MORPHO - Atlas
[Guimond 2000] A. Guimond, J. Meunier, J. Thirion, “Average brain models: A convergence study”, Computer Vision and Image Understanding 77(2) (2000) 192–210.
[Commowick 2004] O. Commowick, G. Malandain and P.Y.Bondiau, “Segmentation automatique des tissus cérébraux en présence de structures pathologiques ”, in Proceedings of the 43èmes journées scientifiques de la Société Française de PhysiqueMédicale (SFPM 2004), June 2004.
[Stefanescu 2004] R. Stefanescu, O. Commowick, G. Malandain, P.Y. Bondiau, N. Ayache, and X. Pennec, “Non Rigid Atlas to Subject Registration with Pathologies for Conformal Brain Radiotherapy”, In C. Barillot, D.R. Haynor, and P. Hellier, editors, Proc. of the 7th Int. Conf on Medical Image Computing and Computer Assisted Intervention MICCAI 2004, volume 3216 of LNCS, SaintMalo, France, pages 704711, September 2004. Springer Verlag.
[Commowick 2005] Olivier Commowick, Radu Stefanescu, Pierre Fillard, Vincent Arsigny, Nicholas Ayache, Xavier Pennec, and Grégoire Malandain. “Incorporating Statistical Measures of Anatomical Variability in Atlas to Subject Registration for Conformal Brain Radiotherapy.” In J. Duncan and G. Gerig, editors, Proceedings of the 8th Int. Conf. On Medical Image Computing and ComputerAssisted Intervention MICCAI 2005, Part II, volume 3750 of LNCS, Palm Springs, CA, USA, October 2629, pages 927934, 2005. Springer Verlag.
[Commowick 2006a] O. Commowick, V. Arsigny, J. Costa, N. Ayache, and G. Malandain, “An Efficient Locally Affine Framework for the Registration of Anatomical Structures”, in Proceedings of the Third IEEE International Symposium on Biomedical Imaging (ISBI 2006), pages 478481, Crystal Gateway Marriott, Arlington, Virginia, USA, 2006.
[Commowick 2006b] O. Commowick and G. Malandain, “Evaluation of Atlas Construction Strategies in the Context of Radiotherapy Planning”, In Proceedings of the SA2PM Workshop (From Statistical Atlases to Personalized Models), Copenhagen, October 2006. Note: Held in conjunction with MICCAI 2006.*
[Commowick 2007a] O. Commowick, “Création et Utilisation d'Atlas Anatomiques Numériques pour la Radiothérapie (Design and Use of Anatomical Atlases for Radiotherapy).”, Thèse de sciences (PhD Thesis), Université de NiceSophia Antipolis, February 2007.
[Commowick 2007b] O. Commowick and G. Malandain, “Efficient selection of the most similar image in a database for critical structures segmentation,” in Proc. MICCAI’07, Part II, Brisbane, Australia, October 2007, number 4792 in LNCS, pp. 203–210.
[Commowick 2008a] Commowick O, Arsigny V, Isambert A, Costa J, Dhermain F, Bidault F, Bondiau PY, Ayache N and Malandain G, “An Efficient Locally Affine Framework for the Smooth Registration of Anatomical Structures.” , Med. Image Anal., 12, p427444,2008a.
[Commowick 2008b] O. Commowick, V. Grégoire, G. Malandain, “Atlasbased delineation of lymph node levels in head and neck computed tomography images.”, Radiotherapy Oncology 87(2) (2008) 281–289.
[Ramus 2009] L. Ramus and G. Malandain, “Using consensus measures for atlas construction.”, In Proceedings of the Sixth IEEE International Symposium on Biomedical Imaging 2009 (ISBI 2009), Boston, MA, July 2009.
[Ramus 2010a] L. Ramus and G. Malandain, “Assessing Selection Methods in the Context of Multiatlas Based Segmentation.”, In Proceedings of the Seventh IEEE International Symposium on Biomedical Imaging 2010 (ISBI'10), 2010.
[Ramus 2010b] Ramus L., Thariat J., Marcy P.Y., Pointreau Y., Bera G., Commowick O., Malandain G., “Contouring Tool, Design and Application of Anatomical Atlases: Cases of head and Neck Cancer ( Outils de contourage, Utilisation et Construction d'Atlas Anatomiques : Exemples des Cancers de la Tete et du Cou).”, Cancer/Radiothérapie, In Press, Corrected Proof, 2010.
[Ramus 2010c] Ramus L., Aouadi S., Gregoire V., Malandain G., “Design and Use of PatientSpecific Atlases For Radiotherapy Planning and the Head and Neck Region.”, poster ESTRO 2010.
[Ramus 2010d] Ramus L., Malandain G., “Construction of Patient Specific Atlases from Locally Most Similar Anatomical Pieces.” Proceedings of the Conf. On Medical Image Computing and ComputerAssisted Intervention MICCAI 2010.
[Ramus 2010e] L. Ramus and G. Malandain. “Multi-atlas based segmentation: Application to the head and neck region for radiotherapy planning.” In MICCAI Workshop Medical Image Analysis for the Clinic - A Grand Challenge, Beijing, China, September 2010. HAL ID: inria-00616150.
[Thariat 2011] J. Thariat, L. Ramus, P. Maingon, G. Odin, V. Grégoire, V. Darcourt, P.Y. Marcy, N. Guevara, M.H. Orlanducci, S. Marcie, G. Poissonnet, A. Bozec, O. Dassonville, F. Demard, L. Castillo, J. Santini, and G. Malandain. “DENTALMAPS: Automatic Dental Delineation for Radiotherapy Planning in Head and Neck Cancer.” Int J Radiat Oncol Biol Phys, 2011.
[Ramus 2011] L. Ramus. “Conception et utilisation d'atlas anatomiques pour la segmentation automatique : application à la radiothérapie des cancers ORL.” Thèse de sciences, Université de Nice Sophia Antipolis, Juillet 2011.
[Costa 2005] J. Costa, H. Delingette, J.C. Diaz et al., “Towards an automatic delineation of lower abdomen structures for conformational radiotherapy based on CT images”, in Proceedings of the 44èmes journées scientifiques de la Société Française de Physique Médicale (SFPM 2005), June 2005.
[Costa 2007a] J. Costa, H. Delingette et N. Ayache, “Automatic Segmentation of the Bladder Using Deformable Models”, in ISBI 2007, Crystal Gateway Marriott, Arlington, Virginia, USA, April 2007.
[Costa 2007b] J. Costa, H. Delingette, S. Novellas and N. Ayache, “Automatic Segmentation of Bladder and Prostate Using Coupled 3D Deformable Models”, in Proceedings of MICCAI, Brisbane, Australia, November 2007.
[Costa 2008] J. Costa, “Segmentation of Anatomical Structures of the Lower Abdomen using 3D Deformable Models. ”, PhD Thesis, École Nationale Supérieure des Mines de Paris, March 2008.
[Bondiau 2004a] PY Bondiau, G Malandain, O Commowick, PY Marcy, S Chanalet, and N Ayache, “Atlas based Automatic Segmentation of MR Images: Validation Study on the Brainstem in Radiotherapy Context”, In 90th Scientific Assembly and Annual Meeting of the Radiological Society of North America (RSNA), Chicago, 2004.
[Bondiau 2005] Bondiau PY, Malandain G, Chanalet S, Marcy PY, Habrand JL, Fauchon F, Paquis P, Courdi A, Commowick O, Rutten I and Ayache N, “Atlasbased automatic segmentation of MR images: validation study on the brainstem in radiotherapy context”, Int J Radiat Oncol Biol Phys, 61(1):28998, January 2005
[Isambert 2006a] Isambert A, Dhermain F, Bonniaud G, Bidault F, Beaudre A, Malandain G, Commowick O, Diaz JC, Bourhis J, Ricard M, Lefkopoulos D., “Evaluation of multimodality image registration software and atlasbased automatic segmentation (ABAS) for delineation of Organs at Risk (OAR) in the brain in conformal radiotherapy (CRT)”, in Proceedings of the journées scientifiques de la Société Française de Physique Médicale, SFPM 2006.
[Isambert 2006b] Isambert, Dhermain, Bidault, Bonniaud, Lery, Malandain, Commowick, Diaz, Bourhis, Lefkopoulos, “Evaluation of Multimodality Image Registration Software and Atlasbased Automatic Segmentation for Delineation of Organs at Risk (OAR) in the Brain in Conformal Radiotherapy (CRT)”, Abstract ASTRO 2006 Philadelphie
[Isambert 2008] A. Isambert, F. Dhermain, F. Bidault, O. Commowick, P.Y. Bondiau, G. Malandain and D. Lefkopoulos., “Evaluation of an atlasbased automatic segmentation software for the delineation of brain organs at risk in a radiation therapy clinical context.”, Radiotherapy Oncology, 87(1):9399, April 2008.
[Isambert 2007] A. Isambert, V. Grégoire, F. Bidault, G. Calais, O. Commowick, G. Malandain, JB. Ruaud, M. Tomsej, C. Bramoulle, J. Bourhis, D. Lefkopoulos, “AtlasBased Automatic Segmentation (ABAS) of head and neck (H&N) structures in conformal radiotherapy (CRT): atlas development and preliminary results in clinical context.”, abstract accepted for oral communication, 9th biennal ESTRO meeting, Barcelona, Sept 2007.
[Sims 2009] Richard Sims, Aurelie Isambert, Vincent Gregoire, Francois Bidault, Lydia Fresco, John Sage, John Mills, Jean Bourhis, Dimitri Lefkopoulos, Olivier Commowick, Mehdi Benkebil, Gregoire Malandain, “A preclinical assessment of an atlas based automatic segmentation tool for the head and neck”, Radiotherapy and Oncology, Volume 93, Issue 3, December 2009, Pages 474478, ISSN 01678140, DOI: 10.1016/j.radonc.2009.08.013.
[Bera 2010] G. Bera, Y. Pointreau, C. Bramoullé, G. Calais, I. Barillot, “Evaluation d’un atlas de segmentation automatique de la sphère ORL”, 21e Congrès national de la Société Française de Radiothérapie Oncologique (SFRO), Octobre 2010. Note: Cancer/Radiothérapie 14(6-7): 658, 2010.
[Kwan 1996] R.K.S. Kwan, A.C. Evans et G.B. Pike. “An Extensible MRI Simulator for PostProcessing Evaluation”, In Visualization in Biomedical Computing (VBC'96), volume 1131 of LNCS, pages 135140, 1996.
[Cocosco 1997] C.A. Cocosco, V. Kollokian, R.K.S. Kwan et A.C. Evans. “BrainWeb : Online Interface to a 3D MRI Simulated Brain Database.”, NeuroImage, vol. 5, no. 4, 1997.
[Kwan 1999] R.K.S. Kwan, A.C. Evans et G.B. Pike. “MRI simulationbased evaluation of imageprocessing and classication methods.”, IEEE Transactions on Medical Imaging, vol. 18, no. 11, pages 108597, Novembre 1999.
[Collins 1998] D.L. Collins, A.P. Zijdenbos, V. Kollokian, J.G. Sled, N.J. Kabani, C.J. Holmes et A.C. Evans. “Design and Construction of a Realistic Digital Brain Phantom. ”, IEEE Transactions on Medical Imaging, vol. 17, no. 3, pages 463468,Juin 1998.
[Park 2003] Hyunjin Park, Peyton Bland et Charles R. Meyer, “Construction of an Abdominal Probabilistic Atlas and its Application in Segmentation.”, IEEE Trans. Med. Imaging, vol. 22, no. 4, pages 483492, 2003.
[Warfield 2004] S. Warfield, K. Zou, W. Wells, “Simultaneous truth and performance level estimation (STAPLE): an algorithm for the validation of image segmentation”, IEEE Transactions on Medical Imaging 23(7) (July 2004) 903–921.
[Rohlfing 2004] Rohlfing, T., Brandt, R., Menzel, R., et al., “Evaluation of atlas selection strategies for atlasbased image segmentation with application to confocal microscopy images of bee brains.”, Neuroimage 21(4) (2004) 1428–42.
[Bondiau 2004b] PierreYves Bondiau. “Mise en oeuvre et évaluation d'outils de fusion d'image en radiothérapie”. Thèse de sciences, Université de NiceSophia Antipolis, November 2004.
[Ripoche 2004] X. Ripoche, J. Atif et A. Osorio. “A 3D discrete deformable model guided by mutual information for medical image segmentation.” In Proceedings of the Medical Imaging Conference 2004. SPIE, 2004.
[Wu 2007] M. Wu, C. Rosano, P. LopezGarcia, et al., “Optimum template selection for atlasbased segmentation,” Neuroimage, vol. 34, no. 4, pp. 1612–8, February 2007.
[Aljabar 2009] Aljabar, P., Heckemann, R., et al., “Multiatlas based segmentation of brain images: atlas selection and its effect on accuracy.” Neuroimage 46(3) (2009) 726–38
[Isgum 2009] Isgum, I., Staring, M., Rutten, A., et al., “Multiatlasbased segmentation with local decision fusion–application to cardiac and aortic segmentation in CT scans.” IEEE TMI 28(7) (2009) 1000–10. [van Rikxoort 2010] van Rikxoort, E.M., Isgum, I., et al., “Adaptive local multiatlas segmentation: application to heart segmentation in chest CT scans.”, MedIA 14(1) (2010) 39–49.
4D Radiotherapy - Adaptive and respiratory
BlockMatching
[Ourselin 2000] S. Ourselin, A. Roche, S. Prima, N. Ayache, “Block Matching: A General Framework to Improve Robustness of Rigid Registration of Medical Images.”, MICCAI, LNCS 1935, Pennsylvanie USA, 557566, 2000.
Locally affine registration
[Arsigny 2006] Arsigny V., Commowick O., Pennec X., Ayache N., “Polyaffine Framework for Locally Rigid or Affine Registration.”, A LogEuclidean.In Proceedings of the Third International Workshop on Biomedical Image Registration (WBIR'06), LNCS, Utrecht, The Netherlands, 9 11 July 2006. Springer.
[Commowick 2006] O. Commowick, V. Arsigny, J. Costa, N. Ayache, and G. Malandain, “An Efficient Locally Affine Framework for the Registration of Anatomical Structures”, in Proceedings of the Third IEEE International Symposium on Biomedical Imaging (ISBI 2006), pages 478481, Crystal Gateway Marriott, Arlington, Virginia, USA, 2006.
[Commowick 2007] O. Commowick, “Création et Utilisation d'Atlas Anatomiques Numériques pour la Radiothérapie (Design and Use of Anatomical Atlases for Radiotherapy).”, Thèse de sciences (PhD Thesis), Université de NiceSophia Antipolis, February 2007.
Optimisation based approaches
[Roche 2000] A. Roche, G. Malandain, N. Ayache, “Unifying Maximum Likelihood Approaches in Medical Image Registration”, International Journal of Imaging Systems and Technology: Special Issue on 3D Imaging, 11(1), 7180, 2000.
Deformable
[Thirion 1998] J.P. Thirion, “Image Matching as a Diffusion Process: an Analogy with Maxwell's Demons.”, Medical Image Analysis, 2( 3), 243260, 1998.
[Bondiau 2004] P.Y.Bondiau, G. Malandain, S.Chanalet, P.Y.Marcy, C. Foa, N. Ayache, “Traitement des Images et Radiothérapie (Image Processing and Radiotherapy)” Cancer/Radiothérapie, 8(2):120129, 2004.
[Isambert 2006] A. Isambert, G. Bonniaud, R. Lery, C. Comtat, J.C. Diaz JC, G. Malandain, D. Lefkopoulos, “Phantombased Evaluation of Multimodality Image Registration Software for Radiotherapy”, 17e Congrès de la Société Française de Radiothérapie Oncologique (SFRO), November 2006. Note: Cancer/Radiothérapie 10(67): 507, 2006.
[Bonniaud 2006] G. Bonniaud, A. Isambert, F. Dhermain, A. Beaudré, I. Ferreira, M. Ricard, D. Lefkopoulos, “Image Registration for Radiation Therapy: Practical Aspects and Quality Control”, Cancer Radiothérapie, 10(5): 222230, 2006.
[Isambert 2008a] A. Isambert, G. Bonniaud, F. Lavielle, G. Malandain, D. Lefkopoulos, “A Phantom Study of the Accuracy of CT, MR and PET Image Registrations with a Block MatchingBased Algorithm”, Cancer Radiothérapie, 12(8): 800808 , 2008.
[Isambert 2008b] A. Isambert, F. Dhermain, F. Bidault, O. Commowick, P.Y. Bondiau, G. Malandain and D. Lefkopoulos., “Evaluation of an atlasbased automatic segmentation software for the delineation of brain organs at risk in a radiation therapy clinical context.”, Radiotherapy Oncology, 87(1):9399, April 2008.
[Sims 2009] R. Sims, A. Isambert, V. Gregoire, F. Bidault, L. Fresco, J. Sage, J. Mills, J. Bourhis, D. Lefkopoulos, O. Commowick, M. Benkebil, G. Malandain, “A preclinical assessment of an atlasbased automatic segmentation tool for the head and neck”, Radiotherapy and Oncology, Volume 93, Issue 3, December 2009, Pages 474478.
Review
[Kessler 2006] M. L. Kessler, “Image Registration and Data Fusion in Radiation Therapy.”, The British Journal of Radiology, 79, 99108, 2006.
Optimisationbased approaches
[Press 1992] Press W.H., Teukolsky S.A., Vetterling W.T., Flannery B.P., “Numerical Recipes in C: The Art of Scientific Computing.”, Cambridge University Press, New York, 1992.
Deformable registration
[Lee 1997] S. Lee, G. Wolberg, and S. Y. Shin, “Scattered Data Interpolation with Multilevel Bsplines.”, IEEE Trans. Visualization Comput. Graph, 1997 July, 3:228244.
[Christensen 2001] Christensen GE, Carlson B, Chao KS, Yin P, Grigsby PW, Nguyen K, Dempsey JF, Lerma FA, Bae KT, Vannier MW, Williamson JF, “Imagebased dose planning of intracavitary brachytherapy: registration of serialimaging studies using deformable anatomic templates.”, Int J Radiat Oncol Biol Phys. 2001 Sep 1;51(1):22743. PMID: 11516873
[Wang 2005] He Wang, Lei Dong, Ming Fwu Lii, Andrew L. Lee, Renaud de Crevoisier, Radhe Mohan, James D. Cox, Deborah A. Kuban, Rex Cheung, “Implementation and validation of a threedimensional deformable registration algorithm for targeted prostate cancer radiotherapy”, International Journal of Radiation Oncology*Biology*Physics, Volume 61, Issue 3, 1 March 2005, Pages 725735.
[Vemuri 2003] B. C. Vemuri, J. Ye, Y. Chen, C. M. Leonard. “Image Registration via LevelSet Motion : Applications to AtlasBased Segmentation.”, Medical Image Analysis, 7(1), 120, 2003.
[Castadot 2008] P. Castadot, J. A. Lee et. al. “Comparison of 12 Deformable Registration Strategies in Adaptive Radiation Therapy for the Treatment of Head and Neck Tumors.”, Radiotherapy and Oncology, 89(1), 112, 2008.
[MuyanOzcelik 2008] P. Muyan Ozcelik et. al., “Fast Deformable Registration on the GPU: A CUDA Implementation of Demons”, ICCSA, 2008.
[Sarrut 2007] D. Sarrut et. al. “A Comparison Framework for Breathing Motion Estimation Methods from 4D Imaging.”, IEEE Transactions on Medical Imaging, 26(12), 16361648, 2007.
[Sarrut 2009] D. Sarrut, J. Vandemeulebroucke. “BLUT: Fast and Low Memory Bspline Image Interpolation”. Comput. Methods Programs Biomed, 2009.
[Brock 2005] Brock KK, Sharpe MB, Dawson LA, Kim SM, Jaffray DA., “Accuracy of finite element model based multiorgan deformable image registration.”, Med Phys. 2005 Jun;32(6):164759.
[Brock 2010] K. Brock, “Results of a MultiInstitution Deformable Registration Accuracy Study (MIDRAS)”, Int. J. Radiat. Oncol. Biol. Phys, 76( 2), 583596, 2010.
2D/2D and 2D/3D
[Aouadi 2008] S. Aouadi, L. Sarry. “Accurate and Precise 2D3D Registration Based on Xray Intensity”. Computer Vision and Image Understanding. 110(1), pp. 134151, 2008.
Registration metric
[Kim 2004] J. Kim, J.A. Fessler, “Intensitybased image registration using robust correlation coefficients”, IEEE Transactions on Medical Imaging 2004, vol. 23, no11, pp. 14301444.
[Meyer 1997] Meyer CR, Boes JL, Kim B, Bland PH, Zasadny KR, Kison PV, Koral K, Frey KA, Wahl RL. “Demonstration of accuracy and clinical versatility of mutual information for automatic multimodality image fusion using affine and thinplate spline warped geometric deformations.”, Med Image Anal. 1997 Apr;1(3):195206.
[Viola 1997] Viola P, Wells WM, “Alignment by Maximization of Mutual Information”, Int J Computer Vision 1997;13754
BlockMatching
[Ourselin 2000] S. Ourselin, A. Roche, S. Prima, N. Ayache, “Block Matching: A General Framework to Improve Robustness of Rigid Registration of Medical Images.”, MICCAI, LNCS 1935, Pennsylvanie USA, 557566, 2000.
Locally affine registration
[Arsigny 2006] Arsigny V., Commowick O., Pennec X., Ayache N., “Polyaffine Framework for Locally Rigid or Affine Registration.”, A LogEuclidean.In Proceedings of the Third International Workshop on Biomedical Image Registration (WBIR'06), LNCS, Utrecht, The Netherlands, 9 11 July 2006. Springer.
[Commowick 2006] O. Commowick, V. Arsigny, J. Costa, N. Ayache, and G. Malandain, “An Efficient Locally Affine Framework for the Registration of Anatomical Structures”, in Proceedings of the Third IEEE International Symposium on Biomedical Imaging (ISBI 2006), pages 478481, Crystal Gateway Marriott, Arlington, Virginia, USA, 2006.
[Commowick 2007] O. Commowick, “Création et Utilisation d'Atlas Anatomiques Numériques pour la Radiothérapie (Design and Use of Anatomical Atlases for Radiotherapy).”, Thèse de sciences (PhD Thesis), Université de NiceSophia Antipolis, February 2007.
Optimisation based approaches
[Roche 2000] A. Roche, G. Malandain, N. Ayache, “Unifying Maximum Likelihood Approaches in Medical Image Registration”, International Journal of Imaging Systems and Technology: Special Issue on 3D Imaging, 11(1), 7180, 2000.
Deformable
[Thirion 1998] J.P. Thirion, “Image Matching as a Diffusion Process: an Analogy with Maxwell's Demons.”, Medical Image Analysis, 2( 3), 243260, 1998.
EPIgray – In vivo measurements using the EPID
Alkattar Zeina, “Evaluation de la dosimétrie In Vivo à base de détecteurs plan de type aS500-II (Varian). Etude de faisabilité et précision en Clinique”, PhD thesis, Université Paris XI, 2009
Berger Lucie “Utilisation d'un système d'imagerie portale électronique avec détecteur au silicium amorphe pour vérifier la dose reçue par les patients en radiothérapie”, PhD thesis, Université de Toulouse, 2006
Boissard P., François P. & Mazal A. “Utilisation des imageurs portals pour la dosimétrie in vivo à l’Institut Curie”, oral presentation - 49ème journées scientifiques de la SFPM, Bordeaux, May ‘10
Boissard P., François P. & Mazal A. “The routine use of in vivo portal dosimetry at the Institut Curie”, oral presentation - 11ème international workshop on portal imaging, Leuven, June ’10
François P, Boissard P, Berger L & Mazal “A In vivo dose verification from back projection of a transit dose measurement on the central axis of photon beams”, Physica Medica in print
Van Elmpt W, McDermott L, Nijsten S, Wendling M, Lambin P & Mijnheer B (2008) “A literature review of electronic portal imaging for radiotherapy dosimetry”, Radiother Oncol 88(3), 289-3
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