Fast And Automatic Curvilinear Reformatting Of Mr Images Of The Brain For Diagnosis Of Dysplastic Lesions

Curvilinear reformatting is known as the best non-invasive technique for diagnosis of dysplastic lesions of the brain. It consists of computing surfaces that follow the brain's curvature at various depths, making the diagnosis possible by visual inspection of the voxel intensities on these surfaces. Traditional approaches require user intervention and present curvature artifacts. We present a new method for curvilinear reformatting that solves both problems. It uses a graph-based approach to segment the brain, extract its envelope, and compute the isosurfaces at all possible depths by euclidean distance transform. It requires no user input, no ad-hoc parameters, and takes less than 1 minute to run on a common PC. © 2006 IEEE.2006486489Barkovich, A.J., Rowley, H.A., Andermann, F., MR in partial epilepsy: Value of high-resolution volumetric techniques (1995) American Journal of Neuroradiology, 16, pp. 339-343. , FebBastos, A.C., Comeau, R.M., Andermann, F., Melanson, D., Cendes, F., Dubeau, F., Fontaine, S., Olivier, A., Diagnosis of subtle focal dysplastic lesions: Curvilinear reformatting from three-dimensional magnetic resonance imaging (1999) Annals of Neurology, 46 (1), pp. 88-94Colombo, N., Tassi, L., Galli, C., Citterio, A., Lo Russo, G., Scialfa, G., Spreafico, R., Focal cortical dysplasias: MR imaging, histopathologic, and clinical correlations in surgically treated patients with epilepsy (2003) American Journal of Neuroradiology, 24, pp. 724-733. , AprBrainSight, , http://www.rogue-research.com/B/epilepsy.htmFrackowiak, R.S.J., Friston, K.J., Frith, C., Dolan, R., Price, C.J., Zeki, S., Ashburner, J., Penny, W.D., (2003) Human Brain Function, , Academic Press, 2nd editionBueno, G., Musse, O., Heitz, F., Armspach, J.P., Three-dimensional segmentation of anatomical structures in MR images on large data bases (2001) Magnetic Resonance Imaging, 19, pp. 73-88Dougherty, E.R., Lotufo, R.A., (2003) Hands-on Morphological Image Processing, , SPIE Press, Bellingham, WAFalcão, A.X., Stolfi, J., Lotufo, R.A., The image foresting transform: Theory, algorithms, and applications (2004) IEEE Trans. on Pattern Analysis and Machine Intelligence, 26 (1), pp. 19-29Falcão, A.X., Bergo, F.P.G., Miranda, P.A.V., Image segmentation by tree pruning (2004) Proc. of the XVII Brazillian Symposium on Computer Graphics and Image Processing., pp. 65-71. , Oct , IEEEFalcão, A.X., Miranda, P.A.V., Bergo, F.P.G., (2005) Automatic Object Detection by Tree Pruning, , Tech. Rep. IC-05-19, Institute of Computing, University of Campinas, SepOtsu, N., A threshold selection method from gray level histograms (1979) IEEE Trans. Systems, Man and Cybernetics, 9, pp. 62-66. , Ma

Visual analytics of magnetic resonance images for supporting detection of cortical lesions and preoperative location of anatomical landmarks

Orientadores: Shin-Ting Wu, Clarissa Lin YasudaTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de ComputaçãoResumo: Com o aumento da qualidade das neuroimagens estruturais torna-se possível uma investigação detalhada da neuroanatomia. Contudo, a utilização de ferramentas computacionais que ajudem no realce e na exploração de neuroimagens ainda é de extrema importância para a identificação de lesões corticais e para a localização pré-operatória de referências anatômicas. A reformatação curvilínea e o janelamento (windowing) são dois exemplos. A reformatação curvilínea permite refatiar curvilinearmente um volume reconstruído a partir de uma imagem 3D e o janelamento, alterar o brilho e o contraste das neuroimagens. No estado da arte, os métodos de reformatação curvilínea são aplicados no diagnóstico para propiciar uma melhor visualização dos giros e sulcos cerebrais, já o janelamento está presente em diversos aplicativos de renderização de neuroimagens por facilitar ajustes interativos dos parâmetros de renderização à percepção subjetiva. Este trabalho foi motivado pela nossa hipótese da existência de uma correspondência entre a neuroanatomia e os padrões de sinais em imagens de ressonância magnética ponderadas em T1 e do potencial uso deste conhecimento no aprimoramento das ferramentas já existentes. Mostramos como essa correspondência pode ser usada para caracterizar estruturas neuroanatômicas que possibilitam a construção de um algoritmo capaz de localizar a região das meninges e de estimar medidas estatísticas, como a média e o desvio-padrão, da substância cinzenta e branca de um cérebro. Uma vez que a reformatação curvilínea é realizada com preservação das meninges, a técnica se torna útil na localização pré-operatória de referências anatômicas (como as estruturas vasculares), para preservação de áreas eloquentes durante uma intervenção cirúrgica. Uma nova forma de janelamento baseada na correspondência identificada pode também realçar a interface substância cinzenta¿branca e, consequentemente, revelar lesões sutis. A análise visual com uso das ferramentas em conjunto se mostrou útil no suporte à localização de lesões corticais e na exposição pré-operatória dos marcadores fiduciais intra-operatórios em imagens anatômicas com contrasteAbstract: As the quality of structural neuroimage improves, a more accurate neuroanatomy investiga- tion becomes feasible. However, computational tools to aid in the enhancement and explo- ration of these neuroimages are still extremely useful for the identification of subtle cortical lesions and pre-operative localization of anatomical landmarks. Curvilinear reformatting and windowing are two examples. Curvilinear reformatting allows reslicing curvilinearly a volume reconstructued from a 3D image, while windowing allows changing the brightness and the contrast of neuroimages. In the current state-of-the-art, curvilinear reformatting is applied to diagnosis for providing a better visualization of complex cerebral cortical folding patterns, and the windowing is used in medical visualization software for facilitating fine adjustments of rendering parameters according to the subjective perception. This work was driven by the hypothesis that there would be a correspondence between the neuroanatomy and the signal patterns from T1-weighted magnetic resonance images, and that the knowledge of this cor- respondence might improve the existing tools. We showed how this correspondence could be used to characterize the anatomical structures that made possible the design of an algorithm for locating the neighborhood of meninges and for computing the statistical measures, such as mean and standard deviation, of grey and white matter. Assuring that the curvilinear reformatting can be performed preserving the meninges, the technique is useful to preopera- tively localize the anatomical landmarks , such as superficial veins. A new way of windowing based on our finding of the neuroanatomy¿imaging signal correspondence can enhance the interface between gray matter and white matter and reveal subtle lesions. Visual analytics using both tools has proven to be helpful in supporting the localization of cortical lesions and in revealing preoperatively the intraoperative fiducial landmarks, such as superficial veins, on contrast-enhanced anatomical imagesDoutoradoEngenharia de ComputaçãoDoutor em Engenharia Elétrica165777/2014-1CNP

Adapted Dynamic Meshes For Deformable Surfaces

Deformable objects play an important role in many applications, such as animation and simulation. Effective computation with deformable surfaces can be achieved through the use of dynamic meshes. In this paper, we introduce a framework for constructing and maintaining a time-varying adapted mesh structure that conforms to the under-lying deformable surface. The adaptation function employs error metrics based on stochastic sampling. Our scheme combines normal and tangential geometric correction with refinement and simplification resolution control. Furthermore, it applies to both parametric and implicit surface descriptions. As the result, we obtain a simple and efficient general scheme that can be used for a wide range of computations. © 2006 IEEE.213220Bergo, F.P.G., Falcão, A.X., Fast and automatic curvilinear reformatting of MR images of the brain for diagnosis of dysplastic lesions (2006) IEEE International Symposium on Biomedical ImagingBerti, G., (2000) Generic software components for Scientific Computing, , PhD thesis, BTU CottbusBotsch, M., Steinberg, S., Bischoff, S., Kobbelt, L., Openmesh - a generic and efficient polygon mesh data structure (2002) OpenSG PLUS SymposiumBowden, R., Mitchell, T., Sahardi, M., Real-time dynamic deformable meshes for volumetric segmentation and visualization (1997) Proc. BMVC, , 11:310-1=319Cohen-Steiner, D., Alliez, P., Desbrun, M., Variational shape approximation (2004) ACM Transactions on Graphics, 23 (3), pp. 905-914. , AugDeCoro, C., Rusinkiewicz, S., Pose-independent simplification of articulated meshes (2005) SI3D '05: Proceedings of the 2005 symposium on Interactive 3D graphics and games, pp. 17-24. , New York, NY, USA, ACM PressDey, T., Edelsbrunner, H., Guha, S., Computational topology (1999) Contemporary mathematics, 223, pp. 109-143. , B. Chazelle, J. E. Goodman, and R. Pollack, editors, Advances in Discrete and Computational Geometry, American Mathematical SocietyDuan, Y., Hua, J., Qin, H., Interactive shape modeling using lagrangian surface flow (2005) Visual Comp, 21 (5), pp. 279-288Duchaineau, M.A., Wolinsky, M., Sigeti, D.E., Miller, M.C., Aldrich, C., Mineev-Weinstein, M.B., Roaming terrain: Real-time optimally adapting meshes (1997) IEEE Visualization '97, pp. 81-88. , NovFabri, A., Giezeman, G.-J., Kettner, L., Schirra, S., Schonherr, S., On the design of CGAL a computational geometry algorithms library (2000) SP&E, 30 (11), pp. 1167-1202L. D. Floriani, P. Magillo, and E. Puppo. Efficient implementation of multi-triangulations. In D. Ebert, H. Hagen, and H. Rushmeier, editors, IEEE Visualization '98, pages 43-50, 1998L. D. Floriani, E. Puppo, and P. Magillo. A formal approach to multiresolution modeling. In W. S. er, R. Klein, and R. Rau, editors, Theory and Practice of Geometric Modeling. SpringerVerlag, 1996Garland, M., Multiresolution modeling: Survey & future opportunities (1999) Eurographics, State of the Art ReportGarland, M., Zhou, Y., Quadric-based simplification in any dimension (2005) ACM Trans. on Graphics, 24 (2), pp. 209-239Hoppe, H., Efficient implementation of progressive meshes (1998) Computers & Graphics, 22 (1), pp. 27-36. , FebruaryKircher, S., Garland, M., Progressive multiresolution meshes for deforming surfaces (2005) 2005 ACM SIGGRAPH / Eurographics Symposium on Computer Animation, pp. 191-200. , JulyKobbelt, L.P., Bareuther, T., Seidel, H.-P., Multiresolution shape deformations for meshes with dynamic vertex connectivity (2000) Computer Graphics Forum, 19 (3)Lindstrom, P., Pascucci, V., Terrain simplification simplified: A general framework for view-dependent out-of-core visualization (2002) IEEE Transactions on Visualization and Computer Graphics, 8 (3), pp. 239-254. , July, SeptemberPuppo, E., Variable resolution triangulations (1998) Computational Geometry Theory and Applications, 11 (34), pp. 219-238P. Schroeder. Subdivision for modeling and animation, 1998. Course notes of Siggraph 98. ACM SIGGRAPHShamir, A., Bajaj, C.L., Pascucci, V., Multi-resolution dynamic meshes with arbitrary deformations (2000) IEEE Visualization, pp. 423-430Velho, L., A dynamic adaptive mesh library based on stellar operators (2004) Journal of Graphics Tools, 9 (2), pp. 1-29Velho, L., Gomes, J., Variable resolution 4-k meshes: Concepts and applications (2000) Comp. Graphics Forum, 19, pp. 195-212Velho, L., Zorin, D., 4-8 subdivision (2001) Computer-Aided Geometric Design, 18 (5), pp. 397-427. , Special Issue on Subdivision TechniquesWelch, W., Witkin, A., Free-form shape design using triangulated surfaces (1994) SIGGRAPH, pp. 247-256Wood, Z.J., Desbrun, M., Schröder, P., Breen, D., Semiregular mesh extraction from volumes (2000) IEEE Visualization 2000, pp. 275-282. , Oc