基于MR图像的大鼠脑自定义模板的构建
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摘要
目的基于大鼠头部高分辨磁共振图像,探讨建立大鼠自定义脑模板的可能性,旨在对图像的基于体素的形态学分析(voxel-based morphometry,VBM)提供研究基础。方法应用首都医科大学中心实验室Micro MR成像仪对18只12周龄正常成年雄性SD大鼠头部成T2像;将公开的大鼠脑模板RAT97 T2W设为初始模板,对图像进行线性配准,得到一个模板;之后将该模板作为非线性配准的初始参考模板图像,进行非线性配准;经过以上两步,得到该组数据的大鼠脑自定义模板;最后将自定义脑模板与RAT97 T2W进行定量比较。结果相比较RAT97 T2W,自定义模板与原始图像整体相似度更高,并且更好地继承了原始图像的信息量。结论与RAT97 T2W相比,应用本方法构建的大鼠脑自定义模板图像结构清晰,保留了原始图像的特殊性,更能代表该组样本大脑的形态结构,适用于该组样本的分析与研究。
Objective To construct a rat brain custom template based on MRI images of rat heads,which is the basis for the statistical analysis of brain images.Methods The data were collected from Micro MRI of Core Facility Center of Capital Medical University.After being preprocessed,each set of the original images was linearly registered with the open rat brain template RAT97 T2W,and a template was obtained after this step,which was used as the initial reference template for nonlinear registration.After nonlinear registration,a rat brain custom template was obtained.Finally,the rat brain custom template was compared with RAT97 T2W quantitatively.Results Compared with RAT97 T2W,the custom template was more similar to the original images,and inherited more information.Conclusions Compared with RAT97 T2W,the custom template preserves the particularity of the original images,and is more suitable for analysis and research of the data.
Objective To construct a rat brain custom template based on MRI images of rat heads,which is the basis for the statistical analysis of brain images.Methods The data were collected from Micro MRI of Core Facility Center of Capital Medical University.After being preprocessed,each set of the original images was linearly registered with the open rat brain template RAT97 T2W,and a template was obtained after this step,which was used as the initial reference template for nonlinear registration.After nonlinear registration,a rat brain custom template was obtained.Finally,the rat brain custom template was compared with RAT97 T2W quantitatively.Results Compared with RAT97 T2W,the custom template was more similar to the original images,and inherited more information.Conclusions Compared with RAT97 T2W,the custom template preserves the particularity of the original images,and is more suitable for analysis and research of the data.
引文
[1]Ashburner J,Friston KJ.Voxel-based morphometry-the methods[J].Neuroimage,2000,11(6 Pt 1):805-821.
[2]Vriend C,Boedhoe P,Rutten S,et al.A smaller amygdala is associated with anxiety in Parkinson’s disease:a combined Free Surfer-VBM study[J].Journal of Neurology Neurosurgery and Psychiatry,2016,87(5):493-500.
[3]Singh S,Modi S,Goyal S,et al.Functional and structural abnormalities associated with empathy in patients with schizophrenia:An f MRI and VBM study[J].Journal of Biosciences,2015,40(2):355-364.
[4]Moon CM,Kim BC,Jeong GW.Effects of donepezil on brain morphometric and metabolic changes in patients with Alzheimer’s disease:a DARTEL-based VBM and(1)H-MRS[J].Magnetic Resonance Imaging,2016,34(7):1008-1016.
[5]Takahashi R,Ishii K,Miyamoto N,et al.Measurement of gray and white matter atrophy in dementia with Lewy bodies using diffeomorphic anatomic registration through exponentiated lie algebra:a comparison with conventional voxel-based morphometry[J].AJNR American Journal of Neuroradiology,2010,31(10):1873-1878.
[6]Pepe A,Dinov I,Tohka J.An automatic framework for quantitative validation of voxel based morphometry measures of anatomical brain asymmetry[J].Neuro Image,2014,100:444-459.
[7]Evans AC,Janke AL,Collins DL,et al.Brain templates and atlases[J].Neuroimage,2012,62(2):911-922.
[8]Uchiyama HT,Seki A,Tanaka D,et al.A study of the standard brain in Japanese children:morphological comparison with the MNI template[J].Brain and Development,2013,35(3):228-235.
[9]Mazziotta J,Toga A,Evans A,et al.A four-dimensional probabilistic atlas of the human brain[J].Journal of the American Medical Informatics Association,2001,8(5):401-430.
[10]Schwarz AJ,Danckaert A,Reese T,et al.A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas:application to pharmacological MRI[J].Neuro Image,2006,32(2):538-550.
[11]Joshi S,Davis B,Jomier M.Unbiased diffeomorphic atlas construction for computational anatomy[J].Neuro Image,2004,23(Suppl 1):S151-160.
[12]杨丽琴.重度抑郁症患者静息态脑功能网络分析及大鼠脑磁共振解剖图像模板的制作[D].北京:中国科学院大学,2013.Yang LQ.Resting state functional brain network analysis in major depressive disorder and construction of an anatomical image template for rat brain[D].Beijing:University of Chinese Academy of Sciences,2013.
[13]聂彬彬,赵书俊,单保慈.动物标准脑模板建立的研究进展[J].中国医学影像技术,2009,25(6):1103-1105.Nie BB,Zhao SJ,Shan BC.Advances of building standard brain template of animals[J].Chinese Journal of Medical Imaging Technology,2009,25(6):1103-1105.
[14]Jenkinson M,Smith S.A global optimization method for robust affine registration of brain images[J].Medical Image Analysis,2001,5(2):143-156.
[15]吴义根,李可.SPM软件包数据处理原理简介——第一部分:基本数学原理[J].中国医学影像技术,2004,20(11):1768-1772.Wu GY,Li K.Basic principle of SPM:an introduction-PartⅠ:review in basic mathematic principle.Chinese Journal of Medical Imaging Technology,2004,20(11):1768-1772.
[16]吴义根,李可.SPM软件包数据处理原理简介—第二部分:应用于PET及f MRI[J].中国医学影像技术,2004,20(11):1772-1775.Wu GY,Li K.Basic principle of SPM:an introduction-PartⅡ:applications to PET and f MRI[J].Chinese Journal of Medical Imaging Technology,2004,20(11):1772-1775.
[17]Avants BB,Epstein CL,Grossman M,et al.Symmetric diffeomorphic image registration with cross-correlation:evaluating automated labeling of elderly and neurodegenerative brain[J].Medical Image Analysis,2008,12(1):26-41.
[18]Fonov V,Evans AC,Botteron K,et al.Unbiased average ageappropriate atlases for pediatric studies[J].Neuroimage,2011,54(1):313-327.
[19]Schweinhardt P,Fransson P,Olson L,et al.A template for spatial normalization of MR images of the rat brain[J].Journal of Neuroscience Methods,2003,129(2):105-113.
[20]Nie BB,Chen K,Zhao SJ,et al.A rat brain MRI template with digital stereotaxic atlas of fine anatomical delineations in paxinos space and its automated application in voxel-wise analysis[J].Human Brain Mapping,2013,34(6):1306-1318.
[21]Lin L,Chen K,Alexander GE,et al.Construction of mouse brain MRI templates using SPM 99[J].Modeling and Control in Biomedical Systems,2003,36(15):113-118.
[22]Lin L.Research on MRM template and atlas framework of mouse brain[D].Arizona:Arizona State University,2006:54-73.
[2]Vriend C,Boedhoe P,Rutten S,et al.A smaller amygdala is associated with anxiety in Parkinson’s disease:a combined Free Surfer-VBM study[J].Journal of Neurology Neurosurgery and Psychiatry,2016,87(5):493-500.
[3]Singh S,Modi S,Goyal S,et al.Functional and structural abnormalities associated with empathy in patients with schizophrenia:An f MRI and VBM study[J].Journal of Biosciences,2015,40(2):355-364.
[4]Moon CM,Kim BC,Jeong GW.Effects of donepezil on brain morphometric and metabolic changes in patients with Alzheimer’s disease:a DARTEL-based VBM and(1)H-MRS[J].Magnetic Resonance Imaging,2016,34(7):1008-1016.
[5]Takahashi R,Ishii K,Miyamoto N,et al.Measurement of gray and white matter atrophy in dementia with Lewy bodies using diffeomorphic anatomic registration through exponentiated lie algebra:a comparison with conventional voxel-based morphometry[J].AJNR American Journal of Neuroradiology,2010,31(10):1873-1878.
[6]Pepe A,Dinov I,Tohka J.An automatic framework for quantitative validation of voxel based morphometry measures of anatomical brain asymmetry[J].Neuro Image,2014,100:444-459.
[7]Evans AC,Janke AL,Collins DL,et al.Brain templates and atlases[J].Neuroimage,2012,62(2):911-922.
[8]Uchiyama HT,Seki A,Tanaka D,et al.A study of the standard brain in Japanese children:morphological comparison with the MNI template[J].Brain and Development,2013,35(3):228-235.
[9]Mazziotta J,Toga A,Evans A,et al.A four-dimensional probabilistic atlas of the human brain[J].Journal of the American Medical Informatics Association,2001,8(5):401-430.
[10]Schwarz AJ,Danckaert A,Reese T,et al.A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas:application to pharmacological MRI[J].Neuro Image,2006,32(2):538-550.
[11]Joshi S,Davis B,Jomier M.Unbiased diffeomorphic atlas construction for computational anatomy[J].Neuro Image,2004,23(Suppl 1):S151-160.
[12]杨丽琴.重度抑郁症患者静息态脑功能网络分析及大鼠脑磁共振解剖图像模板的制作[D].北京:中国科学院大学,2013.Yang LQ.Resting state functional brain network analysis in major depressive disorder and construction of an anatomical image template for rat brain[D].Beijing:University of Chinese Academy of Sciences,2013.
[13]聂彬彬,赵书俊,单保慈.动物标准脑模板建立的研究进展[J].中国医学影像技术,2009,25(6):1103-1105.Nie BB,Zhao SJ,Shan BC.Advances of building standard brain template of animals[J].Chinese Journal of Medical Imaging Technology,2009,25(6):1103-1105.
[14]Jenkinson M,Smith S.A global optimization method for robust affine registration of brain images[J].Medical Image Analysis,2001,5(2):143-156.
[15]吴义根,李可.SPM软件包数据处理原理简介——第一部分:基本数学原理[J].中国医学影像技术,2004,20(11):1768-1772.Wu GY,Li K.Basic principle of SPM:an introduction-PartⅠ:review in basic mathematic principle.Chinese Journal of Medical Imaging Technology,2004,20(11):1768-1772.
[16]吴义根,李可.SPM软件包数据处理原理简介—第二部分:应用于PET及f MRI[J].中国医学影像技术,2004,20(11):1772-1775.Wu GY,Li K.Basic principle of SPM:an introduction-PartⅡ:applications to PET and f MRI[J].Chinese Journal of Medical Imaging Technology,2004,20(11):1772-1775.
[17]Avants BB,Epstein CL,Grossman M,et al.Symmetric diffeomorphic image registration with cross-correlation:evaluating automated labeling of elderly and neurodegenerative brain[J].Medical Image Analysis,2008,12(1):26-41.
[18]Fonov V,Evans AC,Botteron K,et al.Unbiased average ageappropriate atlases for pediatric studies[J].Neuroimage,2011,54(1):313-327.
[19]Schweinhardt P,Fransson P,Olson L,et al.A template for spatial normalization of MR images of the rat brain[J].Journal of Neuroscience Methods,2003,129(2):105-113.
[20]Nie BB,Chen K,Zhao SJ,et al.A rat brain MRI template with digital stereotaxic atlas of fine anatomical delineations in paxinos space and its automated application in voxel-wise analysis[J].Human Brain Mapping,2013,34(6):1306-1318.
[21]Lin L,Chen K,Alexander GE,et al.Construction of mouse brain MRI templates using SPM 99[J].Modeling and Control in Biomedical Systems,2003,36(15):113-118.
[22]Lin L.Research on MRM template and atlas framework of mouse brain[D].Arizona:Arizona State University,2006:54-73.