脊柱MRI图像的分割与三维可视化
摘要
医学图像分割和三维可视化是目前医学图像处理研究领域的一个热点问题,是计算机图形学和图像处理在生物医学工程中的重要应用,在医学诊断和治疗领域具有特殊应用价值。因此,对医学图像分割及三维可视化的研究具有重要的意义。本文主要研究了脊柱MRI(Magnetic Resonance Imaging)图像的分割及三维可视化算法。主要内容如下：
第一,为了有效地对图像进行分割和三维可视化,本文首先对脊柱MRI图像进行预处理,包括图像增强和断层图像插值。采用了基于形态学开、闭运算、顶帽运算的增强算法,增强了脊柱MRI图像的目标区域；通过比较分析几种常用的插值算法,采用基于灰度的线性插值方法对断层图像进行插值,有效地提高了三维重建的质量。
第二,提出了一种适用于脊柱MRI图像的水平集分割方法。首先采用基于先验知识的椎间盘检测算法,定位并分割出椎间盘,利用椎间盘的分割结果对椎骨进行粗分割,以此粗分割作为水平集分割的初始化轮廓；然后用基于RSF(Region Scalable Fitting)的能量模型引导水平集曲线向椎骨边界演化,最终分割出椎骨。为了构造用于三维可视化的体数据,我们分别根据椎间盘检测结果和水平集分割结果构建脊柱窗和椎骨模板,利用椎骨模板和脊柱窗从原始图像序列中提取椎骨和脊柱区域。
第三、我们利用Ray Casting算法对分割出的脊柱和椎骨进行三维重建。利用美国辛辛那提大学医学院提供的脊柱MRI图像数据库进行实验,重建图像清晰,真实地再现了脊柱和椎骨的三维面貌。在文章的最后,我们在Visual C++6.0平台下,实现了基于VTK(Visualization Toolkit)的脊柱和椎骨三维可视化,可以对重建的三维模型交互的进行旋转、平移等操作,具有较强的实用性。
Segmentation and 3D Visualization of medical images are becoming hot topics in medical image processing currently. They are important applications of computer graphics and image processing in biomedical engineering, which have special application value in medical diagnosis and treatment. So research on Segmentation and 3D visualization of medical images has deep significance. This paper centralizes on the segmentation and 3D visualization of spine MRI images. The main work of this paper is as following:
Firstly, we perform image pre-processing including image enhancement and interpolation of slice-images for effective segmentation and 3D visualization of spine MRI images. Morphological operations such as opening, closing and top hat are used to enhance the object regions. After comparing and analyzing several commonly used interpolation algorithms, we use the linear gray-based slice-image interpolation method to improve the quantity of 3D visualization.
Secondly, we propose a level set method based on spine MRI images. At first, we use a knowledge-based disks detection method to locate and segment the disks, the results of disks segmentation are used for rough segmentation of vertebrae, which are taken as the initialization of level set method, then the RSF-based energy model is used to guide the level set evolution towards vertebra boundaries, at last we get the final segmentation of vertebrae. What's more, we separately construct spine window and vertebrae masks according to the results of disks detection and level set segmentation for the next 3D volume data construction. The spine window and vertebra masks are then used to extract the spine and vertebrae regions from original images.
Thirdly, we employ the Ray Casting algorithm to perform 3D reconstruction of the segmented spine and vertebrae. Experiments based on spine MRI images provided by College of Medicine, University of Cincinnati, prove the efficiency of the algorithm, the reconstructed 3D vertebrae have clear 3D profile, and the reconstructed 3D spine could reflect curvature of the spine. In the last of this paper, we implemented the VTK-based 3D visualization of spine and vertebrae under the platform of Visual C++6.0, which has strong practicability, and we can rotate and translate the reconstructed 3D model interactively.
第一,为了有效地对图像进行分割和三维可视化,本文首先对脊柱MRI图像进行预处理,包括图像增强和断层图像插值。采用了基于形态学开、闭运算、顶帽运算的增强算法,增强了脊柱MRI图像的目标区域；通过比较分析几种常用的插值算法,采用基于灰度的线性插值方法对断层图像进行插值,有效地提高了三维重建的质量。
第二,提出了一种适用于脊柱MRI图像的水平集分割方法。首先采用基于先验知识的椎间盘检测算法,定位并分割出椎间盘,利用椎间盘的分割结果对椎骨进行粗分割,以此粗分割作为水平集分割的初始化轮廓；然后用基于RSF(Region Scalable Fitting)的能量模型引导水平集曲线向椎骨边界演化,最终分割出椎骨。为了构造用于三维可视化的体数据,我们分别根据椎间盘检测结果和水平集分割结果构建脊柱窗和椎骨模板,利用椎骨模板和脊柱窗从原始图像序列中提取椎骨和脊柱区域。
第三、我们利用Ray Casting算法对分割出的脊柱和椎骨进行三维重建。利用美国辛辛那提大学医学院提供的脊柱MRI图像数据库进行实验,重建图像清晰,真实地再现了脊柱和椎骨的三维面貌。在文章的最后,我们在Visual C++6.0平台下,实现了基于VTK(Visualization Toolkit)的脊柱和椎骨三维可视化,可以对重建的三维模型交互的进行旋转、平移等操作,具有较强的实用性。
Segmentation and 3D Visualization of medical images are becoming hot topics in medical image processing currently. They are important applications of computer graphics and image processing in biomedical engineering, which have special application value in medical diagnosis and treatment. So research on Segmentation and 3D visualization of medical images has deep significance. This paper centralizes on the segmentation and 3D visualization of spine MRI images. The main work of this paper is as following:
Firstly, we perform image pre-processing including image enhancement and interpolation of slice-images for effective segmentation and 3D visualization of spine MRI images. Morphological operations such as opening, closing and top hat are used to enhance the object regions. After comparing and analyzing several commonly used interpolation algorithms, we use the linear gray-based slice-image interpolation method to improve the quantity of 3D visualization.
Secondly, we propose a level set method based on spine MRI images. At first, we use a knowledge-based disks detection method to locate and segment the disks, the results of disks segmentation are used for rough segmentation of vertebrae, which are taken as the initialization of level set method, then the RSF-based energy model is used to guide the level set evolution towards vertebra boundaries, at last we get the final segmentation of vertebrae. What's more, we separately construct spine window and vertebrae masks according to the results of disks detection and level set segmentation for the next 3D volume data construction. The spine window and vertebra masks are then used to extract the spine and vertebrae regions from original images.
Thirdly, we employ the Ray Casting algorithm to perform 3D reconstruction of the segmented spine and vertebrae. Experiments based on spine MRI images provided by College of Medicine, University of Cincinnati, prove the efficiency of the algorithm, the reconstructed 3D vertebrae have clear 3D profile, and the reconstructed 3D spine could reflect curvature of the spine. In the last of this paper, we implemented the VTK-based 3D visualization of spine and vertebrae under the platform of Visual C++6.0, which has strong practicability, and we can rotate and translate the reconstructed 3D model interactively.
引文
[1]田捷,包尚联,周明全.医学影像处理与分析[M].电子工业出版社.2003
[2]D.C.Williamson, N.A.Thacker, S.R.Williams, M.Pokric. Partial Volume issue Segmentation using Grey-Level Gradient. Medical Image Understanding and Analysis Conference(MIUA),2002.
[3]张海波.医学CT图像的三维分割与可视化研究.山东师范大学.2005
[4]Claudia Chevrefils, Farida Cheriet,Guy Grimard, Carl-Eric Aubin. Watershed segmentation of intervertebral disk and spinal canal from MRI images, ICIAR,2007
[5]Andersson GBL. The epidemiology of spinal disorders. Frymoyer JW, ED. The adult spine: principles and practice. New York:Lippincott-Raven Publisher.1997.93-141
[6]M.Modic, T.Masaryk, J.Ross. Magnetic Resonance Imaging of the Spine. St. Louis, Mo, 1989
[7]Jia Zhong. Automated Vertebra Segmentation and Quantification Algorithm of Whole Spine MRI Images. Biomedical Engineering, University of Cincinnati, USA.2004
[8]McInerney T, Terzopoulos D. Deformable models in medical image analysis:a survey. Medical Image Analysis.1996
[9]P. Smyth, C Taylor, J Adams. Automatic Measurement of Vertebral Shape Using Active Shape Models. The British Machine Vision Conference.1996
[10]T.F. Cootes, C.J. Taylor. Statistical Models of Appearance for Medical Image Analysis and Computer Vision. Proc SPIE Medical Imaging.2001
[11]S.Osher, J.Sethian. Fronts Propagating with Curvature Dependent Speed:Algorithms Based on Hamilton-Jacobi Formulations. Journal of Computational Physics.1988
[13]Chunming.Li, Chenyang.Xu, Changfeng.Gui, Martin D.Fox, Level set evolution without re-initialization, IEEE Conference on Computer Vision and Pattern Recognotion,2005
[14]ChunmingLi, Chiu-Yen Kao, John C.Gore, Zhaohua Ding. Implicit Active Contours Driven by Local Binary Fitting Energy. IEEE Conference on Computer Vision and Pattern Recognotion.2007
[15]ChunmingLi, Chiu-Yen Kao, John C.Gore. Minimization of Region-Scalable Fitting Energy for Image Segmentation. IEEE transactions on image processing.2008
[16]钱海勇.三维医学图像分割方法研究[D].东南大学硕士论文.2006
[17]诸葛斌.医学图像三维重建[M].浙江工商大学出版社.2008
[18]E.Keppel. Approximating Complex Surfaces by Triangulation of Contour Lines. IBM J.Res.Dev,19.1999
[19]G.T.Herman, H.K.Liu. Three-Dimensional Display of Human Organs from Computed Tomograms. CVGIP,1979, Vol.9(1):1-21
[20]William E. Lorensen, Harvey E. Cline. Marching cubes:A high resolution 3D surface construction algorithm. Computer Graphics,21(4) 163-169,1987
[21]Harvey E. Cline, William E. Lorensen, S.Ludke, C.R.Crawford, B.C.Teeter. Two Algorithms for Three-dimensional Reconstruction of Tomograms. Medical Physics, 1988,Vol.22(4):59-64
[22]王隽.基于MRI的脑图像分割和三维重建[D].河北工业大学.2004
[23]王福昌,胡顺田,张宝雷.基于体绘制法的头部CT图像的三维重建[J].计算机与现代化.2007
[24]Marc Levoy. Efficient Ray Tracing of Volume Data. ACM Transactions on Graphics.1990
[25]Laur, P. Hanradhan. Hierarchical Splatting:a progressive refinement algorithm for volume rendering. ACM Transactions on Graphics.1991
[26]Totsuka T, Levoy M. Frequency domain volume rendering. Computer Graphics Proceedings.1993
[27]张尤赛,陈福民.三维医学图像的体绘制技术综述[J].计算机工程与应用.2002
[28]N.Max. Modes Of Direct Volume Rendering. IEEE Trans Visualization and Computer Graph.1995
[29]伍亚军,叶安培,王霄英,付京波,蒋学祥.基于MRI的动物肝脏脉管分割与三维重建.中国医学影像技术.2005
[30]NIH Clinical Center, http://www.cc.nig.gov./cip/sofware.html
[31]3D Slicer. http://www.slicer.org
[32]彭延军,石教英.体绘制技术在医学可视化中的新发展[J].中国图像图形学报,2002,7(12)：1239-1246
[33]邓俊辉,唐泽圣.频域体绘制中的颜色合成[J].软件学报.1996,7(9)：571-576
[34]孙燕.医学图像三维重建的研究[D].吉林大学.2007
[35]阮秋奇.数字图像处理学[M].电子工业出版社.2001
[36]张德丰.Matlab小波分析与工程应用[M].国防工业出版社,230-234
[37]Aboutanos G B, Nikanne J, Watkins N, et al. Model creation and deformation for the automatic segmentation of the brain in MRI Images. IEEE Trans on Biomed. Eng.1999,46(11):1346-1356
[38]许为华,尹学松.医学图像插值算法的研究.计算机仿真.2006,1(7)111-114
[39]Raya S P, Udupa J K. Shape-based interpolation of multi-dimensional objects. IEEE Trans Med Imaging,1990,9(1),32-42
[40]Herman G T, Zheng J S, Bucholtz C A. Shape-based interpolation. Computer Graphics and Applications,1992,12(3),69-79
[41]王群.CT断层图像三维重建中插值技术研究与应用[D].苏州大学.2007
[42]Malladi R,Sethian J A, Vemuri B C. Shape modeling with front propagation:a Level Set approach, IEEE Trans. On PAMI,1995,17(2):pp.158-pp.866
[43]金大年.基于水平集的医学图像分割算法研究[学位论文].第一军医大学.2005
[44]Kimia B B. Conservation laws and a theory of shape, Ph. D thesis, McGil Centre for Intelligent Machines, McGill Univ., Montreal, Canada,1990
[45]Grayson M A. Shortening embedded curves, Annals of Mathematics,1989, 129:pp.71-pp.111
[46]Caselles V, Kimmel R, Sapiro G. Geodesic active contours. International Journal of Computer Vision,1997,22(1):pp.61-pp.79
[47]Sethian J A. Level Set methods and fast marching methods:evolving interfaces in computational geometry,fluid mechanics, computer vision, and materials science. Cambridge University Press,1999
[48]金大年.基于水平集的医学图像分割算法研究[学位论文].第一军医大学.2005
[49]史睿琼.脊柱MRI图像椎间盘定位及椎骨分割算法的研究[学位论文].北京交通大学.2007
[50]赵燕燕.MRI脊柱图像椎间盘分割及定位算法研究[学位论文].北京交通大学.2008
[51]查艳丽.MRI脊柱图像的定位与分割[学位论文].北京交通大学.2008
[52]T. Chan and L. Vese, "Active contours without edges," IEEE Trans.Image Process., vol.10, no.2, pp.266-277, Feb.2001.
[53]M.W.Jones, M.Chen. A new approach to the construction from contour data. Computer Graphics Forum,1994,13(3):75-84
[54]LorenSen W.E, Cline H.E. Marching Cubes:A high-resulution 3D surface construction algorithm. Computer Graphics,1987,21(3):163-169
[55]Cline H.E, Lorenson W.E. Two algorithm for three-dimentional reconstructions of tomograms. Medical Physics,1998,15(3):320-327
[56]Westover L. Footprint Evaluation for Volume Rendering. Computer Graphics,1990,24(4): 367-376
[57]Lacroute P, Levoy M. Fast Volume Rendering using a Shear-Warp Factorization of the Viewing Transformation. Computer Graphics, Proceedings, July 1994:451-458
[58]Cameron G G, Undrill P E. Rendering Volumetric Medical Image Data on a SIMD-architecture Computer. Proceedings of the Third Eurographics Workshop on Rendering, May 1992,135-145
[59]M.A.Westenberg, J.B.T.M.Roerdink. Frequeney Domain Volume Rendering by the Wavelet X-Ray Transform. IEEE Transaetions on Image Proeessing.2000,9(7): 1249-1261
[60]Max N. Optical Models for Direct Volume Rendering. IEEE Transactions on Visualization and Computer Graphics,1995,1(2):99-108
[61]Levy M. Volume Rending:Display of Surfaces from Volume Data. IEEE Computer Graphics and Application. May 1988.29-37.
[62]余松煌,周源华,吴时光编.数字图像处理[M].电子工业出版社.79-81
[63]Levy M. Volume Rendering by Adaptive Refinement. UNC Technical Report.1988, June
[64]Will Schroeder, Ken Martin, Bill Lorensen. The Visualization Toolkit:An Object-Oriented Approach to 3D Graphics. Kitware,2002.
[2]D.C.Williamson, N.A.Thacker, S.R.Williams, M.Pokric. Partial Volume issue Segmentation using Grey-Level Gradient. Medical Image Understanding and Analysis Conference(MIUA),2002.
[3]张海波.医学CT图像的三维分割与可视化研究.山东师范大学.2005
[4]Claudia Chevrefils, Farida Cheriet,Guy Grimard, Carl-Eric Aubin. Watershed segmentation of intervertebral disk and spinal canal from MRI images, ICIAR,2007
[5]Andersson GBL. The epidemiology of spinal disorders. Frymoyer JW, ED. The adult spine: principles and practice. New York:Lippincott-Raven Publisher.1997.93-141
[6]M.Modic, T.Masaryk, J.Ross. Magnetic Resonance Imaging of the Spine. St. Louis, Mo, 1989
[7]Jia Zhong. Automated Vertebra Segmentation and Quantification Algorithm of Whole Spine MRI Images. Biomedical Engineering, University of Cincinnati, USA.2004
[8]McInerney T, Terzopoulos D. Deformable models in medical image analysis:a survey. Medical Image Analysis.1996
[9]P. Smyth, C Taylor, J Adams. Automatic Measurement of Vertebral Shape Using Active Shape Models. The British Machine Vision Conference.1996
[10]T.F. Cootes, C.J. Taylor. Statistical Models of Appearance for Medical Image Analysis and Computer Vision. Proc SPIE Medical Imaging.2001
[11]S.Osher, J.Sethian. Fronts Propagating with Curvature Dependent Speed:Algorithms Based on Hamilton-Jacobi Formulations. Journal of Computational Physics.1988
[13]Chunming.Li, Chenyang.Xu, Changfeng.Gui, Martin D.Fox, Level set evolution without re-initialization, IEEE Conference on Computer Vision and Pattern Recognotion,2005
[14]ChunmingLi, Chiu-Yen Kao, John C.Gore, Zhaohua Ding. Implicit Active Contours Driven by Local Binary Fitting Energy. IEEE Conference on Computer Vision and Pattern Recognotion.2007
[15]ChunmingLi, Chiu-Yen Kao, John C.Gore. Minimization of Region-Scalable Fitting Energy for Image Segmentation. IEEE transactions on image processing.2008
[16]钱海勇.三维医学图像分割方法研究[D].东南大学硕士论文.2006
[17]诸葛斌.医学图像三维重建[M].浙江工商大学出版社.2008
[18]E.Keppel. Approximating Complex Surfaces by Triangulation of Contour Lines. IBM J.Res.Dev,19.1999
[19]G.T.Herman, H.K.Liu. Three-Dimensional Display of Human Organs from Computed Tomograms. CVGIP,1979, Vol.9(1):1-21
[20]William E. Lorensen, Harvey E. Cline. Marching cubes:A high resolution 3D surface construction algorithm. Computer Graphics,21(4) 163-169,1987
[21]Harvey E. Cline, William E. Lorensen, S.Ludke, C.R.Crawford, B.C.Teeter. Two Algorithms for Three-dimensional Reconstruction of Tomograms. Medical Physics, 1988,Vol.22(4):59-64
[22]王隽.基于MRI的脑图像分割和三维重建[D].河北工业大学.2004
[23]王福昌,胡顺田,张宝雷.基于体绘制法的头部CT图像的三维重建[J].计算机与现代化.2007
[24]Marc Levoy. Efficient Ray Tracing of Volume Data. ACM Transactions on Graphics.1990
[25]Laur, P. Hanradhan. Hierarchical Splatting:a progressive refinement algorithm for volume rendering. ACM Transactions on Graphics.1991
[26]Totsuka T, Levoy M. Frequency domain volume rendering. Computer Graphics Proceedings.1993
[27]张尤赛,陈福民.三维医学图像的体绘制技术综述[J].计算机工程与应用.2002
[28]N.Max. Modes Of Direct Volume Rendering. IEEE Trans Visualization and Computer Graph.1995
[29]伍亚军,叶安培,王霄英,付京波,蒋学祥.基于MRI的动物肝脏脉管分割与三维重建.中国医学影像技术.2005
[30]NIH Clinical Center, http://www.cc.nig.gov./cip/sofware.html
[31]3D Slicer. http://www.slicer.org
[32]彭延军,石教英.体绘制技术在医学可视化中的新发展[J].中国图像图形学报,2002,7(12)：1239-1246
[33]邓俊辉,唐泽圣.频域体绘制中的颜色合成[J].软件学报.1996,7(9)：571-576
[34]孙燕.医学图像三维重建的研究[D].吉林大学.2007
[35]阮秋奇.数字图像处理学[M].电子工业出版社.2001
[36]张德丰.Matlab小波分析与工程应用[M].国防工业出版社,230-234
[37]Aboutanos G B, Nikanne J, Watkins N, et al. Model creation and deformation for the automatic segmentation of the brain in MRI Images. IEEE Trans on Biomed. Eng.1999,46(11):1346-1356
[38]许为华,尹学松.医学图像插值算法的研究.计算机仿真.2006,1(7)111-114
[39]Raya S P, Udupa J K. Shape-based interpolation of multi-dimensional objects. IEEE Trans Med Imaging,1990,9(1),32-42
[40]Herman G T, Zheng J S, Bucholtz C A. Shape-based interpolation. Computer Graphics and Applications,1992,12(3),69-79
[41]王群.CT断层图像三维重建中插值技术研究与应用[D].苏州大学.2007
[42]Malladi R,Sethian J A, Vemuri B C. Shape modeling with front propagation:a Level Set approach, IEEE Trans. On PAMI,1995,17(2):pp.158-pp.866
[43]金大年.基于水平集的医学图像分割算法研究[学位论文].第一军医大学.2005
[44]Kimia B B. Conservation laws and a theory of shape, Ph. D thesis, McGil Centre for Intelligent Machines, McGill Univ., Montreal, Canada,1990
[45]Grayson M A. Shortening embedded curves, Annals of Mathematics,1989, 129:pp.71-pp.111
[46]Caselles V, Kimmel R, Sapiro G. Geodesic active contours. International Journal of Computer Vision,1997,22(1):pp.61-pp.79
[47]Sethian J A. Level Set methods and fast marching methods:evolving interfaces in computational geometry,fluid mechanics, computer vision, and materials science. Cambridge University Press,1999
[48]金大年.基于水平集的医学图像分割算法研究[学位论文].第一军医大学.2005
[49]史睿琼.脊柱MRI图像椎间盘定位及椎骨分割算法的研究[学位论文].北京交通大学.2007
[50]赵燕燕.MRI脊柱图像椎间盘分割及定位算法研究[学位论文].北京交通大学.2008
[51]查艳丽.MRI脊柱图像的定位与分割[学位论文].北京交通大学.2008
[52]T. Chan and L. Vese, "Active contours without edges," IEEE Trans.Image Process., vol.10, no.2, pp.266-277, Feb.2001.
[53]M.W.Jones, M.Chen. A new approach to the construction from contour data. Computer Graphics Forum,1994,13(3):75-84
[54]LorenSen W.E, Cline H.E. Marching Cubes:A high-resulution 3D surface construction algorithm. Computer Graphics,1987,21(3):163-169
[55]Cline H.E, Lorenson W.E. Two algorithm for three-dimentional reconstructions of tomograms. Medical Physics,1998,15(3):320-327
[56]Westover L. Footprint Evaluation for Volume Rendering. Computer Graphics,1990,24(4): 367-376
[57]Lacroute P, Levoy M. Fast Volume Rendering using a Shear-Warp Factorization of the Viewing Transformation. Computer Graphics, Proceedings, July 1994:451-458
[58]Cameron G G, Undrill P E. Rendering Volumetric Medical Image Data on a SIMD-architecture Computer. Proceedings of the Third Eurographics Workshop on Rendering, May 1992,135-145
[59]M.A.Westenberg, J.B.T.M.Roerdink. Frequeney Domain Volume Rendering by the Wavelet X-Ray Transform. IEEE Transaetions on Image Proeessing.2000,9(7): 1249-1261
[60]Max N. Optical Models for Direct Volume Rendering. IEEE Transactions on Visualization and Computer Graphics,1995,1(2):99-108
[61]Levy M. Volume Rending:Display of Surfaces from Volume Data. IEEE Computer Graphics and Application. May 1988.29-37.
[62]余松煌,周源华,吴时光编.数字图像处理[M].电子工业出版社.79-81
[63]Levy M. Volume Rendering by Adaptive Refinement. UNC Technical Report.1988, June
[64]Will Schroeder, Ken Martin, Bill Lorensen. The Visualization Toolkit:An Object-Oriented Approach to 3D Graphics. Kitware,2002.