Articles in journal, book chapters

1. Safaa Al-Ali, John Chaussard, Sébastien Li-Thiao-Té, Éric Ogier-Denis, Alice Percy-Du-Sert, Xavier Treton, and Hatem Zaag. Detection of ulcerative colitis lesions from weakly annotated colonoscopy videos using bounding boxes. Gastrointestinal Disorders, 6(1):292-307, March 2024. [bibtex-entry]



2. Olivier Bisson and Xavier Pennec. Differential of the Stretch Tensor for Any Dimension with Applications to Quotient Geodesics. Comptes Rendus. Mathématique, 362(G12):1847-1856, November 2024. Keyword(s): Polar Decomposition, Stretch Tensor, Quotient Geodesics. [bibtex-entry]



3. Anna Calissano, Théodore Papadopoulo, Xavier Pennec, and Samuel Deslauriers-Gauthier. Graph Alignment Exploiting the Spatial Organization Improves the Similarity of Brain Networks. Human Brain Mapping, 45(1):e26554, January 2024. [bibtex-entry]



4. Andrea Chierici, Fabien Lareyre, Benjamin Salucki, Antonio Iannelli, Hervé Delingette, and Juliette Raffort. Vascular liver segmentation: a narrative review on methods and new insights brought by artificial intelligence. Journal of International Medical Research, 52(9), September 2024. Keyword(s): deep learning, deep learning, Vessel segmentation, liver, artificial intelligence, active contour, tracking, machine learning. [bibtex-entry]



5. Yann Fraboni, Martin van Waerebeke, Kevin Scaman, Richard Vidal, Laetitia Kameni, and Marco Lorenzi. Privacy preserving image registration. Medical Image Analysis, 94, May 2024. Keyword(s): Optimization, Federated learning, Machine unlearning. [bibtex-entry]



6. Sebastien Goffart, Andréa Chierici, Lisa Guzzi, Hervé Delingette, Ahmed Alouane, Fabien Lareyre, and Juliette Raffort. Artificial Intelligence to enhance future clinical trials in Vascular Surgery. Annals of Vascular Surgery, 111:331-335, November 2024. [bibtex-entry]



7. Etrit Haxholli and Marco Lorenzi. On Tail Decay Rate Estimation of Loss Function Distributions. Journal of Machine Learning Research, 25(25):1-47, February 2024. Keyword(s): Extreme Value Theory, Tail Modelling, Loss Function Distributions, Peaks-Over-Threshold, Cross-Tail-Estimation, Model Ranking. [bibtex-entry]



8. Justine Labory, Evariste Njomgue-Fotso, and Silvia Bottini. Benchmarking feature selection and feature extraction methods to improve the performances of machine-learning algorithms for patient classification using metabolomics biomedical data. Computational and Structural Biotechnology Journal, 23(1):1274-1287, December 2024. [bibtex-entry]



9. Sébastien Molière, Dimitri Hamzaoui, Guillaume Ploussard, R Mathieu, Gaëlle Fiard, Michael Baboudjian, benjamin granger, Morgan Roupret, Hervé Delingette, and Raphaële Renard-Penna. A Systematic Review of the Diagnostic Accuracy of Deep Learning Models for the Automatic Detection, Localization, and Characterization of Clinically Significant Prostate Cancer on Magnetic Resonance Imaging. European Urology Oncology, 2024. Keyword(s): Artificial intelligence, Deep learning, Diagnostic accuracy, Magnetic resonance imaging, Prostate cancer, Systematic review. [bibtex-entry]



10. Yann Thanwerdas. Permutation-invariant log-Euclidean geometries on full-rank correlation matrices. SIAM Journal on Matrix Analysis and Applications, 45(2):930-953, April 2024. Keyword(s): SPD matrices, elliptope, correlation matrices, log-Euclidean metric, permutationinvariant, cor-inversion, off-log metric, log-scaled metric, quotient-affine metric AMS subject classifications.. [bibtex-entry]



11. Paul Tourniaire, Marius Ilie, Julien Mazières, Anna Vigier, François Ghiringhelli, Nicolas Piton, Jean-Christophe Sabourin, Frédéric Bibeau, Paul Hofman, Nicholas Ayache, and Hervé Delingette. WhARIO: whole-slide-image-based survival analysis for patients treated with immunotherapy. Journal of Medical Imaging, 11(03), May 2024. Keyword(s): Lung cancer LC, Whole slide image classification. [bibtex-entry]



12. Zihao Wang, Yingyu Yang, Yuzhou Chen, Tingting Yuan, Maxime Sermesant, Hervé Delingette, and Ona Wu. Mutual Information Guided Diffusion for Zero-Shot Cross-Modality Medical Image Translation. IEEE Transactions on Medical Imaging, 43(8):2825-2838, March 2024. Keyword(s): Zero-shot learning, cross-modality translation, diffusion model, mutual information. [bibtex-entry]



13. Yingyu Yang, Marie Rocher, Pamela Moceri, and Maxime Sermesant. Echocardiography Analysis with Deep Learning using Priors: Multi-centric Evaluation of Generalisation. Journal of Machine Learning for Biomedical Imaging, 2(November 2024):2293-2325, November 2024. Keyword(s): Image segmentation Image registration Generalisation of deep learning methods priors Echocardiography analysis, Image segmentation, Image registration, Generalisation of deep learning methods, priors, Echocardiography analysis. [bibtex-entry]



14. Irene Balelli, Safaa Al-Ali, Elise Dumas, and Judith Abécassis. Causality: fundamental principles and tools. In Trustworthy AI in Medical Imaging, number Chapitre 14, pages 297-314. November 2024. Keyword(s): Causal learning, Discovery, Inference, Bias, Counfounder, Counterfactual queries. [bibtex-entry]

1. Arnaud Berenbaum, Hervé Delingette, Aurélien Maire, Cécile Poret, Claire Hassen-Khodja, Stéphane Bréant, Christel Daniel, Patricia Martel, Lamiae Grimaldi, Marie Frank, Emmanuel Durand, and Florent Besson. Performance of AI-Based Automated Classifications of Whole-Body FDG PET in Clinical Practice: The CLARITI Project. Applied Sciences, 13(9):5281, May 2023. Keyword(s): FDG PET, artificial intelligence, deep learning, convolutional neural network. [bibtex-entry]



2. Nina Brillat-Savarin, Carine Wu, Laurène Aupin, Camille Thoumin, Dimitri Hamzaoui, and Raphaële Renard-Penna. 3.0 T prostate MRI: Visual assessment of 2D and 3D T2-weighted imaging sequences using PI-QUAL score. European Journal of Radiology, 166:110974, September 2023. [bibtex-entry]



3. Nicolas Cedilnik, Mihaela Pop, Josselin Duchateau, Frédéric Sacher, Pierre Jaïs, Hubert Cochet, and Maxime Sermesant. Efficient Patient-Specific Simulations of Ventricular Tachycardia Based on Computed Tomography-Defined Wall Thickness Heterogeneity. JACC: Clinical Electrophysiology, September 2023. Keyword(s): Cardiac modeling, Electrophysiology modeling, CT, Ventricular tachycardia, Medical simulation. [bibtex-entry]



4. Nikos Chrisochoides, Yixun Liu, Fotis Drakopoulos, Andriy Kot, Panos Foteinos, Christos Tsolakis, Emmanuel Billias, Olivier Clatz, Nicholas Ayache, Andrey Fedorov, Alex Golby, Peter Black, and Ron Kikinis. Comparison of physics-based deformable registration methods for image-guided neurosurgery. Frontiers in Digital Health, 5, December 2023. Keyword(s): Image-guided neurosurgery, physics-based deformable registration, finite element methods (FEM), high performance computing, mesh generation. [bibtex-entry]



5. Quentin Clairon, Chloé Pasin, Irene Balelli, Rodolphe Thiébaut, and Mélanie Prague. Parameter estimation in nonlinear mixed effect models based on ordinary differential equations: An optimal control approach. Computational Statistics, September 2023. Keyword(s): Dynamic population models, Ordinary differential equations, Optimal control theory, Mechanistic models, Nonlinear mixed effects models, Clinical trial analysis. [bibtex-entry]



6. Francesco Cremonesi, Vincent Planat, Varvara Kalokyri, Haridimos Kondylakis, Tiziana Sanavia, Victor Miguel Mateos Resinas, Babita Singh, and Silvia Uribe. The need for multimodal health data modeling: A practical approach for a federated-learning healthcare platform. Journal of Biomedical Informatics, 141:104338, May 2023. Keyword(s): Federated learning, Data model, Healthcare, Omics, Lessons learned, Medical research, Graphical. [bibtex-entry]



7. Hind Dadoun, Hervé Delingette, Anne-Laure Rousseau, Eric de Kerviler, and Nicholas Ayache. Deep Clustering for Abdominal Organ Classification in US imaging. Journal of Medical Imaging, 10(3):034502, 2023. Keyword(s): ultrasound imaging, representation learning, deep clustering, semi-supervised learning. [bibtex-entry]



8. Yann Fraboni, Richard Vidal, Laetitia Kameni, and Marco Lorenzi. A General Theory for Federated Optimization with Asynchronous and Heterogeneous Clients Updates. Journal of Machine Learning Research, 24:1-43, March 2023. Note: Code is available https://github.com/Accenture/Labs-Federated-Learning/tree/asynchronous_FL. [bibtex-entry]



9. Dimitri Hamzaoui, Sarah Montagne, Raphaële Renard-Penna, Nicholas Ayache, and Hervé Delingette. Morphologically-Aware Consensus Computation via Heuristics-based IterATive Optimization (MACCHIatO). Journal of Machine Learning for Biomedical Imaging, 2(UNSURE 2022 Special Issue):361-389, September 2023. Keyword(s): Consensus, Distance, Heuristic, Optimization, STAPLE. [bibtex-entry]



10. Philipp Harms, Peter W. Michor, Xavier Pennec, and Stefan Sommer. Geometry of Sample Spaces. Differential Geometry and its Applications, 90:102029, October 2023. Note: 29 pages, 1 figure. [bibtex-entry]



11. Raabid Hussain, Attila Frater, Roger Calixto, Chadlia Karoui, Jan Margeta, Zihao Wang, Michel Hoen, Hervé Delingette, François Patou, Charles Raffaelli, Clair Vandersteen, and Nicolas Guevara. Anatomical Variations of the Human Cochlea Using an Image Analysis Tool. Journal of Clinical Medicine, 12(2):509, January 2023. Keyword(s): Otology, Cochlea Modeling, Medical Image Analysis, cochlear morphology, cochlear implantation, statistical analysis. [bibtex-entry]



12. Victoriya Kashtanova, Mihaela Pop, Ibrahim Ayed, Patrick Gallinari, and Maxime Sermesant. Simultaneous data assimilation and cardiac electrophysiology model correction using differentiable physics and deep learning. Interface Focus, 13(6), December 2023. Keyword(s): Physics-based learning, Deep Learning, Cardiac electrophysiology, Simulations. [bibtex-entry]



13. Fabien Lareyre, Kak Khee Yeung, Lisa Guzzi, Gilles Di Lorenzo, Arindam Chaudhuri, Christian-Alexander Behrendt, Konstantinos Spanos, and Juliette Raffort. Artificial intelligence in vascular surgical decision making. Seminars in Vascular Surgery, 36(3):448-453, September 2023. Keyword(s): Artificial intelligence, Machine learning, Vascular disease, Decision making, Precision medicine, Artificial intelligence. [bibtex-entry]



14. Sébastien Molière, Dimitri Hamzaoui, Anna Luzurier, Benjamin Granger, Sarah Montagne, Alexandre Allera, Malek Ezziane, Raphaële Quint, Mehdi Kalai, Nicholas Ayache, Hervé Delingette, and Raphaële Renard-Penna. Reference standard for the evaluation of automatic segmentation algorithms: Quantification of inter observer variability of manual delineation of prostate contour on MRI. Diagnostic and Interventional Imaging, August 2023. Keyword(s): Artificial intelligence Inter-reader variability Magnetic resonance imaging Prostate Segmentation. [bibtex-entry]



15. Théodore Soulier, Olivier Colliot, Nicholas Ayache, and Benjamin Rohaut. How will tomorrow's algorithms fuse multimodal data? The example of the neuroprognosis in Intensive Care. Anaesthesia Critical Care & Pain Medicine, pp 101301, September 2023. Keyword(s): Disorders of Consciousness, Neurological Prognosis, Multimodal Data, Artificial Intelligence, Disorders of Consciousness Neurological Prognosis Multimodal Data Artificial Intelligence. [bibtex-entry]



16. Yann Thanwerdas and Xavier Pennec. Bures-Wasserstein minimizing geodesics between covariance matrices of different ranks. SIAM Journal on Matrix Analysis and Applications, 44(3):1447-1476, September 2023. Keyword(s): Covariance matrices, PSD matrices, Bures-Wasserstein, Orbit space, Geodesics, Injection domain, 15B48, 15A63, 53B20, 53C22, 58D17, 53-08, 53A04, 54E50, 58A35. [bibtex-entry]



17. Yann Thanwerdas and Xavier Pennec. O(n)-invariant Riemannian metrics on SPD matrices. Linear Algebra and its Applications, 661:163-201, March 2023. Keyword(s): 53B20, Symmetric Positive Definite matrices, Riemannian geometry, Invariance under orthogonal transformations, Families of metrics, Log-Euclidean metric, Affine-invariant metric, Bures-Wasserstein metric, Kernel metrics. [bibtex-entry]



18. Paul Tourniaire, Marius Ilie, Paul Hofman, Nicholas Ayache, and Hervé Delingette. MS-CLAM: Mixed Supervision for the classification and localization of tumors in Whole Slide Images. Medical Image Analysis, 85:102763, 2023. Keyword(s): Digital Pathology, Mixed Supervision, Deep Learning, Camelyon16, DigestPath2019. [bibtex-entry]



19. Zihao Wang, Zhifei Xu, Jiayi He, Herve Delingette, and Jun Fan. Long Short-Term Memory Neural Equalizer. IEEE Transactions on Signal and Power Integrity, 2:13-22, 2023. [bibtex-entry]



20. Marco Lorenzi, Marie Deprez, Irene Balelli, Ana L Aguila, and Andre Altmann. Integration of Multimodal Data. In Olivier Colliot, editor, Machine Learning for Brain Disorders, volume NM197 of Neuromethods, pages 573 - 597. Springer, 2023. Keyword(s): Multivariate analysis, Latent variable models, Multimodal imaging, -Omics, Imaginggenetics, Partial least squares, Canonical correlation analysis, Variational autoencoders, Sparsity, Interpretability. [bibtex-entry]



21. Buntheng Ly, Mihaela Pop, Hubert Cochet, Nicolas Duchateau, Declan O'regan, and Maxime Sermesant. Outcome Prediction. In AI and Big Data in Cardiology : A Practical Guide, pages 105-133. Springer International Publishing, May 2023. [bibtex-entry]

1. Clément Abi Nader, Federica Ribaldi, Giovanni B Frisoni, Valentina Garibotto, Philippe Robert, Nicholas Ayache, and Marco Lorenzi. SimulAD: A dynamical model for personalized simulation and disease staging in Alzheimer's disease. Neurobiology of Aging, 113:73-83, May 2022. Keyword(s): Alzheimer's disease, Disease progression models, Clinical trials, Biomarkers. [bibtex-entry]



2. Safaa Al-Ali, John Chaussard, Sébastien Li-Thiao-Té, Eric Ogier-Denis, Alice Percy-Du-Sert, Xavier Treton, and Hatem Zaag. AUTOMATIC BLEEDING AND ULCER DETECTION FROM LIMITED QUALITY ANNOTATIONS IN ULCERATIVE COLITIS. Gastroenterology, 28(Supplement_1):S19-S20, February 2022. [bibtex-entry]



3. Carlos Albors, Èric Lluch, Juan Francisco Gomez, Nicolas Cedilnik, Konstantinos Mountris, Tommaso Mansi, Svyatoslav Khamzin, Arsenii Dokuchaev, Olga Solovyova, Esther Pueyo, Maxime Sermesant, Rafael Sebastian, Hernán Morales, and Oscar Camara. Meshless Electrophysiological Modeling of Cardiac Resynchronization Therapy-Benchmark Analysis with Finite-Element Methods in Experimental Data. Applied Sciences, 12(13):6438, July 2022. [bibtex-entry]



4. Benoît Audelan, Dimitri Hamzaoui, Sarah Montagne, Raphaële Renard-Penna, and Hervé Delingette. Robust Bayesian fusion of continuous segmentation maps. Medical Image Analysis, 78:102398, May 2022. Keyword(s): Image segmentation, Data fusion, Consensus, Mixture. [bibtex-entry]



5. Nicholas Ayache. La fée IA au chevet des malades. Pour la Science. Dossier, (hors série 115):18-23, May 2022. Note: The article is available at the following address: https://www.pourlascience.fr/sd/medecine/la-fee-ia-au-chevet-des-malades-23684.php. [bibtex-entry]



6. Tania Marina Bacoyannis, Buntheng Ly, H Cochet, and Maxime Sermesant. Deep learning formulation of ECGI evaluated on clinical data. EP-Europace, 24(Supplement_1), May 2022. Keyword(s): Electrocardiography, Inverse Problem, Deep learning, Computational Modelling, Generative Model, Data Processing, Clinical Evaluation. [bibtex-entry]



7. Irene Balelli, Santiago Silva, and Marco Lorenzi. A Differentially Private Probabilistic Framework for Modeling the Variability Across Federated Datasets of Heterogeneous Multi-View Observations. Journal of Machine Learning for Biomedical Imaging, April 2022. [bibtex-entry]



8. James Benn and Stephen Marsland. The Measurement and Analysis of Shapes. Annals of Global Analysis and Geometry, 62:47-70, April 2022. Keyword(s): Shape, Currents, Hodge theory, Sobolev diffeomorphisms, Euler Equations, Probability densities. [bibtex-entry]



9. Nathan Blanken, Jelmer Wolterink, Herve Delingette, Christoph Brune, Michel Versluis, and Guillaume Lajoinie. Super-Resolved Microbubble Localization in Single-Channel Ultrasound RF Signals Using Deep Learning. IEEE Transactions on Medical Imaging, 41(9):2532-2542, September 2022. [bibtex-entry]



10. Hind Dadoun, Anne-Laure Rousseau, Eric de Kerviler, Jean Michel Correas, Anne-Marie Tissier, Fanny Joujou, Sylvain Bodard, Kemel Khezzane, Constance de Margerie-Mellon, Hervé Delingette, and Nicholas Ayache. Detection, Localization, and Characterization of Focal Liver Lesions in Abdominal US with Deep Learning. Radiology: Artificial Intelligence, 4(3), 2022. [bibtex-entry]



11. Nicolas Guigui and Xavier Pennec. Numerical Accuracy of Ladder Schemes for Parallel Transport on Manifolds. Foundations of Computational Mathematics, 22:757-790, June 2022. [bibtex-entry]



12. Dimitri Hamzaoui, Sarah Montagne, Benjamin Granger, Alexandre Allera, Malek Ezziane, Anna Luzurier, Raphaëlle Quint, Mehdi Kalai, Nicholas Ayache, Hervé Delingette, and Raphaële Renard-Penna. Correction to: Prostate Volume Prediction on MRI: Tools, Accuracy and Variability. European Radiology, 32(7):5035-5035, 2022. Note: Correction about the name of the author Raphaële Renard-Penna. [bibtex-entry]



13. Dimitri Hamzaoui, Sarah Montagne, Benjamin Granger, Alexandre Allera, Malek Ezziane, Anna Luzurier, Raphaële Quint, Mehdi Kalai, Nicholas Ayache, Hervé Delingette, and Raphaele Renard-Penna. Prostate volume prediction on MRI: tools, accuracy and variability. European Radiology, February 2022. Note: The original publication is available at www.springerlink.com: https://link.springer.com/article/10.1007/s00330-022-08554-4. Keyword(s): Prostate, Magnetic Resonance Imaging, Volume, PSA density, Segmentation. [bibtex-entry]



14. Dimitri Hamzaoui, Sarah Montagne, Raphaele Renard-Penna, Nicholas Ayache, and Hervé Delingette. Automatic Zonal Segmentation of the Prostate from 2D and 3D T2-weighted MRI and Evaluation for Clinical Use. Journal of Medical Imaging, 9(2):024001, March 2022. Keyword(s): Prostate, Segmentation, Deep Learning, Lesion, Magnetic Resonance Imaging, Inter-rater Variability. [bibtex-entry]



15. Marius Ilie, Jonathan Benzaquen, Paul Tourniaire, Simon Heeke, Nicholas Ayache, Hervé Delingette, Elodie Long-Mira, Sandra Lassalle, Marame Hamila, Julien Fayada, Josiane Otto, Charlotte Cohen, Abel Gomez Caro, Jean Philippe Berthet, Charles Hugo Marquette, Véronique Hofman, Christophe Bontoux, and Paul Hofman. Deep learning facilitates distinguishing histologic subtypes of pulmonary neuroendocrine tumors on digital whole-slide images. Cancers, 14(7):1740, March 2022. Keyword(s): lung, neuroendocrine carcinoma, deep learning, CNN, HALO-AI. [bibtex-entry]



16. Fabien Lareyre, Christian-Alexander Behrendt, Arindam Chaudhuri, Nicholas Ayache, Juliette Raffort, and Hervé Delingette. Big Data and Artificial Intelligence in Vascular Surgery: Time for Multidisciplinary Cross-Border Collaboration. Angiology, 73(8):697-700, September 2022. [bibtex-entry]



17. Jan Margeta, Raabid Hussain, Paula López Diez, Anika Morgenstern, Thomas Demarcy, Zihao Wang, Dan Gnansia, Octavio Martinez Manzanera, Clair Vandersteen, Hervé Delingette, Andreas Buechner, Thomas Lenarz, François Patou, and Nicolas Guevara. A Web-Based Automated Image Processing Research Platform for Cochlear Implantation-Related Studies. Journal of Clinical Medicine, 11(22):6640, November 2022. Keyword(s): cochlear implant, image analysis, computed tomography, machine learning, deep learning, image segmentation, 3D model, tonotopic mapping, visualization. [bibtex-entry]



18. Mathilde Merle, Florent Collot, Julien Castelneau, Pauline Migerditichan, Mehdi Juhoor, Buntheng Ly, Valery Ozenne, Bruno Quesson, Nejib Zemzemi, Yves Coudière, Pierre Jaïs, Hubert Cochet, and Maxime Sermesant. MUSIC: Cardiac Imaging, Modelling and Visualisation Software for Diagnosis and Therapy. Applied Sciences, 12(12):6145, June 2022. Keyword(s): cardiac imaging, multimodal, electrophysiology, deep learning, biophysical modelling, inverse problems. [bibtex-entry]



19. Adele Myers, Saiteja Utpala, Shubham Talbar, Sophia Sanborn, Christian Shewmake, Claire Donnat, Johan Mathe, Umberto Lupo, Rishi Sonthalia, Xinyue Cui, Tom Szwagier, Arthur Pignet, Andri Bergsson, Soren Hauberg, Dmitriy Nielsen, Stefan Sommer, David Klindt, Erik Hermansen, Melvin Vaupel, Benjamin Dunn, Jeffrey Xiong, Noga Aharony, Itsik Pe'Er, Felix Ambellan, Martin Hanik, Esfandiar Nava-Yazdani, Christoph von Tycowicz, and Nina Miolane. ICLR 2022 Challenge for Computational Geometry & Topology: Design and Results. Proceedings of Machine Learning Research, 196:269-276, November 2022. [bibtex-entry]



20. M Nuñez-Garcia, S Finsterbach, Buntheng Ly, Marco Lorenzi, H Cochet, and Maxime Sermesant. Long-term remodelling and arrhythmogenicity after myocardial infarction using a novel image-based estimator: the Scar Maturation Score. EP-Europace, 24(Supplement_1), May 2022. [bibtex-entry]



21. Jairo Rodrìguez-Padilla, Argyrios Petras, Julie Magat, Jason Bayer, Yann Bihan-Poudec, Dounia El Hamrani, Girish Ramlugun, Aurel Neic, Christoph Augustin, Fanny Vaillant, Marion Constantin, David Benoist, Line Pourtau, Virginie Dubes, Julien Rogier, Louis Labrousse, Olivier Bernus, Bruno Quesson, Michel Haïssaguerre, Matthias Gsell, Gernot Plank, Valéry Ozenne, and Edward Vigmond. Impact of intraventricular septal fiber orientation on cardiac electromechanical function. AJP - Heart and Circulatory Physiology, 322(6):H936-H952, June 2022. Keyword(s): diffusion tensor imaging, electromechanical models, fiber orientation, intraventricular septum, normal structural discontinuities. [bibtex-entry]



22. Marius Schmidt- Mengin, Théodore Soulier, Mariem Hamzaoui, Arya Yazdan-Panah, Benedetta Bodini, Nicholas Ayache, Bruno Stankoff, and Olivier Colliot. Online hard example mining vs. fixed oversampling strategy for segmentation of new multiple sclerosis lesions from longitudinal FLAIR MRI. Frontiers in Neuroscience, 16:100405, 2022. Keyword(s): New lesions segmentation, Deep learning, Hard example mining, Multiple sclerosis, MRI. [bibtex-entry]



23. Yann Thanwerdas and Xavier Pennec. The geometry of mixed-Euclidean metrics on symmetric positive definite matrices. Differential Geometry and its Applications, 81(101867), April 2022. Keyword(s): Symmetric Positive Definite matrices, Riemannian geometry, information geometry, families of metrics, kernel metrics, alpha-Procrustes, mixed-power-Euclidean, mixed-Euclidean, (u, v)-divergence, ($\alpha$, $\beta$)-divergence, 15B48, 53B12, 15A63, 53B20. [bibtex-entry]



24. Yann Thanwerdas and Xavier Pennec. Theoretically and computationally convenient geometries on full-rank correlation matrices. SIAM Journal on Matrix Analysis and Applications, 43(4):1851-1872, December 2022. Keyword(s): SPD matrices, Correlation matrices, Lie group, Lie group actions, Quotient-affine metric, Lie-Cholesky metrics, Poly-hyperbolic-Cholesky metrics, Euclidean-Cholesky metrics, Log-Euclidean-Cholesky metrics. [bibtex-entry]



25. Carine Wu, Sarah Montagne, Dimitri Hamzaoui, Nicholas Ayache, Hervé Delingette, and Raphaële Renard-Penna. Automatic segmentation of prostate zonal anatomy on MRI: a systematic review of the literature. Insights into Imaging, 13(1):202, December 2022. Keyword(s): Artificial intelligence, Deep learning, Magnetic resonance imaging, Prostate cancer. [bibtex-entry]



26. Nicolas Guigui and Xavier Pennec. Parallel transport, a central tool in geometric statistics for computational anatomy: Application to cardiac motion modeling. In Frank Nielsen, Arni S.R. Srinivasa Rao, and C.R. Rao, editors, Geometry and Statistics, volume 46 of Handbook of Statistics, pages 285-326. Elsevier, May 2022. Keyword(s): Parallel transport, longitudinal studies, mean trajectory, cardiac motion analysis, Schild's ladder, pole ladder, Riemannian manifolds. [bibtex-entry]

1. Clément Abi Nader, Nicholas Ayache, Giovanni B Frisoni, Philippe Robert, and Marco Lorenzi. Simulating the outcome of amyloid treatments in Alzheimer's Disease from multi-modal imaging and clinical data. Brain Communications, February 2021. Keyword(s): Alzheimer's Disease, Clinical trials, Disease progression, Amyloid hypothesis, Mental State Examination, FAQ = Functional Assessment Questionnaire, RAVLT = Rey Auditory Verbal Learning Test, CDRSB = Clinical Dementia Rating Scale Sum of Boxes. [bibtex-entry]



2. Tania Bacoyannis, Buntheng Ly, Nicolas Cedilnik, Hubert Cochet, and Maxime Sermesant. Deep Learning Formulation of ECGI Integrating Image & Signal Information with Data-driven Regularisation. EP-Europace, 23(Supplement_1):i55-i62, March 2021. Keyword(s): Electrocardiographic Imaging, Inverse Problem, Deep learning, Computational Modelling, Generative Model. [bibtex-entry]



3. Jaume Banus, Marco Lorenzi, Oscar Camara, and Maxime Sermesant. Biophysics-based statistical learning: Application to heart and brain interactions. Medical Image Analysis, 72, August 2021. Keyword(s): Lumped model, Cardiovascular modelling, Personalisation, White matter damage, Atrial fibrillation, Heart-Brain interaction. [bibtex-entry]



4. Paul Blanc-Durand, Simon Jégou, Salim Kanoun, Alina Berriolo-Riedinger, Caroline M Bodet-Milin, Françoise Kraeber-Bodéré, Thomas Carlier, Steven Le Gouill, René-Olivier Casasnovas, Michel Meignan, and Emmanuel Itti. Fully automatic segmentation of diffuse large B cell lymphoma lesions on 3D FDG-PET/CT for total metabolic tumour volume prediction using a convolutional neural network. European Journal of Nuclear Medicine and Molecular Imaging, pp 1362-1370, 2021. Keyword(s): Convolutional neural network, Deep learning, Lymphoma, Positron emission tomography, Segmentation, Total metabolic tumour volume, U-net. [bibtex-entry]



5. Adrià Casamitjana, Marco Lorenzi, Sebastiano Ferraris, Loïc Peter, Marc Modat, Allison Stevens, Bruce Fischl, Tom Vercauteren, and Juan Eugenio Iglesias. Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas. Medical Image Analysis, October 2021. Keyword(s): nonlinear registration, 3D reconstruction, linear programming, ex vivo MRI, histology. [bibtex-entry]



6. Vien Ngoc Dang, Francesco Galati, Rosa Cortese, Giuseppe Di Giacomo, Viola Marconetto, Prateek Mathur, Karim Lekadir, Marco Lorenzi, Ferran Prados, and Maria A Zuluaga. Vessel-CAPTCHA: an efficient learning framework for vessel annotation and segmentation. Medical Image Analysis, 2021. [bibtex-entry]



7. Marie Deprez, Julien Moreira, Maxime Sermesant, and Marco Lorenzi. Decoding genetic markers of multiple phenotypic layers through biologically constrained Genome-to-Phenome Bayesian Sparse Regression. Frontiers in Molecular Medicine, 2021. Keyword(s): Bayesian, Variational Dropout, Genome, Phenome, Regression, Biological constraint. [bibtex-entry]



8. Véronique Duboc, David Pratella, Marco Milanesio, John Boudjarane, Stéphane Descombes, Véronique Paquis-Flucklinger, and Silvia Bottini. NiPTUNE: an automated pipeline for noninvasive prenatal testing in an accurate, integrative and flexible framework. Briefings in Bioinformatics, September 2021. [bibtex-entry]



9. Nicolas Duchateau, Pamela Moceri, and Maxime Sermesant. Direction-dependent decomposition of 3D right ventricular motion: beware of approximations. Journal of The American Society of Echocardiography, 34(2):201-203, 2021. [bibtex-entry]



10. Sara Garbarino and Marco Lorenzi. Investigating hypotheses of neurodegeneration by learning dynamical systems of protein propagation in the brain. NeuroImage, 235:117980, July 2021. Keyword(s): Neurodegeneration, Causal model, Dynamical systems, Protein propagation, Gaussian process, Brain connectivity. [bibtex-entry]



11. Shuman Jia, Hubert Nivet, Josquin Harrison, Xavier Pennec, Claudia Camaioni, Pierre Jaïs, Hubert Cochet, and Maxime Sermesant. Left atrial shape is independent predictor of arrhythmia recurrence after catheter ablation for atrial fibrillation: A shape statistics study. Heart Rhythm O2, 2(6):622-632, December 2021. Keyword(s): Atrial fibrillation, Catheter ablation, CT, Left atrial shape, Recurrence, Statistical shape modeling. [bibtex-entry]



12. Julian Krebs, Hervé Delingette, Nicholas Ayache, and Tommaso Mansi. Learning a Generative Motion Model from Image Sequences based on a Latent Motion Matrix. IEEE Transactions on Medical Imaging, February 2021. Keyword(s): motion model, deformable registration, conditional variational autoencoder, gaussian process, latent variable model, motion interpolation, motion simulation, tracking. [bibtex-entry]



13. Julian Krebs, Tommaso Mansi, Hervé Delingette, Bin Lou, Joao Lima, Susumu Tao, Luisa Ciuffo, Sanaz Norgard, Barbara Butcher, Wei Lee, Ela Chamera, Timm-Michael Dickfeld, Michael Stillabower, Joseph Marine, Robert Weiss, Gordon Tomaselli, Henry Halperin, Katherine Wu, and Hiroshi Ashikaga. CinE caRdiac magneTic resonAnce to predIct veNTricular arrhYthmia (CERTAINTY). Scientific Reports, 11(1):22683, November 2021. Keyword(s): Cardiac device therapy, Ventricular fibrillation, Ventricular tachycardia. [bibtex-entry]



14. Georgios Lazaridis, Marco Lorenzi, Jibran Mohamed-Noriega, Soledad Aguilar-Munoa, Katsuyoshi Suzuki, Hiroki Nomoto, Sebastien Ourselin, David Garway-Heath, David Crabb, Catey Bunce, Francesca Amalfitano, Nitin Anand, Augusto Azuara-Blanco, Rupert Bourne, David Broadway, Ian Cunliffe, Jeremy Diamond, Scott Fraser, Tuan Ho, Keith Martin, Andrew Mcnaught, Anil Negi, Ameet Shah, Paul Spry, Edward White, Richard Wormald, Wen Xing, and Thierry Zeyen. OCT Signal Enhancement with Deep Learning. Ophthalmology Glaucoma, 4(3):295-304, May 2021. Keyword(s): Deep learning, Glaucoma, Image analysis, OCT, Visual fields. [bibtex-entry]



15. Georgios Lazaridis, Marco Lorenzi, Sebastien Ourselin, and David Garway-Heath. Improving statistical power of glaucoma clinical trials using an ensemble of cyclical generative adversarial networks. Medical Image Analysis, 68:101906, February 2021. Keyword(s): Optical coherence tomography, Deep learning, Perceptual loss, GAN, Label fusion, Statistical power, Clinical trials, Glaucoma. [bibtex-entry]



16. Alice Le Brigant, Nicolas Guigui, Sana Rebbah, and Stéphane Puechmorel. Classifying histograms of medical data using information geometry of beta distributions. IFAC-PapersOnLine, June 2021. Keyword(s): histogram analysis, clustering, medical imaging, Information geometry, classification. [bibtex-entry]



17. Pamela Moceri, Nicolas Duchateau, Delphine Baudouy, Fabien Squara, Sok Sithikun Bun, Emile Ferrari, and Maxime Sermesant. Additional prognostic value of echocardiographic follow-up in pulmonary hypertension - role of 3D right ventricular area strain. European Heart Journal - Cardiovascular Imaging, 2021. Keyword(s): Pulmonary hypertension, right ventricular function, 3D echocardiography, myocardial deformation imaging. [bibtex-entry]



18. Pamela Moceri, Nicolas Duchateau, Benjamin Sartre, Delphine Baudouy, Fabien Squara, Maxime Sermesant, and Emile Ferrari. Value of 3D right ventricular function over 2D assessment in acute pulmonary embolism. Echocardiography, 2021. Keyword(s): pulmonary embolism, right ventricular function, 3D echocardiography, speckle-tracking. [bibtex-entry]



19. Sarah Montagne, Dimitri Hamzaoui, Alexandre Allera, Malek Ezziane, Anna Luzurier, Raphaële Quint, Mehdi Kalai, Nicholas Ayache, Hervé Delingette, and Raphaele Renard Penna. Challenge of prostate MRI segmentation on T2-weighted images: inter-observer variability and impact of prostate morphology. Insights into Imaging, 12(1), June 2021. Keyword(s): Prostate, MRI, Segmentation, Zones, Atlas. [bibtex-entry]



20. Talia M Nir, Jean-Paul Fouche, Jintanat Ananworanich, Beau M Ances, Jasmina Boban, Bruce J Brew, Joga R Chaganti, Linda Chang, Christopher R K Ching, Lucette A Cysique, Thomas Ernst, Joshua Faskowitz, Vikash Gupta, Jaroslaw Harezlak, Jodi M Heaps-Woodruff, Charles H Hinkin, Jacqueline Hoare, John A Joska, Kalpana J Kallianpur, Taylor Kuhn, Hei y Lam, Meng Law, Christine Lebrun-Frénay, Andrew J Levine, Lydiane Mondot, Beau K Nakamoto, Bradford A Navia, Xavier Pennec, Eric C Porges, Lauren E Salminen, Cecilia M Shikuma, Wesley Surento, April D Thames, Victor Valcour, Matteo Vassallo, Adam J Woods, Paul M Thompson, Ronald A Cohen, Robert Paul, Dan J Stein, and Neda Jahanshad. Association of Immunosuppression and Viral Load With Subcortical Brain Volume in an International Sample of People Living With HIV. JAMA Network Open, 4(1):e2031190, January 2021. [bibtex-entry]



21. Maxime Sermesant, Hervé Delingette, Hubert Cochet, Pierre Jaïs, and Nicholas Ayache. Applications of artificial intelligence in cardiovascular imaging. Nature Reviews Cardiology, 18:600-609, March 2021. Keyword(s): Cardiology, Machine learning, Medical imaging. [bibtex-entry]



22. Maxim Stolyarchuk, Julie Ledoux, Elodie Maignant, Alain Trouvé, and Luba Tchertanov. Identification of the Primary Factors Determining the Specificity of the human VKORC1 Recognition by Thioredoxin-fold Proteins. International Journal of Molecular Sciences, 22(2):802, January 2021. Keyword(s): Trx-fold proteins, protein folding, dynamics, molecular recognition, thioldisulphide exchange, protein-protein interactions, PDI-hVKORC1 complex, 3D modelling, molecular dynamics simulation. [bibtex-entry]



23. Zihao Wang, Thomas Demarcy, Clair Vandersteen, Dan Gnansia, Charles Raffaelli, Nicolas Guevara, and Hervé Delingette. Bayesian Logistic Shape Model Inference: application to cochlear image segmentation. Medical Image Analysis, 75:102268, October 2021. Keyword(s): Bayesian Inference, Image Segmentation, Shape Modeling. [bibtex-entry]



24. Zihao Wang, Clair Vandersteen, Thomas Demarcy, Dan Gnansia, Charles Raffaelli, Nicolas Guevara, and Hervé Delingette. Inner-ear Augmented Metal Artifact Reduction with Simulation-based 3D Generative Adversarial Networks. Computerized Medical Imaging and Graphics, 93:101990, October 2021. Keyword(s): Artifact Reduction, Deep Learning, GAN. [bibtex-entry]



25. Zhifei Xu, Zihao Wang, Yin Sun, Chulsoon Hwang, Hervé Delingette, and Jun Fan. Jitter Aware Economic PDN Optimization with a Genetic Algorithm. IEEE Transactions on Microwave Theory and Techniques, June 2021. Note: Corresponding authors: Zihao Wang; Chulsoon Hwang. Keyword(s): PDN, Jitter, PSIJ, Decoupling capacitor, Genetic algorithm, Power integrity. [bibtex-entry]



26. Kevin Zhou, Hoang Ngan Le, Khoa Luu, Hien van Nguyen, and Nicholas Ayache. Deep reinforcement learning in medical imaging: A literature review. Medical Image Analysis, 73:102193, October 2021. [bibtex-entry]



27. Nicholas Ayache. Foreword. In Jean-François Uhl, Joaquim Jorge, Daniel Simoes Lopes, and Pedro F Campos, editors, Digital Anatomy - Applications of Virtual, Mixed and Augmented Reality, Human--Computer Interaction Series. Springer Nature, May 2021. [bibtex-entry]



28. Xavier Pennec. Statistical analysis of organs' shapes and deformations: the Riemannian and the affine settings in computational anatomy. In Jean-François Uhl, Joaquim Jorge, Daniel Simoes Lopes, and Pedro F Campos, editors, Digital Anatomy - Applications of Virtual, Mixed and Augmented Reality, Human--Computer Interaction Series. Springer Nature, May 2021. [bibtex-entry]

1. Benoît Audelan and Hervé Delingette. Unsupervised quality control of segmentations based on a smoothness and intensity probabilistic model. Medical Image Analysis, 68:101895, November 2020. Keyword(s): Unsupervised quality control, Image segmentation, Bayesian learning, Unsupervised quality control. [bibtex-entry]



2. Paul Blanc-Durand, Jean-Baptiste. Schiratti, Kathryn Schutte, Paul Jehanno, Paul Herent, Frédéric Pigneur, Olivier Lucidarme, Y. Benaceur, Alexandre Sadate, Alain Luciani, Olivier Ernst, A. Rouchaud, Maud Creze, Alex Dallongeville, Nathan Banaste, Mehdi Cadi, Imad Bousaid, Nathalie Lassau, and Simon Jégou. Abdominal musculature segmentation and surface prediction from CT using deep learning for sarcopenia assessment. Diagnostic and Interventional Imaging, 101(12):789-794, December 2020. Keyword(s): Convolutional neural networks (CNN), Deep learning, Muscular body bass, Sarcopenia, Tomography, X-ray computed. [bibtex-entry]



3. Emmanuel Chevallier and Nicolas Guigui. A Bi-Invariant Statistical Model Parametrized by Mean and Covariance on Rigid Motions. Entropy, 22(4):432, 2020. Keyword(s): moment-matching estimator, Euclidean groups, density estimation, wrapped distributions, rigid motions, sampling, differential of the exponential. [bibtex-entry]



4. James S Duncan, Michel F Insana, and Nicholas Ayache. Biomedical Imaging and Analysis In the Age of Big Data and Deep Learning. Proceedings of the IEEE, 14:3-10, January 2020. [bibtex-entry]



5. Simon Heeke, Jonathan Benzaquen, Véronique Hofman, Elodie Long-Mira, Virginie Lespinet, Olivier Bordone, Charles-Hugo Marquette, Hervé Delingette, Marius Ilié, and Paul Hofman. Comparison of Three Sequencing Panels Used for the Assessment of Tumor Mutational Burden in NSCLC Reveals Low Comparability. Journal of Thoracic Oncology, 15(9):1535-1540, September 2020. [bibtex-entry]



6. Nina Miolane, Nicolas Guigui, Alice Le Brigant, Johan Mathe, Benjamin Hou, Yann Thanwerdas, Stefan Heyder, Olivier Peltre, Niklas Koep, Hadi Zaatiti, Hatem Hajri, Yann Cabanes, Thomas Gerald, Paul Chauchat, Christian Shewmake, Daniel Brooks, Bernhard Kainz, Claire Donnat, Susan Holmes, and Xavier Pennec. Geomstats: A Python Package for Riemannian Geometry in Machine Learning. Journal of Machine Learning Research, 21(223):1-9, December 2020. Keyword(s): differential geometry, Riemannian geometry, statistics, machine learning, manifold. [bibtex-entry]



7. Pawel Mlynarski, Hervé Delingette, Hamza A Alghamdi, Pierre-Yves Bondiau, and Nicholas Ayache. Anatomically consistent CNN-based segmentation of organs-at-risk in cranial radiotherapy. Journal of Medical Imaging, 7(1):1-21, February 2020. Keyword(s): segmentation, organs at risk, Convolutional Neural Networks, radiotherapy, MRI. [bibtex-entry]



8. Pamela Moceri, Nicolas Duchateau, Stéphane Gillon, Lolita Jaunay, Delphine Baudouy, Fabien Squara, Emile Ferrari, and Maxime Sermesant. 3D right ventricular shape and strain in congenital heart disease patients with right ventricular chronic volume loading. European Heart Journal - Cardiovascular Imaging, 22(10):1174-1181, 2020. [bibtex-entry]



9. Fanny Orlhac, Augustin Lecler, Julien Savatovski, Jessica Goya-Outi, Christophe Nioche, Frédérique Charbonneau, Nicholas Ayache, Frédérique Frouin, Loïc Duron, and Irène Buvat. How can we combat multicenter variability in MR radiomics? Validation of a correction procedure. European Radiology, 2020. [bibtex-entry]



10. Raphaël Sivera, Nicolas Capet, Valeria Manera, Roxane Fabre, Marco Lorenzi, Hervé Delingette, Xavier Pennec, Nicholas Ayache, and Philippe Robert. Voxel-based assessments of treatment effects on longitudinal brain changes in the Multidomain Alzheimer Preventive Trial cohort. Neurobiology of Aging, 94:50-59, October 2020. Keyword(s): Multidomain intervention, Clinical trial, Subjective memory complaint, Deformation-based morphometry. [bibtex-entry]



11. Wen Wei, Emilie Poirion, Benedetta Bodini, Matteo Tonietto, Stanley Durrleman, Olivier Colliot, Bruno Stankoff, and Nicholas Ayache. Predicting PET-derived Myelin Content from Multisequence MRI for Individual Longitudinal Analysis in Multiple Sclerosis. NeuroImage, 223C(117308), December 2020. Keyword(s): Conditional GANs, Attention Mechanism, PET Imaging, Multisequence MRI, Demyelination and Remyelination, Deep Learning, Multiple Sclerosis. [bibtex-entry]



12. Qiao Zheng, Hervé Delingette, Kenneth Fung, Steffen E Petersen, and Nicholas Ayache. Pathological Cluster Identification by Unsupervised Analysis in 3,822 UK Biobank Cardiac MRIs. Frontiers in Cardiovascular Medicine, 7:164, November 2020. Keyword(s): Cluster analysis, Gaussian mixture model, Cine MRI, Cardiac pathology, Feature extraction, UK Biobank, Cardiac motion. [bibtex-entry]



13. Nicholas Ayache. Medical Imaging in the Age of Artificial Intelligence. In Nordlinger B., Villani C., and Rus D., editors, Healthcare and Artificial Intelligence, pages 89-91. Springer International Publishing, March 2020. [bibtex-entry]



14. Nina Miolane, Loïc Devilliers, and Xavier Pennec. Bias on estimation in quotient space and correction methods: Applications to statistics on organ shapes. In Riemannian Geometric Statistics in Medical Image Analysis, number Chap. 9, pages 343-376. Elsevier, 2020. [bibtex-entry]



15. Xavier Pennec. Advances in Geometric Statistics for Manifold Dimension Reduction. In Handbook of Variational Methods for Nonlinear Geometric Data, pages 339-359. Springer International Publishing, April 2020. [bibtex-entry]



16. Xavier Pennec. Manifold-valued image processing with SPD matrices. In Riemannian Geometric Statistics in Medical Image Analysis, number Chap. 3, pages 75-134. Elsevier, 2020. [bibtex-entry]



17. Xavier Pennec and Marco Lorenzi. Beyond Riemannian geometry: The affine connection setting for transformation groups. In Riemannian Geometric Statistics in Medical Image Analysis, number Chap. 5, pages 169-229. Elsevier, 2020. [bibtex-entry]



18. Stefan Sommer, Tom Fletcher, and Xavier Pennec. Introduction to differential and Riemannian geometry. In Riemannian Geometric Statistics in Medical Image Analysis, number Chap. 1, pages 3-37. Elsevier, 2020. [bibtex-entry]

1. Clement Abi Nader, Nicholas Ayache, Philippe Robert, and Marco Lorenzi. Monotonic Gaussian Process for Spatio-Temporal Disease Progression Modeling in Brain Imaging Data. NeuroImage, 2019. Keyword(s): Stochastic variational inference, Clinical trials, Bayesian modeling, Alzheimer's disease, Disease progression modeling, Gaussian Process. [bibtex-entry]



2. Luigi Antelmi, Nicholas Ayache, Philippe Robert, and Marco Lorenzi. Sparse Multi-Channel Variational Autoencoder for the Joint Analysis of Heterogeneous Data. Proceedings of Machine Learning Research, (97):302-311, 2019. [bibtex-entry]



3. Nicholas Ayache and Sara Colantonio. The Digital Health Revolution - Introduction to the Special Theme. ERCIM News, (118):4-5, July 2019. [bibtex-entry]



4. Laurent Bergé, Charles Bouveyron, Marco Corneli, and Pierre Latouche. The Latent Topic Block Model for the Co-Clustering of Textual Interaction Data. Computational Statistics and Data Analysis, 137:247-270, 2019. [bibtex-entry]



5. Christian Callegari, Marco Milanesio, and Pietro Michiardi. Network level perspective in web sessions troubleshooting. International Journal of Communication Systems, 32(6):e3908, April 2019. [bibtex-entry]



6. Paloma Compes, Emeline Tabouret, Amandine Etcheverry, Carole Colin, Romain Appay, Nicolas Cordier, Jean Mosser, Olivier Chinot, Hervé Delingette, Nadine Girard, Henry Dufour, Philippe Metellus, and Dominique Figarella-Branger. Neuro-radiological characteristics of adult diffuse grade II and III insular gliomas classified according to WHO 2016. Journal of Neuro-Oncology, 142(3):511-520, May 2019. Keyword(s): Molecular, Glioma, Neuro-radiology, Insula, Perfusion. [bibtex-entry]



7. Claire Cury, Stanley Durrleman, David Cash, Marco Lorenzi, Jennifer M Nicholas, Martina Bocchetta, John C. van Swieten, Barbara Borroni, Daniela Galimberti, Mario Masellis, Maria Carmela Tartaglia, James Rowe, Caroline Graff, Fabrizio Tagliavini, Giovanni B. Frisoni, Robert Laforce, Elizabeth Finger, Alexandre de Mendonça, Sandro Sorbi, Sébastien Ourselin, Jonathan Rohrer, Marc Modat, Christin Andersson, Silvana Archetti, Andrea Arighi, Luisa Benussi, Sandra Black, Maura Cosseddu, Marie Fallstrm, Carlos G. Ferreira, Chiara Fenoglio, Nick Fox, Morris Freedman, Giorgio Fumagalli, Stefano Gazzina, Robert Ghidoni, Marina Grisoli, Vesna Jelic, Lize Jiskoot, Ron Keren, Gemma Lombardi, Carolina Maruta, Lieke Meeter, Rick van Minkelen, Benedetta Nacmias, Linn Ijerstedt, Alessandro Padovani, Jessica Panman, Michela Pievani, Cristina Polito, Enrico Premi, Sara Prioni, Rosa Rademakers, Veronica Redaelli, Ekaterina Rogaeva, Giacomina Rossi, Martin Rossor, Elio Scarpini, David Tang-Wai, Hakan Thonberg, Pietro Tiraboschi, Ana Verdelho, and Jason Warren. Spatiotemporal analysis for detection of pre-symptomatic shape changes in neurodegenerative diseases: Initial application to the GENFI cohort. NeuroImage, 188:282-290, March 2019. Keyword(s): Clustering, Thalamus, Spatiotemporal geodesic regression, Parallel transport, Computational anatomy, Shape analysis. [bibtex-entry]



8. Thomas Demarcy, Isabelle Pélisson, Dan Gnansia, Hervé Delingette, Nicholas Ayache, Charles Raffaelli, Clair Vandersteen, and Nicolas Guevara. Un modèle de reconstruction tridimensionnelle de la cochlée au service de l'implantation cochléaire. Cahiers de l'audition, 32(4):36-40, July 2019. [bibtex-entry]



9. Rubén Doste, David Soto-iglesias, Gabriel Bernardino, Alejandro Alcaine, Rafael Sebastian, Sophie Giffard-Roisin, Maxime Sermesant, Antonio Berruezo, Damian Sanchez-quintana, and Oscar Camara. A rule-based method to model myocardial fiber orientation in cardiac biventricular geometries with outflow tracts. International Journal for Numerical Methods in Biomedical Engineering, 35(4), March 2019. Keyword(s): Rule-based method, Fiber orientation, Outflow tract, Septum, Electrophysiological simulations, Outflow tract ventricular arrhythmia. [bibtex-entry]



10. Sara Garbarino, Marco Lorenzi, Neil Oxtoby, Elisabeth Vinke, Razvan Marinescu, Arman Eshaghi, M Arfan Ikram, Wiro Niessen, Olga Ciccarelli, Frederik Barkhof, Jonathan Schott, Meike Vernooij, and Daniel Alexander. Differences in topological progression profile among neurodegenerative diseases from imaging data. eLife, 8, December 2019. [bibtex-entry]



11. Simon Heeke, Jonathan Benzaquen, Elodie Long-Mira, Benoît Audelan, Virginie Lespinet, Olivier Bordone, Salomé Lalvée, Katia Zahaf, Michel Poudenx, Olivier Humbert, Henri Montaudié, Pierre-Michel Dugourd, Madleen Chassang, Thierry Passeron, Hervé Delingette, Charles-Hugo Marquette, Véronique Hofman, Albrecht Stenzinger, Marius Ilié, and Paul Hofman. In-House Implementation of Tumor Mutational Burden Testing to Predict Durable Clinical Benefit in Non-Small Cell Lung Cancer and Melanoma Patients. Cancers, 11, 2019. Keyword(s): tumor mutational burden, FoundationOne assay, Oncomine TML assay, lung cancer, melanoma, immunotherapy. [bibtex-entry]



12. Simon Heeke, Hervé Delingette, Youta Fanjat, Elodie Long-Mira, Sandra Lassalle, Véronique Hofman, Jonathan Benzaquen, Charles-Hugo Marquette, Paul Hofman, and Marius Ilié. La pathologie cancéreuse pulmonaire à l'heure de l'intelligence artificielle : entre espoir, désespoir et perspectives. Annales de Pathologie, 39(2):130-136, April 2019. Keyword(s): Pathology, Histology, Lung cancer, Artificial intelligence, Convolutional neural networks, Deep learning, Pathologie Apprentissage profond, Histologie, Cancer broncho-pulmonair, Intelligence artificielle, Réseaux de neurones convolutifs, Apprentissage profond. [bibtex-entry]



13. Paul Hofman, Nicholas Ayache, Pascal Barbry, Michel Barlaud, Audrey Bel, Philippe Blancou, Frédéric Checler, Sylvie Chevillard, Gael Cristofari, Mathilde Demory, Vincent Esnault, Claire Falandry, Eric Gilson, Olivier Guerin, Nicolas Glaichenhaus, Joël Guigay, Marius I. Ilie, Bernard Mari, Charles-Hugo Marquette, Véronique Paquis-Flucklinger, Frédéric Prate, Pierre Saintigny, Barbara Seitz-Polsky, Taycir Skhiri, Ellen van Obberghen-Schilling, Emmanuel Van Obberghen, and Laurent Yvan-Charvet. The OncoAge Consortium: Linking Aging and Oncology from Bench to Bedside and Back Again. Cancers, 11(2):1-11, February 2019. Keyword(s): education, elderly, optimization, research, well-being, aging, cancer. [bibtex-entry]



14. Julian Krebs, Hervé Delingette, Boris Mailhé, Nicholas Ayache, and Tommaso Mansi. Learning a Probabilistic Model for Diffeomorphic Registration. IEEE Transactions on Medical Imaging, pp 2165-2176, February 2019. Keyword(s): deformable registration, deformation transport, latent variable model, probabilistic encoding, conditional variational autoencoder, deep learning. [bibtex-entry]



15. R azvan Marinescu, Arman Eshaghi, Marco Lorenzi, Alexandra Young, Neil Oxtoby, Sara Garbarino, Sebastian Crutch, and Daniel Alexander. DIVE: A spatiotemporal progression model of brain pathology in neurodegenerative disorders. NeuroImage, 192:166-177, May 2019. [bibtex-entry]



16. Pawel Mlynarski, Hervé Delingette, Antonio Criminisi, and Nicholas Ayache. 3D Convolutional Neural Networks for Tumor Segmentation using Long-range 2D Context. Computerized Medical Imaging and Graphics, 73:60-72, February 2019. Keyword(s): Brain tumor, Multisequence MRI, Segmentation, 3D Convolutional Neural Networks, Ensembles of models. [bibtex-entry]



17. Pawel Mlynarski, Hervé Delingette, Antonio Criminisi, and Nicholas Ayache. Deep Learning with Mixed Supervision for Brain Tumor Segmentation. Journal of Medical Imaging, July 2019. Keyword(s): Semi-supervised learning, tumor, segmentation, Convolutional Neural Networks, Convolutional N..., Semi-supervised..., MRI. [bibtex-entry]



18. Roch Molléro, Xavier Pennec, Hervé Delingette, Nicholas Ayache, and Maxime Sermesant. Population-based priors in cardiac model personalisation for consistent parameter estimation in heterogeneous databases. International Journal for Numerical Methods in Biomedical Engineering, 35(2):e3158, February 2019. Keyword(s): Cardiac Electromechanical Modeling, Parameter Estimation, Personalised modeling, Parameter Selection. [bibtex-entry]



19. Fanny Orlhac, Charles Bouveyron, and Nicholas Ayache. Radiomics: How to Make Medical Images Speak?. ERCIM News, (118):7-8, July 2019. [bibtex-entry]



20. Fanny Orlhac, Frédérique Frouin, Christophe Nioche, Nicholas Ayache, and Irène Buvat. Validation of A Method to Compensate Multicenter Effects Affecting CT Radiomics. Radiology, 291(1):53-59, April 2019. [bibtex-entry]



21. Maxime Sermesant. Improving Cardiac Arrhythmia Therapy with Medical Imaging. ERCIM News, (118):10-11, July 2019. [bibtex-entry]



22. Raphaël Sivera, Hervé Delingette, Marco Lorenzi, Xavier Pennec, and Nicholas Ayache. A model of brain morphological changes related to aging and Alzheimer's disease from cross-sectional assessments. NeuroImage, 198:255-270, September 2019. Keyword(s): Imaging biomarkers, Aging, Spatio-temporal model, Brain morphology, Deformations, Alzheimer's disease. [bibtex-entry]



23. Masateru Takigawa, Josselin Duchateau, Frederic Sacher, Ruairidh Martin, Konstantinos Vlachos, Takeshi Kitamura, Maxime Sermesant, Nicolas Cedilnik, Ghassen Cheniti, Antonio Frontera, Nathaniel Thompson, Calire Martin, Grégoire Massoullié, Felix Bourier, Anna Lam, Michael Wolf, William Escande, Clémentine André, Thomas Pambrun, Arnaud Denis, Nicolas Derval, Mélèze Hocini, Michel Haïssaguerre, Hubert Cochet, and Pierre Jaïs. Are wall thickness channels defined by computed tomography predictive of isthmuses of postinfarction ventricular tachycardia?. Heart Rhythm, 16(11):1661-1668, June 2019. Keyword(s): Wall thickness, Isthmus, High-resolution mapping, Contrart-enhanced multidetector computed tomography, MUSIC, Myocardial infarction, Ventricular tachycardia. [bibtex-entry]



24. Wen Wei, Emilie Poirion, Benedetta Bodini, Stanley Durrleman, Nicholas Ayache, Bruno Stankoff, and Olivier Colliot. Predicting PET-derived Demyelination from Multimodal MRI using Sketcher-Refiner Adversarial Training for Multiple Sclerosis. Medical Image Analysis, 58(101546), December 2019. Keyword(s): Multimodal MRI, PET Imaging, Adversarial Training, Multiple Sclerosis. [bibtex-entry]



25. Wen Wei, Emilie Poirion, Benedetta Bodini, Stanley Durrleman, Olivier Colliot, Bruno Stankoff, and Nicholas Ayache. Fluid-attenuated inversion recovery MRI synthesis from multisequence MRI using three-dimensional fully convolutional networks for multiple sclerosis. Journal of Medical Imaging, 6(01), February 2019. Keyword(s): MR Images, FLAIR Synthesis, 3D Fully Convolutional Networks, Multiple Sclerosis, Deep Learning. [bibtex-entry]



26. Wilhelm Wimmer, Lukas Anschuetz, Stefan Weder, Franca Wagner, Hervé Delingette, and Marco Caversaccio. Human bony labyrinth dataset: Co-registered CT and micro-CT images, surface models and anatomical landmarks. Data in Brief, 27:104782, December 2019. Keyword(s): Anatomy, Cochlea, Inner ear, Morphology, Semicircular canals, Vestibule. [bibtex-entry]



27. Qiao Zheng, Hervé Delingette, and Nicholas Ayache. Explainable cardiac pathology classification on cine MRI with motion characterization by semi-supervised learning of apparent flow. Medical Image Analysis, 56:80-95, 2019. Keyword(s): Deep learn- ing, Cine MRI, Classifi-cation, Motion, Semi-supervised learning, Deep learn-ing, Cardiac pathology, Neural network, Apparent flow, Classifi- cation. [bibtex-entry]

1. Martino Alessandrini, Bidisha Chakraborty, Brecht Heyde, Olivier Bernard, Mathieu de Craene, Maxime Sermesant, and Jan d'Hooge. Realistic Vendor-Specific Synthetic Ultrasound Data for Quality Assurance of 2-D Speckle Tracking Echocardiography: Simulation Pipeline and Open Access Database. IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, 65(3):411-422, March 2018. [bibtex-entry]



2. Fabien Almairac, Denys Fontaine, Thomas Demarcy, Hervé Delingette, Stephanie Beuil, and Charles Raffaelli. Motor cortex neurovascular coupling: inputs from ultra--high-frequency ultrasound imaging in humans. Journal of Neurosurgery, pp 1-7, November 2018. Keyword(s): Motor cortex, Ultrasound, Imaging methodology, Clinical neurophysiology, Diagnostic technique, Cerebral blood flow, Neurovascular coupling. [bibtex-entry]



3. Jonathan Benzaquen, Jacques Boutros, Charles Marquette, Hervé Delingette, and Paul Hofman. Lung Cancer Screening, Towards a Multidimensional Approach: Why and How?. Cancers, 10, 2018. Keyword(s): screening, lung cancer, artificial intelligence. [bibtex-entry]



4. Olivier Bernard, Alain Lalande, Clement Zotti, Frederic Cervenansky, Xin Yang, Pheng-Ann Heng, Irem Cetin, Karim Lekadir, Oscar Camara, Miguel Angel Gonzalez Ballester, Gerard Sanroma, Sandy Napel, Steffen Petersen, Georgios Tziritas, Elias Grinias, Mahendra Khened, Varghese Alex Kollerathu, Ganapathy Krishnamurthi, Marc-Michel Rohé, Xavier Pennec, Maxime Sermesant, Fabian Isensee, Paul Jager, Klaus H Maier-Hein, Peter M. Full, Ivo Wolf, Sandy Engelhardt, Chrisitan Baumgartner, Lisa Koch, Jelmer Wolterink, Ivana Isgum, Yeonggul Jang, Yoonmi Hong, Jay Patravali, Shubham Jain, Olivier Humbert, and Pierre-Marc Jodoin. Deep Learning Techniques for Automatic MRI Cardiac Multi-structures Segmentation and Diagnosis: Is the Problem Solved?. IEEE Transactions on Medical Imaging, 37(11):2514-2525, May 2018. Keyword(s): MRI, Lleft and right ventricles, Cardiac segmentation and diagnosis, Myocardium, Deep learning. [bibtex-entry]



5. Rocio Cabrera Lozoya, Benjamin Berte, Hubert Cochet, Pierre Jaïs, Nicholas Ayache, and Maxime Sermesant. Model-based Feature Augmentation for Cardiac Ablation Target Learning from Images. IEEE Transactions on Biomedical Engineering, pp 1, March 2018. Keyword(s): intracardiac electrogram modelling, cardiac elec-, Index Terms-radio-frequency ablation planning, trophysiology modelling, electroanatomical mapping. [bibtex-entry]



6. Nicolas Cedilnik, Josselin Duchateau, Rémi Dubois, Frédéric Sacher, Pierre Jaïs, Hubert Cochet, and Maxime Sermesant. Fast Personalized Electrophysiological Models from CT Images for Ventricular Tachycardia Ablation Planning. EP-Europace, 20, November 2018. Keyword(s): Computed Tomography, Computational Modelling, Catheter Ablation, Myocardial Infarction, Sudden Cardiac Death, Electrophysiology. [bibtex-entry]



7. Marco Corneli, Charles Bouveyron, Pierre Latouche, and Fabrice Rossi. The dynamic stochastic topic block model for dynamic networks with textual edges. Statistics and Computing, 2018. Keyword(s): Dynamic random graph, model based clustering, non homogeneous Poisson process, stochastic block model, topic modeling, latent Dirichlet allocation. [bibtex-entry]



8. Nicolas Duchateau, Maxime Sermesant, Hervé Delingette, and Nicholas Ayache. Model-based generation of large databases of cardiac images: synthesis of pathological cine MR sequences from real healthy cases. IEEE Transactions on Medical Imaging, 37:755-766, 2018. Keyword(s): validation, magnetic resonance., biomechanical modeling, Image synthesis and simulation, myocardial infarct, large database for machine learning. [bibtex-entry]



9. Leman Feng, Pierre Alliez, Laurent Busé, Hervé Delingette, and Mathieu Desbrun. Curved Optimal Delaunay Triangulation. ACM Transactions on Graphics, 37(4):16, August 2018. Keyword(s): Bézier elements ACM Reference Format:, Mesh generation, Bézier elements, Additional Key Words and Phrases: Higher-order meshing, Optimal Delau-nay Triangulations, CCS Concepts: $\bullet$ Mathematics of computing $\rightarrow$ Mesh generation, higher order finite elements, Optimal Delaunay Triangulations, Higher-order meshing. [bibtex-entry]



10. Sebastiano Ferraris, Johannes van Der Merwe, Lennart van Der Veeken, Ferran Prados, Juan Eugenio Iglesias, Marco Lorenzi, Andrew Melbourne, Marc M Modat, Willy Gsell, Jan Deprest, and Tom Vercauteren. A magnetic resonance multi-atlas for the neonatal rabbit brain. NeuroImage, 179:187 - 198, October 2018. [bibtex-entry]



11. Sophie Giffard-Roisin, Hervé Delingette, Thomas Jackson, Jessica Webb, Lauren Fovargue, Jack Lee, Christopher A Rinaldi, Reza Razavi, Nicholas Ayache, and Maxime Sermesant. Transfer Learning from Simulations on a Reference Anatomy for ECGI in Personalised Cardiac Resynchronization Therapy. IEEE Transactions on Biomedical Engineering, 20, 2018. Keyword(s): Cardiac Electrophysiology, Inverse Problem of ECG, Personalisation, ECG Imaging, Index Terms-Cardiac Electrophysiology, In- verse Problem of ECG. [bibtex-entry]



12. Pietro Gori, Olivier Colliot, Linda Marrakchi Kacem, Yulia Worbe, Alexandre Routier, Cyril Poupon, Andreas Hartmann, Nicholas Ayache, and Stanley Durrleman. Double diffeomorphism: combining morphometry and structural connectivity analysis. IEEE Transactions on Medical Imaging, 37(9):2033-2043, September 2018. Keyword(s): Neural circuits, Structural connectivity, Diffeomorphisms, Multi-object, Atlas, Shape, Morphometry, Complex, Tourette. [bibtex-entry]



13. Rashed Karim, Lauren-Emma Blake, Jiro Inoue, Qian Tao, Shuman Jia, R. James James Housden, Pranav Bhagirath, Jean-Luc Duval, Marta Varela, Jonathan Behar, Loïc Cadour, Rob J van Der Geest, Hubert Cochet, Maria Drangova, Maxime Sermesant, Reza Razavi, Oleg Aslanidi, Ronak Rajani, and Kawal S. Rhode. Algorithms for left atrial wall segmentation and thickness -- Evaluation on an open-source CT and MRI image database. Medical Image Analysis, 50:36 - 53, December 2018. Keyword(s): Myocardium, Left atrial wall thickness, Left atrium, Atrial fibrillation. [bibtex-entry]



14. Marco Lorenzi, Andre Altmann, Boris Gutman, Selina Wray, Charles Arber, Derrek D Hibar, Neda J Jahanshad, Jonathan Schott, Daniel Alexander, Paul M. Thompson, and Sébastien Ourselin. Susceptibility of brain atrophy to TRIB3 in Alzheimer's disease, evidence from functional prioritization in imaging genetics. Proceedings of the National Academy of Sciences of the United States of America, 115(12):3162-3167, 2018. Keyword(s): bioinformatics, phenotype, imaging-genetics, Alzheimer's disease, genotype, GWA. [bibtex-entry]



15. Kristin Mcleod, Kristin Tondel, Lilian Calvet, M Sermesant, and Xavier Pennec. Cardiac Motion Evolution Model for Analysis of Functional Changes Using Tensor Decomposition and Cross-Sectional Data. IEEE Transactions on Biomedical Engineering, 65(12):2769 - 2780, December 2018. Keyword(s): tensor decomposition, evolution modelling, Cardiac motion tracking, non-rigid image registration, spatio-temporal alignment, N-way PLS, atlas, population statistics, Tetralogy of Fallot. [bibtex-entry]



16. Nina Miolane, Susan Holmes, and Xavier Pennec. Topologically constrained template estimation via Morse-Smale complexes controls its statistical consistency. SIAM Journal on Applied Algebra and Geometry, 2(2):348-375, 2018. [bibtex-entry]



17. Pamela Moceri, Nicolas Duchateau, Delphine Baudouy, Elie-Dan Schouver, Sylvie Leroy, Fabien Squara, Emile Ferrari, and Maxime Sermesant. Three-dimensional right-ventricular regional deformation and survival in pulmonary hypertension. European Heart Journal - Cardiovascular Imaging, 19:450-458, 2018. Keyword(s): pulmonary hypertension, speckle-tracking imaging, three-dimensional echocardiography. [bibtex-entry]



18. Pamela Moceri, Maxime Sermesant, Delphine Baudouy, Emile Ferrari, and Nicolas Duchateau. Right Ventricular Function Evolution With Pregnancy in Repaired Tetralogy of Fallot. Canadian Journal of Cardiology, 34(10):1369.e9 - 1369.e11, October 2018. Keyword(s): Pregnancy, Echocardiography, Right Ventricular Function, 3D speckle-tracking imaging, Key-words: Tetralogy of Fallot. [bibtex-entry]



19. Christophe Nioche, Fanny Orlhac, Sarah Boughdad, Sylvain Reuzé, Jessica Goya-Outi, Charlotte Robert, Claire Pellot-Barakat, Michael Soussan, Frédérique Frouin, and Irene Buvat. LIFEx: A Freeware for Radiomic Feature Calculation in Multimodality Imaging to Accelerate Advances in the Characterization of Tumor Heterogeneity. Cancer Research, 78(16):4786 - 4789, August 2018. [bibtex-entry]



20. Fanny Orlhac, Frédérique Frouin, Christophe Nioche, Nicholas Ayache, and Irene Buvat. Validation of a method to compensate multicenter effects affecting CT radiomic features. Radiology, 2018. [bibtex-entry]



21. F Orlhac, P.-A Mattei, C. Bouveyron, and N Ayache. Class-specific Variable Selection in High-Dimensional Discriminant Analysis through Bayesian Sparsity. Journal of Chemometrics, pp e3097, November 2018. [bibtex-entry]



22. Xavier Pennec. Barycentric Subspace Analysis on Manifolds. Annals of Statistics, 46(6A):2711-2746, July 2018. Keyword(s): Manifold, Flag of subspaces, Frechet mean, Barycenter, Subspaces, Pricipal Component Analysis. [bibtex-entry]



23. Marc-Michel Rohé, Maxime Sermesant, and Xavier Pennec. Low-Dimensional Representation of Cardiac Motion Using Barycentric Subspaces: a New Group-Wise Paradigm for Estimation, Analysis, and Reconstruction. Medical Image Analysis, 45:1-12, April 2018. Keyword(s): Cardiac motion, Low-dimensional analysis, Registration, Image synthesis. [bibtex-entry]



24. Sergio Sanchez-Martinez, Nicolas Duchateau, Tamas Erdei, Gabor Kunszt, Svend Aakhus, Anna Degiovanni, Paolo Marino, Erberto Carluccio, Gemma Piella, Alan Fraser, and Bart Bijnens. Machine learning analysis of left ventricular function to characterize heart failure with preserved ejection fraction. Circulation: Cardiovascular Imaging, 11(4), April 2018. Keyword(s): Excercise echocardiography, Heart failure with preservec ejection fraction, Myocardial velocity, Machine learning, Non-invasive diagnostic heart failure. [bibtex-entry]



25. Marzia A Scelzi, Raiyan R Khan, Marco Lorenzi, Christopher Leigh, Michael D Greicius, Jonathan M. Schott, Sébastien Ourselin, and Andre Altmann. Genetic study of multimodal imaging Alzheimer's disease progression score implicates novel loci. Brain - A Journal of Neurology, 141(7):2167 - 2180, July 2018. [bibtex-entry]



26. Avan A Suinesiaputra, Pierre A Ablin, Xènia A Albà, Martino Alessandrini, Jack A Allen, Wenjia Bai, Serkan Cimen, Peter Claes, Brett R Cowan, Jan d'Hooge, Nicolas Duchateau, Jan Ehrhardt, Alejandro F. Frangi, Ali A Gooya, Vicente Grau, Karim Lekadir, Allen A Lu, Anirban A Mukhopadhyay, Ilkay Oksuz, Nripesh Parajuli, Xavier Pennec, Marco Pereañez, Catarina Pinto, Paolo Piras, Marc-Michel Rohé, Daniel R Rueckert, Dennis Säring, Maxime Sermesant, Kaleem Siddiqi, Mahdi Tabassian, Luciano Teresi, Sotirios A Tsaftaris, Matthias Wilms, Alistair A Young, Xingyu Zhang, and Pau Medrano-Gracia. Statistical shape modeling of the left ventricle: myocardial infarct classification challenge. IEEE Journal of Biomedical and Health Informatics, 22(3):503-515, March 2018. Keyword(s): statistical shape analysis, classification, myocardial infarct, Cardiac modeling. [bibtex-entry]



27. Qiao Zheng, Hervé Delingette, Nicolas Duchateau, and Nicholas Ayache. 3D Consistent & Robust Segmentation of Cardiac Images by Deep Learning with Spatial Propagation. IEEE Transactions on Medical Imaging, 37:2137-2148, April 2018. Keyword(s): deep learning, spatial propagation, Cardiac segmentation, 3D consistency, neural network. [bibtex-entry]



28. Yitian Zhou, Sophie Giffard-Roisin, Mathieu de Craene, Sorina Camarasu-Pop, Jan d'Hooge, Martino Alessandrini, Denis Friboulet, Maxime Sermesant, and Olivier Bernard. A Framework for the Generation of Realistic Synthetic Cardiac Ultrasound and Magnetic Resonance Imaging Sequences from the same Virtual Patients. IEEE Transactions on Medical Imaging, 37(3):741-754, 2018. Keyword(s): cardiac strain, Multimodal cardiac imaging, synthetic sequences, electromechanical model, motion estimation, numerical simulation. [bibtex-entry]



29. Nicholas Ayache. L'imagerie médicale à l'heure de l'intelligence artificielle. In Cédric Villani and Bernard Nordlinger, editors, Santé et intelligence artificielle, pages 151-154. CNRS Editions, October 2018. [bibtex-entry]



30. Charles Bouveyron. Apprentissage statistique en grande dimension et application au diagnostic oncologique par radiomique. In Cédric Villani and Bernard Nordlinger, editors, Santé et intelligence artificielle, pages 179-189. CNRS Editions, October 2018. [bibtex-entry]

1. Jan L. Bruse, Elena Cervi, Kristin Mcleod, Giovanni Biglino, Maxime Sermesant, Xavier Pennec, Andrew Taylor, Silvia Schievano, and Tain-Yen Hsia. Looks Do Matter! Aortic Arch Shape After Hypoplastic Left Heart Syndrome Palliation Correlates With Cavopulmonary Outcomes. Annals of Thoracic Surgery, 103(2):645 - 654, February 2017. [bibtex-entry]



2. Jan L. Bruse, Abbas Khushnood, Kristin Mcleod, Giovanni Biglino, Maxime Sermesant, Xavier Pennec, Andrew M. Taylor, Tain-Yen Hsia, and Silvia Schievano. How successful is successful? Aortic arch shape after successful aortic coarctation repair correlates with left ventricular function. Journal of Thoracic and Cardiovascular Surgery, 153(2):418 - 427, February 2017. [bibtex-entry]



3. Jan L. Bruse, Maria A. Zuluaga, Abbas Khushnood, Kristin Mcleod, Hopewell N. Ntsinjana, Tain-Yen Hsia, Maxime Sermesant, Xavier Pennec, Andrew M. Taylor, and Silvia Schievano. Detecting clinically meaningful shape clusters in medical image data: metrics analysis for hierarchical clustering applied to healthy and pathological aortic arches. IEEE Transactions on Biomedical Engineering, pp 1 - 13, February 2017. [bibtex-entry]



4. Thomas Demarcy, Clair Vandersteen, Nicolas Guevara, Charles Raffaelli, Dan Gnansia, Nicholas Ayache, and Hervé Delingette. Automated analysis of human cochlea shape variability from segmented $\mu$CT images. Computerized Medical Imaging and Graphics, 59(July 2017):1 - 12, 2017. Keyword(s): cochlear implant, human cochlea, anatomy, shape variability, modiolar axis. [bibtex-entry]



5. Loïc Devilliers, Stéphanie Allassonnière, Alain Trouvé, and Xavier Pennec. Inconsistency of template estimation by minimizing of the variance/pre-variance in the quotient space. Entropy, 19(6):article 288, June 2017. Keyword(s): quotient space, Fréchet mean, Hilbert space, deformable model, regularization, template estimation, inconsistency. [bibtex-entry]



6. Loïc Devilliers, Stéphanie Allassonnière, Alain Trouvé, and Xavier Pennec. Template estimation in computational anatomy: Fréchet means in top and quotient spaces are not consistent. SIAM Journal on Imaging Sciences, 10(3):1139-1169, August 2017. Keyword(s): Fréchet mean, Hilbert space, quotient space, Template, manifold, empirical Fréchet mean, inconsistency, group action, consistency bias. [bibtex-entry]



7. Sophie Giffard-Roisin, Thomas Jackson, Lauren Fovargue, Jack Lee, Hervé Delingette, Reza Razavi, Nicholas Ayache, and Maxime Sermesant. Non-Invasive Personalisation of a Cardiac Electrophysiology Model from Body Surface Potential Mapping. IEEE Transactions on Biomedical Engineering, 64(9):2206 - 2218, September 2017. Note: Selected for the TBME highlights, sept. 2017rlhttps://tbme.embs.org/2017/08/24/non-invasive-personalisation-cardiac-electrophysiology-model-body-surface-potential-mapping/. Keyword(s): ECG Imaging, Parameter estimation, In- verse Problem of ECG, Cardiac Electrophysiology, Personalisation. [bibtex-entry]



8. Pietro Gori, Olivier Colliot, Linda Marrakchi-Kacem, Yulia Worbe, Cyril Poupon, Andreas Hartmann, Nicholas Ayache, and Stanley Durrleman. A Bayesian Framework for Joint Morphometry of Surface and Curve meshes in Multi-Object Complexes. Medical Image Analysis, 35:458-474, January 2017. Keyword(s): complex, fiber bundle, morphometry, shape, Bayesian, varifolds, atlas, multi - object. [bibtex-entry]



9. Bishesh Khanal, Nicholas Ayache, and Xavier Pennec. Simulating Longitudinal Brain MRIs with known Volume Changes and Realistic Variations in Image Intensity. Frontiers in Neuroscience, 11(Article 132):18, February 2017. Keyword(s): simulated database, biomechanical simulation, Neurodegeneration, biophysical modelling, synthetic images, synthetic. [bibtex-entry]



10. Loïc Le Folgoc, Hervé Delingette, Antonio Criminisi, and Nicholas Ayache. Sparse Bayesian registration of medical images for self-tuning of parameters and spatially adaptive parametrization of displacements. Medical Image Analysis, 36:79 - 97, February 2017. Keyword(s): Cardiac Imaging, Automatic Relevance Determination, Bayesian modelling, Sparse, Registration. [bibtex-entry]



11. Marco Lorenzi, Maurizio Filippone, Giovanni Frisoni, Daniel C Alexander, and Sébastien Ourselin. Probabilistic disease progression modeling to characterize diagnostic uncertainty: application to staging and prediction in Alzheimer's disease. NeuroImage, October 2017. [bibtex-entry]



12. Alex F. Mendelson, Maria A. Zuluaga, Marco Lorenzi, Brian F. Hutton, and Sébastien Ourselin. Selection bias in the reported performances of AD classification pipelines. Neuroimage-Clinical, 14:400 - 416, 2017. Keyword(s): Alzheimer's disease, Classification, Cross validation, Selection bias, Overfitting, ADNI. [bibtex-entry]



13. Nina Miolane. Les maths de l'espace-temps qui décrivent et dépassent le cerveau. Interstices, February 2017. Keyword(s): anatomie cérébrale, anatomie numérique, modélisation mathématique, géométrie riemannienne, cortex visuel, neuroimagerie, image 3D, perception visuelle. [bibtex-entry]



14. Nina Miolane, Susan Holmes, and Xavier Pennec. Template Shape Estimation: Correcting an Asymptotic Bias. SIAM Journal on Imaging Sciences, 10(2):808 - 844, 2017. Keyword(s): geometry, quotient space, manifold, template, bias, shape, consistency. [bibtex-entry]



15. Roch Molléro, Xavier Pennec, Hervé Delingette, Alan Garny, Nicholas Ayache, and Maxime Sermesant. Multifidelity-CMA: a multifidelity approach for efficient personalisation of 3D cardiac electromechanical models. Biomechanics and Modeling in Mechanobiology, pp 1-16, September 2017. Keyword(s): Finite Element Mechanical modeling, Parameter Estimation, Reduced Model, Cardiac Electromechanical Modeling, Multi-fidelity Modeling. [bibtex-entry]



16. Naiara Rodriguez-Florez, Jan L. Bruse, Alessandro Borghi, Herman Vercruysse, Juling Ong, Greg James, Xavier Pennec, David J. Dunaway, Owase Jeelani, and Silvia Schievano. Statistical shape modelling to aid surgical planning: associations between surgical parameters and head shapes following spring-assisted cranioplasty. International Journal of Computer Assisted Radiology and Surgery, pp 1-11, May 2017. [bibtex-entry]



17. Sergio Sanchez-Martinez, Nicolas Duchateau, Tamas Erdei, Alan Fraser, Bart Bijnens, and Gemma Piella. Characterization of myocardial motion patterns by unsupervised multiple kernel learning. Medical Image Analysis, 35:70-82, 2017. Keyword(s): echocardiography, pattern analysis, multiple kernel learning, Myocardial motion. [bibtex-entry]



18. Walther Schulze, Zhong Chen, Jatin Relan, Danila Potyagaylo, Martin W. Krueger, Rashed Karim, Manav Sohal, Anoop Shetty, Yingliang Ma, Nicholas Ayache, Maxime Sermesant, Hervé Delingette, Julian Bostock, Reza Razavi, Kawal S. Rhode, and Christopher A. Rinaldi. ECG imaging of ventricular tachycardia: evaluation against simultaneous non-contact mapping and CMR-derived grey zone. Medical and Biological Engineering and Computing, 55(6):979 - 990, June 2017. Keyword(s): Clinical validation, Non-contact mapping, ECG imaging, Ventricular tachycardia, Inverse problem of ECG. [bibtex-entry]



19. David Soto-Iglesias, Nicolas Duchateau, Constantine Butakoff, David Andreu, Juan Fernández-Armenta, Bart Bijnens, Antonio Berruezo, Marta Sitges, and Oscar Camara. Quantitative analysis of electro-anatomical maps: application to an experimental model of LBBB/CRT. IEEE Journal of Translational Engineering in Health and Medicine, 5:1900215, 2017. Keyword(s): electro - anatomical mapping system, quantitative pattern analysis, left bundle branch block, subject - specific 2D and 3D data representation, Cardiac resynchronization therapy, lead placement. [bibtex-entry]



20. Zhiyu Tian and Chenyang Xu. Finiteness of fundamental groups. Compositio Mathematica, 153(02):257-273, February 2017. [bibtex-entry]



21. Stéphanie Marchesseau, Simon Chatelin, and Hervé Delingette. Nonlinear Biomechanical Model of the Liver. In Yohan Payan and Jacques Ohayon, editors, Biomechanics of Living Organs. Hyperelastic Constitutive Laws for Finite Element Modeling, pages 243 - 265. Elsevier, 2017. [bibtex-entry]

1. Martino Alessandrini, Brecht Heyde, Sandro Queirós, Szymon Cygan, Maria Zontak, Oudom Somphone, Olivier Bernard, Maxime Sermesant, Hervé Delingette, Daniel Barbosa, Mathieu de Craene, Matthew O'Donnell, and Jan d'Hooge. Detailed Evaluation of Five 3D Speckle Tracking Algorithms Using Synthetic Echocardiographic Recordings. IEEE Transactions on Medical Imaging, 35(8):1915-1926, 2016. [bibtex-entry]



2. Chloé Audigier, Tommaso Mansi, Hervé Delingette, Saikiran Rapaka, Tiziano Passerini, Viorel Mihalef, Marie-Pierre Jolly, Raoul Pop, Michele Diana, Luc Soler, Ali Kamen, Dorin Comaniciu, and Nicholas Ayache. Comprehensive Pre-Clinical Evaluation of a Multi-physics Model of Liver Tumor Radiofrequency Ablation. International Journal of Computer Assisted Radiology and Surgery, December 2016. [bibtex-entry]



3. Nicholas Ayache. Medical Imaging Informatics: Towards a Personalized Computational Patient. IMIA Yearbook of Medical Informatics, 25(Suppl. 1):S8-S9, 2016. [bibtex-entry]



4. Nicholas Ayache and James Duncan. 20th anniversary of the medical image analysis journal (MedIA). Medical Image Analysis, 33:1-3, October 2016. [bibtex-entry]



5. Jan L. Bruse, Kristin Mcleod, Giovanni Biglino, Hopewell N. Ntsinjana, Claudio Capelli, Tain-Yen Hsia, Maxime Sermesant, Xavier Pennec, Andrew M. Taylor, and Silvia Schievano. A statistical shape modelling framework to extract 3D shape biomarkers from medical imaging data: assessing arch morphology of repaired coarctation of the aorta. BMC Medical Imaging, 16(1), May 2016. [bibtex-entry]



6. Jan Bruse, Hopewell Ntsinjana, Claudio Capelli, Giovanni Biglino, Kristin Mcleod, Maxime Sermesant, Xavier Pennec, Tain-Yen Hsia, Silvia Schievano, and Andrew Taylor. CMR-based 3D statistical shape modelling reveals left ventricular morphological differences between healthy controls and arterial switch operation survivors. Journal of Cardiovascular Magnetic Resonance, 18(S1), December 2016. [bibtex-entry]



7. Rocìo Cabrera-Lozoya, Benjamin Berte, Hubert Cochet, Pierre Jaïs, Nicholas Ayache, and Maxime Sermesant. Image-based Biophysical Simulation of Intracardiac Abnormal Ventricular Electrograms. IEEE Transactions on Biomedical Engineering, PP(99), 2016. Keyword(s): electroanatomical mapping, intracar-diac electrogram modelling, radiofrequency ablation planning, cardiac electrophysiology modelling. [bibtex-entry]



8. Radomir Chabiniok, Vicky Y. Wang, Myrianthi Hadjicharalambous, Liya Asner, Jack Lee, Maxime Sermesant, Ellen Kuhl, Alistair A. Young, Philippe Moireau, Martyn P. Nash, Dominique Chapelle, and David Nordsletten. Multiphysics and multiscale modelling, data-model fusion and integration of organ physiology in the clinic: ventricular cardiac mechanics. Interface Focus, 6(2), 2016. Keyword(s): translational cardiac modelling, patient-specific modelling, heart mechanics, cardiac mechanics, data-model fusion. [bibtex-entry]



9. Zhong Chen, Rocìo Cabrera-Lozoya, Jatin Relan, Manav Sohal, Anoop Shetty, Rashed Karim, Hervé Delingette, Jaswinder Gill, Kawal Rhode, Nicholas Ayache, Peter Taggart, Christopher Aldo Rinaldi, Maxime Sermesant, and Reza Razavi. Biophysical modelling predicts ventricular tachycardia inducibility and circuit morphology: A combined clinical validation and computer modelling approach. Journal of Cardiovascular Electrophysiology, 27(7):851-860, 2016. Keyword(s): cardiac magnetic resonance imaging, conductivity, APD restitution, computer modelling, Ventricular tachycardia. [bibtex-entry]



10. Nicolas Cordier, Hervé Delingette, Matthieu Lê, and Nicholas Ayache. Extended Modality Propagation: Image Synthesis of Pathological Cases. IEEE Transactions on Medical Imaging, PP(99), July 2016. Keyword(s): patch-based, multi-atlas, glioma, generative model, medical image simulation, modality synthesis. [bibtex-entry]



11. Nicolas Duchateau, Mathieu de Craene, Pascal Allain, Eric Saloux, and Maxime Sermesant. Infarct localization from myocardial deformation: Prediction and uncertainty quantification by regression from a low-dimensional space. IEEE Transactions on Medical Imaging, 35(10):2340-2352, 2016. Keyword(s): biomechanical modeling, delayed-enhancement, pattern recognition & classification, Index Terms-Myocardial infarct, dimensionality reduction, computer-aided diagnosis, ultrasound. [bibtex-entry]



12. Dan Gnansia, Thomas Demarcy, Clair Vandersteen, Charles Raffaelli, Nicolas Guevara, Hervé Delingette, and Nicholas Ayache. Optimal electrode diameter in relation to volume of the cochlea. European Annals of Otorhinolaryngology, Head and Neck Diseases, 133, Supplement 1:S66-S67, June 2016. Keyword(s): Cochlear implant, Electrode-array, Hearing preservation, Soft surgery, Electrode-array design, Image processing, Computed tomography, Inner ear, Anatomy. [bibtex-entry]



13. Pietro Gori, Olivier Colliot, Linda Marrakchi-Kacem, Yulia Worbe, Fabrizio de Vico Fallani, Mario Chavez, Cyril Poupon, Andreas Hartmann, Nicholas Ayache, and Stanley Durrleman. Parsimonious Approximation of Streamline Trajectories in White Matter Fiber Bundles. IEEE Transactions on Medical Imaging, PP(99), 2016. Keyword(s): Index Terms-Diffusion weighted imaging, Brain, Connectivity analysis, Dimensionality reduction, Registration, Tractography, Visualization. [bibtex-entry]



14. Mehdi Hadj-Hamou, Marco Lorenzi, Nicholas Ayache, and Xavier Pennec. Longitudinal Analysis of Image Time Series with Diffeomorphic Deformations: A Computational Framework Based on Stationary Velocity Fields. Frontiers in Neuroscience, 10(236):18, June 2016. Keyword(s): non-linear registration, deformation-based morphometry, longitudinal study, diffeomorphism parametrized by stationary velocity fields, statistical analysis, reproducible research. [bibtex-entry]



15. Bishesh Khanal, Marco Lorenzi, Nicholas Ayache, and Xavier Pennec. A biophysical model of brain deformation to simulate and analyze longitudinal MRIs of patients with Alzheimer's disease. NeuroImage, 134:35-52, July 2016. Keyword(s): longitudinal modeling, simulation of atrophy, longitudinal MRIs simulation, biophysical model, Alzheimer's disease. [bibtex-entry]



16. Loïc Le Folgoc, Hervé Delingette, Antonio Criminisi, and Nicholas Ayache. Quantifying Registration Uncertainty with Sparse Bayesian Modelling. IEEE Transactions on Medical Imaging, PP(99), December 2016. Keyword(s): MCMC, Uncertainty Quantification, Registration, Sparse Bayesian Learning, Reversible Jump, Automatic Relevance Determination. [bibtex-entry]



17. Matthieu Lê, Hervé Delingette, Jayashree Kalpathy-Cramer, Elizabeth R Gerstner, Tracy Batchelor, Jan Unkelbach, and Nicholas Ayache. MRI Based Bayesian Personalization of a Tumor Growth Model. IEEE Transactions on Medical Imaging, 35(10):2329-2339, April 2016. Keyword(s): bayesian, personalization, Index Terms-tumor growth, glioblastoma, reaction-diffusion, LBM, Monte Carlo. [bibtex-entry]



18. Matthieu Lê, Hervé Delingette, Jayashree Kalpathy-Cramer, Elizabeth R Gerstner, Tracy Batchelor, Jan Unkelbach, and Nicholas Ayache. Personalized Radiotherapy Planning Based on a Computational Tumor Growth Model. IEEE Transactions on Medical Imaging, pp 11, 2016. Keyword(s): Index Terms-Radiotherapy planning, computational tu-, mor growth model, personalization, uncertainty, segmentation, glioblastoma. [bibtex-entry]



19. Matthieu Lê, Jan Unkelbach, Nicholas Ayache, and Hervé Delingette. Sampling Image Segmentations for Uncertainty Quantification. Medical Image Analysis, 34:42-51, December 2016. Note: Accepted for publication to the journal Elsevier Medical Image Analysis. Keyword(s): Gaussian process, brain tumor, uncertainty, radiotherapy planning, Segmentation. [bibtex-entry]



20. Nerea Mangado, Mario Ceresa, Nicolas Duchateau, Hans Martin Kjer, Sergio Vera, Hector Dejea Velardo, Pavel Mistrik, Rasmus R. Paulsen, Jens Fagertun, Jérôme Noailly, Gemma Piella, and Miguel Ángel González Ballester. Automatic model generation framework for computational simulation of cochlear implantation. Annals of Biomedical Engineering, 44(8):2453-2463, 2016. [bibtex-entry]



21. Hugo Talbot, Federico Spadoni, Christian Duriez, Maxime Sermesant, Stéphane Cotin, and Hervé Delingette. Interactive Training System for Interventional Electrocardiology Procedures. Medical Image Analysis, 8789:11-19, 2016. Keyword(s): Endovascular Navigation, Training Simulator, Interactive Simulation, Real-Time Electrophysiology. [bibtex-entry]



22. Anant S. Vemuri, Stéphane Nicolau, Adrien Sportes, Jacques Marescaux, Luc Soler, and Nicholas Ayache. Inter-Operative Biopsy Site Relocalization in Endoluminal Surgery. IEEE Transactions on Biomedical Engineering, 63(9):1862-1873, September 2016. Keyword(s): video synchronization, Computer assisted intervention, gastro-intestinal (GI) endoscopy, biopsy relocalization, Barrett's Oesophagus, electromagnetic tracking. [bibtex-entry]



23. Antoine Verger, Yalcin Yagdigul, Axel van Der Gucht, Sylvain Poussier, Eric Guedj, Louis Maillard, Grégoire Malandain, Gabriela Hossu, Renaud Fay, Gilles Karcher, and Pierre-Yves Marie. Temporal epilepsy lesions may be detected by the voxel-based quantitative analysis of brain FDG-PET images using an original block-matching normalization software. Annals of Nuclear Medicine, 30(4):272-278, May 2016. Keyword(s): Block-matching algorithm, FDG-PET, Mesial temporal lobe epilepsy, Spatial normalization, Statistical parametric mapping. [bibtex-entry]



24. Seigo Yamashita, Hubert Cochet, Frédéric Sacher, Saagar Mahida, Benjamin Berte, Darren Hooks, Jean-Marc Sellal, Nora Al Jefairi, Antonio Frontera, Yuki Komatsu, Han S Lim, Sana Amraoui, Arnaud Denis, Nicolas Derval, Maxime Sermesant, François Laurent, Mélèze Hocini, Michel Haïssaguerre, Michel Montaudon, and Pierre Jais. Impact of New Technologies and Approaches for Post--Myocardial Infarction Ventricular Tachycardia Ablation During Long-Term Follow-Up. Circulation. Arrhythmia and electrophysiology, 9(7), July 2016. Keyword(s): Myocardial infarction, Infarction, Heart failure, Catheter ablation, Ventricular tachycardia. [bibtex-entry]



25. Seigo Yamashita, Frédéric Sacher, Saagar Mahida, Benjamin Berte, Han S Lim, Yuki Komatsu, Sana Amraoui, Arnaud Denis, Nicolas Derval, François Laurent, Maxime Sermesant, Michel Montaudon, Mélèze Hocini, Michel Haïssaguerre, Pierre Jais, and Hubert Cochet. Image Integration to Guide Catheter Ablation in Scar-Related Ventricular Tachycardia. Journal of Cardiovascular Electrophysiology, 27(6):699 - 708, June 2016. Keyword(s): Scar-related ventricular tachycardia, Ablation, CMR, MDCT, Imaging. [bibtex-entry]



26. Nicolas Duchateau, Gemma Piella, Alejandro Frangi, and Mathieu de Craene. Learning pathological deviations from a normal pattern of myocardial motion: Added value for CRT studies?. In Guorong Wu, Dinggang Shen, and Mert Sabuncu, editors, Machine learning and medical imaging, 1st Edition, pages 365-382. Elsevier, 2016. [bibtex-entry]

1. Martino Alessandrini, Mathieu de Craene, Olivier Bernard, Sophie Giffard-Roisin, Pascal Allain, Juergen Weese, Eric Saloux, Hervé Delingette, Maxime Sermesant, and Jan d'Hooge. A Pipeline for the Generation of Realistic 3D Synthetic Echocardiographic Sequences: Methodology and Open-access Database.. IEEE Transactions on Medical Imaging, 34(7):1436-1451, 2015. [bibtex-entry]



2. A Amelot, E Stretton, Hervé Delingette, Nicholas Ayache, S Froelich, and E Mandonnet. Expert-validated CSF segmentation of MNI atlas enhances accuracy of virtual glioma growth patterns. Journal of Neuro-Oncology, 121(2):381-387, January 2015. [bibtex-entry]



3. Chloé Audigier, Tommaso Mansi, Hervé Delingette, Saikiran Rapaka, Viorel Mihalef, Daniel Carnegie, Emad Boctor, Michael Choti, Ali Kamen, Nicholas Ayache, and Dorin Comaniciu. Efficient Lattice Boltzmann Solver for Patient-Specific Radiofrequency Ablation of Hepatic Tumors. IEEE Transactions on Medical Imaging, 34(issue 7):p 1576-1589, 2015. Keyword(s): Radio Frequency ablation, Patient-Specific Simulation, Lattice Boltzmann Method, Heat Transfer, Computational Fluid Dynamics, Therapy Planning. [bibtex-entry]



4. Mariem Ben Abdallah, Jihene Malek, Ahmad Taher Azar, Philippe Montesinos, Hafedh Belmabrouk, Julio Esclarìn Monreal, and Karl Krissian. Automatic Extraction of Blood Vessels in the Retinal Vascular Tree Using Multiscale Medialness. International Journal of Biomedical Imaging, 2015:1-16, 2015. Keyword(s): Distance transform, similarity measures, contours. [bibtex-entry]



5. Thomas Benseghir, Grégoire Malandain, and Régis Vaillant. A tree-topology preserving pairing for 3D/2D registration. International Journal of Computer Assisted Radiology and Surgery, 10(6):913-923, 2015. Note: Information Processing in Computer-Assisted Interventions (IPCAI) 2015 Special Issue. Keyword(s): Registration, Tree, Coronary Arteries, X-ray, Navigation, Iterative Closest Curve. [bibtex-entry]



6. David M. Cash, Chris Frost, Leonardo O. Iheme, Devrim Ünay, Melek Kandemir, Jurgen Fripp, Olivier Salvado, Pierrick Bourgeat, Martin Reuter, Bruce Fischl, Marco Lorenzi, Giovanni B. Frisoni, Xavier Pennec, Ronald K. Pierson, Jeffrey L. Gunter, Matthew L. Senjem, Clifford R. Jack, Nicolas Guizard, Vladimir S. Fonov, D. Louis Collins, Marc Modat, Jorge M. Cardoso, Kelvin K. Leung, Hongzhi Wang, Sandhitsu R. Das, Paul A. Yushkevich, Ian B. Malone, Nick C. Fox, Jonathan M. Schott, and Sebastien Ourselin. Assessing atrophy measurement techniques in dementia: Results from the MIRIAD atrophy challenge. NeuroImage, 123:149-164, December 2015. [bibtex-entry]



7. Hubert Cochet, Arnaud Denis, Yuki Komatsu, Amir S. Jadidi, Tassadit Aït Ali, Frédéric Sacher, Nicolas Derval, Jatin Relan, Maxime Sermesant, Olivier Corneloup, Mélèze Hocini, Michel Haïssaguerre, François Laurent, Michel Montaudon, and Pierre Jaïs. Automated Quantification of Right Ventricular Fat at Contrast-enhanced Cardiac Multidetector CT in Arrhythmogenic Right Ventricular Cardiomyopathy. Radiology, 275(3):683-91, June 2015. [bibtex-entry]



8. Nicolas Cordier, Hervé Delingette, and Nicholas Ayache. A patch-based approach for the segmentation of pathologies: Application to glioma labelling. IEEE Transactions on Medical Imaging, 35(4):11, December 2015. Keyword(s): patch-based, multi-atlas, glioma, segmentation. [bibtex-entry]



9. Marco Lorenzi, Nicholas Ayache, and Xavier Pennec. Regional flux analysis for discovering and quantifying anatomical changes: An application to the brain morphometry in Alzheimer's disease. NeuroImage, 115:224-234, July 2015. [bibtex-entry]



10. Marco Lorenzi, Xavier Pennec, Giovanni B. Frisoni, and Nicholas Ayache. Disentangling normal aging from Alzheimer's disease in structural magnetic resonance images. Neurobiology of Aging, 36:S42-S52, January 2015. [bibtex-entry]



11. Jan Margeta, Antonio Criminisi, Rocio Cabrera Lozoya, Daniel C. Lee, and Nicholas Ayache. Fine-tuned convolutional neural nets for cardiac MRI acquisition plane recognition. Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, August 2015. Note: This is an electronic version of an article published inComputer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualizationon 13 August 2015, by Taylor & Francis, DOI: 10.1080/21681163.2015.1061448.Available online at: http://www.tandfonline.com/10.1080/21681163.2015.1061448. Keyword(s): Transfer learning, Fine-tuning, SSFP, Planes of acquisition, Machine learning, Cardiac magnetic resonance, Convolutional neural networks, Magnetic resonance, Cardiac imaging, Deep learning. [bibtex-entry]



12. Kristin Mcleod, Maxime Sermesant, Philipp Beerbaum, and Xavier Pennec. Spatio-Temporal Tensor Decomposition of a Polyaffine Motion Model for a Better Analysis of Pathological Left Ventricular Dynamics. IEEE Transactions on Medical Imaging, 34(7):1562-1675, July 2015. Keyword(s): cardiac modelling, atlas, non-rigid image registration, motion tracking, population statistics, tensor decomposition, spatio-temporal alignment, Tetralogy of Fallot. [bibtex-entry]



13. Bjoern H Menze, Koen van Leemput, Danial Lashkari, Tammy Riklin-Raviv, Ezequiel Geremia, Esther Alberts, Philipp Gruber, Susanne Wegener, Marc-André Weber, Gabor Szekely, Nicholas Ayache, and Polina Golland. A generative probabilistic model and discriminative extensions for brain lesion segmentation -- with application to tumor and stroke. IEEE Transactions on Medical Imaging, November 2015. [bibtex-entry]



14. Nina Miolane and Xavier Pennec. Computing Bi-Invariant Pseudo-Metrics on Lie Groups for Consistent Statistics. Entropy, 17(4):1850-1881, April 2015. [bibtex-entry]



15. Catalina Tobon-Gomez, Arjan J. Geers, Jochen Peters, Jürgen Weese, Karen Pinto, Rashed Karim, Mohammed Ammar, Abdelaziz Daoudi, Jan Margeta, Zulma Sandoval, Birgit Stender, Yefeng Zheng, Maria A Zuluaga, Julian Betancur, Nicholas Ayache, Mohammed Amine Chikh, Jean-Louis Dillenseger, Michael B. Kelm, Saïd Mahmoudi, Sébastien Ourselin, Alexander Schlaefer, Tobias Schaeffter, Reza Razavi, and Kawal S. Rhode. Benchmark for Algorithms Segmenting the Left Atrium From 3D CT and MRI Datasets. IEEE Transactions on Medical Imaging, 34(7):1460-1473, July 2015. Keyword(s): Benchmark testing, automatic segmentations, atrial fibrillation ablation guidance, anatomical regions, 3D CT datasets, Left Atrial Segmentation Challenge, left atrial surface, ground truth, image segmentation, LA appendage trunk, LASC, LA segmentation, left atrial anatomy, left atrium, Magnetic Resonance Imaging, Measurement, medical image processing, MRI datasets, multiple input data, physiological models, pulmonary vein proximal sections, region growing approach, Shape, standardisation framework, statistical analysis, statistical models, biomedical MRI, biophysical modelling, blood vessels, cardiovascular disease, cardiovascular system, Computed Tomography, computerised tomography, diseases, Educational institutions, electroanatomical mapping systems, evaluation code, fibrosis quantification. [bibtex-entry]



16. Clair Vandersteen, Thomas Demarcy, Coralie Roger, Eric Fontas, Charles Raffaelli, Nicholas Ayache, Hervé Delingette, and Nicolas Guevara. Impact of the surgical experience on cochleostomy location: a comparative temporal bone study between endaural and posterior tympanotomy approaches for cochlear implantation. European Archives of Oto-Rhino-Laryngology, pp 1-7, 2015. Keyword(s): Cochlear implantation, Cochleostomy, Minimally invasive surgery, Endaural approach, Learning skills, Surgery resident, Compétences d'apprentissage, Voie endaurale, Chirurgie mini-invasive, Cochléostomie, Implantation cochléaire, Interne en chirurgie. [bibtex-entry]



17. Ken C.L. Wong, Maxime Sermesant, Kawal Rhode, Matthew Ginks, C. Aldo Rinaldi, Reza Razavi, Hervé Delingette, and Nicholas Ayache. Velocity-based cardiac contractility personalization from images using derivative-free optimization. Journal of the mechanical behavior of biomedical materials, 43:35-52, March 2015. Keyword(s): parameter estimation, model personalization, derivative-free optimization, Cardiac contractility, cardiac electromechanical model. [bibtex-entry]



18. Hervé Delingette and Nicholas Ayache. Building Patient-Specific Physical and Physiological Computational Models from Medical Images. In Paragios, Nikos, Duncan, Jim, Ayache, and Nicholas, editors, Handbook of Biomedical Imaging: Methodologies and Clinical Research, pages 169-182. Springer US, 2015. [bibtex-entry]



19. Xavier Pennec and Pierre Fillard. Statistical Computing on Non-Linear Spaces for Computational Anatomy. In Paragios, Nikos, Duncan, Jim, Ayache, and Nicholas, editors, Handbook of Biomedical Imaging: Methodologies and Clinical Research, pages 147-168. Springer, 2015. [bibtex-entry]

1. Romain Guibert, Kristin Mcleod, Alfonso Caiazzo, Tommaso Mansi, Miguel Angel Fernández, Maxime Sermesant, Xavier Pennec, Irene Vignon-Clementel, Younes Boudjemline, and Jean-Frédéric Gerbeau. Group-wise Construction of Reduced Models for Understanding and Characterization of Pulmonary Blood Flows from Medical Images. Medical Image Analysis, 18(1):63-82, 2014. Keyword(s): Computational fluid dynamics, Pulmonary artery, Tetralogy of Fallot, Atlas construction, Proper orthogonal decomposition. [bibtex-entry]



2. Antoine Iannessi, Pierre Yves Marcy, Olivier Clatz, Nicholas Ayache, and Pierre Fillard. Touchless User Interface for Intraoperative Image Control: Almost There. Radiographics, 34(4), July 2014. [bibtex-entry]



3. A Iannessi, P.-y Marcy, O Clatz, P Fillard, and N Ayache. Touchless intra-operative display for interventional radiologist. Diagnostic and Interventional Imaging, 2014. Keyword(s): User-computer interface, Gesture, CT-scan, Interventional radiology, Sterility. [bibtex-entry]



4. Y. Komatsu, A. Jadidi, F. Sacher, A. Denis, M. Daly, N. Derval, A. Shah, H. Lehrmann, C.-I. Park, R. Weber, T. Arentz, G. Pache, Maxime Sermesant, Nicholas Ayache, J. Relan, M. Montaudon, F. Laurent, M. Hocini, M. Haissaguerre, P. Jais, and Hubert Cochet. Relationship Between MDCT-Imaged Myocardial Fat and Ventricular Tachycardia Substrate in Arrhythmogenic Right Ventricular Cardiomyopathy. Journal of the American Heart Association, 3(4):10, 2014. [bibtex-entry]



5. Herve Lombaert, Leo Grady, Xavier Pennec, Nicholas Ayache, and Farida Cheriet. Spectral Log-Demons: Diffeomorphic Image Registration with Very Large Deformations. International Journal of Computer Vision, 107(3):254-271, May 2014. [bibtex-entry]



6. Bjoern Menze, Andras Jakab, Stefan Bauer, Jayashree Kalpathy-Cramer, Keyvan Farahani, Justin Kirby, Yuliya Burren, Nicole Porz, Johannes Slotboom, Roland Wiest, Levente Lanczi, Elisabeth Gerstner, Marc-Andre Weber, Tal Arbel, Brian Avants, Nicholas Ayache, Patricia Buendia, Louis Collins, Nicolas Cordier, Jason Corso, Antonio Criminisi, Tilak Das, Hervé Delingette, Cagatay Demiralp, Christopher Durst, Michel Dojat, Senan Doyle, Joana Festa, Florence Forbes, Ezequiel Geremia, Ben Glocker, Polina Golland, Xiaotao Guo, Andac Hamamci, Khan Iftekharuddin, Raj Jena, Nigel John, Ender Konukoglu, Danial Lashkari, Jose Antonio Mariz, Raphael Meier, Sergio Pereira, Doina Precup, S. J. Price, Tammy Riklin-Raviv, Syed Reza, Michael Ryan, Lawrence Schwartz, Hoo-Chang Shin, Jamie Shotton, Carlos Silva, Nuno Sousa, Nagesh Subbanna, Gabor Szekely, Thomas Taylor, Owen Thomas, Nicholas Tustison, Gozde Unal, Flor Vasseur, Max Wintermark, Dong Hye Ye, Liang Zhao, Binsheng Zhao, Darko Zikic, Marcel Prastawa, Mauricio Reyes, and Koen van Leemput. The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS). IEEE Transactions on Medical Imaging, 34(10):1993-2024, October 2014. [bibtex-entry]



7. Antonio Porras, Martino Alessandrini, Mathieu de Craene, Nicolas Duchateau, Marta Sitges, Bart Bijnens, Hervé Delingette, Maxime Sermesant, Jan d'Hooge, Alejandro Frangi, and Gemma Piella. Improved Myocardial Motion Estimation Combining Tissue Doppler and B-Mode Echocardiographic Images. IEEE Transactions on Medical Imaging, 33(11):2098 - 2106, June 2014. Keyword(s): Echocardiography, free form deformation (FFD), image registration, motion estimation. [bibtex-entry]



8. Adityo Prakosa, Maxime Sermesant, Pascal Allain, Nicolas Villain, Christopher Aldo Rinaldi, Kawal Rhode, Reza Razavi, Hervé Delingette, and Nicholas Ayache. Cardiac Electrophysiological Activation Pattern Estimation from Images using a Patient-Specific Database of Synthetic Image Sequences. IEEE Transactions on Biomedical Engineering, 61(2):235 - 245, 2014. [bibtex-entry]



9. Avan Suinesiaputra, Brett Cowan, Ahmed O. Al-Agamy, Mustafa A. Alattar, Nicholas Ayache, Ahmed S. Fahmy, Ayman M. Khalifa, Pau Medrano-Gracia, Marie-Pierre Jolly, Alan H. Kadish, Daniel C. Lee, Jan Margeta, Simon K. Warfield, and Alistair Young. A Collaborative Resource to Build Consensus for Automated Left Ventricular Segmentation of Cardiac MR Images. Medical Image Analysis, 18(1):50-62, 2014. [bibtex-entry]



10. Yuliya Tarabalka, Guillaume Charpiat, Ludovic Brucker, and Bjoern Menze. Spatio-Temporal Video Segmentation with Shape Growth or Shrinkage Constraint. IEEE Transactions on Image Processing, 23(9):3829-3840, September 2014. [bibtex-entry]



11. A. Frangi, Denis Friboulet, Nicholas Ayache, H. Delingette, T. Glatard, C. Hoogendoorn, L. Humbert, K. Lekadir, I. Larrabide, Y. Martelli, F. Peyrin, X. Planes, Maxime Sermesant, M.C. Villa-Uriol, T. Whitmarsh, and D. Atkinson. Image Based Modelling. In Peter Coveney, Vanessa Diaz, Peter Hunter, and Marco Viceconti, editors, Computational Biomedicine, pages 59 - 82. Oxford University Press, 2014. [bibtex-entry]



12. Marco Lorenzi and Xavier Pennec. Discrete Ladders for Parallel Transport in Transformation Groups with an Affine Connection Structure. In Frank Nielsen, editor, Geometric Theory of Information, Signals and Communication Technology, pages 243-271. Springer, 2014. [bibtex-entry]

1. Marine Breuilly, Grégoire Malandain, Julien Guglielmi, Robert Marsault, Thierry Pourcher, Philippe R. Franken, and Jacques Darcourt. Amplitude-based data selection for optimal retrospective reconstruction in micro-SPECT. Physics in Medicine and Biology, 58(8):2657-2674, April 2013. [bibtex-entry]



2. François Chung and Hervé Delingette. Regional Appearance Modeling based on the Clustering of Intensity Profiles. Computer Vision and Image Understanding, 117(6):705-717, 2013. [bibtex-entry]



3. Hubert Cochet, Y. Komatsu, F. Sacher, A. Jadidi, D. Scherr, M. Riffaud, N. Derval, A. Shah, L. Roten, P. Pascale, Jatin Relan, Maxime Sermesant, Nicholas Ayache, M. Montaudon, F. Laurent, M. Hocini, M. Haïssaguerre, and Pierre Jaïs. Integration of Merged Delayed-Enhanced Magnetic Resonance Imaging and Multi-Detector Computed Tomography for the Guidance of Ventricular Tachycardia Ablation: A Pilot Study. Journal of Cardiovascular Electrophysiology, 24(4):419-426, April 2013. [bibtex-entry]



4. Stanley Durrleman, Xavier Pennec, Alain Trouvé, José Braga, Guido Gerig, and Nicholas Ayache. Toward a Comprehensive Framework for the Spatiotemporal Statistical Analysis of Longitudinal Shape Data. International Journal of Computer Vision, 103(1):22-59, May 2013. [bibtex-entry]



5. Alejandro F. Frangi, D. Rod Hose, Peter J. Hunter, Nicholas Ayache, and Dana Brooks. Guest Editorial Special Issue on Medical Imaging and Image Computing in Computational Physiology. IEEE Transactions on Medical Imaging, 32(1):1-7, January 2013. [bibtex-entry]



6. Amir S. Jadidi, Hubert Cochet, Ashok J. Shah, Steven J. Kim, Edward Duncan, Shinsuke Miyazaki, Maxime Sermesant, Heiko Lehrmann, Matthieu Lederlin, Nick Linton, Andrei Forclaz, Isabelle Nault, Lena Rivard, Matthew Wright, Xingpeng Liu, Daniel Scherr, Stephen B. Wilton, Laurent Roten, Patrizio Pascale, Nicolas Derval, Frédéric Sacher, Sebastian Knecht, Cornelius Keyl, Mélèze Hocini, Michel Montaudon, François Laurent, Michel Haïssaguerre, and Pierre Jaïs. Inverse relationship between fractionated electrograms and atrial fibrosis in persistent atrial fibrillation: combined magnetic resonance imaging and high-density mapping. Journal of the American College of Cardiology, 62(9):802-812, 2013. [bibtex-entry]



7. Yuki Komatsu, Hubert Cochet, Amir Jadidi, Frédéric Sacher, Ashok Shah, Nicolas Derval, Daniel Scherr, Patrizio Pascale, Laurent Roten, Arnaud Denis, Khaled Ramoul, Shinsuke Miyazaki, Matthew Daly, Matthieu Riffaud, Maxime Sermesant, Jatin Relan, Nicholas Ayache, Steven Kim, Michel Montaudon, François Laurent, Mélèze Hocini, Michel Haïssaguerre, and Pierre Jaïs. Regional myocardial wall thinning at multidetector computed tomography correlates to arrhythmogenic substrate in postinfarction ventricular tachycardia: assessment of structural and electrical substrate. Circulation. Arrhythmia and electrophysiology, 6(2):342-350, 2013. [bibtex-entry]



8. Benedetta Leonardi, Andrew Taylor, Tommaso Mansi, Ingmar Voigt, Maxime Sermesant, Xavier Pennec, Nicholas Ayache, Younes Boudjemline, and Giacomo Pongiglione. Computational modelling of the right ventricle in repaired tetralogy of Fallot: can it provide insight into patient treatment?. European Heart Journal - Cardiovascular Imaging, 14(4):381-6, April 2013. [bibtex-entry]



9. Marco Lorenzi, Nicholas Ayache, Giovanni B. Frisoni, and Xavier Pennec. LCC-Demons: a robust and accurate symmetric diffeomorphic registration algorithm. NeuroImage, 81(1):470-483, 2013. [bibtex-entry]



10. Marco Lorenzi and Xavier Pennec. Efficient Parallel Transport of Deformations in Time Series of Images: from Schild's to Pole Ladder. Journal of Mathematical Imaging and Vision, 50(1-2):5-17, October 2013. [bibtex-entry]



11. Marco Lorenzi and Xavier Pennec. Geodesics, Parallel Transport & One-parameter Subgroups for Diffeomorphic Image Registration. International Journal of Computer Vision, 105(2):111-127, November 2013. [bibtex-entry]



12. Stéphanie Marchesseau, Hervé Delingette, Maxime Sermesant, Rocio Cabrera Lozoya, Catalina Tobon-Gomez, Philippe Moireau, Rosa Maria Figueras I Ventura, Karim Lekadir, Alfredo Hernandez, Mireille Garreau, Erwan Donal, Christophe Leclercq, Simon G. Duckett, Kawal Rhode, Christopher Aldo Rinaldi, Alejandro F. Frangi, Reza Razavi, Dominique Chapelle, and Nicholas Ayache. Personalization of a Cardiac Electromechanical Model using Reduced Order Unscented Kalman Filtering from Regional Volumes. Medical Image Analysis, 17(7):816-829, May 2013. [bibtex-entry]



13. Stéphanie Marchesseau, Hervé Delingette, Maxime Sermesant, Michel Sorine, Kawal Rhode, Simon G. Duckett, Christopher Aldo Rinaldi, Reza Razavi, and Nicholas Ayache. Preliminary Specificity Study of the Bestel-Clément-Sorine Electromechanical Model of the Heart using Parameter Calibration from Medical Images. Journal of the mechanical behavior of biomedical materials, 20:259-271, 2013. [bibtex-entry]



14. Bjoern Menze, Georg Langs, Zhuowen Tu, and Antonio Criminisi. Whole-body anatomy localization via classification and regression forests. Medical Image Analysis, 17(8):1282, December 2013. [bibtex-entry]



15. Katja E. Odening, Bernd A. Jung, Corinna N. Lang, Rocio Cabrera Lozoya, David Ziupa, Marius Menza, Jatin Relan, Gerlind Franke, Stefanie Perez Feliz, Gideon Koren, Manfred Zehender, Christoph Bode, Michael Brunner, Maxime Sermesant, and Daniela Föll. Spatial Correlation of Action Potential Duration and Diastolic Dysfunction in Transgenic and Drug-induced LQT2 Rabbits. Heart Rhythm, 10(10):1533-1541, 2013. Note: Focus Issue: Sudden Cardiac Death. [bibtex-entry]



16. Xavier Pennec, Sarang Joshi, and Mads Nielsen. Mathematical Methods for Medical Imaging. International Journal of Computer Vision, 105(2):109-110, August 2013. [bibtex-entry]



17. A. Prakosa, Maxime Sermesant, H. Delingette, S. Marchesseau, E. Saloux, Pascal Allain, N. Villain, and Nicholas Ayache. Generation of Synthetic but Visually Realistic Time Series of Cardiac Images Combining a Biophysical Model and Clinical Images. IEEE Transactions on Medical Imaging, 32(1):99-109, January 2013. [bibtex-entry]



18. Islem Rekik, Stéphanie Allassonnière, Olivier Clatz, Ezequiel Geremia, Erin Stretton, Hervé Delingette, and Nicholas Ayache. Tumor Growth Parameters Estimation and Source Localization From a Unique Time Point: Application to Low-grade Gliomas. Computer Vision and Image Understanding, 117(3):238-249, 2013. [bibtex-entry]



19. Stefan Sommer, François Lauze, Mads Nielsen, and Xavier Pennec. Sparse Multi-Scale Diffeomorphic Registration: the Kernel Bundle Framework. Journal of Mathematical Imaging and Vision, 46(3):292-308, 2013. [bibtex-entry]



20. Stefan Sommer, Mads Nielsen, Sune Darkner, and Xavier Pennec. Higher-order momentum distributions and locally affine LDDMM registration. SIAM Journal on Imaging Sciences, 6(1):341-367, February 2013. [bibtex-entry]



21. Hugo Talbot, Stéphanie Marchesseau, Christian Duriez, Maxime Sermesant, Stéphane Cotin, and Hervé Delingette. Towards an Interactive Electromechanical Model of the Heart. Interface Focus, 3(2):4, April 2013. Keyword(s): electrophysiology cardiac mechanics training simulation interactive SOFA framework. [bibtex-entry]



22. Catalina Tobon-Gomez, Nicolas Duchateau, Rafael Sebastian, Stéphanie Marchesseau, Oscar Camara, Erwan Donal, Mathieu de Craene, Ali Pashaei, Jatin Relan, Martin Steghofer, Pablo Lamata, Hervé Delingette, Simon G. Duckett, Mireille Garreau, Alfredo Hernandez, Kawal S. Rhode, Maxime Sermesant, Nicholas Ayache, Christophe Leclercq, Reza Razavi, Nicolas P. Smith, and Alejandro F. Frangi. Understanding the mechanisms amenable to CRT response: from pre-operative multimodal image data to patient-specific computational models. Medical and Biological Engineering and Computing, pp 1-16, 2013. [bibtex-entry]



23. Catalina Tobon-Gomez, Mathieu de Craene, Kristin Mcleod, Lennart Tautz, Wenzhe Shi, Anja Hennemuth, Adityo Prakosa, Hengui Wang, Gerald Carr-White, Sergio Kapetanakis, Albert Lutz, Vernon Rasche, Tobias Schaeffter, Constantin Butakoff, Oskar Friman, Tommaso Mansi, Maxime Sermesant, Xiahai Zhuang, Sébastien Ourselin, Hans Otto Peitgen, Xavier Pennec, Reza Razavi, Daniel Rueckert, Alejandro F. Frangi, and Kawal Rhode. Benchmarking framework for myocardial tracking and deformation algorithms: an open access database. Medical Image Analysis, 17(6):632-648, 2013. [bibtex-entry]



24. Nicolas Toussaint, Christian T. Stoeck, Tobias Schaeffter, Sebastian Kozerke, Maxime Sermesant, and Philip G. Batchelor. In vivo human cardiac fibre architecture estimation using shape-based diffusion tensor processing. Medical Image Analysis, 2013. Note: In press. Keyword(s): Diffusion tensor imaging. [bibtex-entry]



25. Jan Unkelbach, Bjoern Menze, Ender Konukoglu, Florian Dittmann, Nicholas Ayache, and Helen Shi. Radiotherapy planning for glioblastoma based on a tumor growth model: implications for spatial dose redistribution. Physics in Medicine and Biology, December 2013. [bibtex-entry]



26. Jan Unkelbach, Bjoern Menze, Ender Konukoglu, Florian Dittmann, Matthieu Le, Nicholas Ayache, and Helen Shi. Radiotherapy planning for glioblastoma based on a tumor growth model: improving target volume delineation. Physics in Medicine and Biology, December 2013. [bibtex-entry]



27. Irina Vidal-Migallón, Olivier Commowick, Xavier Pennec, Julien Dauguet, and Tom Vercauteren. GPU & CPU implementation of Young - Van Vliet's Recursive Gaussian Smoothing Filter. Insight Journal, pp 16, July 2013. Note: Open peer-review journal. Open code / open data. Keyword(s): GPU, OpenCL, Recursive Gaussian Smoothing. [bibtex-entry]



28. Jürgen Weese, Nicholas Ayache, and Nicolas P. Smith. Personalized Cardiac Modeling and Simulations in euHeart. Medical and Biological Engineering and Computing, 2013. Note: Editorial. [bibtex-entry]



29. Mathieu de Craene, Stéphanie Marchesseau, Brecht Heyde, Hang Gao, M. Alessandrini, Olivier Bernard, Gemma Piella, Antonio Porras, Lennart Tautz, Anja Hennemuth, Adityo Prakosa, Hervé Liebgott, Oudom Somphone, Pascal Allain, S. Makram Ebeid, Hervé Delingette, Maxime Sermesant, Jan d'Hooge, and Eric Saloux. 3D strain assessment in ultrasound (straus): A synthetic comparison of five tracking methodologies. IEEE Transactions on Medical Imaging, 32(9):1632 - 1646, 2013. [bibtex-entry]



30. Ezequiel Geremia, Darko Zikic, Olivier Clatz, Bjoern H. Menze, Ben Glocker, Ender Konukoglu, Jamie Shotton, O. M. Thomas, S. J. Price, Tilak Das, Raj Jena, Nicholas Ayache, and Antonio Criminisi. Classification Forests for Semantic Segmentation of Brain Lesions in Multi-channel MRI. In Criminisi, Antonio, Shotton, and J., editors, Decision Forests for Computer Vision and Medical Image Analysis, Advances in Computer Vision and Pattern Recognition, pages 245-260. Springer London, 2013. [bibtex-entry]



31. Kristin Mcleod, Tommaso Mansi, Maxime Sermesant, Giacomo Pongiglione, and Xavier Pennec. Statistical Shape Analysis of Surfaces in Medical Images Applied to the Tetralogy of Fallot Heart. In Frederic Cazals and Pierre Kornprobst, editors, Modeling in Computational Biology and Biomedicine, Lectures Notes in Mathematical and Computational Biology, pages 165-191. Springer, 2013. [bibtex-entry]

1. Barbara André, Tom Vercauteren, Anna M. Buchner, Murli Krishna, Nicholas Ayache, and Michael B. Wallace. Software for Automated Classification of probe-based Confocal Laser Endomicroscopy Videos of Colorectal Polyps. World Journal of Gastroenterology, October 2012. [bibtex-entry]



2. Barbara André, Tom Vercauteren, Anna M. Buchner, Michael B. Wallace, and Nicholas Ayache. Learning Semantic and Visual Similarity for Endomicroscopy Video Retrieval. IEEE Transactions on Medical Imaging, 31(6):1276-1288, June 2012. [bibtex-entry]



3. R. Blanc, Christof Seiler, G. Székely, L. Nolte, and Mauricio Reyes. Statistical Model Based Shape Prediction from a Combination of Direct Observations and Various Surrogates. Medical Image Analysis (MedIA), 16(6):1156-1166, 2012. [bibtex-entry]



4. H. Cochet, Y. Komatsu, F. Sacher, A. Jadidi, D. Scherr, M. Riffaud, N. Derval, A. Shah, L. Roten, P. Pascale, Jatin Relan, Maxime Sermesant, Nicholas Ayache, M. Montaudon, F. Laurent, M. Hocini, M. Haïssaguerre, and P. Jaïs. Integration of Merged Delayed-Enhanced Magnetic Resonance Imaging and Multi-Detector Computed Tomography for the Guidance of Ventricular Tachycardia Ablation: A Pilot Study. Journal of Cardiovascular Electrophysiology, 2012. ISSN: 1540-8167. Keyword(s): ventricular tachycardia, MRI, computed tomography, catheter ablation, myocardial infarction, cardiomyopathy. [bibtex-entry]



5. Hervé Delingette, F. Billet, Ken C. L. Wong, Maxime Sermesant, Kawal Rhode, M. Ginks, C. Aldo Rinaldi, Reza Razavi, and Nicholas Ayache. Personalization of Cardiac Motion and Contractility From Images Using Variational Data Assimilation. Biomedical Engineering, IEEE Transactions on, 59(1):20 -24, jan. 2012. ISSN: 0018-9294. [bibtex-entry]



6. Stanley Durrleman, Xavier Pennec, Alain Trouvé, Nicholas Ayache, and José Braga. Comparison of the endocranial ontogenies between chimpanzees and bonobos via temporal regression and spatiotemporal registration. Journal of Human Evolution, 62(1):74 - 88, 2012. ISSN: 0047-2484. Keyword(s): Endocranium. [bibtex-entry]



7. B. Michael Kelm, Frederik O. Kaster, A. Henning, Marc-André Weber, P. Bachert, P. Boesiger, Fred A. Hamprecht, and Bjoern H. Menze. Using spatial prior knowledge in the spectral fitting of MRS images. NMR in Biomedicine, 25(1):1-13, 2012. HAL ID: inria-00616193. [bibtex-entry]



8. Hervé Lombaert, Jean-Marc Peyrat, Pierre Croisille, Stanislas Rapacchi, Laurent Fanton, Farida Cheriet, Patrick Clarysse, Isabelle Magnin, Hervé Delingette, and Nicholas Ayache. Human Atlas of the Cardiac Fiber Architecture: Study on a Healthy Population. IEEE Trans. on Medical Imaging, 31(7):1436-1447, 2012. [bibtex-entry]



9. Stéphanie Marchesseau, Hervé Delingette, Maxime Sermesant, and Nicholas Ayache. Fast Parameter Calibration of a Cardiac Electromechanical Model from Medical Images based on the Unscented Transform. Biomechanics and Modeling in Mechanobiology, 2012. [bibtex-entry]



10. Christophe Person, Valérie Louis-Dorr, Sylvain Poussier, Olivier Commowick, Grégoire Malandain, Louis Maillard, Didier Wolf, Nicolas Gilet, Véronique Roch, Gilles Karcher, and Pierre-Yves Marie. Voxel-based quantitative analysis of brain images from F-18 Fluorodeoxyglucose Positron Emission Tomography with a Block-Matching algorithm for spatial normalization. Clinical Nuclear Medicine, 37(3):268-273, 2012. HAL ID: hal-00651731. [bibtex-entry]



11. M. Pop, Maxime Sermesant, G. Liu, Jatin Relan, Tommaso Mansi, A. Soong, Jean-Marc Peyrat, M.V. Truong, P. Fefer, Elliot R. McVeigh, Hervé Delingette, A.J. Dick, Nicholas Ayache, and G.A Wright. Construction of 3D MR image-based computer models of pathologic hearts, augmented with histology and optical fluorescence imaging to characterize action potential propagation. Medical Image Analysis, 16(2):505-523, February 2012. [bibtex-entry]



12. L. Ritacco, Christof Seiler, G. Farfalli, L. Nolte, Mauricio Reyes, D. Muscolo, and L. Tinao. Validity of an Automatic Measure Protocol in Distal Femur for Allograft Selection from a Three-Dimensional Virtual Bone Bank System. Cell and Tissue Banking, 2012. Note: To appear. [bibtex-entry]



13. Roberta Rossi, Michela Pievani, Marco Lorenzi, Marina Boccardi, Rossella Beneduce, Stefano Bignotti, Genoveffa Borsci, Maria Cotelli, Panteleimon Giannakopoulos, Laura R. Magni, Luciana Rillosi, Sandra Rosini, Giuseppe Rossi, and Giovanni B. Frisoni. Structural brain features of borderline personality and bipolar disorders. Psychiatry Research: Neuroimaging, 12:S0925-4927, 2012. [bibtex-entry]



14. Christof Seiler, A. Gazdhar, Mauricio Reyes, L.M. Benneker, T. Geiser, K.A. Siebenrock, and B. Gantenbein-Ritter. Time-Lapse Microscopy and Classification of 2D Human Mesenchymal Stem Cells Based on Cell Shape Picks Up Myogenic from Osteogenic and Adipogenic Differentiation. Journal of Tissue Engineering and Regenerative Medicine, 2012. Note: To appear. [bibtex-entry]



15. Christof Seiler, Xavier Pennec, and Mauricio Reyes. Capturing the Multiscale Anatomical Shape Variability with Polyaffine Transformation Trees. Medical Image Analysis (MedIA), 16(7):1371-1384, 2012. [bibtex-entry]



16. Maxime Sermesant, R. Chabiniok, P. Chinchapatnam, Tommaso Mansi, F. Billet, P. Moireau, Jean-Marc Peyrat, Ken C. L. Wong, Jatin Relan, Kawal Rhode, M. Ginks, P. Lambiase, Hervé Delingette, M. Sorine, C. Aldo Rinaldi, D. Chapelle, Reza Razavi, and Nicholas Ayache. Patient-specific electromechanical models of the heart for the prediction of pacing acute effects in CRT: A preliminary clinical validation. Medical Image Analysis, 16(1):201-215, 2012. [bibtex-entry]



17. Juliette Thariat, Pierre-Yves Marcy, A. Lacout, Liliane Ramus, T. Girinsky, Y. Pointreau, and Grégoire Malandain. Radiotherapy and radiology: joint efforts for modern radiation planning and practice. Diagn Interv Imaging, 93(5):342-50, May 2012. [Abstract] [bibtex-entry]



18. Juliette Thariat, Liliane Ramus, Philippe Maingon, Guillaume Odin, Vincent Gregoire, Vincent Darcourt, Nicolas Guevara, Marie-Helene Orlanducci, Serge Marcie, Gilles Poissonnet, Pierre-Yves Marcy, Alex Bozec, Olivier Dassonville, Laurent Castillo, Francois Demard, Jose Santini, and Grégoire Malandain. DENTALMAPS: Automatic Dental Delineation for Radiotherapy Planning in Head-and-neck Cancer. Int J Radiat Oncol Biol Phys, 82(5):1858-65, April 2012. [Abstract] [bibtex-entry]



19. Florian Vichot, H. Cochet, Benoit Bleuzé, Nicolas Toussaint, P. Jaïs, and Maxime Sermesant. Cardiac Interventional Guidance using Multimodal Data Processing and Visualisation: medInria as an Interoperability Platform. Midas Journal, 2012. Keyword(s): Standards, Data Formats, Registration, Visualisation. [Abstract] [bibtex-entry]



20. François Faure, Christian Duriez, Hervé Delingette, Jérémie Allard, Benjamin Gilles, Stéphanie Marchesseau, Hugo Talbot, Hadrien Courtecuisse, Guillaume Bousquet, Igor Peterlik, and Stéphane Cotin. SOFA: A Multi-Model Framework for Interactive Physical Simulation. In Yohan Payan, editor, Soft Tissue Biomechanical Modeling for Computer Assisted Surgery. Springer, June 2012. HAL ID: hal-00681539. [bibtex-entry]



21. Xavier Pennec and Vincent Arsigny. Exponential Barycenters of the Canonical Cartan Connection and Invariant Means on Lie Groups. In Frederic Barbaresco, Amit Mishra, and Frank Nielsen, editors, Matrix Information Geometry, pages 123-166. Springer, May 2012. ISBN: 978-3-642-30231-2. HAL ID: hal-00699361. [Abstract] [bibtex-entry]

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] [bibtex-entry]



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. [bibtex-entry]



3. N. Ayache, H. Delingette, and M. Sermesant. Le coeur numérique personnalisé. Bulletin de l'Académie Nationale de Médecine, 195(8), November 2011. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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] [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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] [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]



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. [bibtex-entry]

1. M Cohen, C Lebrun, D Aufauvre, S Chanalet, C Filleau-Bertogliatti, W Camu, P Thomas, G Malandain, and P Clavelou. [Longitudinal study of health related quality of life in multiple sclerosis: correlation with MRI parameters]. Rev Neurol (Paris), 166(11):894-900, November 2010. Note: [In French]. Keyword(s): Adolescent, Adult, Atrophy, Brain, pathology, Cognition, physiology, Contrast Media, Disease Progression, Female, Gadolinium, Humans, Image Processing Computer-Assisted, Interferon Type I, therapeutic use, Longitudinal Studies, Magnetic Resonance Imaging, Male, Middle Aged, Multiple Sclerosis Chronic Progressive, pathology, Neuropsychological Tests, Quality of Life, Recombinant Proteins, Young Adult. [Abstract] [bibtex-entry]



2. Hervé Delingette and Maxime Sermesant. Le coeur numérique. Doc Sciences, 13:26-33, October 2010. [bibtex-entry]



3. Romain Fernandez, Pradeep Das, Vincent Mirabet, Eric Moscardi, Jan Traas, Jean-Luc Verdeil, Grégoire Malandain, and Christophe Godin. Imaging plant growth in 4-D: robust tissue reconstruction and lineaging at cell resolution. Nature Methods, 7(7):547-553, 2010. [Abstract] [bibtex-entry]



4. Damien Galanaud, Stéphane Haik, Marius George Linguraru, Jean-Philippe Ranjeva, Baptiste Faucheux, Elsa Kaphan, Nicholas Ayache, Jacques Chiras, Patrick Cozzone, Didier Dormont, and Jean-Philippe Brandel. Combined diffusion imaging and MR Spectroscopy in Human Prion Diseases. AJNR. American journal of neuroradiology, 31(7):1311-8, 2010. [Abstract] [bibtex-entry]



5. D. Gianni, S. McKeever, T. Yu, R. Britten, Hervé Delingette, A. Frangi, P. Hunter, and Nic Smith. Sharing and reusing cardiovascular anatomical models over the Web: a step towards the implementation of the virtual physiological human project. Philos Transact of the Royal Society A Mathematical Physical Engineering Sciences, 368:3039-3056, June 2010. [bibtex-entry]



6. Ender Konukoglu, Olivier Clatz, Pierre-Yves Bondiau, Hervé Delingette, and Nicholas Ayache. Extrapolating Glioma Invasion Margin in Brain Magnetic Resonance Images: Suggesting New Irradiation Margins. Medical Image Analysis, 14(2):111-125, 2010. [bibtex-entry]



7. Ender Konukoglu, Olivier Clatz, Bjoern H. Menze, Marc-André Weber, Bram Stieltjes, Emmanuel Mandonnet, Hervé Delingette, and Nicholas Ayache. Image Guided Personalization of Reaction-Diffusion Type Tumor Growth Models Using Modified Anisotropic Eikonal Equations. IEEE Transactions on Medical Imaging, 29(1):77-95, 2010. [bibtex-entry]



8. Marco Lorenzi, Michael Donohue, Donata Paternico, Cristina Scarpazza, Susanne Ostrowitzki, Olivier Blin, Elaine Irving, and G. Frisoni. Enrichment through biomarkers in clinical trials of Alzheimer's drugs in patients with mild cognitive impairment. Neurobiology of Aging, pp 1443-51, August 2010. Note: Special Issue on ADNI. [bibtex-entry]



9. Stéphanie Marchesseau, T. Heimann, Simon Chatelin, Rémy Willinger, and Hervé Delingette. Fast porous visco-hyperelastic soft tissue model for surgery simulation: application to liver surgery. Progress in Biophysics and Molecular Biology, 103(2-3):185-196, 2010. [bibtex-entry]



10. Markand D. Patel, Nicolas Toussaint, Geoffrey D. Charles-Edwards, Jean-Pierre Lin, and Philip G. Batchelor. Distribution and Fibre Field Similarity Mapping of the Human Anterior Commissure Fibres by Diffusion Tensor Imaging. Magnetic Resonance Materials in Physics, Biology and Medicine, February 2010. [bibtex-entry]



11. Jean-Marc Peyrat, Hervé Delingette, Maxime Sermesant, Chenyang Xu, and Nicholas Ayache. Registration of 4D Cardiac CT Sequences Under Trajectory Constraints With Multichannel Diffeomorphic Demons. IEEE Transactions on Medical Imaging, 29(7):1351-1368, July 2010. [bibtex-entry]



12. Liliane Ramus, Juliette Thariat, Pierre-Yves Marcy, Yoann Pointreau, Guillaume Bera, Olivier Commowick, and Grégoire Malandain. Outils de contourage, utilisation et construction d'atlas anatomiques : exemples des cancers de la tete et du cou. Cancer radiothérapie, 14(3):206-12, 2010. Note: In French. [Abstract] [bibtex-entry]



13. Tammy Riklin-Raviv, Koen Van Leemput, Bjoern H. Menze, William M. Wells, and Polina Golland. Segmentation of image ensembles via latent atlases. Medical Image Analysis, 14(5):654-65, 2010. [bibtex-entry]



14. Boon Thye Thomas Yeo, Mert Sabuncu, Tom Vercauteren, Nicholas Ayache, Bruce Fischl, and Polina Golland. Spherical Demons: Fast Diffeomorphic Landmark-Free Surface Registration. IEEE Transactions on Medical Imaging, 29(3):650-668, March 2010. Note: PMID:19709963. [Abstract] [bibtex-entry]



15. Ender Konukoglu, Olivier Clatz, Hervé Delingette, and Nicholas Ayache. Personalization of Reaction-Diffusion Tumor Growth Models in MR Images: Application to Brain Gliomas Characterization and Radiotherapy Planning. In Thomas S. Deisboeck and Georgios Stamatakos, editors, Multiscale Cancer Modeling, Chapman & Hall/CRC Mathematical & Computational Biology. CRC Press, December 2010. [bibtex-entry]



16. Maxime Sermesant and Reza Razavi. Personalized Computational Models of the Heart for Cardiac Resynchronization Therapy. In Roy C.P. Kerckhoffs, editor, Patient-Specific Modeling of the Cardiovascular System, pages 167-182. Springer New York, 2010. ISBN: 978-1-4419-6691-9. Keyword(s): Life Sciences. [bibtex-entry]

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]

1. Neculai Archip, Olivier Clatz, Stephen Whalen, Simon Dimaio, Peter Black, Alexandra Golby, Ferenc Jolesz, and Simon Warfield. Compensation of geometric distortion effects on intraoperative magnetic resonance imaging for enhanced visualization in image-guided neurosurgery. Neurosurgery, 62(3 supl. 1):209-15, March 2008. [bibtex-entry]



2. Jonathan Boisvert, Farida Cheriet, Xavier Pennec, Hubert Labelle, and Nicholas Ayache. Articulated Spine Models for 3D Reconstruction from Partial Radiographic Data. IEEE Transactions on Bio-Medical Engineering, 55(11):2565-2574, November 2008. [bibtex-entry]



3. Jonathan Boisvert, Farida Cheriet, Xavier Pennec, Hubert Labelle, and Nicholas Ayache. Geometric Variability of the Scoliotic Spine using Statistics on Articulated Shape Models. IEEE Transactions on Medical Imaging, 27(4):557-568, 2008. [bibtex-entry]



4. Jonathan Boisvert, Farida Cheriet, Xavier Pennec, Hubert Labelle, and Nicholas Ayache. Principal Deformations Modes of Articulated Models for the Analysis of 3D Spine Deformities. Electronic Letters on Computer Vision and Image Analysis, 7(4):13-31, December 2008. [bibtex-entry]



5. Pierre-Yves Bondiau, Olivier Clatz, Maxime Sermesant, Pierre-Yves Marcy, Hervé Delingette, Marc Frenay, and Nicholas Ayache. Biocomputing: numerical simulation of glioblastoma growth using diffusion tensor imaging. Physics in Medicine and Biology, 53(4):879-93, February 2008. [bibtex-entry]



6. P. Chinchapatnam, K.S. Rhode, M. Ginks, C.A. Rinaldi, P. Lambiase, R. Razavi, S. Arridge, and M. Sermesant. Model-Based Imaging of Cardiac Apparent Conductivity and Local Conduction Velocity for Diagnosis and Planning of Therapy. IEEE Transactions on Medical Imaging, 27(11):1631-1642, 2008. [bibtex-entry]



7. Olivier Commowick, Vincent Arsigny, Aurélie Isambert, Jimena Costa, Frédéric Dhermain, François Bidault, Pierre-Yves Bondiau, Nicholas Ayache, and Grégoire Malandain. An efficient locally affine framework for the smooth registration of anatomical structures. Medical Image Analysis, 12(4):427-41, August 2008. Keyword(s): Algorithms, Brain, anatomy & histology, Diagnostic Imaging, methods, Humans, Image Processing Computer-Assisted, Radiotherapy Planning Computer-Assisted, methods, Sensitivity and Specificity. [Abstract] [bibtex-entry]



8. Olivier Commowick, Vincent Grégoire, and Grégoire Malandain. Atlas-Based Delineation of Lymph Node Levels in Head and Neck Computed Tomography Images. Radiotherapy Oncology, 87(2):281-289, 2008. [bibtex-entry]



9. H. Delingette. Triangular Springs for Modeling Nonlinear Membranes. IEEE Transactions on Visualization and Computer Graphics, 14(2), March/April 2008. [bibtex-entry]



10. Stanley Durrleman, Xavier Pennec, Alain Trouvé, Paul Thompson, and Nicholas Ayache. Inferring brain variability from diffeomorphic deformations of currents: an integrative approach. Medical Image Analysis, 12(5):626-637, 2008. [bibtex-entry]



11. Tristan Glatard, Johan Montagnat, David Emsellem, and Diane Lingrand. A Service-Oriented Architecture enabling dynamic services grouping for optimizing distributed workflows execution. Future Generation Computer Systems, 7(24):720-730, July 2008. [bibtex-entry]



12. Tristan Glatard, Johan Montagnat, Diane Lingrand, and Xavier Pennec. Flexible and efficient workflow deployment of data-intensive applications on GRIDS with MOTEUR. International Journal of High Performance Computing Applications, 3(22):347-360, August 2008. Note: Special issue on Workflow Systems in Grid Environments. [bibtex-entry]



13. S Haik, D Galanaud, MG Linguraru, K Peoc'h, N Privat, BA Faucheux, N Ayache, JJ Hauw, D Dormont, and JP Brandel. In Vivo Detection of Thalamic Gliosis: A Pathoradiologic Demonstration in Familial Fatal Insomnia. Archives of Neurology, 65(4):545-549, April 2008. [Abstract] [bibtex-entry]



14. H. Hufnagel, X. Pennec, J. Ehrhardt, N. Ayache, and H. Handels. Generation of a Statistical Shape Model with Probabilistic Point Correspondences and EM-ICP. International Journal for Computer Assisted Radiology and Surgery, 2(5):265-273, March 2008. [bibtex-entry]



15. A Isambert, G Bonniaud, F Lavielle, G Malandain, and D Lefkopoulos. A phantom study of the accuracy of CT, MR and PET image registrations with a block matching-based algorithm. Cancer radiothérapie, 12(8):800-8, December 2008. Keyword(s): Algorithms, Automation, Brain, pathology, Head, Humans, Magnetic Resonance Imaging, methods, Phantoms Imaging, Positron-Emission Tomography, methods, Radiotherapy Planning Computer-Assisted, methods, Software, Tomography X-Ray Computed, methods. [Abstract] [bibtex-entry]



16. Aurélie Isambert, Frédéric Dhermain, François Bidault, Olivier Commowick, Pierre-Yves Bondiau, Grégoire Malandain, and Dimitri Lefkopoulos. Evaluation of an atlas-based automatic segmentation software for the delineation of brain organs at risk in a radiation therapy clinical context. Radiotherapy Oncology, 87(1):93-9, April 2008. Keyword(s): Algorithms, Brain Neoplasms, pathology, Female, Humans, Image Interpretation Computer-Assisted, methods, Magnetic Resonance Imaging, Male, Middle Aged, ROC Curve, Retrospective Studies, Software, Tomography X-Ray Computed. [Abstract] [bibtex-entry]



17. Emmanuel Mandonnet, Johan Pallud, Olivier Clatz, Hugues Duffau, and Laurent Capelle. Computational Modelling of the WHO Grade II Glioma Dynamics: Principles and Applications to Surgical Strategy. Neurosurgical Review, 31(3):263-9, July 2008. [bibtex-entry]



18. Johan Montagnat, Tristan Glatard, Isabel Campos Plasencia, Francisco Castejon, Xavier Pennec, Giuliano Taffoni, Vladimir Voznesensky, and Claudio Vuerli. Workflow-based data parallel applications on the EGEE production grid infrastructure. Journal of Grid Computing, 6(4):369-383, December 2008. [bibtex-entry]



19. D R Rutgers, P Fillard, G Paradot, M Tadie, P Lasjaunias, and D Ducreux. Diffusion tensor imaging characteristics of the corpus callosum in mild, moderate, and severe traumatic brain injury. AJNR. American journal of neuroradiology, 29(9):1730-5, October 2008. Keyword(s): Adult, Anisotropy, Brain Concussion, diagnosis, Brain Injuries, diagnosis, Corpus Callosum, injuries, Diffuse Axonal Injury, diagnosis, Diffusion Magnetic Resonance Imaging, Female, Follow-Up Studies, Humans, Image Processing Computer-Assisted, Male, Middle Aged, Nerve Fibers, pathology, Young Adult. [Abstract] [bibtex-entry]



20. D R Rutgers, F Toulgoat, J Cazejust, P Fillard, P Lasjaunias, and D Ducreux. White matter abnormalities in mild traumatic brain injury: a diffusion tensor imaging study. AJNR. American journal of neuroradiology, 29(3):514-9, March 2008. Keyword(s): Adult, Brain, pathology, Brain Injuries, pathology, Demyelinating Diseases, pathology, Diffusion Magnetic Resonance Imaging, methods, Female, Humans, Male, Nerve Fibers Myelinated, pathology, Reproducibility of Results, Sensitivity and Specificity. [Abstract] [bibtex-entry]



21. M Sermesant, J M Peyrat, P Chinchapatnam, F Billet, T Mansi, K Rhode, H Delingette, R Razavi, and N Ayache. Toward patient-specific myocardial models of the heart. Heart Failure Clinics, 4(3):289-301, July 2008. [bibtex-entry]



22. Ender Konukoglu, Xavier Pennec, Olivier Clatz, and Nicholas Ayache. Tumor Growth Modeling in Oncological Image Analysis. In I. Bankman, editor, Handbook of Medical Image Processing and Analysis - New edition, chapter 18, pages 297-307. Academic Press, December 2008. ISBN: 13: 978-0-12-373904-9. [bibtex-entry]



23. X. Pennec. Statistical computing on manifolds: from Riemannian geometry to computational anatomy. In Frank Nielsen, editor, Emerging Trends in Visual Computing, volume 5416 of LNCS, pages 347-386. Springer, 2008. ISBN: 978-3-642-00825-2. [bibtex-entry]



24. Xavier Pennec, Nicholas Ayache, and Jean-Philippe Thirion. Landmark-based registration using features identified through differential geometry. In I. Bankman, editor, Handbook of Medical Image Processing and Analysis - New edition, chapter 34, pages 565-578. Academic Press, December 2008. ISBN: 13: 978-0-12-373904-9. Keyword(s): registration, matching, validation, uncertainty. [bibtex-entry]



25. Tom Vercauteren, Nicholas Ayache, Nicolas Savoire, Grégoire Malandain, and Aymeric Perchant. Processing of In Vivo Fibered Confocal Microscopy Video Sequences. In Jens Rittscher, Raghu Machiraju, and Stephen T. C. Wong, editors, Microscopic Image Analysis for Life Science Applications, chapter 19, pages 441-463. Artech House, 2008. [bibtex-entry]

1. Elsa Angelini, Olivier Clatz, Emmanuel Mandonnet, Ender Konukoglu, Laurent Capelle, and Hugues Duffau. Glioma Dynamics and Computational Models: A Review of Segmentation, Registration, and In Silico Growth Algorithms and their Clinical Applications. Current Medical Imaging Reviews, 3(4):262-176, 2007. [bibtex-entry]



2. Neculai Archip, Olivier Clatz, Stephen Whalen, Dan Kacher, Andriy Fedorov, Andriy Kot, Nikos Chrisochoides, Ferenc Jolesz, Alexandra Golby, Peter Black, and Simon Warfield. Non-rigid alignment of preoperative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery. NeuroImage, 35(2):609-24, April 2007. [bibtex-entry]



3. Vincent Arsigny, Pierre Fillard, Xavier Pennec, and Nicholas Ayache. Geometric Means in a Novel Vector Space Structure on Symmetric Positive-Definite Matrices. SIAM Journal on Matrix Analysis and Applications, 29(1):328-347, 2007. Keyword(s): DT-MRI, Tensors, Riemannian geometry, Lie groups, interpolation, Log-Euclidean metrics. [bibtex-entry]



4. M. A. Audette, H. Delingette, A. Fuchs, O. Burgert, and K. Chinzei. A topologically faithful, tissue-guided, spatially varying meshing strategy for computing patient-specific head models for endoscopic pituitary surgery simulation. Journal of Computer Aided Surgery, 12(1):43-52, January 2007. [bibtex-entry]



5. Valentin Becker, Tom Vercauteren, Claus Hann von Weyern, Christian Prinz, Roland M. Schmid, and Alexander Meining. High Resolution Miniprobe-based Confocal Microscopy in Combination with Video-mosaicing. Gastrointestinal Endoscopy, 66(5):1001-1007, November 2007. [bibtex-entry]



6. Olivier Clatz, Stéphane Litrico, Hervé Delingette, Philippe Paquis, and Nicholas Ayache. Dynamic Model of Communicating Hydrocephalus for Surgery Simulation. IEEE Transactions on Bio-Medical Engineering, 54(4):755-758, April 2007. [bibtex-entry]



7. Julien Dauguet, Thierry Delzescaux, Françoise Condé, Jean-François Mangin, Nicholas Ayache, Philippe Hantraye, and Vincent Frouin. Three-dimensional reconstruction of stained histological slices and 3D non-linear registration with in-vivo MRI for whole baboon brain. Journal of Neuroscience Methods, 164(1):191-204, 2007. [bibtex-entry]



8. D. Ducreux, P. Fillard, D. Facon, A. Ozanne, J.-F. Lepeintre, J. Renoux, M. Tadié, and P. Lasjaunias. Diffusion Tensor Magnetic Resonance Imaging and Fiber Tracking in Spinal Cord Lesions: Current and Future Indications. Neuroimaging Clinics of North America, 17(1):137-147, February 2007. [bibtex-entry]



9. Pierre Fillard, Vincent Arsigny, Xavier Pennec, Kiralee M. Hayashi, Paul M. Thompson, and Nicholas Ayache. Measuring Brain Variability by Extrapolating Sparse Tensor Fields Measured on Sulcal Lines. NeuroImage, 34(2):639-650, January 2007. Note: Also as INRIA Research Report 5887, April 2006. PMID: 17113311. [bibtex-entry]



10. Pierre Fillard, Xavier Pennec, Vincent Arsigny, and Nicholas Ayache. Clinical DT-MRI Estimation, Smoothing and Fiber Tracking with Log-Euclidean Metrics. IEEE Transactions on Medical Imaging, 26(11):1472-1482, November 2007. [bibtex-entry]



11. Marius G. Linguraru, Miguel A. González Ballester, and Nicholas Ayache. Deformable Atlases for the Segmentation of Internal Brain Nuclei in Magnetic Resonance Imaging. International Journal of Computers, Communication and Control, 2(1):26-36, 2007. [bibtex-entry]



12. Marius George Linguraru, Tom Vercauteren, Mauricio Reyes Aguirre, Miguel Ángel González Ballester, and Nicholas Ayache. Segmentation Propagation from Deformable Atlases for Brain Mapping and Analysis. Brain Research Journal, 1(4):269-287, 2007. [bibtex-entry]



13. Jean-Marc Peyrat, Maxime Sermesant, Xavier Pennec, Hervé Delingette, Chenyang Xu, Eliot R. McVeigh, and Nicholas Ayache. A Computational Framework for the Statistical Analysis of Cardiac Diffusion Tensors: Application to a Small Database of Canine Hearts. IEEE Transactions on Medical Imaging, 26(11):1500-1514, November 2007. [bibtex-entry]



14. A. Pitiot, H. Delingette, and P.M. Thompson. Learning Shape Correspondence for n-D curves. International Journal of Computer Vision, 71(1):71-88, January 2007. [bibtex-entry]



15. M Reyes, G Malandain, P M Koulibaly, M A Gonzalez-Ballester, and J Darcourt. Model-based respiratory motion compensation for emission tomography image reconstruction. Physics in Medicine and Biology, 52(12):3579-600, June 2007. [Abstract] [bibtex-entry]



16. Luc Thiberville, Sophie Moreno-Swirc, Tom Vercauteren, Eric Peltier, Charlotte Cavé, and Geneviève Bourg Heckly. In Vivo Imaging of the Bronchial Wall Microstructure Using Fibered Confocal Fluorescence Microscopy. American journal of respiratory and critical care medicine, 175(1):22-31, January 2007. Note: Chosen for the cover of the AJRCCM paper issue. PMID: 17023733. [bibtex-entry]



17. Jérôme Yelnik, Eric Bardinet, Didier Dormont, Grégoire Malandain, Sébastien Ourselin, Dominique Tandé, Carine Karachi, Nicholas Ayache, Philippe Cornu, and Yves Agid. A three-dimensional, histological and deformable atlas of the human basal ganglia. I. Atlas construction based on immunohistochemical and MRI data. NeuroImage, 34(2):618-38, January 2007. [Abstract] [bibtex-entry]



18. Grégoire Malandain. Applications de la géométrie discrète en imagerie médicale. In Géométrie discrète et images numériques, Traités IC2, pages 371-379. Hermès, 2007. [bibtex-entry]

1. Vincent Arsigny, Pierre Fillard, Xavier Pennec, and Nicholas Ayache. Log-Euclidean Metrics for Fast and Simple Calculus on Diffusion Tensors. Magnetic Resonance in Medicine, 56(2):411-421, August 2006. Keyword(s): DT-MRI, Tensors, Riemannian geometry, Lie groups, interpolation, Log-Euclidean metrics. [bibtex-entry]



2. C Bensa, C Bertogliati, S Chanalet, G Malandain, P Bedoucha, and C Lebrun. Early detection of cognitive impairment in relapsing-remitting multiple sclerosis: functional-anatomical correlations and longitudinal follow-up. Revue Neurologique, 162(12):1221-31, December 2006. Note: [In French]. [Abstract] [bibtex-entry]



3. Christophe Blondel, Grégoire Malandain, Régis Vaillant, and Nicholas Ayache. Reconstruction of Coronary Arteries from a Single Rotational X-Ray Projection Sequence. IEEE Transactions on Medical Imaging, 25(5):653-663, May 2006. Keyword(s): Angiocardiography, Coronarography, Image Motion Analysis, Image Reconstruction, Tomography. [Abstract] [bibtex-entry]



4. Francis Cassot, Frederic Lauwers, Céline Fouard, Steffen Prohaska, and Valerie Lauwers-Cances. A novel three-dimensional computer-assisted method for a quantitative study of microvascular networks of the human cerebral cortex. Microcirculation, 13(1):1-18, January 2006. [Abstract] [bibtex-entry]



5. Olivier Clatz, Emmanuel Mandonnet, Stéphane Chanalet, Christine Lebrun, Ender Konukoglu, Hervé Delingette, Nicholas Ayache, and Pierre-Yves Bondiau. Modèles Biomathématiques de Croissance Des Gliomes : Recherche en Informatique et Perspectives en Neuro-oncologie. Neurologies, 9(93):665-667, 2006. [bibtex-entry]



6. O. Colliot, T. Mansi, N. Bernasconi, V. Naessens, D. Klironomos, and A. Bernasconi. Segmentation of focal cortical dysplasia lesions on MRI using level set evolution. NeuroImage, 32(4):1621-1630, October 2006. [Abstract] [bibtex-entry]



7. Hervé Delingette and Nicholas Ayache. La simulation de Chirurgie Hépatique. Pour la science, 52(52):106-109, July 2006. Keyword(s): Simulation. [bibtex-entry]



8. Hervé Delingette, Xavier Pennec, Luc Soler, Jacques Marescaux, and Nicholas Ayache. Computational Models for Image Guided, Robot-Assisted and Simulated Medical Interventions. Proceedings of the IEEE, 94(9):1678- 1688, September 2006. [bibtex-entry]



9. Denis Ducreux, Frédéric Dhermain, and Pierre Fillard. [Functional MRI in brain tumours]. Cancer radiothérapie, 10(6-7):330-3, November 2006. Note: [In French]. Keyword(s): Brain, anatomy & histology, Brain Mapping, Brain Neoplasms, pathology, Humans, Magnetic Resonance Imaging, methods, Prognosis. [Abstract] [bibtex-entry]



10. Denis Ducreux, Jean-Francois Lepeintre, Pierre Fillard, C. Loureiro, Marc Tadié, and Pierre Lasjaunias. MR diffusion tensor imaging and fiber tracking in 5 spinal cord astrocytomas. AJNR. American journal of neuroradiology, 27(1):214-6, January 2006. Keyword(s): Adult, Astrocytoma, diagnosis, Diffusion Magnetic Resonance Imaging, Female, Humans, Image Processing Computer-Assisted, Imaging Three-Dimensional, Male, Nerve Fibers, pathology, Spinal Cord, pathology, Spinal Cord Neoplasms, diagnosis. [Abstract] [bibtex-entry]



11. Céline Fouard, Grégoire Malandain, Steffen Prohaska, and Malte Westerhoff. Blockwise Processing Applied to Brain Microvascular Network Study. IEEE Transactions on Medical Imaging, 25(10):1319-1328, 2006. [Abstract] [bibtex-entry]



12. M. Liberatore, C. Denier, Pierre Fillard, M.C. Petit-Lacour, F. Benoudiba, Pierre Lasjaunias, and Denis Ducreux. [Diffusion tensor imaging and tractography of central pontine myelinolysis]. J Neuroradiol, 33(3):189-193, June 2006. Note: [In French]. Keyword(s): Adult, Anorexia, complications, Diffusion Magnetic Resonance Imaging, Female, Humans, Myelinolysis Central Pontine, diagnosis, Pyramidal Tracts, pathology. [Abstract] [bibtex-entry]



13. M.G. Linguraru, N. Ayache, E. Bardinet, M.A. González Ballester, D. Galanaud, S. Haïk, B.A. Faucheux, J.J. Hauw, P. Cozzone, D. Dormont, and J.P. Brandel. Differentiation of sCJD and vCJD Forms by Automated Analysis of Basal Ganglia Intensity Distribution in Multisequence MRI of the Brain - Definition and Evaluation of New MRI-based Ratios. IEEE Transactions on Medical Imaging, 25(8):1052-1067, 2006. [bibtex-entry]



14. M.G. Linguraru, K. Marias, R. English, and J.M. Brady. A Biologically Inspired Algorithm for Microcalcification Cluster Detection. Medical Image Analysis, 10(6), 2006. [bibtex-entry]



15. Valérie Moreau-Villéger, Hervé Delingette, Maxime Sermesant, Hiroshi Ashikaga, Elliot McVeigh, and Nicholas Ayache. Building Maps of Local Apparent Conductivity of the Epicardium with a 2D Electrophysiological Model of the Heart. IEEE Transactions on Bio-Medical Engineering, 53(8):1457-1466, August 2006. [bibtex-entry]



16. Xavier Pennec. Intrinsic Statistics on Riemannian Manifolds: Basic Tools for Geometric Measurements. Journal of Mathematical Imaging and Vision, 25(1):127-154, July 2006. Note: A preliminary appeared as INRIA RR-5093, January 2004. Keyword(s): Fréchet means, Statistics, Lie groups, Riemannian geometry. [bibtex-entry]



17. Xavier Pennec, Pierre Fillard, and Nicholas Ayache. A Riemannian Framework for Tensor Computing. International Journal of Computer Vision, 66(1):41-66, January 2006. Note: A preliminary version appeared as INRIA Research Report 5255, July 2004. Keyword(s): Tensors, regularization, PDE, geometry, Riemannian geometry. [Abstract] [bibtex-entry]



18. Alain Pitiot, Eric Bardinet, Paul M. Thompson, and Grégoire Malandain. Piecewise Affine Registration of Biological Images for Volume Reconstruction. Medical Image Analysis, 10(3):465-483, June 2006. Keyword(s): registration, clustering, reconstruction, histology, MRI. [Abstract] [bibtex-entry]



19. J Renoux, D Facon, P Fillard, I Huynh, P Lasjaunias, and D Ducreux. MR diffusion tensor imaging and fiber tracking in inflammatory diseases of the spinal cord. AJNR. American journal of neuroradiology, 27(9):1947-51, October 2006. Keyword(s): Adult, Anisotropy, Diagnosis Differential, Diffusion Magnetic Resonance Imaging, Female, Humans, Image Enhancement, Image Processing Computer-Assisted, Male, Middle Aged, Multiple Sclerosis, diagnosis, Myelitis, diagnosis, Myelitis Transverse, diagnosis, Nerve Fibers, pathology, Neurologic Examination, Prospective Studies, Reference Values, Sarcoidosis, diagnosis, Spinal Cord, pathology. [Abstract] [bibtex-entry]



20. Gilles Scarella, Olivier Clatz, Stéphane Lanteri, Grégory Beaume, Steve Oudot, Jean-Philippe Pons, Serge Piperno, Patrick Joly, and Joe Wiart. Realistic numerical modelling of human head tissue exposure to electromagnetic waves from cellular phones. Comptes Rendus de l'Académie des Sciences - Physics, 7(5):501-508, June 2006. [Abstract] [bibtex-entry]



21. Maxime Sermesant, Hervé Delingette, and Nicholas Ayache. An Electromechanical Model of the Heart for Image Analysis and Simulation. IEEE Transactions on Medical Imaging, 25(5):612-625, 2006. [bibtex-entry]



22. Maxime Sermesant, Philippe Moireau, Oscar Camara, Jacques Sainte-Marie, Rado Andriantsimiavona, Robert Cimrman, Derek L. Hill, Dominique Chapelle, and Reza Razavi. Cardiac function estimation from MRI using a heart model and data assimilation: Advances and difficulties. Medical Image Analysis, 10(4):642-656, 2006. [bibtex-entry]



23. Arjan W Simonetti, Vedat A Elezi, Regine Farion, Gregoire Malandain, Christoph Segebarth, Chantal Remy, and Emmanuel L Barbier. A low temperature embedding and section registration strategy for 3D image reconstruction of the rat brain from autoradiographic sections. Journal of Neuroscience Methods, 158(2):242-50, December 2006. [Abstract] [bibtex-entry]



24. Tom Vercauteren, Aymeric Perchant, Grégoire Malandain, Xavier Pennec, and Nicholas Ayache. Robust Mosaicing with Correction of Motion Distortions and Tissue Deformation for In Vivo Fibered Microscopy. Medical Image Analysis, 10(5):673-692, October 2006. Note: Annual Medical Image Analysis (MedIA) Best Paper Award 2006. PMID: 16887375. [bibtex-entry]

1. Vincent Arsigny, Xavier Pennec, and Nicholas Ayache. Polyrigid and Polyaffine Transformations: a Novel Geometrical Tool to Deal with Non-Rigid Deformations - Application to the registration of histological slices. Medical Image Analysis, 9(6):507-523, December 2005. Keyword(s): Non-rigid registration, Histological slices, Polyaffine transformations, Ordinary differential equations. [bibtex-entry]



2. J.-D. Boissonnat, R. Chaine, P. Frey, G. Malandain, S. Salmon, E. Saltel, and M. Thiriet. From arteriographies to computational flow in saccular aneurisms: the INRIA experience. Medical Image Analysis, 9(2):133-143, April 2005. Keyword(s): 3D reconstruction, Aneurism, Finite element method, Mesh adaptation, Pulsatile flow. [Abstract] [bibtex-entry]



3. Pierre-Yves Bondiau, Gregoire Malandain, Stephane Chanalet, Pierre-Yves Marcy, Jean-Louis Habrand, Francois Fauchon, Philippe Paquis, Adel Courdi, Olivier Commowick, Isabelle Rutten, and Nicholas Ayache. Atlas-based automatic segmentation of MR images: validation study on the brainstem in radiotherapy context. Int J Radiat Oncol Biol Phys, 61(1):289-98, January 2005. Keyword(s): Algorithms, Anatomical Atlas, methods, Brain Neoplasms, pathology, Brain Stem, anatomy & histology, Humans, Image Interpretation Computer-Assisted, methods, Magnetic Resonance Imaging, methods, Medical Illustration, Observer Variation, Reproducibility of Results, Sensitivity and Specificity. [Abstract] [bibtex-entry]



4. Olivier Clatz, Hervé Delingette, Ion-Florin Talos, Alexandra J. Golby, Ron Kikinis, Ferenc Jolesz, Nicholas Ayache, and Simon Warfield. Robust Non-Rigid Registration to Capture Brain Shift from Intra-Operative MRI. IEEE Transactions on Medical Imaging, 24(11):1417-1427, Nov. 2005. Keyword(s): Non-rigid registration, intra-operative magnetic resonance imaging, finite element model, brain shift. [Abstract] [bibtex-entry]



5. Olivier Clatz, Maxime Sermesant, Pierre-Yves Bondiau, Hervé Delingette, Simon K. Warfield, Grégoire Malandain, and Nicholas Ayache. Realistic Simulation of the 3D Growth of Brain Tumors in MR Images Coupling Diffusion with Mass Effect. IEEE Transactions on Medical Imaging, 24(10):1334-1346, October 2005. Keyword(s): Tumor, brain, growth, model, simulation. [Abstract] [bibtex-entry]



6. H. Delingette and N. Ayache. Hepatic Surgery Simulation. Communications of the ACM, 48(2):31-36, February 2005. [bibtex-entry]



7. D. Ducreux, I. Huynh, P. Fillard, J. Renoux, M.C. Petit-Lacour, K. Marsot-Dupuch, and P. Lasjaunias. Brain MR Diffusion Tensor Imaging and Fibre Tracking to Differentiate Between Two Diffuse Axonal Injuries. Neuroradiology, 47(8):604-608, August 2005. [bibtex-entry]



8. D. Facon, A. Ozanne, P. Fillard, J.-F. Lepeintre, C. Tournoux-Facon, and D. Ducreux. MR Diffusion Tensor Imaging and Fiber Tracking in Spinal Cord Compression. AJNR. American journal of neuroradiology, 26:1587-1594, 2005. [bibtex-entry]



9. C. Forest, H. Delingette, and N. Ayache. Removing Tetrahedra from manifold tetrahedralisation : application to real-time surgical simulation. Medical Image Analysis, 9(2):113-122, April 2005. Keyword(s): Surgical simulation, Topological modifications, Manifold meshes. [Abstract] [bibtex-entry]



10. Céline Fouard and Grégoire Malandain. 3-D chamfer distances and norms in anisotropic grids. Image and Vision Computing, 23(2):143-158, February 2005. Keyword(s): chamfer distance, anisotropic lattice, Farey triangulation. [Abstract] [bibtex-entry]



11. C. Germain, V. Breton, P. Clarysse, Y. Gaudeau, T. Glatard, E. Jeannot, Y. Legré, C. Loomis, I. Magnin, J. Montagnat, J.-M. Moureau, A. Osorio, X. Pennec, and R. Texier. Grid-Enabling Medical Image Analysis. Journal of Clinical Monitoring and Computing, 19(4-5):339-349, October 2005. [bibtex-entry]



12. Grégoire Malandain and Mauricio Reyes. La tomographie en mouvement. Pour la science, 338:132-137, December 2005. [bibtex-entry]



13. J. Montagnat and H. Delingette. 4D Deformable Models with temporal constraints : application to 4D cardiac image segmentation. Medical Image Analysis, 9(1):87-100, February 2005. [bibtex-entry]



14. V Muthurangu, D Atkinson, M Sermesant, M E Miquel, S Hegde, R Johnson, R Andriantsimiavona, A M Taylor, E Baker, R Tulloh, D Hill, and R S Razavi. Measurement of total pulmonary arterial compliance using invasive pressure monitoring and MR flow quantification during MR-guided cardiac catheterization. American journal of physiology. Heart and circulatory physiology, 289(3):1301-1306, September 2005. [Abstract] [bibtex-entry]



15. Stéphane Nicolau, Alain Garcia, Xavier Pennec, Luc Soler, and Nicholas Ayache. An augmented reality system to guide radio-frequency tumor ablation. Computer Animation and Virtual World (previously the Journal of Visualization and Computer Animation), 16(1):1-10, 2005. [bibtex-entry]



16. Xavier Pennec. Recaler pour mieux soigner. Pour la science, 338:126-131, December 2005. [bibtex-entry]



17. K. Rhode, M. Sermesant, D. Brogan, S. Hegde, J. Hipwell, P. Lambiase, E. Rosenthal, C. Bucknall, S. Qureshi, J. Gill, R. Razavi, and D. Hill. A system for real-time XMR guided cardiovascular intervention. IEEE Transactions on Medical Imaging, 24(11):1428-1440, 2005. [bibtex-entry]



18. M. Sermesant, K. Rhode, G. Sanchez-Ortiz, O. Camara, R. Andriantsimiavona, S. Hegde, D. Rueckert, P. Lambiase, C. Bucknall, E. Rosenthal, H. Delingette, D. Hill, N. Ayache, and R. Razavi. Simulation of Cardiac Pathologies using an Electromechanical Biventricular Model and XMR Interventional Imaging. Medical Image Analysis, 9(5):467-480, 2005. [bibtex-entry]



19. Radu Stefanescu, Xavier Pennec, and Nicholas Ayache. A Grid Service for the Interactive Use of a Parallel Non-Rigid Registration Algorithm of Medical Images. Methods of Information in Medicine, 44(2), 2005. Keyword(s): grid service, registration, non-rigid, parallel. [bibtex-entry]



20. Xavier Pennec, Alexis Roche, Pascal Cathier, and Nicholas Ayache. Non-Rigid MR/US Registration for Tracking Brain Deformations. In R.S. Blum and Zh. Liu, editors, Multi-Sensor Image Fusion and Its Applications, volume 26 of Signal Processing and Communications, chapter 4, pages 107-143. CRC Press - Taylor and Francis, July 2005. Keyword(s): registration, matching, ultrasound, motion tracking, deformations, magnetic resonance, correlation ratio, robust estimation, multimodal. [bibtex-entry]



21. A. Pitiot, H. Delingette, and P.M. Thompson. Automated Image Segmentation: Issues and Applications. In Cornelius T. Leondes, editor, Medical Imaging Systems Technology, volume 3. World Scientific, 2005. [bibtex-entry]

1. J. Annese, A. Pitiot, I.D. Dinov, and A.W. Toga. A myelo-architectonic method for the structural classification of cortical areas. NeuroImage, 21(1):15-26, January 2004. Keyword(s): Myelo-architecture, Cerebral cortex, Cortical areas. [Abstract] [bibtex-entry]



2. Christophe Blondel, Régis Vaillant, Grégoire Malandain, and Nicholas Ayache. 3-D tomographic reconstruction of coronary arteries using a precomputed 4-D motion field. Physics in Medicine and Biology, 49(11):2197-2208, 2004. [bibtex-entry]



3. P.Y. Bondiau, G. Malandain, S. Chanalet, P.Y. Marcy, C. Foa, and N. Ayache. Traitement des images et radiothérapie. Cancer radiothérapie, 8(2):120-129, 2004. [Abstract] [bibtex-entry]



4. P. Cachier and N. Ayache. Isotropic energies, filters and splines for vectorial regularization. Journal of Mathematical Imaging and Vision, 20(3):251-265, May 2004. Keyword(s): vector field regularization, non-rigid registration, convolution filter, spline. [bibtex-entry]



5. H. Delingette. Réalité Virtuelle et Médecine. Centraliens, 552:17-18, February 2004. [bibtex-entry]



6. Miguel Angel González Ballester, Xavier Pennec, Marius George Linguraru, and Nicholas Ayache. Generalized Image Models and Their Application as Statistical Models of Images. Medical Image Analysis, 8(3):361-369, September 2004. [bibtex-entry]



7. Isabelle Klein, Jessica Dubois, Jean-François Mangin, Ferath Kherif, Guillaume Flandin, Jean-Baptiste Poline, Michel Denis, Stephen M. Kosslyn, and Denis LeBihan. Retinotopic organization of visual mental images as revealed by functional magnetic resonance imaging. Cognitive Brain Research, 22(1):26-31, December 2004. [Abstract] [bibtex-entry]



8. C Lebrun, D Rey, S Chanalet, V Bourg, C Bensa, M Chatel, N Ayache, and G Malandain. The contribution of automatic anatomical matching of sequential brain MRI scans in the monitoring of multiple sclerosis lesions. Revue Neurologique, 160(8-9):805-10, September 2004. Note: In French. Keyword(s): multiple sclerosis. [Abstract] [bibtex-entry]



9. A. MacKenzie-Graham, E.F. Lee, I.D. Dinov, M. Bota, D.W. Shattuck, S. Ruffins, H. Yuan, F. Konstantinidis, A. Pitiot, Y. Ding, G. Hu, R.E. Jacobs, and A.W. Toga. A multimodal, multidimensional atlas of the C57BL/6J mouse brain. Journal of Anatomy, 204(2):93-102, February 2004. [Abstract] [bibtex-entry]



10. Grégoire Malandain, Éric Bardinet, Koen Nelissen, and Wim Vanduffel. Fusion of autoradiographs with an MR volume using 2-D and 3-D linear transformations. NeuroImage, 23(1):111-127, September 2004. [Abstract] [bibtex-entry]



11. R.R. Peeters, P. Kornprobst, M. Nikolova, S. Sunaert, T. Vieville, G. Malandain, R. Deriche, O. Faugeras, M. Ng, and P. Van Hecke. The use of superresolution techniques to reduce slice thickness in functional MRI. International Journal of Imaging Systems and Technology, 14(3):131-138, 2004. Note: Special issue on High Resolution Image Reconstruction. Keyword(s): fMRI, Super-Resolution algorithm, SNR. [Abstract] [bibtex-entry]



12. A. Pitiot, H. Delingette, P. M. Thompson, and N. Ayache. Expert Knowledge Guided Segmentation System for Brain MRI. NeuroImage, 23(supplement 1):S85-S96, 2004. Note: Special Issue: Mathematics in Brain Imaging. [bibtex-entry]



13. M. Sermesant, K. Rhode, S. Hegde, G. Sanchez-Ortiz, D. Rueckert, P. Lambiase, C. Bucknall, D. Hill, and R. Razavi. Electromechanical Modelling of the Myocardium using XMR Interventional Imaging. Journal of Cardiovascular Magnetic Resonance, 6(1):123-125, 2004. Note: Abstract. [bibtex-entry]



14. Olivier Simon, Ferath Kherif, Guillaume Flandin, Jean-Baptiste Poline, Denis Rivière, Jean-François Mangin, Denis LeBihan, and Stanislas Dehaene. Automatized clustering and functional geometry of human parietofrontal networks for language, space, and number. NeuroImage, 23(3):1192-1202, November 2004. [Abstract] [bibtex-entry]



15. Luc Soler, Nicholas Ayache, Stéphane Nicolau, Xavier Pennec, Clément Forest, Hervé Delingette, and Jacques Marescaux. Traitement d'images médicales pour la planification, la simulation et l'aide intra-opératoire des actes chirurgicaux. La Revue de l'Electricité et de l'Electronique, pp 64-71, janvier 2004. [bibtex-entry]



16. Radu Stefanescu, Xavier Pennec, and Nicholas Ayache. Grid Powered Nonlinear Image Registration with Locally Adaptive Regularization. Medical Image Analysis, 8(3):325-342, September 2004. Keyword(s): non-rigid registration, adaptive regularization, grid, parallel. [bibtex-entry]



17. Radu Stefanescu, Xavier Pennec, and Nicholas Ayache. Grid-Enabled Non-Rigid Registration of Medical Images. Parallel Processing Letters, 14(2):197-216, 2004. Keyword(s): grid, non-rigid registration, parallel, cluster. [bibtex-entry]



18. H. Delingette and N. Ayache. Soft Tissue Modeling for Surgery Simulation. In N. Ayache, editor, Computational Models for the Human Body, Handbook of Numerical Analysis (Ed : Ph. Ciarlet), pages 453-550. Elsevier, 2004. [bibtex-entry]



19. Luc Soler, Nicholas Ayache, Stéphane Nicolau, Xavier Pennec, Clément Forest, Hervé Delingette, Didier Mutter, and Jacques Marescaux. Traitements d'images médicales pour la planification, la simulation et l'aide intra-opératoire des actes chirurgicaux. In M. Faupel, P. Smigielski, and R. Grzymala, editors, Imagerie et Photonique pour les sciences du vivant et la médecine, pages 19-31. Edition Fontis Media, 2004. ISBN: 2-88476-005-9. [bibtex-entry]

1. N. Ayache. Epidaure: a Research Project in Medical Image Analysis, Simulation and Robotics at INRIA. IEEE Transactions on Medical Imaging, 22(10):1185-1201, October 2003. [bibtex-entry]



2. Pierre-Yves Bondiau, Grégoire Malandain, Pierre Chauvel, Frédérique Peyrade, Adel Courdi, Nicole Iborra, Jean-Pierre Caujolle, and Pierre Gastaud. Automatic three-dimensional model for protontherapy of the eye: Preliminary results. Medical Physics, 30(6):1013-1020, June 2003. [Abstract] [bibtex-entry]



3. Pascal Cachier, Eric Bardinet, Didier Dormont, Xavier Pennec, and Nicholas Ayache. Iconic Feature Based Nonrigid Registration: The PASHA Algorithm. Computer Vision and Image Understanding, 89(2-3):272-298, Feb.-march 2003. Note: Special Issue on Nonrigid Registration. Keyword(s): registration, matching, similarity measures, deformations. [bibtex-entry]



4. Olivier Clatz, Hervé Delingette, Eric Bardinet, Didier Dormont, and Nicholas Ayache. Création d'un Modèle Biomécanique Spécifique du Cerveau par l'Analyse d'Images et son Application à la Neurochirurgie Stéréotaxique. Mécanique et Industrie, 4(4):429-433, 2003. Note: Numéro spécial CFM 2003. [bibtex-entry]



5. P Hellier, C Barillot, I Corouge, B Gibaud, G Le Goualher, D L Collins, A Evans, G Malandain, N Ayache, G E Christensen, and H J Johnson. Retrospective evaluation of intersubject brain registration. IEEE Transactions on Medical Imaging, 22(9):1120-30, September 2003. [Abstract] [bibtex-entry]



6. Ferath Kherif, Jean-Baptiste Poline, Sébastien Meriaux, Habib Benali, Guillaume Flandin, and Matthew Brett. Group analysis in functional neuroimaging: selecting subjects using similarity measures. NeuroImage, 20(4):2197-2208, December 2003. Keyword(s): fMRI, Group analysis, Multivariate analysis, Statistical analysis. [Abstract] [bibtex-entry]



7. Pierre-Jean Lahaye, Jean-Baptiste Poline, Guillaume Flandin, Silke Dodel, and Line Garnero. Functional connectivity: studying nonlinear, delayed interactions between BOLD signals. NeuroImage, 20(2):962-974, October 2003. Keyword(s): fMRI. [bibtex-entry]



8. J. Montagnat, M. Sermesant, H. Delingette, G. Malandain, and N. Ayache. Anisotropic filtering for model-based segmentation of 4D cylindrical echocardiographic images. Pattern Recognition Letters, 24(4-5):815-828, February 2003. Note: Special Issue on Ultrasonic Image Processing and Analysis. Keyword(s): anisotropic diffusion, 4D, Heart, segmentation, ultrasound, medical images, motion tracking. [bibtex-entry]



9. Xavier Pennec, Pascal Cachier, and Nicholas Ayache. Tracking Brain Deformations in Time-Sequences of 3D US Images. Pattern Recognition Letters, 24(4-5):801-813, February 2003. Note: Special Issue on Ultrasonic Image Processing and Analysis. Keyword(s): registration, matching, ultrasound, motion tracking, deformations. [bibtex-entry]



10. G. Picinbono, H. Delingette, and N. Ayache. Non-Linear Anisotropic Elasticity for Real-Time Surgery Simulation. Graphical Models, 65(5):305-321, September 2003. Keyword(s): journal, simulation. [bibtex-entry]



11. Maxime Sermesant, Clément Forest, Xavier Pennec, Hervé Delingette, and Nicholas Ayache. Deformable biomechanical models: Application to 4D cardiac image analysis. Medical Image Analysis, 7(4):475-488, December 2003. [bibtex-entry]



12. J. Yelnik, P. Damier, S. Demeret, D. Gervais, E. Bardinet, B.P. Bejjani, C. Francois, J.L. Houeto, I. Arnule, D. Dormont, D. Galanaud, B. Pidoux, P. Cornu, and Y. Agid. Localization of stimulating electrodes in patients with Parkinson disease by using a three-dimensional atlas-magnetic resonance imaging coregistration method. Journal of Neurosurgery, 99(1):89-99, July 2003. [Abstract] [bibtex-entry]

1. M. A. González Ballester, A. Zisserman, and M. Brady. Estimation of the Partial Volume Effect in MRI. Medical Image Analysis, 6(4):389-405, December 2002. [bibtex-entry]



2. P. Jannin, J.M. Fitzpatrick, D.J. Hawkes, X. Pennec, R. Shahidi, and M.W. Vannier. Validation of Medical Image Processing in Image-guided Therapy. IEEE Transactions on Medical Imaging, 21(12):1445-1449, December 2002. [bibtex-entry]



3. Carine Karachi, Chantal François, Karine Parain, Eric Bardinet, Dominique Tandé, Etienne Hirsch, and Jérôme Yelnik. Three-dimensional cartography of functional territories in the human striatopallidal complex by using calbindin immunoreactivity. Journal of Comparative Neurology, 450(2):122-134, August 2002. [Abstract] [bibtex-entry]



4. Ferath Kherif, Jean-Baptiste Poline, Guillaume Flandin, Habib Benali, Olivier Simon, Stanislas Dehaene, and Keith J. Worsley. Multivariate Model Specification for fMRI Data. NeuroImage, 16(4):1068-1083, August 2002. Keyword(s): fMRI, model selection, multivariate analysis. [bibtex-entry]



5. Grégoire Malandain and Jean-Daniel Boissonnat. Computing the Diameter of a Point Set. International Journal of Computational Geometry & Applications, 12(6):489-510, December 2002. Keyword(s): computational geometry, diameter, width, approximation, point sets, furthest neighbors, double normal. [Abstract] [bibtex-entry]



6. G. Picinbono, H. Delingette, and N. Ayache. Modèle déformable élastique non-linéaire pour la simulation de chirurgie en temps réel. Les Comptes Rendus de l'Académie des Sciences (CRAS), C.R. Biologies, 325(4):335-344, 2002. Keyword(s): journal, simulation. [bibtex-entry]



7. G. Picinbono, J-C. Lombardo, H. Delingette, and N. Ayache. Improving realism of a surgery simulator: linear anisotropic elasticity, complex interactions and force extrapolation. Journal of Visualisation and Computer Animation, 13(3):147-167, July 2002. Keyword(s): journal, simulation. [bibtex-entry]



8. Alain Pitiot, Paul M. Thompson, and Arthur W. Toga. Adaptive Elastic Segmentation of Brain MRI via Shape Model Guided Evolutionary Programming. IEEE Transactions on Medical Imaging, 21(8):910-923, August 2002. Keyword(s): MRI. [bibtex-entry]



9. S. Prima, S. Ourselin, and N. Ayache. Computation of the Mid-Sagittal Plane in 3D Brain Images. IEEE Transactions on Medical Imaging, 21(2):122-138, February 2002. Keyword(s): registration, matching. [bibtex-entry]



10. David Rey, Gérard Subsol, Hervé Delingette, and Nicholas Ayache. Automatic Detection and Segmentation of Evolving Processes in 3D Medical Images: Application to Multiple Sclerosis. Medical Image Analysis, 6(2):163-179, June 2002. Keyword(s): Automation, Brain, pathology, Human, Image Processing Computer-Assisted, methods, Imaging Three-Dimensional, methods, Magnetic Resonance Imaging, methods, Models Neurological, Multiple Sclerosis, diagnosis, Reproducibility of Results, Sensitivity and Specificity, Support Non-U.S. Gov't. [Abstract] [bibtex-entry]



11. N. Ayache. Medical Imaging Informatics. From Digital Anatomy to Virtual Scapels and Image Guided Therapy. In R Haux and C Kulikowski, editors, Medical Imaging Informatics (IMIA Yearbook of Medical Informatics). Schattauer Verlagsgesellschaft mbH, Stuttgart, 2002. ISBN: 3-7945-2193-5. [bibtex-entry]



12. G. Subsol, B. Mafart, A. Silvestre, and M.A. de Lumley. 3D Image Processing for the Study of the Evolution of the Shape of the Human Skull: Presentation of the Tools and Preliminary Results. In B. Mafart, H. Delingette, and G. Subsol, editors, Three-Dimensional Imaging in Paleoanthropology and Prehistoric Archaeology, pages 37-45. BAR International Series 1049, 2002. [bibtex-entry]

1. H. Delingette and J. Montagnat. Shape and Topology Constraints on Parametric Active Contours. Computer Vision and Image Understanding, 83(2):140-171, 2001. Keyword(s): journal, reconstruction. [bibtex-entry]



2. A. Guimond, A. Roche, N. Ayache, and J. Meunier. Multimodal Brain Warping Using the Demons Algorithm and Adaptative Intensity Corrections. IEEE Transactions on Medical Imaging, 20(1):58-69, 2001. Keyword(s): registration, matching, deformations. [Abstract] [bibtex-entry]



3. M.G. Linguraru and J.M. Brady. An Anisotropic Diffusion Approach for Early Detection of Breast Cancer. Acta Universitatis Cibiniensis, Technical Series, XLIII:49-60, 2001. [bibtex-entry]



4. Y. Machida, Y. Hamamura, M. A. González Ballester, S. Nozaki, K. Okamoto, S. Uchizono, N. Ichinose, Y. Kassai, H. Kanazawa, and Y. Usui. Development of MR Parallel Imaging, SPEEDER (in Japanese). Medical Review, 83:52-58, November 2001. [bibtex-entry]



5. O. Migneco, M. Benoit, P.M. Koulibaly, I. Dygai, C. Bertogliati, P. Desvignes, Ph. Robert, G. Malandain, F. Bussière, and J. Darcourt. Perfusion brain SPECT and Statistical Parametric Mapping analysis indicate that apathy is a cingulate syndrome: a study in Alzheimer's disease and non-demented patients. NeuroImage, 13(5):896-902, 2001. Keyword(s): apathy, cingulate, statistical parametric mapping, ECD. [Abstract] [bibtex-entry]



6. J. Montagnat, H. Delingette, and N. Ayache. A review of deformable surfaces: topology, geometry and deformation. Image and Vision Computing, 19(14):1023-1040, December 2001. Keyword(s): journal, reconstruction. [bibtex-entry]



7. Sébastien Ourselin, Alexis Roche, Gérard Subsol, Xavier Pennec, and Nicholas Ayache. Reconstructing a 3D Structure from Serial Histological Sections. Image and Vision Computing, 19(1-2):25-31, January 2001. Keyword(s): registration, matching, histology. [bibtex-entry]



8. Alexis Roche, Xavier Pennec, Grégoire Malandain, and Nicholas Ayache. Rigid Registration of 3D Ultrasound with MR Images: a New Approach Combining Intensity and Gradient Information. IEEE Transactions on Medical Imaging, 20(10):1038-1049, October 2001. Keyword(s): registration, ultrasound, magnetic resonance, correlation ratio, robust estimation, multimodal. [Abstract] [bibtex-entry]



9. L Soler, H Delingette, G Malandain, J Montagnat, N Ayache, C Koehl, O Dourthe, B Malassagne, M Smith, D Mutter, and J Marescaux. Fully automatic anatomical, pathological, and functional segmentation from CT scans for hepatic surgery. Comput Aided Surg, 6(3):131-42, 2001. Keyword(s): Human, Image Processing Computer-Assisted, methods, Liver, anatomy & histology, Support Non-U.S. Gov't, Surgery Computer-Assisted, Tomography X-Ray Computed. [Abstract] [bibtex-entry]

1. N. Ayache. Imagerie et robotique médicales: du microscope informatique au simulateur de chirurgie. Technique et Science Informatiques, 19(1), January 2000. [bibtex-entry]



2. S. Cotin, H. Delingette, and N. Ayache. A Hybrid Elastic Model allowing Real-Time Cutting, Deformations and Force-Feedback for Surgery Training and Simulation. The Visual Computer, 16(8):437-452, 2000. Keyword(s): journal, simulation. [bibtex-entry]



3. J. Duncan and N. Ayache. Medical Image Analysis: Progress over two decades and the challenges ahead. IEEE Transactions on Pattern Analysis and Machine Intelligence, 22(1):85-106, 2000. [bibtex-entry]



4. M. A. González Ballester, A. Zisserman, and M. Brady. Segmentation and Measurement of Brain Structures in MRI Including Confidence Bounds. Medical Image Analysis, 4(3):189-200, 2000. [bibtex-entry]



5. A. Guimond, J. Meunier, and J.-P. Thirion. Average Brain Models: A Convergence Study. Computer Vision and Image Understanding, 77(2):192-210, 2000. Keyword(s): atlas. [bibtex-entry]



6. K. Krissian, G. Malandain, N. Ayache, R. Vaillant, and Y. Trousset. Model-Based Detection of Tubular Structures in 3D Images. Computer Vision and Image Understanding, 80(2):130-171, 2000. Keyword(s): filtering, vessel detection, multiscale analysis, segmentation. [Abstract] [bibtex-entry]



7. A. Roche, G. Malandain, and N. Ayache. Unifying Maximum Likelihood Approaches in Medical Image Registration. International Journal of Imaging Systems and Technology, 11(1):71-80, 2000. Note: Special Issue on 3D Imaging. Keyword(s): registration, matching, similarity measures. [bibtex-entry]



8. L Soler, H Delingette, G Malandain, N Ayache, C Koehl, J M Clement, O Dourthe, and J Marescaux. An automatic virtual patient reconstruction from CT-scans for hepatic surgical planning. Stud Health Technol Inform, 70:316-22, 2000. Keyword(s): Computer Graphics, Computer Simulation, Hepatectomy, Human, Image Processing Computer-Assisted, Liver Diseases, radiography, Tomography X-Ray Computed, User-Computer Interface. [Abstract] [bibtex-entry]



9. J.-P. Thirion, S. Prima, G. Subsol, and N. Roberts. Statistical Analysis of Normal and Abnormal Dissymmetry in Volumetric Medical Images. Medical Image Analysis, 4(2):111-121, June 2000. Keyword(s): Aphasia, pathology, Brain, anatomy & histology, Computer Simulation, Epilepsies Partial, pathology, Human, Image Processing Computer-Assisted, Imaging Three-Dimensional, Laterality, Magnetic Resonance Imaging, Male. [Abstract] [bibtex-entry]



10. Xavier Pennec, Nicholas Ayache, and Jean-Philippe Thirion. Landmark-based registration using features identified through differential geometry. In I. Bankman, editor, Handbook of Medical Imaging, chapter 31, pages 499-513. Academic Press, September 2000. Keyword(s): registration, matching, validation, uncertainty. [bibtex-entry]

1. N. Ayache and G. Subsol. El Cerebro in Cuatro Dimensiones. Mundo Cientifico, 203:30-33, July 1999. [bibtex-entry]



2. N. Ayache and G. Subsol. Le cerveau en quatre dimensions. La Recherche, 320:46-49, May 1999. [bibtex-entry]



3. S. Cotin, H. Delingette, and N. Ayache. Real-time elastic deformations of soft tissues for surgery simulation. IEEE Transactions on Visualization and Computer Graphics, 5(1):62-73, January-March 1999. Keyword(s): journal, simulation. [bibtex-entry]



4. H. Delingette. General Object Reconstruction based on Simplex Meshes. International Journal of Computer Vision, 32(2):111-146, September 1999. Keyword(s): journal, reconstruction. [bibtex-entry]



5. J.-L. Dugelay, K. Fintzel, S. Valente, and H. Delingette. Clonage de visage et spatialisation video : Outils pour la téléconférence virtuelle. Traitement du signal, 16(1):60-72, July 1999. Keyword(s): journal, reconstruction. [bibtex-entry]



6. S. Ourselin, C. Sattonnet, A. Roche, and G. Subsol. Automatic alignement of histological sections for 3D reconstruction and analysis. Analytical Cellular Pathology, 18(3):123, 1999. Note: Abstracts of the 1999 Annual Meeting of the Association Française de Cytométrie, Dijon, 12-15 October 1999. Keyword(s): registration, matching, histology, MRI. [bibtex-entry]



7. J.-P. Thirion and G. Calmon. Deformation Analysis to Detect and Quantify Active Lesions in Three-Dimensional Medical Image Sequences. IEEE Transactions on Medical Imaging, 18(5):429-441, 1999. Keyword(s): Lesion, mass effect, motion field analysis, multiple sclerosis, stereology, volume measurement. [bibtex-entry]



8. J. Webb, A. Guimond, N. Roberts, P. Eldridge, D. Chadwick, J. Meunier, and J.-P. Thirion. Automatic detection of hippocampal atrophy on magnetic resonance images. Magnetic Resonance Imaging, 17(8):1149-1161, April 1999. [bibtex-entry]

1. Nicholas Ayache. L'analyse automatique des images médicales, état de l'art et perspectives. Annales de l'Institut Pasteur, 9(1):13-21, avril--juin 1998. Note: Numéro spécial sur les progrès récents de l'imagerie médicale. [bibtex-entry]



2. N. Ayache, S. Cotin, H. Delingette, J.-M. Clément, J. Marescaux, and M. Nord. Simulation of Endoscopic Surgery. Journal of Minimally Invasive Therapy and Allied Technologies (MITAT), 7(2):71-77, July 1998. Keyword(s): journal, simulation. [bibtex-entry]



3. Eric Bardinet, Laurent D. Cohen, and Nicholas Ayache. A parametric deformable model to fit unstructured 3D data. Computer Vision and Image Understanding, 71(1):39-54, 1998. [bibtex-entry]



4. Serge Benayoun and Nicholas Ayache. Dense non-rigid motion estimation in sequences of medical images using differential constraints. International Journal of Computer Vision, 26(1):25-40, 1998. Keyword(s): registration, matching, deformations, motion tracking. [bibtex-entry]



5. J. Declerck, J. Feldmar, and N. Ayache. Definition of a four-dimensional continuous planispheric transformation for the tracking and the analysis of left-ventricle motion. Medical Image Analysis, 2(2):197-213, June 1998. Keyword(s): Motion tracking, Heart, 4D. [bibtex-entry]



6. H. Delingette. Towards Realistic Soft Tissue Modeling in Medical Simulation. Proceedings of the IEEE, pp 512-523, April 1998. Note: Special Issue on Surgery Simulation. Keyword(s): journal, simulation. [bibtex-entry]



7. Márta Fidrich. Iso-surface Extraction in $n$-D applied to Tracking Feature Curves across Scale. Image and Vision Computing, 16(8):545-556, 1998. [bibtex-entry]



8. Márta Fidrich and Jean-Philippe Thirion. Stability of Corner Points in Scale Space: The Effect of Small Non-Rigid Deformations. Computer Vision and Image Understanding, 72(1):72-83, 1998. [bibtex-entry]



9. G. Malandain and S. Fernández-Vidal. Euclidean Skeletons. Image and Vision Computing, 16(5):317-327, April 1998. [bibtex-entry]



10. J Marescaux, J M Clement, V Tassetti, C Koehl, S Cotin, Y Russier, D Mutter, H Delingette, and N Ayache. Virtual reality applied to hepatic surgery simulation: the next revolution. Annals of Surgery, 228(5):627-34, November 1998. Keyword(s): Computer Simulation, Digestive System Surgical Procedures, methods, Image Processing Computer-Assisted, Liver, surgery, Support Non-U.S. Gov't, journal, simulation. [Abstract] [bibtex-entry]



11. J Marescaux, J M Clement, M Vix, Y Russier, V Tassetti, D Mutter, S Cotin, and N Ayache. [A new concept in surgery of the digestive tract: surgical procedure assisted by computer, from virtual reality to telemanipulation]. Chirurgie, 123(1):16-24, February 1998. Note: In french. Keyword(s): Anatomy Cross-Sectional, Computer Simulation, English Abstract, Forecasting, Hepatectomy, instrumentation, Human, Image Processing Computer-Assisted, instrumentation, Liver Neoplasms, surgery, Phantoms Imaging, Robotics, instrumentation, Surgical Procedures Operative, trends, User-Computer Interface. [Abstract] [bibtex-entry]



12. J. Montagnat and H. Delingette. Globally constrained deformable models for 3D object reconstruction. Signal Processing, 71(2):173-186, 1998. Keyword(s): journal, reconstruction. [bibtex-entry]



13. Xavier Pennec. Toward a generic framework for recognition based on uncertain geometric features. Videre: Journal of Computer Vision Research, 1(2):58-87, 1998. Keyword(s): registration, matching, uncertainty. [bibtex-entry]



14. Xavier Pennec and Nicholas Ayache. A geometric algorithm to find small but highly similar 3D substructures in proteins. Bioinformatics, 14(6):516-522, 1998. Keyword(s): registration, matching, protein structure. [bibtex-entry]



15. Xavier Pennec and Nicholas Ayache. Uniform distribution, distance and expectation problems for geometric features processing. Journal of Mathematical Imaging and Vision, 9(1):49-67, July 1998. Note: A preliminary version appeared as INRIA Research Report 2820, March 1996. Keyword(s): statistics, geometry, Riemannian geometry. [bibtex-entry]



16. L. Robert and G. Malandain. Fast Binary Image Processing Using Binary Decision Diagrams. Computer Vision and Image Understanding, 72(1):1-9, October 1998. [bibtex-entry]



17. L. Soler, G. Malandain, and H. Delingette. Segmentation automatique : application aux angioscanners 3D du foie. Traitement du signal, 15(5):411-431, 1998. Keyword(s): journal, reconstruction. [bibtex-entry]



18. G. Subsol, J.-Ph. Thirion, and N. Ayache. A Scheme for Automatically Building 3D Morphometric Anatomical Atlases: application to a Skull Atlas. Medical Image Analysis, 2(1):37-60, 1998. Keyword(s): registration, matching, atlas, deformations, Algorithms, Anatomy Artistic, methods, Comparative Study, Craniofacial Abnormalities, pathology, Diagnosis Computer-Assisted, methods, Human, Medical Illustration, Skull, anatomy & histology. [Abstract] [bibtex-entry]



19. J.-P. Thirion. Image matching as a diffusion process: an analogy with Maxwell's demons. Medical Image Analysis, 2(3):243-260, 1998. Keyword(s): registration, matching, deformations, Algorithms, Animals, Brain, anatomy & histology, Computer Simulation, Diagnostic Imaging, methods, Dogs, Heart, anatomy & histology, Human, Image Processing Computer-Assisted, methods, Models Theoretical, Thermodynamics. [Abstract] [bibtex-entry]



20. Nicholas Ayache, Stephane Cotin, and Hervé Delingette. Surgery Simulation with visual and haptic feedback. In Y. Shirai and S. Hirose, editors, Robotics Research, the Eigth International Symposium, pages 311-316. Springer, 1998. Keyword(s): workshop, simulation. [bibtex-entry]



21. G. Subsol. Crest Lines for Curve Based Warping. In A. W. Toga, editor, Brain Warping, chapter 13, pages 225-246. Academic Press, 1998. [bibtex-entry]



22. J.-P. Thirion. Diffusing Models and Applications. In A. W. Toga, editor, Brain Warping, chapter 9, pages 143-155. Academic Press, 1998. Keyword(s): registration, matching. [bibtex-entry]

1. P Chauvel, W Sauerwein, N Bornfeld, W Friedrichs, N Brassart, A Courdi, J Herault, J P Pignol, P Y Bondiau, and G Malandain. Clinical and technical requirements for proton treatment planning of ocular diseases. The SERAG (South Europe Radiotherapy Group). Front Radiat Ther Oncol, 30:133-42, 1997. Keyword(s): Comparative Study, Conjunctival Neoplasms, diagnosis, Dose-Response Relationship Radiation, Follow-Up Studies, Fundus Oculi, Human, Image Processing Computer-Assisted, Magnetic Resonance Imaging, Melanoma, diagnosis, Neoplasm Recurrence Local, diagnosis, Predictive Value of Tests, Protons, therapeutic use, Radiotherapy Planning Computer-Assisted, methods, Retrospective Studies, Tomography X-Ray Computed, Treatment Outcome, Uveal Neoplasms, diagnosis. [bibtex-entry]



2. S. Cotin, H. Delingette, N. Ayache, J.M. Clement, J. Marescaux, and M. Nord. Simulation Active de Chirurgie Endoscopique. Revue Européenne de Technologie Biomédicale (RBM), 19(5):167-172, 1997. Keyword(s): journal, simulation. [bibtex-entry]



3. J. Declerck, J. Feldmar, M.L. Goris, and F. Betting. Automatic registration and alignment on a template of cardiac stress & rest SPECT reoriented images. IEEE Transactions on Medical Imaging, 16(6):727-737, 1997. Keyword(s): registration, matching, deformations. [bibtex-entry]



4. H. Delingette. Réalité virtuelle et médecine. Revue de la société des électriciens et des électroniciens (REE), 8:43-45, September 1997. Keyword(s): journal, simulation. [bibtex-entry]



5. J. Feldmar, N. Ayache, and F. Betting. 3D-2D projective registration of free-form curves and surfaces. Journal of Computer Vision and Image Understanding, 65(3):403-424, 1997. [bibtex-entry]



6. J. Feldmar, J. Declerck, G. Malandain, and N. Ayache. Extension of the ICP Algorithm to Non-Rigid Intensity-Based Registration of 3D Volumes. Computer Vision and Image Understanding, 66(2):193-206, May 1997. Keyword(s): registration, matching, deformations. [bibtex-entry]



7. Alexandre Guimond, Gérard Subsol, and Jean-Philippe Thirion. Automatic MRI Database Exploration and Applications. International Journal of Pattern Recognition and Artificial Intelligence, 11(8):1345-1366, December 1997. [bibtex-entry]



8. André Guéziec, Xavier Pennec, and Nicholas Ayache. Medical Image Registration using Geometric Hashing. IEEE Computational Science and Engineering, 4(4):29-41, Oct-Dec 1997. Note: Special issue on Geometric Hashing. Keyword(s): registration, matching. [bibtex-entry]



9. J Marescaux, J M Clement, M Nord, Y Russier, V Tassetti, D Mutter, S Cotin, and N Ayache. [A new concept in digestive surgery: the computer assisted surgical procedure, from virtual reality to telemanipulation]. Bull Acad Natl Med, 181(8):1609-21, November 1997. Keyword(s): review, survey, review, survey, Computer Simulation, Digestive System Surgical Procedures, English Abstract, Human, Telemedicine, User-Computer Interface. [Abstract] [bibtex-entry]



10. Xavier Pennec and Jean-Philippe Thirion. A Framework for Uncertainty and Validation of 3D Registration Methods based on Points and Frames. International Journal of Computer Vision, 25(3):203-229, December 1997. Keyword(s): registration, matching, uncertainty, statistics, validation. [bibtex-entry]



11. L Picard, E Maurincomme, M Soderman, J Feldmar, R Anxionnat, L Launay, K Ericson, G Malandain, S Bracard, E Kerrien, O Flodmark, and N Ayache. X-ray angiography in stereotactic conditions: techniques and interest for interventional neuroradiology. Stereotact Funct Neurosurg, 68(1-4 Pt 1):117-20, 1997. Keyword(s): Angiography Digital Subtraction, methods, Carotid Arteries, anatomy & histology, Cerebral Angiography, methods, Human, Image Enhancement, Magnetic Resonance Angiography, methods, Radiology Interventional, methods, Stereotaxic Techniques. [Abstract] [bibtex-entry]



12. G. Quatrehomme, S. Cotin, G. Subsol, H. Delingette, Y. Garidel, G. Grévin, and M. Fidrich. A Fully Three-Dimensional Method for Facial Reconstruction Based on Deformable Models. Journal of Forensic Sciences, 42(4):649-652, July 1997. Keyword(s): journal, medical. [bibtex-entry]



13. G. Subsol, N. Roberts, M. Doran, and J.-Ph. Thirion. Automatic Analysis of Cerebral Atrophy. Magnetic Resonance Imaging, 15(8):917-927, 1997. [bibtex-entry]



14. J. West, J. M. Fitzpatrick, M. Y. Wang, B. M. Dawant, C. R. Maurer, Jr., R. M. Kessler, R. J. Maciunas, C. Barillot, D. Lemoine, A. Collignon, F. Maes, P. Suetens, D. Vandermeulen, P. A. van den Elsen, S. Napel, T. S. Sumanaweera, B. Harkness, P. F. Hemler, D. L. G. Hill, D. J. Hawkes, C. Studholme, J. B. A. Maintz, M. A. Viergever, G. Malandain, X. Pennec, M. E. Noz, G. Q. Maguire, Jr., M. Pollack, C. A. Pelizzari, R. A. Robb, D. Hanson, and R. P. Woods. Comparison and evaluation of retrospective intermodality brain image registration techniques. Journal of Computer Assisted Tomography, 21(4):554-566, 1997. Keyword(s): registration, matching, multimodal, validation, uncertainty. [Abstract] [bibtex-entry]