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Publications of year 2009

Books and proceedings

  1. Nicholas Ayache, Hervé Delingette, and Maxime Sermesant, editors. Functional Imaging and Modeling of the Heart - FIMH 2009, volume 5528 of LNCS, Nice, France, June 2009. Springer. Note: 537 pages. [bibtex-entry]


Thesis

  1. Ender Konukoglu. Modeling Glioma Growth and Personalizing Growth Models in Medical Images. PhD Thesis, Université Nice Sophia-Antipolis, February 2009. [bibtex-entry]


  2. Jean-Marc Peyrat. Comparison of Cardiac Anatomy and Function: Statistics on Fibre Architecture from DT-MRI and Registration of 4D CT Images. PhD Thesis, Nice Sophia Antipolis University, November 2009. [bibtex-entry]


  3. Jean-Christophe Souplet. Évaluation de l'atrophie et de la charge lésionnelle sur des séquences IRM de patients atteints de sclérose en plaques. Thèse de sciences (PhD Thesis), Université de Nice -- Sophia-Antipolis, January 2009. [bibtex-entry]


Articles in journal, book chapters

  1. Vincent Arsigny, Olivier Commowick, Nicholas Ayache, and Xavier Pennec. A Fast and Log-Euclidean Polyaffine Framework for Locally Linear Registration. Journal of Mathematical Imaging and Vision, 33(2):222-238, 2009. [bibtex-entry]


  2. Éric Bardinet, Manik Bhattacharjee, Didier Dormont, Bernard Pidoux, Grégoire Malandain, Michael Schupbach, Nicholas Ayache, Philippe Cornu, Yves Agid, and Jerome Yelnik. A three-dimensional histological atlas of the human basal ganglia. II. Atlas deformation strategy and evaluation in deep brain stimulation for Parkinson disease.. Journal of Neurosurgery, 110(2):208-19, February 2009. Keyword(s): Basal Ganglia, pathology, Brain Mapping, methods, Deep Brain Stimulation, methods, Humans, Image Interpretation Computer-Assisted, methods, Imaging Three-Dimensional, methods, Magnetic Resonance Imaging, methods, Medical Illustration, Microelectrodes, Microscopy, Parkinson Disease, pathology, Red Nucleus, pathology, Sensitivity and Specificity, Substantia Nigra, pathology, Subthalamic Nucleus, pathology. [Abstract] [bibtex-entry]


  3. Caroline Brun, Natasha Leporé, Xavier Pennec, Agatha D Lee, Marina Barysheva, Sarah K Madsen, Christina Avedissian, Yi-Yu Chou, Greig I. de Zubicaray, Katie McMahon, Margaret Wright, Arthur W. Toga, and Paul M. Thompson. Mapping the Regional Influence of Genetics on Brain Structure Variability - A Tensor-Based Morphometry Study. NeuroImage, 48(1):37-49, October 2009. [bibtex-entry]


  4. Jaydev P. Desai and Nicholas Ayache. Editorial: Special Issue on Medical Robotics. International Journal of Robotics Research, 28(9):1099-1100, 2009. [bibtex-entry]


  5. Stanley Durrleman, Xavier Pennec, Alain Trouvé, and Nicholas Ayache. Statistical Models on Sets of Curves and Surfaces based on Currents. Medical Image Analysis, 13(5):793-808, October 2009. [bibtex-entry]


  6. Heike Hufnagel, Jan Ehrhardt, Xavier Pennec, Nicholas Ayache, and Heinz Handels. Computation of a Probabilistic Statistical Shape Model in a Maximum-a-posteriori Framework. Methods of Information in Medicine, 48(4):314-319, 2009. [bibtex-entry]


  7. Arno Klein, Jesper Andersson, Babak A. Ardekani, John Ashburner, Brian Avants, Ming-Chang Chiang, Gary E. Christensen, D. Louis Collins, Pierre Hellier, Joo Hyun Song, Mark Jenkinson, Claude Lepage, Daniel Rueckert, Paul M. Thompson, Tom Vercauteren, Roger P. Woods, J. John Mann, and Ramin V. Parsey. Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration. NeuroImage, 46(3):786-802, July 2009. [bibtex-entry]


  8. S. Nicolau, Xavier Pennec, Luc Soler, X. Buy, A. Gangi, Nicholas Ayache, and J. Marescaux. An Augmented Reality System for Liver Thermal Ablation: Design and Evaluation on Clinical Cases. Medical Image Analysis, 13(3):494-506, June 2009. [bibtex-entry]


  9. Mihaela Pop, Maxime Sermesant, D Lepiller, M V Truong, Elliot McVeigh, Eugene Crystal, Alexander Dick, Hervé Delingette, Nicholas Ayache, and Graham Wright. Fusion of optical imaging and MRI for the evaluation and adjustment of macroscopic models of cardiac electrophysiology: A feasibility study. Medical Image Analysis, 13(2):370-80, April 2009. [bibtex-entry]


  10. R Sims, A Isambert, V Gregoire, F Bidault, L Fresco, J Sage, J Mills, J Bourhis, D Lefkopoulos, Olivier Commowick, M Benkebil, and Grégoire Malandain. A pre-clinical assessment of an atlas-based automatic segmentation tool for the head and neck. Radiotherapy Oncology, 93(3):474-8, December 2009. [Abstract] [bibtex-entry]


  11. Jean-Christophe Souplet, Christine Lebrun, Stéphane Chanalet, Nicholas Ayache, and Grégoire Malandain. Revue des approches de segmentation des lésions de sclérose en plaques dans les séquences conventionnelles IRM. Revue Neurologique, 165(1):7-14, 2009. Note: In french. [bibtex-entry]


  12. Tom Vercauteren, Xavier Pennec, Aymeric Perchant, and Nicholas Ayache. Diffeomorphic Demons: Efficient Non-parametric Image Registration. NeuroImage, 45(1, Supp.1):S61-S72, March 2009. [bibtex-entry]


  13. Boon Thye Thomas Yeo, Tom Vercauteren, Pierre Fillard, Jean-Marc Peyrat, Xavier Pennec, Polina Golland, Nicholas Ayache, and Olivier Clatz. DT-REFinD: Diffusion Tensor Registration with Exact Finite-Strain Differential. IEEE Transactions on Medical Imaging, 28(12):1914-1928, December 2009. Note: PMID:19556193. [bibtex-entry]


  14. Nicholas Ayache, Olivier Clatz, Hervé Delingette, Grégoire Malandain, Xavier Pennec, and Maxime Sermesant. Asclepios: a Research Project-Team at INRIA for the Analysis and Simulation of Biomedical Images. In Y. Bertot, G. Huet, J.-J. Lévy, and G. Plotkin, editors, From semantics to computer science: essays in honor of Gilles Kahn, pages 415-436. Cambridge University Press, 2009. [bibtex-entry]


  15. C. Germain-Renaud, V. Breton, P. Clarysse, B. Delhay, Y. Gaudeau, T. Glatard, E. Jannot, Y. Legré, Johan Montagnat, J.-M. Moureau, A. Osorio, Xavier Pennec, J. Schaerer, and R. Texier. Grid Analysis of Radiological Data. In Mario Cannataro, editor, Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare, pages 363-391. IGI Global, 2009. Note: IGI-Global Medical Information Science Discoveries Research Award 2009. [bibtex-entry]


  16. Tommaso Mansi, Barbara André, Michael Lynch, Maxime Sermesant, Hervé Delingette, Younes Boudjemline, and Nicholas Ayache. Virtual Pulmonary Valve Replacement Interventions with a Personalised Cardiac Electromechanical Model. In Nadia Magnenat-Thalmann, Jian J. Zhang, and David D. Feng, editors, Recent Advances in the 3D Physiological Human, pages 201-210. Springer, November 2009. ISBN: 978-1-84882-564-2. [bibtex-entry]


  17. Jérôme Schmid, Anders Sandholm, François Chung, Daniel Thalmann, Hervé Delingette, and Nadia Magnenat-Thalmann. Musculoskeletal simulation model generation from MRI datasets and motion capture data. In Nadia Magnenat-Thalmann, Jian J. Zhang, and David D. Feng, editors, Recent Advances in the 3D Physiological Human, pages 3-19. Springer, February 2009. ISBN: 978-1-84882-564-2. [bibtex-entry]


  18. Christof Seiler, P. Büchler, L.-P. Nolte, R. Paulsen, and Mauricio Reyes. Hierarchical Markov Random Fields Applied to Model Soft Tissue Deformations on Graphics Hardware. In J. J. Zhang N. Magnenat-Thalmann and D. D. Feng, editors, Recent Advances in the 3D Physiological Human, pages 133-148. Springer, 2009. ISBN: 978-1-84882-564-2. [bibtex-entry]


Conference articles

  1. Barbara André, Tom Vercauteren, Aymeric Perchant, Michael B. Wallace, Anna M. Buchner, and Nicholas Ayache. Endomicroscopic image retrieval and classification using invariant visual features. In Proceedings of the Sixth IEEE International Symposium on Biomedical Imaging 2009 (ISBI'09), Boston, MA, pages 346-349, August 2009. IEEE. [bibtex-entry]


  2. Barbara André, Tom Vercauteren, Aymeric Perchant, Michael B. Wallace, Anna M. Buchner, and Nicholas Ayache. Introducing space and time in local feature-based endomicroscopic image retrieval. In Proceedings of the MICCAI Workshop - Medical Content-based Retrieval for Clinical Decision (MCBR-CDS'09), volume 5853 of Lecture Notes in Computer Science, pages 18-30, February 2009. Springer. [bibtex-entry]


  3. Florence Billet, Maxime Sermesant, Hervé Delingette, and Nicholas Ayache. Cardiac Motion Recovery and Boundary Conditions Estimation by Coupling an Electromechanical Model and Cine-MRI Data. In Proceedings of Functional Imaging and Modeling of the Heart 2009 (FIMH'09), volume 5528 of LNCS, pages 376-385, 3-5 June 2009. [bibtex-entry]


  4. R. Blanc, Mauricio Reyes, Christof Seiler, and G. Székely. Conditional Variability of Statistical Shape Models Based on Surrogate Variables. In Proceedings of Medical Image Computing and Computer Assisted Intervention 2009 (MICCAI), volume 5762 of LNCS, pages 84-91, September 2009. Springer, Heidelberg. [bibtex-entry]


  5. C.C. Brun, N. Leporé, X. Pennec, Yi-Yu Chou, A.D. Lee, M. Barysheva, G.I. de Zubicaray, K.L. McMahon, M.J. Wright, A.W. Toga, and P.M. Thompson. A Lagrangian formulation for statistical fluid registration. In Proceedings of the Sixth IEEE International Symposium on Biomedical Imaging 2009 (ISBI'09), pages 975-978, 2009. IEEE. [bibtex-entry]


  6. François Chung and Hervé Delingette. Multimodal Prior Appearance Models based on Regional Clustering of Intensity Profiles. In Guang-Zhong Yang, David Hawkes, Daniel Rueckert, Alison Noble, and Chris Taylor, editors, Medical Image Computing and Computer-Assisted Intervention (MICCAI'09), Part II, volume 5762 of Lecture Notes in Computer Science, London, UK, pages 1051-1058, September 2009. Springer. [bibtex-entry]


  7. François Chung, Jérôme Schmid, Olivier Clatz, Nadia Magnenat-Thalmann, and Hervé Delingette. Reconstruction 3D des structures anatomiques des membres inférieurs. In ORASIS'09, June 2009. [bibtex-entry]


  8. Olivier Commowick, Simon K. Warfield, and Grégoire Malandain. Using Frankenstein's Creature Paradigm to Build a Patient Specific Atlas. In Guang-Zhong Yang, David Hawkes, Daniel Rueckert, Alison Noble, and Chris Taylor, editors, Medical Image Computing and Computer-Assisted Intervention (MICCAI'09), Part II, volume 5762 of Lecture Notes in Computer Science, London, UK, pages 993-1000, September 2009. Springer. [bibtex-entry]


  9. Stanley Durrleman, Pierre Fillard, Xavier Pennec, Alain Trouvé, and Nicholas Ayache. A Statistical Model of White Matter Fiber Bundles based on Currents. In Jerry L. Prince, Dzung L. Pham, and Kyle J. Myers, editors, Proceedings of Information Processing in Medical Imaging (IPMI'09), volume 5636 of LNCS, pages 114-125, 2009. [bibtex-entry]


  10. Stanley Durrleman, Xavier Pennec, Alain Trouvé, Guido Gerig, and Nicholas Ayache. Spatiotemporal Atlas Estimation for Developmental Delay Detection in Longitudinal Datasets. In Guang-Zhong Yang, David Hawkes, Daniel Rueckert, Alison Noble, and Chris Taylor, editors, Medical Image Computing and Computer-Assisted Intervention (MICCAI'09), Part I, volume 5761 of Lecture Notes in Computer Science, London, UK, pages 297-304, September 2009. Springer. [bibtex-entry]


  11. V. Gorbunova, Stanley Durrleman, P. Lo, Xavier Pennec, and M. de Bruijne. Curve- and surface-based registration of lung CT images via currents. In M. Brown, M. de Bruijne, B. van Ginneken, A. Kiraly, J.M. Kuhnigk, C. Lorenz, J.R. McClelland, K. Mori, A.P. Reeves, and J. Reinhardt, editors, Proc. of Second International Workshop on Pulmonary Image Analysis, London United Kingdom, pages 15-25, 2009. [bibtex-entry]


  12. Tobias Heimann, François Chung, Hans Lamecker, and Hervé Delingette. Subject-Specific Ligament Models: Towards Real-Time Simulation of the Knee Joint. In Computational Biomechanics for Medicine IV Workshop 2009, September 2009. [bibtex-entry]


  13. Heike Hufnagel, Jan Ehrhardt, Xavier Pennec, and Heinz Handels. Application of a Probabilistic Statistical Shape Model to Automatic Segmentation. In World Congress on Medical Physics and Biomedical Engineering, WC 2009, München, volume 25/4 of IFMBE Proceedings, pages 2181-2184, 2009. Springer. [bibtex-entry]


  14. Heike Hufnagel, Jan Ehrhardt, Xavier Pennec, Alexander Schmidt-Richberg, and Heinz Handels. Level Set Segmentation Using a Point-Based Statistical Shape Model Relying on Correspondence Probabilities. In Proc. of MICCAI Workshop Probabilistic Model for Medical Image Analysis (PMMIA'09), 2009. [bibtex-entry]


  15. D. Kainmüller, Hans Lamecker, H. Seim, M. Zinser, and S. Zachow. Automatic Extraction of Mandibular Nerve and Bone from Cone-Beam CT Data. In Guang-Zhong Yang, David Hawkes, Daniel Rueckert, Alison Noble, and Chris Taylor, editors, Proc. Medical Image Computing and Computer Assisted Intervention, volume 5762 of Lecture Notes in Computer Science, pages 76-83, 2009. Springer. [bibtex-entry]


  16. Hans Lamecker, Tommaso Mansi, Jatin Relan, Florence Billet, Maxime Sermesant, Nicholas Ayache, and Hervé Delingette. Adaptive Tetrahedral Meshing for Personalized Cardiac Simulations. In MICCAI Workshop on Cardiovascular Interventional Imaging and Biophysical Modelling (CI2BM09), London United Kingdom, pages 149-158, 2009. Keyword(s): elements, modeling, mesh quality, mesh size control. [Abstract] [bibtex-entry]


  17. Tommaso Mansi, Stanley Durrleman, Boris Bernhardt, Maxime Sermesant, Hervé Delingette, Ingmar Voigt, Philipp Lurz, Andrew M Taylor, Julie Blanc, Younes Boudjemline, Xavier Pennec, and Nicholas Ayache. A Statistical Model of Right Ventricle in Tetralogy of Fallot for Prediction of Remodelling and Therapy Planning. In Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI'09), volume 5761 of Lecture Notes in Computer Science, London, UK, pages 214-221, September 2009. Springer. [bibtex-entry]


  18. Tommaso Mansi, Jean-Marc Peyrat, Maxime Sermesant, Hervé Delingette, Julie Blanc, Younes Boudjemline, and Nicholas Ayache. Physically-Constrained Diffeomorphic Demons for the Estimation of 3D Myocardium Strain from Cine-MRI. In Proceedings of Functional Imaging and Modeling of the Heart 2009 (FIMH'09), volume 5528 of LNCS, pages 201-210, 3-5 June 2009. [bibtex-entry]


  19. Mihaela Pop, Maxime Sermesant, Tommaso Mansi, Eugene Crystal, Jay Detsky, _Yuesong Yang, Paul Fefer, Elliot McVeigh, Alexander Dick, Nicholas Ayache, and Graham Wright. Characterization of Post-infarct Scars in a Porcine Model - a Combined Experimental and Theoretical Study. In Proceedings of Functional Imaging and Modeling of the Heart 2009 (FIMH'09), volume 5528 of LNCS, pages 1-10, 3-5 June 2009. [bibtex-entry]


  20. Liliane Ramus and Grégoire Malandain. Using consensus measures for atlas construction. In Proceedings of the Sixth IEEE International Symposium on Biomedical Imaging 2009 (ISBI'09), Boston, MA, July 2009. [bibtex-entry]


  21. Jatin Relan, Maxime Sermesant, Hervé Delingette, Mihaela Pop, Graham Wright, and Nicholas Ayache. Quantitative comparison of two cardiac electrophysiology models using personalisation to optical and MR data. In IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'09), Boston, MA, pages 1027-1030, July 2009. Keyword(s): bioelectric phenomena, biomedical MRI, biomedical optical imaging, cardiology, image resolution, medical image processing, physiological modelsAliev-Panfilov model, MRI, cardiac models, depolarisation, electrophysiology, optical imaging, phenomenological model, porcine healthy heart, repolarisation, spatial resolution, temporal resolution. [bibtex-entry]


  22. Jatin Relan, Maxime Sermesant, Mihaela Pop, Hervé Delingette, Michel Sorine, Graham Wright, and Nicholas Ayache. Parameter Estimation of a 3D Cardiac Electrophysiology Model Including the Restitution Curve Using Optical and MR Data. In Olaf Dössel and Wolfgang C. Schlegel, editors, World Congress on Medical Physics and Biomedical Engineering, volume 25/IV of IFMBE Proceedings, Munich, Germany, pages 1716-1719, September 2009. Springer. [bibtex-entry]


  23. Jatin Relan, Maxime Sermesant, Mihaela Pop, Hervé Delingette, Michel Sorine, Graham Wright, and Nicholas Ayache. Volumetric Prediction of Cardiac Electrophysiology using a Heart Model Personalised to Surface Data. In MICCAI Workshop on Cardiovascular Interventional Imaging and Biophysical Modelling - CI2BM09, London, UK, pages 19-27, 2009. [bibtex-entry]


  24. Tammy Riklin-Raviv, Bjoern H. Menze, Koen Van Leemput, Bram Stieltjes, Marc-André Weber, Nicholas Ayache, William M. Wells, and Polina Golland. Joint segmentation via patient-specific latent anatomy model. In MICCAI Workshop on Probabilistic Methods in Medical Image Analysis (PMMIA'09)), London, UK, September 2009. [bibtex-entry]


  25. Mert Sabuncu, Boon Thye Thomas Yeo, Tom Vercauteren, Koen Van Leemput, and Polina Golland. Asymmetric Image-Template Registration. In Guang-Zhong Yang, David Hawkes, Daniel Rueckert, Alison Noble, and Chris Taylor, editors, Medical Image Computing and Computer-Assisted Intervention (MICCAI'09), Part I, volume 5761 of Lecture Notes in Computer Science, London, UK, pages 565-573, September 2009. Springer. Note: PMID:20426033. [bibtex-entry]


  26. Maxime Sermesant, Florence Billet, Radomir Chabiniok, Tommaso Mansi, Phani Chinchapatnam, Philippe Moireau, Jean-Marc Peyrat, Kawal Rhode, Matt Ginks, Pier Lambiase, Simon Arridge, Hervé Delingette, Michel Sorine, Aldo Rinaldi, Dominique Chapelle, Reza Razavi, and Nicholas Ayache. Personalised Electromechanical Model of the Heart for the Prediction of the Acute Effects of Cardiac Resynchronisation Therapy. In Proceedings of Functional Imaging and Modeling of the Heart 2009 (FIMH'09), volume 5528 of LNCS, pages 239-248, 3-5 June 2009. [bibtex-entry]


  27. N. Toussaint, S. Durrleman, M. Sermesant, S. Kozerke, and P. Batchelor. Error Assessment on myocardial fiber orientations from DTI measurements. In Book of Abstracts, European Society of Magnetic Resonance in Medicine (ESMRMB) 26th Annual Scientific Meeting, volume 22, Antalya, Turkey, pages 59, 2009. [bibtex-entry]


Internal reports

  1. Stanley Durrleman, Xavier Pennec, Guido Gerig, Alain Trouvé, and Nicholas Ayache. Spatiotemporal Atlas Estimation for Developmental Delay Detection in Longitudinal Datasets. Research report RR-6952, INRIA, 2009. [bibtex-entry]


Manuals, booklets

  1. Nadia Magnenat-Thalmann, Jérôme Schmid, Hervé Delingette, Marco Agus, and José Antonio Iglesias Guitián. 3D Anatomical Modelling and Simulation Concepts. Eurographics 2009 Course Notes, Eurographics 2009, Munich, August 2009. [bibtex-entry]


Miscellaneous

  1. Barbara André, Tom Vercauteren, Aymeric Perchant, Michael B. Wallace, Anna M. Buchner, and Nicholas Ayache. Endomicroscopic image retrieval and classification using invariant visual features. Pesented as a poster at the third edition of the International Computer Vision Summer School 2009 (ICVSS'09), July 2009. [bibtex-entry]


  2. Florence Dru and Tom Vercauteren. An ITK Implementation of the Symmetric Log-Domain Diffeomorphic Demons Algorithm. Insight Journal -- 2009 January - June, May 2009. [bibtex-entry]


  3. Tommaso Mansi, Barbara André, Maxime Sermesant, Hervé Delingette, Nicholas Ayache, and Younes Boudjemline. Simulation personnalisée de replacements valvulaires pulmonaires grâce à l'utilisation d'un modèle mathématique du coeur. Archives de Pédiatrie - Congrès des Sociétés Françaises Médico-chirurgicales Pédiatriques, June 2009. [bibtex-entry]


  4. J. Relan, M. Sermesant, and H. Delingette, M. Pop, M. Sorine, G.A. Wright, and N. Ayache. Personalisation of 3D Cardiac Electrophysiology Models for valid Predictions: A Step Towards Patient-Specific Ventricular Tachycardia Modelling. The Cardiac Physiome: Multi-scale and Multi-physics Mathematical Modelling Applied to the Heart, Cambridge, UK, July 2009. [bibtex-entry]


  5. Christof Seiler, S. Weber, W. Schmidt, F. Fischer, N. Reimers, and Mauricio Reyes. Automatic Landmark Propagation for Left and Right Symmetry Assessment of Tibia and Femur: A Computational Anatomy Based Approach. CAOS, Boston, USA, June 2009. Note: Abstract. [bibtex-entry]



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