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Publications of year 2011

Books and proceedings

  1. Xavier Pennec, Sarang Joshi, and Mads Nielsen, editors. Proceedings of the Third International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Modelling Biological Shape Variability, Toronto, Canada, September 2011.
    @proceedings{Pennec:MFCAProcs:11,
    address = {Toronto, Canada},
    editor = {Pennec, Xavier and Joshi, Sarang and Nielsen, Mads},
    month = {September},
    title = {Proceedings of the Third International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Modelling Biological Shape Variability},
    url = {http://www-sop.inria.fr/asclepios/events/MFCA11/Proceedings/MFCA11_Proceedings.pdf},
    url-hal = {https://hal.inria.fr/hal-00813806},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-pays = {US},
    x-proceedings = {yes},
    x-scientific-popularization = {no},
    year = {2011} 
    }
    


Thesis

  1. Barbara André. Smart Atlas for Endomicroscopy Diagnosis Support: A Clinical Application of Content-Based Image Retrieval. Ph.D. Thesis, Ecole Nationale Supérieure des Mines de Paris, October 2011.
    @phdthesis{Andre:PhD:11,
    author = {Barbara Andr\'e},
    month = {October},
    school = {Ecole Nationale Sup\'erieure des Mines de Paris},
    title = {Smart Atlas for Endomicroscopy Diagnosis Support: A Clinical Application of Content-Based Image Retrieval},
    type = {Ph.D. Thesis},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Barbara.Andre/PhD-Thesis-Barbara-ANDRE.pdf},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  2. François Chung. Regional appearance modeling for deformable model-based image segmentation. Ph.D. Thesis, Ecole Nationale Supérieure des Mines de Paris, January 2011.
    @phdthesis{Chung:PhD:11,
    author = {Fran\c{c}ois Chung},
    hal-identifiant = {pastel-00575796},
    month = {January},
    school = {Ecole Nationale Sup\'erieure des Mines de Paris},
    title = {Regional appearance modeling for deformable model-based image segmentation},
    type = {Ph.D. Thesis},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Francois.Chung/Phd-Thesis_Francois-Chung.pdf},
    url-hal = {http://pastel.archives-ouvertes.fr/pastel-00575796/en/},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  3. Liliane 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.
    @phdthesis{Ramus:PhD:11,
    author = {Liliane Ramus},
    month = {Juillet},
    school = {Universit\'e de Nice Sophia Antipolis},
    title = {Conception et utilisation d'atlas anatomiques pour la segmentation automatique : application \`a la radioth\'erapie des cancers ORL},
    type = {Th\`ese de sciences},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Liliane.Ramus/These_Liliane_Ramus.pdf},
    x-international-audience = {no},
    year = {2011} 
    }
    


Articles in journal, book chapters

  1. Barbara André, Tom Vercauteren, Anna M. Buchner, Michael B. Wallace, and Nicholas Ayache. A Smart Atlas for Endomicroscopy using Automated Video Retrieval. Medical Image Analysis, 15(4):460-476, August 2011. Keyword(s): Content-Based Video Retrieval (CBVR), Endomicroscopy, Bag-of-Visual-Words (BoW), Video-mosaicing.
    Abstract:
    To support the challenging task of early epithelial cancer diagnosis from in vivo endomicroscopy, we propose a content-based video retrieval method that uses an expert-annotated database. Motivated by the recent successes of non-medical content-based image retrieval, we first adjust the standard Bag-of-Visual-Words method to handle single endomicroscopic images. A local dense multi-scale description is proposed to keep the proper level of invariance, in our case to translations, in-plane rotations and affine transformations of the intensities. Since single images may have an insufficient field-of-view to make a robust diagnosis, we introduce a video-mosaicing technique that provides large field-of-view mosaic images. To remove outliers, retrieval is followed by a geometrical approach that captures a statistical description of the spatial relationships between the local features. Building on image retrieval, we then focus on efficient video retrieval. Our approach avoids the time-consuming parts of the video-mosaicing by relying on coarse registration results only to account for spatial overlap between images taken at different times. To evaluate the retrieval, we perform a simple nearest neighbors classification with leave-one-patient-out cross-validation. From the results of binary and multi-class classification, we show that our approach outperforms, with statistical significance, several state-of-the art methods. We obtain a binary classification accuracy of 94.2%, which is quite close to clinical expectations.

    @article{Andre:MEDIA:11,
    abstract = {To support the challenging task of early epithelial cancer diagnosis from in vivo endomicroscopy, we propose a content-based video retrieval method that uses an expert-annotated database. Motivated by the recent successes of non-medical content-based image retrieval, we first adjust the standard Bag-of-Visual-Words method to handle single endomicroscopic images. A local dense multi-scale description is proposed to keep the proper level of invariance, in our case to translations, in-plane rotations and affine transformations of the intensities. Since single images may have an insufficient field-of-view to make a robust diagnosis, we introduce a video-mosaicing technique that provides large field-of-view mosaic images. To remove outliers, retrieval is followed by a geometrical approach that captures a statistical description of the spatial relationships between the local features. Building on image retrieval, we then focus on efficient video retrieval. Our approach avoids the time-consuming parts of the video-mosaicing by relying on coarse registration results only to account for spatial overlap between images taken at different times. To evaluate the retrieval, we perform a simple nearest neighbors classification with leave-one-patient-out cross-validation. From the results of binary and multi-class classification, we show that our approach outperforms, with statistical significance, several state-of-the art methods. We obtain a binary classification accuracy of 94.2%, which is quite close to clinical expectations.},
    author = {Barbara Andr\'e and Tom Vercauteren and Anna M. Buchner and Michael B. Wallace and Nicholas Ayache},
    doi = {10.1016/j.media.2011.02.003},
    hal-identifiant = {inria-00616190},
    journal = {Medical Image Analysis},
    keywords = {Content-Based Video Retrieval (CBVR), Endomicroscopy, Bag-of-Visual-Words (BoW), Video-mosaicing},
    month = {August},
    number = {4},
    pages = {460--476},
    title = {A Smart Atlas for Endomicroscopy using Automated Video Retrieval},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Barbara.Andre/ANDRE-MedIA2011-published.pdf},
    url-hal = {https://hal.inria.fr/inria-00616190},
    volume = {15},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  2. Nicholas Ayache, Olivier Clatz, Hervé Delingette, Grégoire Malandain, Xavier Pennec, and Maxime Sermesant. Vers un patient numérique personnalisé pour le diagnostic et la thérapie guidés par l'image. Médecine / Sciences, 27:208-213, March 2011.
    @article{Ayache:MedScience:11,
    author = {Nicholas Ayache and Olivier Clatz and Herv\'e Delingette and Gr\'egoire Malandain and Xavier Pennec and Maxime Sermesant},
    hal-identifiant = {inria-00616192},
    journal = {M\'edecine / Sciences},
    month = {March},
    pages = {208--213},
    publisher = {EDK France},
    title = {Vers un patient num\'erique personnalis\'e pour le diagnostic et la th\'erapie guid\'es par l'image},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Delingette/Asclepios-Medecine-sciences2011.pdf},
    url-hal = {http://hal.inria.fr/inria-00616192/en/},
    volume = {27},
    x-editorial-board = {no},
    x-international-audience = {no},
    x-invited-conference = {yes},
    x-scientific-popularization = {yes},
    year = {2011} 
    }
    


  3. N. Ayache, H. Delingette, and M. Sermesant. Le coeur numérique personnalisé. Bulletin de l'Académie Nationale de Médecine, 195(8), November 2011.
    @article{BANMayache2011,
    author = {N. Ayache and H. Delingette and M. Sermesant},
    journal = {Bulletin de l'Acad{\'e}mie Nationale de M{\'e}decine},
    month = {November},
    number = {8},
    title = {Le c{\oe}ur num{\'e}rique personnalis{\'e}},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/Ayache-et-al-Academie-Medecine-24Oct2011.pdf},
    volume = {195},
    year = {2011} 
    }
    


  4. Caroline Brun, Natasha Leporé, Xavier Pennec, Yi-Yu Chou, Agatha Lee, Greig De Zubicaray, Katie Mcmahon, Margaret Wright, James C. Gee, and Paul Thompson. A nonconservative Lagrangian framework for statistical fluid registration-SAFIRA.. IEEE Transactions on Medical Imaging, 30(2):184-202, February 2011. Note: PMID: 20813636.
    @article{Brun:TMI:2011,
    author = {Brun, Caroline and Lepor{\'e}, Natasha and Pennec, Xavier and Chou, Yi-Yu and Lee, Agatha and De Zubicaray, Greig and Mcmahon, Katie and Wright, Margaret and Gee, James C. and Thompson, Paul},
    doi = {10.1109/TMI.2010.2067451},
    journal = {{IEEE Transactions on Medical Imaging}},
    month = {February},
    note = {PMID: 20813636},
    number = {2},
    pages = {184-202},
    pmid = {20813636},
    publisher = {IEEE},
    title = {{A nonconservative Lagrangian framework for statistical fluid registration-SAFIRA.}},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Brun_TMI09.pdf},
    url-hal = {https://hal.inria.fr/inria-00616099},
    volume = {30},
    year = {2011} 
    }
    


  5. O. Camara, M. Sermesant, P. Lamata, L. Wang, M. Pop, J. Relan, M. De Craene, H. Delingette, H. Liu, S. Niederer, A. Pashaei, G. Plank, D. Romero, R. Sebastian, K.C.L. Wong, H. Zhang, N. Ayache, A.F. Frangi, P. Shi, N.P. Smith, and G.A. Wright. Inter-Model Consistency and Complementarity: Learning from ex-vivo Imaging and Electrophysiological Data towards an Integrated Understanding of Cardiac Physiology. Progress in Biophysics and Molecular Biology, 107:122-133, 2011.
    @article{Camara:PBMB:2011,
    author = {O. Camara and M. Sermesant and P. Lamata and L. Wang and M. Pop and J. Relan and M. De Craene and H. Delingette and H. Liu and S. Niederer and A. Pashaei and G. Plank and D. Romero and R. Sebastian and K.C.L. Wong and H. Zhang and N. Ayache and A.F. Frangi and P. Shi and N.P. Smith and G.A. Wright},
    hal-identifiant = {inria-00616197},
    journal = {Progress in Biophysics and Molecular Biology},
    pages = {122-133},
    title = {Inter-Model Consistency and Complementarity: Learning from ex-vivo Imaging and Electrophysiological Data towards an Integrated Understanding of Cardiac Physiology},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/PBMBcamara2011.pdf},
    url-hal = {https://hal.inria.fr/inria-00616197},
    volume = {107},
    year = {2011} 
    }
    


  6. François Chung, Jérôme Schmid, Nadia Magnenat-Thalmann, and Hervé Delingette. Comparison of statistical models performance in case of segmentation using a small amount of training datasets. The Visual Computer, 27(2):141-151, February 2011. Note: 10.1007/s00371-010-0536-9.
    @article{Chung:TVCJ:2011,
    author = {Fran\c{c}ois Chung and J\'er\^ome Schmid and Nadia Magnenat-Thalmann and Herv\'e Delingette},
    hal-identifiant = {inria-00616199},
    journal = {The Visual Computer},
    month = {February},
    note = {10.1007/s00371-010-0536-9},
    number = {2},
    pages = {141-151},
    title = {Comparison of statistical models performance in case of segmentation using a small amount of training datasets},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Francois.Chung/comparison_of_statistical_models_performance_in_case_of_segmentation_using_a_small_amount_of_training_datasets.pdf},
    url-hal = {https://hal.inria.fr/inria-00616199},
    volume = {27},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-pays = {CH},
    year = {2011} 
    }
    


  7. Hervé Delingette, Florence Billet, Ken C.L. Wong, Maxime Sermesant, S. Rhode, Kawal, Matt Ginks, C.A. Rinaldi, Reza Razavi, and Nicholas Ayache. Personalization of Cardiac Motion and Contractility from Images using Variational Data Assimilation. IEEE Transactions on Biomedical Engineering, 2011. Note: In Press.
    Abstract:
    Personalization is a key aspect of biophysical models in order to impact clinical practice. In this paper, we propose a personalization method of electromechanical models of the heart from cine-MR images based on the adjoint method. After estimation of electrophysiological parameters, the cardiac motion is estimated based on a proactive electromechanical model. Then cardiac contractilities on two or three regions are estimated by minimizing the discrepancy between measured and simulation motion. Evaluation of the method on three patients with infarcted or dilated myocardium is provided.

    @article{delingette:inria-00616183,
    abstract = {{Personalization is a key aspect of biophysical models in order to impact clinical practice. In this paper, we propose a personalization method of electromechanical models of the heart from cine-MR images based on the adjoint method. After estimation of electrophysiological parameters, the cardiac motion is estimated based on a proactive electromechanical model. Then cardiac contractilities on two or three regions are estimated by minimizing the discrepancy between measured and simulation motion. Evaluation of the method on three patients with infarcted or dilated myocardium is provided.}},
    affiliation = {ASCLEPIOS - INRIA Sophia Antipolis , BIPOP - INRIA Grenoble Rh{\^o}ne-Alpes / LJK Laboratoire Jean Kuntzmann , Division of Imaging Sciences , NIHR Biomedical Research Centre [London]},
    author = {Delingette, Herv{\'e} and Billet, Florence and Wong, Ken C.L. and Sermesant, Maxime and Rhode, Kawal, S. and Ginks, Matt and Rinaldi, C.A. and Razavi, Reza and Ayache, Nicholas},
    journal = {IEEE Transactions on Biomedical Engineering},
    language = {Anglais},
    note = {In Press },
    publisher = {undefined or unknown publisher},
    title = {{Personalization of Cardiac Motion and Contractility from Images using Variational Data Assimilation}},
    url-hal = {http://hal.inria.fr/inria-00616183},
    year = {2011} 
    }
    


  8. Stanley Durrleman, Pierre Fillard, Xavier Pennec, Alain Trouvé, and Nicholas Ayache. Registration, Atlas Estimation and Variability Analysis of White Matter Fiber Bundles Modeled as Currents. NeuroImage, 55(3):1073-1090, 2011. ISSN: 1053-8119. Keyword(s): Computational Anatomy.
    @article{Durrleman:NImg:11,
    author = {Stanley Durrleman and Pierre Fillard and Xavier Pennec and Alain Trouv\'e and Nicholas Ayache},
    doi = {10.1016/j.neuroimage.2010.11.056},
    hal-identifiant = {inria-00541930},
    issn = {1053-8119},
    journal = {NeuroImage},
    keywords = {Computational Anatomy},
    number = {3},
    pages = {1073-1090},
    title = {Registration, Atlas Estimation and Variability Analysis of White Matter Fiber Bundles Modeled as Currents},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Stanley.Durrleman/Durrleman_NImg10.pdf},
    url-hal = {http://hal.inria.fr/inria-00541930/en/},
    volume = {55},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  9. Ezequiel Geremia, Olivier Clatz, Bjoern H. Menze, Ender Konukoglu, Antonio Criminisi, and Nicholas Ayache. Spatial Decision Forests for MS Lesion Segmentation in Multi-Channel Magnetic Resonance Images. NeuroImage, 57(2):378-90, July 2011.
    @article{Geremia:NeuroImage:11,
    author = {Ezequiel Geremia and Olivier Clatz and Bjoern H. Menze and Ender Konukoglu and Antonio Criminisi and Nicholas Ayache},
    hal-identifiant = {inria-00616194},
    journal = {NeuroImage},
    month = {July},
    pages = {378-90},
    title = {Spatial Decision Forests for MS Lesion Segmentation in Multi-Channel Magnetic Resonance Images},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Ezequiel.Geremia/Geremia-MS-NeuroImage-2011.pdf},
    url-hal = {https://hal.inria.fr/inria-00616194},
    volume = {57(2)},
    year = {2011} 
    }
    


  10. BM Kelm, FO Kaster, A Henning, MA Weber, P Bachert, P Boesiger, FA Hamprecht, and BH Menze. Using spatial prior knowledge in the spectral fitting of MRS images. NMR in Biomedicine, [Epub ahead of print], 2011.
    @article{kelm:NBM:11,
    author = {BM Kelm and FO Kaster and A Henning and MA Weber and P Bachert and P Boesiger and FA Hamprecht and BH Menze},
    hal-identifiant = {inria-00616193},
    journal = {NMR in Biomedicine},
    title = {Using spatial prior knowledge in the spectral fitting of MRS images},
    url = {http://people.csail.mit.edu/menze/papers/kelm_10_using.pdf},
    url-hal = {https://hal.inria.fr/inria-00616193},
    volume = {[Epub ahead of print]},
    year = {2011} 
    }
    


  11. E. Konukoglu, J. Relan, U. Cilingir, B. Menze, P. Chinchapatnam, A. Jadidi, H. Cochet, M. Hocini, H. Delingette, P. Jaïs, M. Haïssaguerre, N. Ayache, and M. Sermesant. Efficient Probabilistic Model Personalization Integrating Uncertainty on Data and Parameters: Application to Eikonal-Diffusion Models in Cardiac Electrophysiology. Progress in Biophysics and Molecular Biology, 107(1):134-146, October 2011.
    @article{Konukoglu:PBMB:2011,
    author = {E. Konukoglu and J. Relan and U. Cilingir and B. Menze and P. Chinchapatnam and A. Jadidi and H. Cochet and M. Hocini and H. Delingette and P. Ja\"is and M. Ha\"issaguerre and N. Ayache and M. Sermesant},
    doi = {10.1016/j.pbiomolbio.2011.07.002},
    hal-identifiant = {inria-00616198},
    journal = {Progress in Biophysics and Molecular Biology},
    month = {Oct},
    number = {1},
    pages = {134-146},
    title = {Efficient Probabilistic Model Personalization Integrating Uncertainty on Data and Parameters: Application to Eikonal-Diffusion Models in Cardiac Electrophysiology},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/KonukogluPBMB2011.pdf},
    url-hal = {https://hal.inria.fr/inria-00616198},
    volume = {107},
    year = {2011} 
    }
    


  12. Georg Langs, Bjoern H. Menze, Danial Lashkari, and Polina Golland. Detecting stable distributed patterns of brain activation using Gini contrast. NeuroImage, 56:497-507, 2011.
    @article{Langs:Neuroimage:2011,
    author = {Georg Langs and Bjoern H. Menze and Danial Lashkari and Polina Golland},
    hal-identifiant = {inria-00616195},
    journal = {NeuroImage},
    pages = {497-507},
    title = {Detecting stable distributed patterns of brain activation using Gini contrast},
    url = {http://people.csail.mit.edu/langs/Georg_Langs/index_files/rf_rev.pdf},
    url-hal = {https://hal.inria.fr/inria-00616195},
    volume = {56},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-pays = {US},
    year = {2011} 
    }
    


  13. Marco Lorenzi, Alberto Beltramello, Nicola Mercuri, Elisa Canu, Giada Zoccatelli, Francesca Pizzini, Franco Alessandrini, Maria Cotelli, Sandra Rosini, Daniela Costardi, Carlo Caltagirone, and Giovanni Frisoni. Effect of memantine on resting state default mode network activity in Alzheimer's disease. Drugs and Aging, 28(3):205-217, 2011.
    @article{Lorenzi:DaA10:11,
    author = {Marco Lorenzi and Alberto Beltramello and Nicola Mercuri and Elisa Canu and Giada Zoccatelli and Francesca Pizzini and Franco Alessandrini and Maria Cotelli and Sandra Rosini and Daniela Costardi and Carlo Caltagirone and Giovanni Frisoni},
    journal = {Drugs and Aging},
    number = {3},
    pages = {205--217},
    title = {Effect of memantine on resting state default mode network activity in Alzheimer's disease},
    url-hal = {https://hal.inria.fr/inria-00616182},
    volume = {28},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-pays = {IT},
    x-proceedings = {yes},
    year = {2011} 
    }
    


  14. Tommaso Mansi, Xavier Pennec, Maxime Sermesant, Hervé Delingette, and Nicholas Ayache. iLogDemons: A Demons-Based Registration Algorithm for Tracking Incompressible Elastic Biological Tissues. International Journal of Computer Vision, 92(1):92-111, 2011.
    @article{Mansi:IJCV:11,
    author = {Tommaso Mansi and Xavier Pennec and Maxime Sermesant and Herv\'e Delingette and Nicholas Ayache},
    doi = {10.1007/s11263-010-0405-z},
    hal-identifiant = {inria-00616187},
    journal = {International Journal of Computer Vision},
    number = {1},
    pages = {92--111},
    title = {{iLogDemons}: A Demons-Based Registration Algorithm for Tracking Incompressible Elastic Biological Tissues},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Tommaso.Mansi/mansi10IJCV.pdf},
    url-hal = {https://hal.inria.fr/inria-00616187},
    volume = {92},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  15. Tommaso Mansi, Ingmar Voigt, Benedetta Leonardi, Xavier Pennec, Stanley Durrleman, Maxime Sermesant, Hervé Delingette, Andrew M. Taylor, Younes Boudjemline, Giacomo Pongiglione, and Nicholas Ayache. A Statistical Model for Quantification and Prediction of Cardiac Remodelling: Application to Tetralogy of Fallot. IEEE Transactions on Medical Imaging, 9(30):1605-1616, September 2011.
    @article{Mansi:TMI:11,
    author = {Tommaso Mansi and Ingmar Voigt and Benedetta Leonardi and Xavier Pennec and Stanley Durrleman and Maxime Sermesant and Herv\'e Delingette and Andrew M. Taylor and Younes Boudjemline and Giacomo Pongiglione and Nicholas Ayache},
    doi = {10.1109/TMI.2011.2135375},
    hal-identifiant = {inria-00616185},
    journal = {IEEE Transactions on Medical Imaging},
    month = {September},
    number = {30},
    pages = {1605--1616},
    title = {A Statistical Model for Quantification and Prediction of Cardiac Remodelling: Application to Tetralogy of Fallot},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Tommaso.Mansi/MansiTMI2011.pdf},
    url-hal = {https://hal.inria.fr/inria-00616185},
    volume = {9},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  16. Keelin Murphy, Bram van Ginneken, Joseph M. Reinhardt, Sven Kabus, Kai Ding, Xiang Deng, Kunlin Cao, Kaifang Du, Gary E. Christensen, Vincent Garcia, Tom Vercauteren, Nicholas Ayache, Olivier Commowick, Gregoire Malandain, Ben Glocker, Nikos Paragios, Nassir Navab, Vladlena Gorbunova, Jon Sporring, Marleen de Bruijne, Xiao Han, Mattias P. Heinrich, Julia A. Schnabel, Mark Jenkinson, Cristian Lorenz, Marc Modat, Jamie R. McClelland, Sebastien Ourselin, Sascha E.A. Muenzing, Max A. Viergever, Dante De Nigris, D. Louis Collins, Tal Arbel, Marta Peroni, Rui Li, Gregory C. Sharp, Alexander Schmidt-Richberg, Jan Ehrhardt, Rene Werner, Dirk Smeets, Dirk Loeckx, Gang Song, Nicholas Tustison, Brian Avants, James C. Gee, Marius Staring, Stefan Klein, Berend C. Stoel, Martin Urschler, Manuel Werlberger, Jef Vandemeulebroucke, Simon Rit, David Sarrut, and Josien P.W. Pluim. Evaluation of registration methods on thoracic CT: the EMPIRE10 challenge. IEEE Trans Med Imaging, 30(11):1901-20, November 2011.
    Abstract:
    EMPIRE10 (Evaluation of Methods for Pulmonary Image REgistration 2010) is a public platform for fair and meaningful comparison of registration algorithms which are applied to a database of intrapatient thoracic CT image pairs. Evaluation of nonrigid registration techniques is a nontrivial task. This is compounded by the fact that researchers typically test only on their own data, which varies widely. For this reason, reliable assessment and comparison of different registration algorithms has been virtually impossible in the past. In this work we present the results of the launch phase of EMPIRE10, which comprised the comprehensive evaluation and comparison of 20 individual algorithms from leading academic and industrial research groups. All algorithms are applied to the same set of 30 thoracic CT pairs. Algorithm settings and parameters are chosen by researchers expert in the configuration of their own method and the evaluation is independent, using the same criteria for all participants. All results are published on the EMPIRE10 website (http://empire10.isi.uu.nl). The challenge remains ongoing and open to new participants. Full results from 24 algorithms have been published at the time of writing. This paper details the organization of the challenge, the data and evaluation methods and the outcome of the initial launch with 20 algorithms. The gain in knowledge and future work are discussed.

    @article{murphy:itmi:2011,
    abstract = {EMPIRE10 (Evaluation of Methods for Pulmonary Image REgistration 2010) is a public platform for fair and meaningful comparison of registration algorithms which are applied to a database of intrapatient thoracic CT image pairs. Evaluation of nonrigid registration techniques is a nontrivial task. This is compounded by the fact that researchers typically test only on their own data, which varies widely. For this reason, reliable assessment and comparison of different registration algorithms has been virtually impossible in the past. In this work we present the results of the launch phase of EMPIRE10, which comprised the comprehensive evaluation and comparison of 20 individual algorithms from leading academic and industrial research groups. All algorithms are applied to the same set of 30 thoracic CT pairs. Algorithm settings and parameters are chosen by researchers expert in the configuration of their own method and the evaluation is independent, using the same criteria for all participants. All results are published on the EMPIRE10 website (http://empire10.isi.uu.nl). The challenge remains ongoing and open to new participants. Full results from 24 algorithms have been published at the time of writing. This paper details the organization of the challenge, the data and evaluation methods and the outcome of the initial launch with 20 algorithms. The gain in knowledge and future work are discussed.},
    author = {Keelin Murphy and van Ginneken, Bram and Joseph M. Reinhardt and Sven Kabus and Kai Ding and Xiang Deng and Kunlin Cao and Kaifang Du and Gary E. Christensen and Vincent Garcia and Tom Vercauteren and Nicholas Ayache and Olivier Commowick and Gregoire Malandain and Ben Glocker and Nikos Paragios and Nassir Navab and Vladlena Gorbunova and Jon Sporring and de Bruijne, Marleen and Xiao Han and Mattias P. Heinrich and Julia A. Schnabel and Mark Jenkinson and Cristian Lorenz and Marc Modat and Jamie R. McClelland and Sebastien Ourselin and Sascha E.A. Muenzing and Max A. Viergever and Dante De Nigris and D. Louis Collins and Tal Arbel and Marta Peroni and Rui Li and Gregory C. Sharp and Alexander Schmidt-Richberg and Jan Ehrhardt and Rene Werner and Dirk Smeets and Dirk Loeckx and Gang Song and Nicholas Tustison and Brian Avants and James C. Gee and Marius Staring and Stefan Klein and Berend C. Stoel and Martin Urschler and Manuel Werlberger and Jef Vandemeulebroucke and Simon Rit and David Sarrut and Josien P.W. Pluim},
    doi = {10.1109/TMI.2011.2158349},
    hal-identifiant = {inserm-00607794},
    journal = {IEEE Trans Med Imaging},
    month = {November},
    number = {11},
    pages = {1901-20},
    pmid = {21632295},
    title = {Evaluation of registration methods on thoracic CT: the EMPIRE10 challenge},
    url-hal = {http://www.hal.inserm.fr/inserm-00607794},
    volume = {30},
    year = {2011} 
    }
    


  17. E. Pernod, M. Sermesant, E. Konukoglu, J. Relan, H. Delingette, and N. Ayache. A Multi-Front Eikonal Model of Cardiac Electrophysiology for Interactive Simulation of Radio-Frequency Ablation. Computers and Graphics, 35:431-440, 2011.
    @article{Pernod:CG:2011,
    author = {E. Pernod and M. Sermesant and E. Konukoglu and J. Relan and H. Delingette and N. Ayache},
    hal-identifiant = {inria-00616180},
    journal = {Computers and Graphics},
    pages = {431--440},
    title = {A Multi-Front Eikonal Model of Cardiac Electrophysiology for Interactive Simulation of Radio-Frequency Ablation},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/CG-VCBM-2011.pdf},
    url-hal = {https://hal.inria.fr/inria-00616180},
    volume = {35},
    year = {2011} 
    }
    


  18. K.M Pohl, E. Konukoglu, S. Novellas, N. Ayache, A. Fedorov, I.-F. Talos, A. Golby, W.M. Wells, R. Kikinis, and P.M. Black. A New Metric for Detecting Change in Slowly Evolving Brain Tumors: Validation in Meningioma Patients. Neurosurgery, 68(1 Suppl Operative):225-33, March 2011.
    @article{Pohl:Neurosurgery:11,
    author = {K.M Pohl and E. Konukoglu and S. Novellas and N. Ayache and A. Fedorov and I.-F. Talos and A. Golby and W.M. Wells and R. Kikinis and P.M. Black},
    hal-identifiant = {inria-00616196},
    journal = {Neurosurgery},
    month = {March},
    pages = {225-33},
    publisher = {EDK France},
    title = {A New Metric for Detecting Change in Slowly Evolving Brain Tumors: Validation in Meningioma Patients},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Kilian.Pohl/pohl-Neurosurgery-2011.pdf},
    url-hal = {https://hal.inria.fr/inria-00616196},
    volume = {68(1 Suppl Operative)},
    year = {2011} 
    }
    


  19. M. Pop, M. Sermesant, T. Mansi, E. Crystal, S. Ghate, J. Peyrat, I. Lashevsky, Beiping Qiang, E. McVeigh, N. Ayache, and G.A. Wright. Correspondence Between Simple 3-D MRI-Based Computer Models and In-Vivo EP Measurements in Swine With Chronic Infarctions. Biomedical Engineering, IEEE Transactions on, 58(12):3483-3486, dec. 2011. ISSN: 0018-9294.
    @article{Pop:TBME:2011,
    author = {Pop, M. and Sermesant, M. and Mansi, T. and Crystal, E. and Ghate, S. and Peyrat, J. and Lashevsky, I. and Beiping Qiang and McVeigh, E. and Ayache, N. and Wright, G.A.},
    doi = {10.1109/TBME.2011.2168395},
    issn = {0018-9294},
    journal = {Biomedical Engineering, IEEE Transactions on},
    month = {dec.},
    number = {12},
    pages = {3483-3486},
    title = {Correspondence Between Simple 3-D MRI-Based Computer Models and In-Vivo EP Measurements in Swine With Chronic Infarctions},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/IEEE_TBME_Mihaela2011.pdf},
    url-hal = {https://hal.inria.fr/hal-00813802},
    volume = {58},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  20. Jatin Relan, Phani Chinchapatnam, Maxime Sermesant, Kawal Rhode, Matt Ginks, Hervé Delingette, C. Aldo Rinaldi, Reza Razavi, and Nicholas Ayache. Coupled Personalization of Cardiac Electrophysiology Models for Prediction of Ischaemic Ventricular Tachycardia. Journal of the Royal Society Interface Focus, 1(3):396-407, 2011.
    @article{Relan:IF:2011,
    author = {Jatin Relan and Phani Chinchapatnam and Maxime Sermesant and Kawal Rhode and Matt Ginks and Herv\'e Delingette and C. Aldo Rinaldi and Reza Razavi and Nicholas Ayache},
    hal-identifiant = {inria-00616188},
    journal = {Journal of the Royal Society Interface Focus},
    number = {3},
    pages = {396--407},
    title = {Coupled Personalization of Cardiac Electrophysiology Models for Prediction of Ischaemic Ventricular Tachycardia},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Jatin.Relan/RSFS-2010-0041_Manuscript.pdf},
    url-hal = {https://hal.inria.fr/inria-00616188},
    volume = {1},
    year = {2011} 
    }
    


  21. Jatin Relan, Mihaela Pop, Hervé Delingette, Graham Wright, Nicholas Ayache, and Maxime Sermesant. Personalisation of a Cardiac Electrophysiology Model using Optical Mapping and MRI for Prediction of Changes with Pacing. IEEE Transactions on Bio-Medical Engineering, 58(12):3339-3349, 2011.
    @article{Relan:TBME:11,
    author = {Jatin Relan and Mihaela Pop and Herv\'e Delingette and Graham Wright and Nicholas Ayache and Maxime Sermesant},
    hal-identifiant = {inria-00616184},
    journal = {IEEE Transactions on Bio-Medical Engineering},
    number = {12},
    pages = {3339--3349},
    title = {Personalisation of a Cardiac Electrophysiology Model using Optical Mapping and MRI for Prediction of Changes with Pacing},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Jatin.Relan/TBME-00761-2010-R2-preprint.pdf},
    url-hal = {https://hal.inria.fr/inria-00616184},
    volume = {58},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-language = {English},
    x-proceedings = {yes},
    year = {2011} 
    }
    


  22. Kawal Rhode and Maxime Sermesant. Modeling and Registration for Electrophysiology Procedures Based on Three-Dimensional Imaging. Current Cardiovascular Imaging Reports, 4:116-126, 2011.
    @article{Sermesant:CCIR:11,
    author = {Kawal Rhode and Maxime Sermesant},
    hal-identifiant = {inria-00616181},
    journal = {Current Cardiovascular Imaging Reports},
    pages = {116-126},
    title = {Modeling and Registration for Electrophysiology Procedures Based on Three-Dimensional Imaging},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/ModelRegistrationEP.pdf},
    url-hal = {https://hal.inria.fr/inria-00616181},
    volume = {4},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  23. N. Smith, A. de Vecchi, M. McCormick, D. Nordsletten, O. Camara, A.F. Frangi, H. Delingette, M. Sermesant, J. Relan, N. Ayache, M. W. Krueger, W. Schulze, R. Hose, I. Valverde, P. Beerbaum, C. Staicu, M. Siebes, J. Spaan, P. Hunter, J. Weese, H. Lehmann, D. Chapelle, and R. Razavi. euHeart: Personalized and integrated cardiac care using patient-specific cardiovascular modelling. Journal of the Royal Society Interface Focus, 1(3):349-364, 2011. ISSN: 2042-8898.
    @article{Smith:IF:2011,
    author = {N. Smith and de Vecchi, A. and M. McCormick and D. Nordsletten and O. Camara and A.F. Frangi and H. Delingette and M. Sermesant and J. Relan and N. Ayache and M. W. Krueger and W. Schulze and R. Hose and I. Valverde and P. Beerbaum and C. Staicu and M. Siebes and J. Spaan and P. Hunter and J. Weese and H. Lehmann and D. Chapelle and R. Razavi},
    hal-identifiant = {inria-00616189},
    issn = {2042-8898},
    journal = {Journal of the Royal Society Interface Focus},
    number = {3},
    pages = {349--364},
    publisher = {The Royal Society},
    title = {euHeart: Personalized and integrated cardiac care using patient-specific cardiovascular modelling},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/FOCUSsmith2011.pdf},
    url-hal = {https://hal.inria.fr/inria-00616189},
    volume = {1},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  24. C. Öhman, D. M. Espino, T. Heimann, M. Baleani, H. Delingette, and M. Viceconti. Subject-specific knee joint model: Design of an experiment to validate a multi-body finite element model. The Visual Computer, 27:153-159, 2011.
    @article{Ohman:VisualComputer:11,
    author = {C. \"Ohman and D. M. Espino and T. Heimann and M. Baleani and H. Delingette and M. Viceconti},
    hal-identifiant = {inria-00616200},
    journal = {The Visual Computer},
    pages = {153--159},
    title = {Subject-specific knee joint model: Design of an experiment to validate a multi-body finite element model},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Delingette/Ohman_et_al_Vis_comput_11.pdf},
    url-hal = {https://hal.inria.fr/inria-00616200},
    volume = {27},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-pays = {IT},
    year = {2011} 
    }
    


  25. T. Heimann and Hervé Delingette. Model-based segmentation. In Thomas Martin Deserno, editor, Biomedical Image Processing. Springer, 2011. ISBN: 978-3-642-15815-5.
    @incollection{Delingette:RABIPA:10,
    author = {T. Heimann and Herv\'e Delingette},
    booktitle = {Biomedical Image Processing},
    editor = {Deserno, Thomas Martin},
    hal-identifiant = {inria-00616063},
    isbn = {978-3-642-15815-5},
    publisher = {Springer},
    title = {Model-based segmentation},
    url = {http://www-sop.inria.fr/members/Herve.Delingette/Publications/Delingette-RABIPA-2010.pdf},
    url-hal = {https://hal.inria.fr/inria-00616063},
    x-international-audience = {yes},
    x-pays = {DE},
    year = {2011} 
    }
    


  26. B H Menze, E Stretton, E Konukoglu, and N. Ayache. Image-based modeling of tumor growth in patients with glioma.. In C S Garbe, R Rannacher, U Platt, and T Wagner, editors, Optimal control in image processing. Springer, Heidelberg/Germany, 2011.
    @incollection{menze_11_image-based,
    author = {B H Menze and E Stretton and E Konukoglu and N. Ayache},
    booktitle = {Optimal control in image processing},
    editor = {C S Garbe and R Rannacher and U Platt and T Wagner},
    publisher = {Springer, Heidelberg/Germany},
    title = {Image-based modeling of tumor growth in patients with glioma.},
    url = {http://people.csail.mit.edu/menze/papers/menze_11_image-based.pdf},
    url-hal = {https://hal.inria.fr/hal-00825866},
    year = {2011} 
    }
    


Conference articles

  1. Barbara André, Tom Vercauteren, and Nicholas Ayache. Content-Based Retrieval in Endomicroscopy: Toward an Efficient Smart Atlas for Clinical Diagnosis. In Proceedings of the MICCAI Workshop - Medical Content-based Retrieval for Clinical Decision (MCBR-CDS'11), LNCS, 2011. Springer.
    @inproceedings{Andre:MCBRCDS:11,
    author = {Barbara Andr\'e and Tom Vercauteren and Nicholas Ayache},
    booktitle = {Proceedings of the MICCAI Workshop - Medical Content-based Retrieval for Clinical Decision (MCBR-CDS'11)},
    publisher = {Springer},
    series = {LNCS},
    title = {Content-Based Retrieval in Endomicroscopy: Toward an Efficient Smart Atlas for Clinical Diagnosis},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Barbara.Andre/BarbaraANDRE_MCBR-CDS_11.pdf},
    url-hal = {https://hal.inria.fr/hal-00813791},
    x-international-audience = {yes},
    x-invited-conference = {yes},
    x-pays = {US},
    x-proceedings = {yes},
    year = {2011} 
    }
    


  2. Barbara André, Tom Vercauteren, Anna M. Buchner, Michael B. Wallace, and Nicholas Ayache. Retrieval evaluation and distance learning from perceived similarity between endomicroscopy videos. In Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI), LNCS, pages 8p, 2011. Springer, Heidelberg.
    @inproceedings{Andre:MICCAI:11,
    author = {Barbara Andr\'e and Tom Vercauteren and Anna M. Buchner and Michael B. Wallace and Nicholas Ayache},
    booktitle = {Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI)},
    hal-identifiant = {inria-00598301},
    pages = {8p},
    publisher = {Springer, Heidelberg},
    series = {LNCS},
    title = {Retrieval evaluation and distance learning from perceived similarity between endomicroscopy videos},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Barbara.Andre/Barbara_ANDRE_MICCAI11_CameraReadyFinal.pdf},
    url-hal = {https://hal.inria.fr/inria-00598301},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-proceedings = {yes},
    x-scientific-popularization = {no},
    year = {2011} 
    }
    


  3. S. Bonaretti, Christof Seiler, C. Boichon, P. Bchler, and Mauricio Reyes. Mesh-based vs. Image-based Statistical Model of Appearance of the Human Femur: A Preliminary Comparison Study for the Creation of Finite Element Meshes. In Mesh Processing in Medical Image Analysis Workshop MICCAI, 2011.
    @inproceedings{BonarettiSeiler:WorkshopMICCAI:11,
    author = {S. Bonaretti and Christof Seiler and C. Boichon and P. B\"chler and Mauricio Reyes},
    booktitle = {Mesh Processing in Medical Image Analysis Workshop MICCAI},
    title = {Mesh-based vs. Image-based Statistical Model of Appearance of the Human Femur: A Preliminary Comparison Study for the Creation of Finite Element Meshes},
    url-hal = {https://hal.inria.fr/hal-00813794},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-proceedings = {no},
    x-scientific-popularization = {no},
    year = {2011} 
    }
    


  4. H. Cochet, A. S. Jadidi, O. Corneloup, M. Lederlin, J. Relan, M. Montaudon, M. Sermesant, P. Jaïs, and F. Laurent. Myocardial Scar Modeling from Delayed Enhancement MRI: Usefulness for the Guidance of Ventricular Tachycardia Mapping and Ablation. In Radiological Society of North America, RSNA'11, November 2011.
    @inproceedings{Hubert:RSNA:11,
    author = {H. Cochet and A. S. Jadidi and O. Corneloup and M. Lederlin and J. Relan and M. Montaudon and M. Sermesant and P. Ja\"is and F. Laurent},
    booktitle = {Radiological Society of North America, RSNA'11},
    month = {November},
    title = {Myocardial Scar Modeling from Delayed Enhancement {MRI}: Usefulness for the Guidance of Ventricular Tachycardia Mapping and Ablation},
    url-hal = {https://hal.inria.fr/hal-00813795},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  5. H. Cochet, A. S. Jadidi, F. Sacher, N. Derval, M. Sermesant, J. Relan, S. J. Kim, P. Bordachar, P. Ritter, M. Hocini, M. Montaudon, F. Laurent, N. Ayache, M. Haïssaguerre, and P. Jais. Ventricular Scar At Cardiac CT Correlates To Critical Isthmuses Of Ventricular Tachycardia Circuits And Sites Of Slow Conduction During Sinus Rhythm - Evidence For Clinical Use Of CT Integration Into 3D Mapping Systems. In Heart Rhythm Society '11, May 2011.
    @inproceedings{Hubert:HeartRhythm:11,
    author = {H. Cochet and A. S. Jadidi and F. Sacher and N. Derval and M. Sermesant and J. Relan and S. J. Kim and P. Bordachar and P. Ritter and M. Hocini and M. Montaudon and F. Laurent and N. Ayache and M. Ha\"issaguerre and P. Jais},
    booktitle = {Heart Rhythm Society '11},
    hal-identifiant = {inria-00616206},
    month = {May},
    title = {Ventricular Scar At Cardiac CT Correlates To Critical Isthmuses Of Ventricular Tachycardia Circuits And Sites Of Slow Conduction During Sinus Rhythm - Evidence For Clinical Use Of CT Integration Into 3D Mapping Systems},
    url-hal = {https://hal.inria.fr/inria-00616206},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  6. B. Gibaud, F. Ahmad, C. Barillot, F. Michel, B. Wali, B. Batrancourt, M. Dojat, P. Girard, A. Gaignard, D. Lingrand, J. Montagnat, J. Rojas Balderrama, G. Malandain, X. Pennec, D. Godard, G. Kassel, and M. Pélégrini-Issac. A federated system for sharing and reuse of images and image processing tools in neuroimaging. In Proc. of Computer Assisted Radiology and Surgery 2011 (CARS 2011), June 2011.
    @inproceedings{Gibaud:CARS:11,
    author = {B. Gibaud and F. Ahmad and C. Barillot and F. Michel and B. Wali and B. Batrancourt and M. Dojat and P. Girard and A. Gaignard and D. Lingrand and J. Montagnat and J. Rojas Balderrama and G. Malandain and X. Pennec and D. Godard and G. Kassel and M. P{\'e}l{\'e}grini-Issac},
    booktitle = {Proc. of Computer Assisted Radiology and Surgery 2011 (CARS 2011)},
    month = {June},
    title = {A federated system for sharing and reuse of images and image processing tools in neuroimaging},
    url-hal = {https://hal.archives-ouvertes.fr/hal-00690921},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  7. A. S. Jadidi, H. Cochet, F. Sacher, S. J. Kim, M. Sermesant, J. Relan, N. Derval, S. Miyazaki, A. Shah, D. Scherr, S. B. Wilton, P. Pascale, L. Roten, M. Pederson, S. Knecht, P. Bordachar, P. Ritter, M. Hocini, M. Montaudon, F. Laurent, N. Ayache, M. Haïssaguerre, and P. Jaïs. Ventricular Scar imaging at MRI Correlates to Critical Isthmuses of Ventricular Tachycardia Circuits and Sites of Slow Conduction during Sinus Rhythm - Utility of integrating MR-data into 3D Mapping Systems. In Heart Rhythm Society '11, May 2011.
    @inproceedings{Amir:HeartRhythm:11,
    author = {A. S. Jadidi and H. Cochet and F. Sacher and S. J. Kim and M. Sermesant and J. Relan and N. Derval and S. Miyazaki and A. Shah and D. Scherr and S. B. Wilton and P. Pascale and L. Roten and M. Pederson and S. Knecht and P. Bordachar and P. Ritter and M. Hocini and M. Montaudon and F. Laurent and N. Ayache and M. Ha\"issaguerre and P. Ja\"is},
    booktitle = {Heart Rhythm Society '11},
    month = {May},
    title = {Ventricular Scar imaging at MRI Correlates to Critical Isthmuses of Ventricular Tachycardia Circuits and Sites of Slow Conduction during Sinus Rhythm - Utility of integrating MR-data into 3D Mapping Systems},
    url-hal = {https://hal.inria.fr/inria-00616207},
    x-international-audience = {yes},
    year = {2011} 
    }
    


  8. Herve Lombaert, Jean-Marc Peyrat, Pierre Croisille, Stanislas Rapacchi, Laurent Fanton, Patrick Clarysse, Hervé Delingette, and Nicholas Ayache. Statistical Analysis of the Human Cardiac Fiber Architecture from DT-MRI. In Leon Axel and Dimitris Metaxas, editors, Proceedings of FIMH Conference 2011, volume 6666 of LNCS, pages 171-179, May 2011. Springer. Note: Best Paper Award.
    @inproceedings{Lombaert:FIMH:11,
    author = {Herve Lombaert and Jean-Marc Peyrat and Pierre Croisille and Stanislas Rapacchi and Laurent Fanton and Patrick Clarysse and Herv\'e Delingette and Nicholas Ayache},
    booktitle = {Proceedings of FIMH Conference 2011},
    editor = {Leon Axel and Dimitris Metaxas},
    hal-identifiant = {inria-00616208},
    month = {May},
    note = {Best Paper Award},
    pages = {171--179},
    publisher = {Springer},
    series = {LNCS},
    title = {Statistical Analysis of the Human Cardiac Fiber Architecture from DT-MRI},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Delingette/FIMH-lombaert.pdf},
    url-hal = {https://hal.inria.fr/inria-00616208},
    volume = {6666},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-pays = {USA},
    x-proceedings = {yes},
    year = {2011} 
    }
    


  9. Herve Lombaert, Jean-Marc Peyrat, Laurent Fanton, Farida Cheriet, Hervé Delingette, Nicholas Ayache, Patrick Clarysse, Isabelle Magnin, and Pierre Croisille. Statistical Atlas of Human Cardiac Fibers: Comparison with Abnormal Hearts. In Proceedings of STACOM Workshop at MICCAI 2011, September 2011. Springer.
    @inproceedings{Lombaert:STACOM:11a,
    author = {Herve Lombaert and Jean-Marc Peyrat and Laurent Fanton and Farida Cheriet and Herv\'e Delingette and Nicholas Ayache and Patrick Clarysse and Isabelle Magnin and Pierre Croisille},
    booktitle = {Proceedings of STACOM Workshop at MICCAI 2011},
    hal-identifiant = {inria-00616208},
    month = {September},
    publisher = {Springer},
    title = {Statistical Atlas of Human Cardiac Fibers: Comparison with Abnormal Hearts},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Delingette/MICCAI-STACOM-Lombaert-Abnormal-Hearts.pdf},
    url-hal = {https://hal.inria.fr/hal-00813799},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-pays = {CA},
    x-proceedings = {yes},
    year = {2011} 
    }
    


  10. Herve Lombaert, Jean-Marc Peyrat, Laurent Fanton, Farida Cheriet, Hervé Delingette, Nicholas Ayache, Patrick Clarysse, Isabelle Magnin, and Pierre Croisille. Variability of the Human Cardiac Laminar Structure. In Proceedings of STACOM Workshop at MICCAI 2011, September 2011. Springer.
    @inproceedings{Lombaert:STACOM:11b,
    author = {Herve Lombaert and Jean-Marc Peyrat and Laurent Fanton and Farida Cheriet and Herv\'e Delingette and Nicholas Ayache and Patrick Clarysse and Isabelle Magnin and Pierre Croisille},
    booktitle = {Proceedings of STACOM Workshop at MICCAI 2011},
    hal-identifiant = {inria-00616208},
    month = {September},
    publisher = {Springer},
    title = {Variability of the Human Cardiac Laminar Structure},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Delingette/MICCAI-STACOM-Lombaert-Laminar-Sheet.pdf},
    url-hal = {https://hal.inria.fr/hal-00813800},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-pays = {CA},
    x-proceedings = {yes},
    year = {2011} 
    }
    


  11. Herve Lombaert, Jean-Marc Peyrat, Stanislas Rapacchi, Laurent Fanton, Herve Delingette, Nicholas Ayache, and Pierre Croisille. Human Statistical Atlas of Cardiac Fiber Architecture from DT-MRI. In Proceedings of Intl. Soc. Mag. Reson. Med. (ISMRM) 2011, volume 19, pages 280, May 2011.
    @inproceedings{Lombaert:ISMRM:11,
    author = {Herve Lombaert and Jean-Marc Peyrat and Stanislas Rapacchi and Laurent Fanton and Herve Delingette and Nicholas Ayache and Pierre Croisille},
    booktitle = {Proceedings of Intl. Soc. Mag. Reson. Med. (ISMRM) 2011},
    hal-identifiant = {inria-00616212},
    month = {May},
    pages = {280},
    title = {Human Statistical Atlas of Cardiac Fiber Architecture from DT-MRI},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Delingette/ISMRM-lombaert.pdf},
    url-hal = {https://hal.inria.fr/inria-00616212},
    volume = {19},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-pays = {CA},
    x-proceedings = {yes},
    year = {2011} 
    }
    


  12. Marco Lorenzi, Nicholas Ayache, Giovanni B. Frisoni, and Xavier Pennec. Mapping the effects of A$\beta_{1-42}$ levels on the longitudinal changes in healthy aging: hierarchical modeling based on stationary velocity fields. In Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI), volume 6892 of LNCS, pages 663-670, 2011. Springer.
    @inproceedings{Lorenzi:MICCAI:11,
    author = {Marco Lorenzi and Nicholas Ayache and Giovanni B. Frisoni and Xavier Pennec},
    booktitle = {Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI)},
    doi = {10.1007/978-3-642-23629-7_81},
    hal-identifiant = {inria-00616213},
    pages = {663--670},
    publisher = {Springer},
    series = {LNCS},
    title = {Mapping the effects of {A$\beta_{1-42}$} levels on the longitudinal changes in healthy aging: hierarchical modeling based on stationary velocity fields},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Marco.Lorenzi/LorenziMICCAI2011.pdf},
    url-hal = {http://hal.inria.fr/inria-00616213/en/},
    volume = {6892},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-proceedings = {yes},
    x-scientific-popularization = {no},
    year = {2011} 
    }
    


  13. Marco Lorenzi, Nicholas Ayache, and Xavier Pennec. Schilds Ladder for the parallel transport of deformations in time series of images. In G. Szekely and H. Hahn, editors, Proceedings of Information Processing in Medical Imaging (IPMI'11), volume 6801 of LNCS, pages 463-474, 2011. Note: Honorable Mention (runner-up) for the Erbsmann Award.
    @inproceedings{Lorenzi:IPMI:11,
    author = {Marco Lorenzi and Nicholas Ayache and Xavier Pennec},
    booktitle = {Proceedings of Information Processing in Medical Imaging (IPMI'11)},
    editor = {G. Szekely and H. Hahn},
    hal-identifiant = {inria-00616210},
    note = {Honorable Mention (runner-up) for the Erbsmann Award},
    pages = {463--474},
    series = {LNCS},
    title = {Schilds Ladder for the parallel transport of deformations in time series of images},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Marco.Lorenzi/IPMI2011-Lorenzi.pdf},
    url-hal = {https://hal.inria.fr/inria-00616210},
    volume = {6801},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-proceedings = {yes},
    x-scientific-popularization = {no},
    year = {2011} 
    }
    


  14. Marco Lorenzi and Xavier Pennec. Geodesics, parallel transport & one-parameter subgroups. In 3rd MICCAI workshop on Mathematical Foundations of Computational Anatomy Workshop, September 2011.
    @inproceedings{Lorenzi:MFCA:11,
    author = {Marco Lorenzi and Xavier Pennec},
    booktitle = {3rd MICCAI workshop on Mathematical Foundations of Computational Anatomy Workshop},
    hal-identifiant = {inria-00616202},
    month = {September},
    title = {Geodesics, parallel transport \& one-parameter subgroups},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Marco.Lorenzi/LorenziMFCA2011c.pdf},
    url-hal = {http://hal.inria.fr/inria-00616202/en/},
    x-editorial-board = {yes},
    x-international-audience = {no},
    x-invited-conference = {no},
    year = {2011} 
    }
    


  15. Marco Lorenzi, Xavier Pennec, and Giovanni B. Frisoni. Monitoring the brain's longitudinal changes in clinical trials for Alzheimers disease: a robust and reliable non-rigid registration framework. In Alzheimer's Association 2011 International Conference on Alzheimer's Disease (AAICAD), 2011.
    @inproceedings{Lorenzi:AAICAD:11,
    author = {Marco Lorenzi and Xavier Pennec and Giovanni B. Frisoni},
    booktitle = {Alzheimer's Association 2011 International Conference on Alzheimer's Disease (AAICAD)},
    hal-identifiant = {inria-00616203},
    title = {Monitoring the brain's longitudinal changes in clinical trials for Alzheimers disease: a robust and reliable non-rigid registration framework},
    url-hal = {https://hal.inria.fr/inria-00616203},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-proceedings = {no},
    x-scientific-popularization = {no},
    year = {2011} 
    }
    


  16. Jan Margeta, Ezequiel Geremia, Antonio Criminisi, and Nicholas Ayache. Layered Spatio-temporal Forests for Left Ventricle Segmentation from 4D Cardiac MRI Data. In Proceedings of STACOM Workshop at MICCAI 2011, September 2011. Springer.
    @inproceedings{Margeta:STACOM:11,
    author = {Jan Margeta and Ezequiel Geremia and Antonio Criminisi and Nicholas Ayache},
    booktitle = {Proceedings of STACOM Workshop at MICCAI 2011},
    hal-identifiant = {hal-00646674},
    month = {September},
    publisher = {Springer},
    title = {Layered Spatio-temporal Forests for Left Ventricle Segmentation from 4D Cardiac MRI Data},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Jan.Margeta/MargetaMICCAI-STACOM2011.pdf},
    url-hal = {http://hal.inria.fr/hal-00646674/en/},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-pays = {CA},
    x-proceedings = {yes},
    year = {2011} 
    }
    


  17. Bjoern H. Menze, Koen Van Leemput, Antti Honkela, Ender Konukoglu, Marc-Andre Weber, Nicholas Ayache, and Polina Golland. A Generative Approach for Image-Based Modeling of Tumor Growth. In G. Szekely and H. Hahn, editors, Proceedings of Information Processing in Medical Imaging (IPMI'11), LNCS 6801, pages 13p, 2011.
    @inproceedings{Menze:IPMI:11,
    author = {Bjoern H. Menze and Van Leemput, Koen and Antti Honkela and Ender Konukoglu and Marc-Andre Weber and Nicholas Ayache and Polina Golland},
    booktitle = {Proceedings of Information Processing in Medical Imaging (IPMI'11)},
    editor = {G. Szekely and H. Hahn},
    hal-identifiant = {inria-00616211},
    pages = {13p},
    series = {LNCS 6801},
    title = {A Generative Approach for Image-Based Modeling of Tumor Growth},
    url = {http://people.csail.mit.edu/menze/papers/menze_11_generative.pdf},
    url-hal = {https://hal.inria.fr/inria-00616211},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-proceedings = {yes},
    x-scientific-popularization = {no},
    year = {2011} 
    }
    


  18. Xavier Pennec and Marco Lorenzi. Which parallel transport for the statistical analysis of longitudinal deformations?. In Colloque GRETSI '11, September 2011.
    @inproceedings{Pennec:GRETSI:11,
    author = {Xavier Pennec and Marco Lorenzi},
    booktitle = {Colloque GRETSI '11},
    hal-identifiant = {inria-00616204},
    month = {September},
    title = {Which parallel transport for the statistical analysis of longitudinal deformations?},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/GRETSI11_Pennec_Lorenzi.pdf},
    url-hal = {https://hal.inria.fr/inria-00616204},
    x-editorial-board = {yes},
    x-international-audience = {no},
    x-invited-conference = {yes},
    year = {2011} 
    }
    


  19. Mihaela Pop, Maxime Sermesant, Jean-Marc Peyrat, Eugene Crystal, Sudip Ghate, Tommaso Mansi, Ilan Lashevsky, Beiping Qiang, Elliot R. McVeigh, Nicholas Ayache, and Graham A. Wright. A 3D MRI-Based Cardiac Computer Model to Study Arrhythmia and Its In-vivo Experimental Validation. In FIMH, pages 195-205, 2011.
    @inproceedings{Pop:FIMH:2011,
    author = {Mihaela Pop and Maxime Sermesant and Jean-Marc Peyrat and Eugene Crystal and Sudip Ghate and Tommaso Mansi and Ilan Lashevsky and Beiping Qiang and Elliot R. McVeigh and Nicholas Ayache and Graham A. Wright},
    booktitle = {FIMH},
    hal-identifiant = {inria-00616205},
    pages = {195-205},
    title = {A 3D MRI-Based Cardiac Computer Model to Study Arrhythmia and Its In-vivo Experimental Validation},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/Pop-FIMH2011.pdf},
    url-hal = {https://hal.inria.fr/inria-00616205},
    year = {2011} 
    }
    


  20. Adityo Prakosa, Maxime Sermesant, Hervé Delingette, Eric Saloux, Pascal Allain, Pascal Cathier, Patrick Etyngier, Nicolas Villain, and Nicholas Ayache. Synthetic Echocardiographic Image Sequences for Cardiac Inverse Electro-Kinematic Learning. In Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI), LNCS, Toronto, Canada, pages 8p, September 2011. Springer, Heidelberg.
    @inproceedings{prakosa:MICCAI:2011,
    address = {Toronto, Canada},
    author = {Adityo Prakosa and Maxime Sermesant and Herv\'e Delingette and Eric Saloux and Pascal Allain and Pascal Cathier and Patrick Etyngier and Nicolas Villain and Nicholas Ayache},
    booktitle = {Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI)},
    hal-identifiant = {inria-00616214},
    month = {September},
    pages = {8p},
    publisher = {Springer, Heidelberg},
    series = {LNCS},
    title = {Synthetic Echocardiographic Image Sequences for Cardiac Inverse Electro-Kinematic Learning},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Adityo.Prakosa/PrakosaMICCAI11.pdf},
    url-hal = {https://hal.inria.fr/inria-00616214},
    x-international-audience = {yes},
    x-proceedings = {yes},
    year = {2011} 
    }
    


  21. J. Relan, M. Sermesant, H. Delingette, and N. Ayache. Personalisation of a 3D Ventricular Electrophysiological Model, Using Endocardial and Epicardial Contact Mapping and MRI. In Statistical Atlases and Computational Models of the Heart. Imaging and Modelling Challenges - Second International Workshop, STACOM 2011, Held in Conjunction with MICCAI 2011, pages 14-22, 2011.
    @inproceedings{Relan:STACOM:11,
    author = {J. Relan and M. Sermesant and H. Delingette and N. Ayache},
    bibsource = {DBLP, http://dblp.uni-trier.de},
    booktitle = {Statistical Atlases and Computational Models of the Heart. Imaging and Modelling Challenges - Second International Workshop, STACOM 2011, Held in Conjunction with MICCAI 2011},
    crossref = {DBLP:conf/miccai/2011stacom},
    ee = {http://dx.doi.org/10.1007/978-3-642-28326-0_2},
    pages = {14-22},
    title = {Personalisation of a 3{D} Ventricular Electrophysiological Model, Using Endocardial and Epicardial Contact Mapping and {MRI}},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Jatin.Relan/STACOM_II_Jatin_Relan.pdf},
    url-hal = {https://hal.inria.fr/hal-00813804},
    year = {2011} 
    }
    


  22. Christof Seiler, Xavier Pennec, and Mauricio Reyes. Geometry-Aware Multiscale Image Registration Via OBBTree-Based Polyaffine Log-Demons. In Proceedings of Medical Image Computing and Computer Assisted Intervention 2011 (MICCAI), volume 6892 of LNCS, pages 631-638, September 2011. Springer, Heidelberg. Note: Young Scientist Award.
    @inproceedings{Seiler:MICCAI:11,
    author = {Christof Seiler and Xavier Pennec and Mauricio Reyes},
    booktitle = {Proceedings of Medical Image Computing and Computer Assisted Intervention 2011 (MICCAI)},
    doi = {10.1007/978-3-642-23629-7\_77},
    hal-identifiant = {inria-00616215},
    month = {September},
    note = {Young Scientist Award},
    pages = {631-638},
    publisher = {Springer, Heidelberg},
    series = {LNCS},
    title = {Geometry-Aware Multiscale Image Registration Via OBBTree-Based Polyaffine Log-Demons},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Christof.Seiler/SeilerOBBTreeMultiscalePolyLogDemonsMICCAI2011.pdf},
    url-hal = {https://hal.inria.fr/inria-00616215},
    volume = {6892},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-proceedings = {yes},
    year = {2011} 
    }
    


  23. Christof Seiler, Xavier Pennec, Lucas Ritacco, and Mauricio Reyes. Femur Specific Polyaffine Model to Regularize the Log-Domain Demons Registration. In Benoit M. Dawant and David R. Haynor, editors, Proceedings of SPIE Medical Imaging '11, volume 7962, pages Paper 7962-15, January 2011. SPIE Publishing. ISBN: 9780819485045.
    @inproceedings{Seiler:SPIE:11,
    author = {Christof Seiler and Xavier Pennec and Lucas Ritacco and Mauricio Reyes},
    booktitle = {Proceedings of SPIE Medical Imaging '11},
    editor = {Benoit M. Dawant and David R. Haynor},
    hal-identifiant = {inria-00616216},
    isbn = {9780819485045},
    month = {January},
    pages = {Paper 7962-15},
    publisher = {SPIE Publishing},
    title = {Femur Specific Polyaffine Model to Regularize the Log-Domain Demons Registration},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Christof.Seiler/SeilerFemurPolyaffineLogDemonsSPIE2011.pdf},
    url-hal = {https://hal.inria.fr/inria-00616216},
    volume = {7962},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-pays = {CH},
    x-proceedings = {yes},
    year = {2011} 
    }
    


  24. Viviana Siless, Pamela Guevara, Xavier Pennec, and Pierre Fillard. Joint T1 and Brain Fiber Diffeomorphic Registration Using the Demons. In Tianming Liu, Dinggang Shen, Luis Ibanez, and Xiaodong Tao, editors, Multimodal Brain Image Analysis (First Int. MICCAI Workshop on), volume 7012 of Lecture Notes in Computer Science, pages 10-18, 2011. Springer. ISBN: 978-3-642-24445-2. Keyword(s): Registration - neural fibers - diffeomorphism - Demons Algorithm - intensity-base registration - tensor-base registration.
    Abstract:
    Non-linear image registration is one of the most challenging task in medical image analysis. In this work, we propose an extension of the well-established diffeomorphic Demons registration algorithm to take into account geometric constraints. Combining the deformation field induced by the image and the geometry, we define a mathematically sound framework to jointly register images and geometric descriptors such as fibers or sulcal lines. We demonstrate this framework by registering simultaneously T 1 images and 50 fiber bundles consistently extracted in 12 subjects. Results show the improvement of fibers alignment while maintaining, and sometimes improving image registration. Further comparisons with non-linear T 1 and tensor registration demonstrate the superiority of the Geometric Demons over their purely iconic counterparts.

    @inproceedings{SILESS:MBIA:2011,
    abstract = {{Non-linear image registration is one of the most challenging task in medical image analysis. In this work, we propose an extension of the well-established diffeomorphic Demons registration algorithm to take into account geometric constraints. Combining the deformation field induced by the image and the geometry, we define a mathematically sound framework to jointly register images and geometric descriptors such as fibers or sulcal lines. We demonstrate this framework by registering simultaneously T 1 images and 50 fiber bundles consistently extracted in 12 subjects. Results show the improvement of fibers alignment while maintaining, and sometimes improving image registration. Further comparisons with non-linear T 1 and tensor registration demonstrate the superiority of the Geometric Demons over their purely iconic counterparts.}},
    affiliation = {Laboratoire de Neuroimagerie Assist{\'e}e par Ordinateur - LNAO , PARIETAL - INRIA Saclay - Ile de France , ASCLEPIOS - INRIA Sophia Antipolis},
    author = {Siless, Viviana and Guevara, Pamela and Pennec, Xavier and Fillard, Pierre},
    booktitle = {{Multimodal Brain Image Analysis (First Int. MICCAI Workshop on)}},
    doi = {10.1007/978-3-642-24446-9\_2 },
    editor = {Liu, Tianming and Shen, Dinggang and Ibanez, Luis and Tao, Xiaodong },
    hal-identifiant = {inria-00627971},
    isbn = {978-3-642-24445-2 },
    keywords = {Registration - neural fibers - diffeomorphism - Demons Algorithm - intensity-base registration - tensor-base registration},
    pages = {10-18},
    pdf = {http://hal.inria.fr/inria-00627971/PDF/Joint\_T1\_and\_Brain\_Fiber\_Diffeomorphic\_Registration\_Using\_the\_Demons\_.pdf},
    publisher = {Springer},
    series = {Lecture Notes in Computer Science },
    title = {{Joint T1 and Brain Fiber Diffeomorphic Registration Using the Demons}},
    url-hal = {https://hal.inria.fr/inria-00627971},
    volume = {7012},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-language = {Anglais},
    year = {2011} 
    }
    


  25. Stefan Sommer, François Lauze, Mads Nielsen, and Xavier Pennec. A Multi-scale Kernel Bundle for LDDMM: Towards Sparse Deformation Description Across Space and Scales. In Gabor Szekely and Horst Hahn, editors, Proceedings of Information Processing in Medical Images IPMI'11, volume 6801 of LNCS, pages 624-635, July 2011. Springer.
    @inproceedings{Sommer:IPMI:11,
    author = {Stefan Sommer and Fran\c{c}ois Lauze and Mads Nielsen and Xavier Pennec},
    booktitle = {Proceedings of Information Processing in Medical Images IPMI'11},
    doi = {10.1007/978-3-642-22092-0_51},
    editor = {Gabor Szekely and Horst Hahn},
    hal-identifiant = {inria-00616209},
    month = {July},
    pages = {624--635},
    publisher = {Springer},
    series = {LNCS},
    title = {A Multi-scale Kernel Bundle for {LDDMM}: Towards Sparse Deformation Description Across Space and Scales},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Sommer.IPMI11.pdf},
    url-hal = {https://hal.inria.fr/inria-00616209},
    volume = {6801},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-pays = {DK},
    x-proceedings = {yes},
    year = {2011} 
    }
    


  26. Stefan Sommer, François Lauze, Mads Nielsen, and Xavier Pennec. Kernel Bundle EPDiff: Evolution Equations for Multi-Scale Diffeomorphic Image Registration. In A.M. Bruckstein, B. ter Haar Romeny, A.M. Bronstein, and M.M. Bronstein, editors, Scale Space and Variational Methods in Computer Vision, volume 6667 of Lecture Notes in Computer Science, Ein-Gedi, Israël, June 2011. Springer.
    Abstract:
    In the LDDMM framework, optimal warps for image registration are found as end-points of critical paths for an energy functional, and the EPDiff equations describe the evolution along such paths. The Large Deformation Diffeomorphic Kernel Bundle Mapping (LDDKBM) extension of LDDMM allows scale space information to be automatically incorporated in registrations and promises to improve the standard framework in several aspects. We present the mathematical foundations of LDDKBM and derive the KB-EPDiff evolution equations, which provide optimal warps in this new framework. To illustrate the resulting diffeomorphism paths, we give examples showing the decoupled evolution across scales and how the method automatically incorporates deformation at appropriate scales.

    @inproceedings{Sommer:SSVM:2011,
    abstract = {{In the LDDMM framework, optimal warps for image registration are found as end-points of critical paths for an energy functional, and the EPDiff equations describe the evolution along such paths. The Large Deformation Diffeomorphic Kernel Bundle Mapping (LDDKBM) extension of LDDMM allows scale space information to be automatically incorporated in registrations and promises to improve the standard framework in several aspects. We present the mathematical foundations of LDDKBM and derive the KB-EPDiff evolution equations, which provide optimal warps in this new framework. To illustrate the resulting diffeomorphism paths, we give examples showing the decoupled evolution across scales and how the method automatically incorporates deformation at appropriate scales.}},
    address = {Ein-Gedi, Isra{\"e}l},
    affiliation = {Department of computer Science [Copenhagen] - DIKU , ASCLEPIOS - INRIA Sophia Antipolis},
    audience = {internationale },
    author = {Sommer, Stefan and Lauze, Fran{\c c}ois and Nielsen, Mads and Pennec, Xavier},
    booktitle = {{Scale Space and Variational Methods in Computer Vision}},
    editor = {Bruckstein, A.M. and ter Haar Romeny, B. and Bronstein, A.M. and Bronstein, M.M. },
    hal-identifiant = {hal-00644965},
    month = {June},
    pdf = {http://hal.inria.fr/hal-00644965/PDF/Sommer.SSVM11.pdf},
    publisher = {Springer},
    series = {Lecture Notes in Computer Science },
    title = {{Kernel Bundle EPDiff: Evolution Equations for Multi-Scale Diffeomorphic Image Registration}},
    url-hal = {https://hal.inria.fr/hal-00644965},
    volume = {6667},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-language = {Anglais},
    x-pays = {DK},
    x-proceedings = {yes},
    year = {2011} 
    }
    


Internal reports

  1. Barbara André, Tom Vercauteren, M. Buchner, Anna, B. Wallace, Michael, and Nicholas Ayache. Learning Semantic and Visual Similarity for Endomicroscopy Video Retrieval. Rapport de recherche RR-7722, INRIA, August 2011. Keyword(s): probe-based Confocal Laser Endomicroscopy (pCLE), Content- Based Image Retrieval (CBIR), Bag-of-Visual-Words (BoW) method, semantic learning, similarity distance learning.
    Abstract:
    Traditional Content-Based Image Retrieval (CBIR) systems only deliver visual outputs that are not directly interpretable by the physicians. Our objective is to provide a system for endomicroscopy video retrieval which delivers both visual and semantic outputs that are consistent with each other. In a previous study, we developed an adapted bag-of-visual-words method for endomicroscopy retrieval that computes a visual signature for each video. In this study, we first leverage semantic ground-truth data to transform these visual signatures into semantic signatures that reflect how much the presence of each semantic concept is expressed by the visual words describing the videos. Using cross-validation, we demonstrate that our visual-word-based semantic signatures enable a recall performance which is significantly higher than those of several state-of-the-art methods in CBIR. In a second step, we propose to improve retrieval relevance by learning, from a perceived similarity ground truth, an adjusted similarity distance. Our distance learning method allows to improve, with statistical significance, the correlation with the perceived similarity. Our resulting retrieval system is efficient in providing both visual and semantic information that are correlated with each other and clinically interpretable by the endoscopists.

    @techreport{andre:inria-00618057,
    abstract = {{Traditional Content-Based Image Retrieval (CBIR) systems only deliver visual outputs that are not directly interpretable by the physicians. Our objective is to provide a system for endomicroscopy video retrieval which delivers both visual and semantic outputs that are consistent with each other. In a previous study, we developed an adapted bag-of-visual-words method for endomicroscopy retrieval that computes a visual signature for each video. In this study, we first leverage semantic ground-truth data to transform these visual signatures into semantic signatures that reflect how much the presence of each semantic concept is expressed by the visual words describing the videos. Using cross-validation, we demonstrate that our visual-word-based semantic signatures enable a recall performance which is significantly higher than those of several state-of-the-art methods in CBIR. In a second step, we propose to improve retrieval relevance by learning, from a perceived similarity ground truth, an adjusted similarity distance. Our distance learning method allows to improve, with statistical significance, the correlation with the perceived similarity. Our resulting retrieval system is efficient in providing both visual and semantic information that are correlated with each other and clinically interpretable by the endoscopists.}},
    affiliation = {ASCLEPIOS - INRIA Sophia Antipolis , Mauna Kea Technologies , Hospital of the University of Pennsylvania - HUP , Mayo Clinic},
    author = {Andr{\'e}, Barbara and Vercauteren, Tom and Buchner, Anna, M. and Wallace, Michael, B. and Ayache, Nicholas},
    institution = {INRIA},
    keywords = {probe-based Confocal Laser Endomicroscopy (pCLE), Content- Based Image Retrieval (CBIR), Bag-of-Visual-Words (BoW) method, semantic learning, similarity distance learning},
    language = {Anglais},
    month = {August},
    number = {RR-7722},
    pdf = {http://hal.inria.fr/inria-00618057/PDF/RR-7722.pdf},
    title = {{Learning Semantic and Visual Similarity for Endomicroscopy Video Retrieval}},
    type = {Rapport de recherche},
    url-hal = {http://hal.inria.fr/inria-00618057},
    year = {2011} 
    }
    


  2. M. W. Krueger, J. Relan, H. Delingette, W. Schulze, G. Seemann, and O. Dössel. Model Personalization for AF and VT simulations. Deliverables D6.2.2, European project euHeart, January 2011.
    @techreport{euHeart:WP06:11,
    author = {M. W. Krueger and J. Relan and H. Delingette and W. Schulze and G. Seemann and O. D\"ossel},
    institution = {European project euHeart},
    month = {January},
    title = {Model Personalization for AF and VT simulations},
    type = {Deliverables D6.2.2},
    url-hal = {https://hal.inria.fr/hal-00813797},
    year = {2011} 
    }
    


  3. M. W. Krueger, W. Schulze, G. Seemann, O. Dössel, J. Relan, H. Delingette, M. Sermesant, and N. Ayache. Planning of Radiofrequency Ablation for patients with Atrial Fibrillation. Deliverables D6.3.1, European project euHeart, June 2011.
    @techreport{euHeart:WP06:2011_AF,
    author = {M. W. Krueger and W. Schulze and G. Seemann and O. D\"ossel and J. Relan and H. Delingette and M. Sermesant and N. Ayache},
    institution = {European project euHeart},
    month = {June},
    title = {Planning of Radiofrequency Ablation for patients with Atrial Fibrillation},
    type = {Deliverables {D}6.3.1},
    url-hal = {https://hal.inria.fr/hal-00813798},
    year = {2011} 
    }
    


  4. J. Relan, H. Delingette, M. Sermesant, N. Ayache, M. W. Krueger, W. Schulze, G. Seemann, and O. Dössel. Planning of RadioFrequency Ablation for patients with Ventricular Tachycardia. Deliverables D6.3.2, European project euHeart, June 2011.
    @techreport{euHeart:WP06:2011_Part2,
    author = {J. Relan and H. Delingette and M. Sermesant and N. Ayache and M. W. Krueger and W. Schulze and G. Seemann and O. D\"ossel},
    institution = {European project euHeart},
    month = {June},
    title = {Planning of RadioFrequency Ablation for patients with Ventricular Tachycardia},
    type = {Deliverables {D}6.3.2},
    url-hal = {https://hal.inria.fr/hal-00813803},
    year = {2011} 
    }
    


Miscellaneous

  1. Barbara André, Tom Vercauteren, Anna M. Buchner, Muhammad Waseem Shahid, Michael B. Wallace, and Nicholas Ayache. Toward a structured training system for probe-based Confocal Laser Endomicroscopy (pCLE) on Barrett's Esophagus: a video retrieval approach to estimate diagnosis difficulty. Gastroenterology (DDW 2011), 2011.
    @misc{Andre:DDW:2011,
    author = {Barbara Andr\'e and Tom Vercauteren and Anna M. Buchner and Muhammad Waseem Shahid and Michael B. Wallace and Nicholas Ayache},
    howpublished = {Gastroenterology (DDW 2011)},
    title = {Toward a structured training system for probe-based Confocal Laser Endomicroscopy (pCLE) on Barrett's Esophagus: a video retrieval approach to estimate diagnosis difficulty},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Barbara.Andre/ANDRE_DDW11_Abstract.pdf},
    url-hal = {https://hal.inria.fr/hal-00825867},
    x-pays = {US},
    year = {2011} 
    }
    


  2. Michel Dojat, Mélanie Pélégrini-Issac, Farooq Ahmad, Christian Barillot, Bénédicte Batrancourt, Alban Gaignard, Bernard Gibaud, Pascal Girard, David Godard, Gilles Kassel, Diane Lingrand, Grégoire Malandain, Franck Michel, Johan Montagnat, Xavier Pennec, Javier Balderrama, and Bacem Wali. NeuroLOG: A framework for the sharing and reuse of distributed tools and data in neuroimaging. 17th Annual Meeting of the Organization for Human Brain Mapping (OHBM), June 26-30, 2011.
    @misc{Dojat:HBM:11,
    address = {Quebec, Canada},
    author = {Dojat, Michel and P{\'e}l{\'e}grini-Issac, M{\'e}lanie and Ahmad, Farooq and Barillot, Christian and Batrancourt, B{\'e}n{\'e}dicte and Gaignard, Alban and Gibaud, Bernard and Girard, Pascal and Godard, David and Kassel, Gilles and Lingrand, Diane and Malandain, Gr{\'e}goire and Michel, Franck and Montagnat, Johan and Pennec, Xavier and Balderrama, Javier and Wali, Bacem},
    howpublished = {17th Annual Meeting of the Organization for Human Brain Mapping (OHBM), June 26-30},
    title = {NeuroLOG: A framework for the sharing and reuse of distributed tools and data in neuroimaging},
    url = {http://neurolog.i3s.unice.fr/_media/public_namespace/hbm11-def.pdf},
    url-hal = {https://hal.inria.fr/hal-00813796},
    x-editorial-board = {no},
    x-international-audience = {yes},
    x-invited-conference = {no},
    x-proceedings = {no},
    x-scientific-popularization = {no},
    year = {2011} 
    }
    



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