的准确性在83%的范围内，但对白色物质束的准确性仅为54%，对脑室的准确性为44%。增加扩散张量参数图像提高了大灰质结构（>5%）、白色物质（10%）和脑室（15%）的准确性。马尔可夫随机场分割的使用进一步提高了C57 BL/6菌株的总体准确性6%，因此Hc和CPu的Dice系数达到93%，白色物质为79%，脑室为68%，黑质为80%。我们展示了广泛使用的C57 BL/6菌株和两种测试菌株（BXD 29，APP/TTA）的分割管道。这种方法似乎很有前途的表征人类神经和精神疾病的小鼠模型的时间变化，并可能提供其他临床前成像，如功能磁共振成像和分子成像的解剖约束。这是第一次证明，多个MR成像模式结合多元分割方法导致小鼠大脑解剖分割的显着改善。
Sophisticated image analysis methods have been developed for the human brain, but such tools still need to be adapted and optimized for quantitative small animal imaging. We propose a framework for quantitative anatomical phenotyping in mouse models of neurological and psychiatric conditions. The framework encompasses an atlas space, image acquisition protocols, and software tools to register images into this space. We show that a suite of segmentation tools designed for human neuroimaging can be incorporated into a pipeline for segmenting mouse brain images acquired with multispectral magnetic resonance imaging (MR) protocols. We present a flexible approach for segmenting such hyperimages, optimizing registration, and identifying optimal combinations of image channels for particular structures. Brain imaging with T1, T2* and T2 contrasts yielded accuracy in the range of 83% for hippocampus and caudate putamen (Hc and CPu), but only 54% in white matter tracts, and 44% for the ventricles. The addition of diffusion tensor parameter images improved accuracy for large gray matter structures (by >5%), white matter (10%), and ventricles (15%). The use of Markov random field segmentation further improved overall accuracy in the C57BL/6 strain by 6%; so Dice coefficients for Hc and CPu reached 93%, for white matter 79%, for ventricles 68%, and for substantia nigra 80%. We demonstrate the segmentation pipeline for the widely used C57BL/6 strain, and two test strains (BXD29, APP/TTA). This approach appears promising for characterizing temporal changes in mouse models of human neurological and psychiatric conditions, and may provide anatomical constraints for other preclinical imaging, e.g. fMRI and molecular imaging. This is the first demonstration that multiple MR imaging modalities combined with multivariate segmentation methods lead to significant improvements in anatomical segmentation in the mouse brain.
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DOI：
10.1023/b:visi.0000043755.93987.aa
发表时间：
2005-02-01
影响因子：
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作者：
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