Publications of Xavier Pennec

1. Nicolas Guigui, Nina Miolane, and Xavier Pennec. Introduction to Riemannian Geometry and Geometric Statistics: from basic theory to implementation with Geomstats, volume 16 of Foundations and Trends® in Machine Learning. Know Publishers, February 2023. Keyword(s): Riemannian Geometry, Geometric Statistics, Python Library. [bibtex-entry]



2. Xavier Pennec, Stephan Sommer, and Tom Fletcher. Riemannian Geometric Statistics in Medical Image Analysis. Academic Press, 2020. [bibtex-entry]



3. Dajiang Zhu, Jingwen Yan, Heng Huang, Li Shen, Paul M. Thompson, Carl-Fredrik Westin, Xavier Pennec, Sarang Joshi, Mads Nielsen, Tom Fletcher, Stanley Durrleman, and Stefan Sommer. Multimodal Brain Image Analysis and Mathematical Foundations of Computational Anatomy, volume 11846 of Lecture Notes in Computer Science (LNCS). Springer, October 2019. Keyword(s): Biomedical imaging, Statistics of surfaces, Computational anatomy, Approximation methods, Artificial intelligence, Image fusion, Image processing, Image reconstruction, Image registration, Image segmentation, Imaging genetics, Machine learning, Neural networks, Principal component analysis, Statistical models. [bibtex-entry]



4. Math in the Black Forest: Workshop on New Directions in Shape Analysis, November 2018. Published by the authors. Note: 27 pages, 4 figures. [bibtex-entry]



5. Jorge M. Cardoso, Tal Arbel, Enzo Ferrante, Xavier Pennec, Dalca Adrian V., Sarah Parisot, Sarang Joshi, Nematollah K. Batmanghelich, Aristeidis Sotiras, Mads Nielsen, Mert Sabuncu, Fletcher Tom, Li Shen, Stanley Durrleman, and Stefan Sommer. Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics, volume 10551 of Lecture Notes in Computer Science. September 2017. Keyword(s): Artificial intelligence, Bayesian networks, Clustering algorithms, Cluster analysis, Learning systems, Data mining, Face recognition, Feature selection, Geometry, Image analysis, Image processing, Image reconstruction, Medical images, Medical imaging, Neural networks, Pattern recognition, Signal processing, Computer vision, Classification. [bibtex-entry]



6. Stanley Durrleman, Thomas P. Fletcher, Guido Gerig, Marc Niethammer, and Xavier Pennec, editors. Spatio-temporal Image Analysis for Longitudinal and Time-Series Image Data, volume 8682 of Lecture notes in computer science, Cambridge, United States, January 2015. Springer International Publishing. [bibtex-entry]



7. Pennec, Xavier, Joshi, Sarang, Nielsen, Mads, Fletcher, Thomas P., Durrleman, Stanley, Sommer, and Stefan, editors. Proceedings of the fifth international workshop on Mathematical Foundations of Computational Anatomy (MFCA 2015), Munich, Germany, August 2015. [bibtex-entry]



8. Xavier Pennec, Sarang Joshi, Mads Nielsen, Thomas P. Fletcher, Stanley Durrleman, and Stefan Sommer. Proceedings of the Fourth International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Biological Shape Variability Modeling (MFCA 2013), Nagoya, Japan. Inria, August 2013. [bibtex-entry]



9. Xavier Pennec, Sarang Joshi, and Mads Nielsen, editors. Proceedings of the Third International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Modelling Biological Shape Variability, Toronto, Canada, September 2011. [bibtex-entry]



10. Xavier Pennec and Sarang Joshi, editors. Proceedings of the Second International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Modelling Biological Shape Variability, New York, USA, September 2008. [bibtex-entry]



11. Xavier Pennec and Sarang Joshi, editors. Proceedings of the First International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Modelling Biological Shape Variability, Copenhagen, Denmark, October 2006. [bibtex-entry]

1. Xavier Pennec. Statistical Computing on Manifolds for Computational Anatomy. Habilitation à diriger des recherches, Université Nice Sophia-Antipolis, December 2006. Keyword(s): Tensors, regularization, PDE, geometry, Riemannian geometry, Registration, statistics, manifolds. [bibtex-entry]



2. Xavier Pennec. L'incertitude dans les problèmes de reconnaissance et de recalage -- Applications en imagerie médicale et biologie moléculaire. Thèse de sciences (PhD thesis), Ecole Polytechnique, Palaiseau (France), December 1996. Keyword(s): registration, matching, statistics, validation, geometry, Riemannian geometry, medical images, protein structure. [bibtex-entry]

1. Tom Szwagier, Pierre-Alexandre Mattei, Charles Bouveyron, and Xavier Pennec. Parsimonious Gaussian mixture models with piecewise-constant eigenvalue profiles. Statistics and Computing, 36(3):95, February 2026. Keyword(s): Model Selection, EM Algorithm, Eigenvalues, Parsimonious Models, Gaussian Mixture Models. [bibtex-entry]



2. Tom Szwagier and Xavier Pennec. The curse of isotropy: from principal components to principal subspaces. Statistical Science, 2025. Keyword(s): Flag Manifolds, Parsimonious Models, Interpretability, Isotropy, Principal Component Analysis. [bibtex-entry]



3. 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): Stretch Tensor, Polar Decomposition, Quotient Geodesics. [bibtex-entry]



4. 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]



5. 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]



6. 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): 54E50, Covariance matrices, PSD matrices, 58A35, Bures-Wasserstein, 53A04, 53-08, 58D17, 53C22, 53B20, 15A63, 15B48, Injection domain, Geodesics, Orbit space. [bibtex-entry]



7. 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]



8. 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]



9. 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): mixed-Euclidean, Symmetric Positive Definite matrices, Riemannian geometry, information geometry, families of metrics, kernel metrics, alpha-Procrustes, mixed-power-Euclidean, $\beta$)-divergence, (u, v)-divergence, ($\alpha$, 53B20, 15A63, 53B12, 15B48. [bibtex-entry]



10. 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): Correlation matrices, Lie group, Lie group actions, Quotient-affine metric, Lie-Cholesky metrics, Poly-hyperbolic-Cholesky metrics, Euclidean-Cholesky metrics, Log-Euclidean-Cholesky metrics, SPD matrices. [bibtex-entry]



11. 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): Riemannian manifolds, pole ladder, Schild's ladder, cardiac motion analysis, mean trajectory, longitudinal studies, Parallel transport. [bibtex-entry]



12. 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): Statistical shape modeling, Recurrence, Left atrial shape, CT, Catheter ablation, Atrial fibrillation. [bibtex-entry]



13. 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]



14. 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]



15. 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]



16. 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): Deformation-based morphometry, Subjective memory complaint, Clinical trial, Multidomain intervention. [bibtex-entry]



17. 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]



18. 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]



19. 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]



20. 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]



21. 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]



22. 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 Selection, Personalised modeling, Parameter Estimation. [bibtex-entry]



23. 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): Spatio-temporal model, Brain morphology, Aging, Imaging biomarkers, Alzheimer's disease, Deformations. [bibtex-entry]



24. 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): Deep learning, MRI, Lleft and right ventricles, Myocardium, Cardiac segmentation and diagnosis. [bibtex-entry]



25. 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): population statistics, Tetralogy of Fallot, tensor decomposition, atlas, N-way PLS, spatio-temporal alignment, non-rigid image registration, Cardiac motion tracking, evolution modelling. [bibtex-entry]



26. 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]



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



28. 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): Image synthesis, Registration, Low-dimensional analysis, Cardiac motion. [bibtex-entry]



29. 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): myocardial infarct, Cardiac modeling, classification, statistical shape analysis. [bibtex-entry]



30. 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]



31. 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]



32. 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]



33. 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): regularization, deformable model, template estimation, inconsistency, Hilbert space, Fréchet mean, quotient space. [bibtex-entry]



34. 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): inconsistency, group action, empirical Fréchet mean, consistency bias, manifold, Template, quotient space, Hilbert space, Fréchet mean. [bibtex-entry]



35. 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): synthetic, synthetic images, biophysical modelling, Neurodegeneration, biomechanical simulation, simulated database. [bibtex-entry]



36. 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): template, bias, shape, consistency, manifold, quotient space, geometry. [bibtex-entry]



37. 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]



38. 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]



39. 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]



40. 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]



41. 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): reproducible research, statistical analysis, diffeomorphism parametrized by stationary velocity fields, longitudinal study, deformation-based morphometry, non-linear registration. [bibtex-entry]



42. 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): Alzheimer's disease, biophysical model, longitudinal MRIs simulation, simulation of atrophy, longitudinal modeling. [bibtex-entry]



43. 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]



44. 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]



45. 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]



46. 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): Tetralogy of Fallot, spatio-temporal alignment, tensor decomposition, population statistics, motion tracking, non-rigid image registration, atlas, cardiac modelling. [bibtex-entry]



47. 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]



48. 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]



49. 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): Proper orthogonal decomposition, Atlas construction, Tetralogy of Fallot, Pulmonary artery, Computational fluid dynamics. [bibtex-entry]



50. 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]



51. 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]



52. 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]



53. 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]



54. 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]



55. 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]



56. 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]



57. 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]



58. 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]



59. 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]



60. 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]



61. 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]



62. 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]



63. 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]



64. 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]



65. 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]



66. 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]



67. 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]



68. 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]



69. 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]



70. 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]



71. 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]



72. 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]



73. 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]



74. 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]



75. 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]



76. 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]



77. 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]



78. 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]



79. 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]



80. 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]



81. 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]



82. 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]



83. 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]



84. 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]



85. 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]



86. 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]



87. 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]



88. 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]



89. 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]



90. 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]



91. 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]



92. 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]



93. 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]



94. 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]



95. 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]



96. 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]



97. 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]



98. 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]



99. 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]



100. 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]



101. 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]



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



103. 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]



104. 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]



105. 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]



106. 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]



107. 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]



108. 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]



109. 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]



110. 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]



111. 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]



112. 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]



113. 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]



114. 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]



115. 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]



116. 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]



117. 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]



118. 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]



119. 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]



120. 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]



121. 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]



122. 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]

1. Olivier Bisson, Yanis Aeschlimann, Samuel Deslauriers-Gauthier, and Xavier Pennec. Log-Euclidean Frameworks for Smooth Brain Connectivity Trajectories. In Lecture Notes in Computer Science (LNCS), volume 16035, Saint-Malo (France), France, pages 194-204, October 2025. Keyword(s): Correlation matrices, Riemannian geometry, Log-Euclidean polynomial regression. [bibtex-entry]



2. Tom Szwagier, Guillaume Olikier, and Xavier Pennec. Eigengap Sparsity for Covariance Parsimony. In Proc. of the 7th International Conference on Geometric Science of Information - GSI'25, volume LNCS 16034 of Lecture Notes in Computer Science, Saint-Malo (35400), France, pages pp 50-59, October 2025. Keyword(s): Isotonic regression, Monotone cone, Flag manifolds, Eigengaps, Parsimony, Covariance estimation. [bibtex-entry]



3. Morten Akhoj, Xavier Pennec, and Stefan Sommer. Tangent phylogenetic PCA. In Lecture Notes in Computer Science, volume 13886 of Lecture Notes in Computer Science, Levi Ski Resort (Lapland), Finland, pages 77-90, April 2023. Springer Nature Switzerland. [bibtex-entry]



4. Anna Calissano, Elodie Maignant, and Xavier Pennec. Towards Quotient Barycentric Subspaces. In Lecture Notes in Computer Science, volume 14071 of Lecture Notes in Computer Science, Saint-Malo (France), France, pages 366-374, August 2023. Springer Nature Switzerland. Keyword(s): Object Oriented Data Analysis, Graph Space, Barycentric Subspace Analysis, Quotient Space, Discrete Group. [bibtex-entry]



5. Elodie Maignant, Alain Trouvé, and Xavier Pennec. Riemannian Locally Linear Embedding with Application to Kendall Shape Spaces. In Lecture Notes in Computer Science, volume 14071 of Lecture Notes in Computer Science, Saint-Malo, (France), France, pages 12-20, August 2023. Springer Nature Switzerland. Keyword(s): Shape Spaces, Optimisation on Quotient Manifolds, Locally Linear Embedding. [bibtex-entry]



6. Tom Szwagier and Xavier Pennec. Rethinking the Riemannian Logarithm on Flag Manifolds as an Orthogonal Alignment Problem. In Lecture Notes in Computer Science, volume 14071 of Lecture Notes in Computer Science, Saint-Malo, (France), France, pages 375-383, August 2023. Springer Nature Switzerland. Keyword(s): Flag manifolds Riemannian logarithm Orthogonal alignment Procrustes analysis, Procrustes analysis, Orthogonal alignment, Riemannian logarithm, Flag manifolds. [bibtex-entry]



7. Yann Thanwerdas and Xavier Pennec. Characterization of Invariant Inner Products. In Lecture Notes in Computer Science, volume LNCS-14071 of Geometric Science of Information: 6th International Conference, GSI 2023, St. Malo, France, August 30 -- September 1, 2023, Proceedings, Part I, Saint Malo, France, France, pages 384-391, August 2023. Springer Nature Switzerland. Keyword(s): Invariant Riemannian metric, Group action, Representation theory, Invariant inner product, Invariant inner product Invariant Riemannian metric Group action Representation theory. [bibtex-entry]



8. Nicolas Guigui, Elodie Maignant, Alain Trouvé, and Xavier Pennec. Parallel Transport on Kendall Shape Spaces. In Lecture Notes in Computer Science, volume 12829 of Lecture Notes in Computer Science, Paris, France, pages 103-110, July 2021. Springer. [bibtex-entry]



9. Nicolas Guigui, Pamela Moceri, Maxime Sermesant, and Xavier Pennec. Cardiac Motion Modeling with Parallel Transport and Shape Splines. In IEEE 18th International Symposium on Biomedical Imaging (ISBI), 2021, IEEE 18th International Symposium on Biomedical Imaging (ISBI), 2021, Nice, France, pages pp. 1394-1397, April 2021. IEEE. Keyword(s): LDDMM, Cardiac Modelling, Shape Analysis. [bibtex-entry]



10. Nicolas Guigui and Xavier Pennec. A reduced parallel transport equation on Lie Groups with a left-invariant metric. In Lecture Notes in Computer Science, volume 12829 of Lecture Notes in Computer Science, Paris, France, pages 119-126, July 2021. Springer, Cham. [bibtex-entry]



11. Florent Jousse, Xavier Pennec, Hervé Delingette, and Matilde Gonzalez. Geodesic squared exponential kernel for non-rigid shape registration. In FG 2021 - IEEE International Conference on Automatic Face and Gesture Recognition, JODHPUR, India, December 2021. [bibtex-entry]



12. Yann Thanwerdas and Xavier Pennec. Geodesics and Curvature of the Quotient-Affine Metrics on Full-Rank Correlation Matrices. In Proceedings of Geometric Science of Information, volume 12829 of Proceedings of Geometric Science of Information, Paris, France, pages 93-102, July 2021. Springer, Cham. Keyword(s): Riemannian geometry, Quotient-affine metric, Quotient manifold, SPD matrices, Correlation matrices. [bibtex-entry]



13. Nina Miolane, Nicolas Guigui, Hadi Zaatiti, Christian Shewmake, Hatem Hajri, Daniel Brooks, Alice Le Brigant, Johan Mathe, Benjamin Hou, Yann Thanwerdas, Stefan Heyder, Olivier Peltre, Niklas Koep, Yann Cabanes, Thomas Gerald, Paul Chauchat, Bernhard Kainz, Claire Donnat, Susan Holmes, and Xavier Pennec. Introduction to Geometric Learning in Python with Geomstats. In Meghann Agarwal, Chris Calloway, Dillon Niederhut, and David Shupe, editors, SciPy 2020 - 19th Python in Science Conference, Austin, Texas, United States, pages 48-57, July 2020. Keyword(s): machine learning, manifold, statistics, Index Terms-differential geometry. [bibtex-entry]



14. Nicolas Guigui, Shuman Jia, Maxime Sermesant, and Xavier Pennec. Symmetric Algorithmic Components for Shape Analysis with Diffeomorphisms. In International Conference on Geometric Science of Information, volume Lecture Notes in Computer Science 11712 of Proceedings of Geometric Science of Information, Toulouse, France, pages 759-768, August 2019. F. Nielsen and F. Barbaresco, Springer. Keyword(s): Shape Registration, Parallel Transport, Symmetric Spaces. [bibtex-entry]



15. Yann Thanwerdas and Xavier Pennec. Exploration of Balanced Metrics on Symmetric Positive Definite Matrices. In International Conference on Geometric Science of Information, volume Lecture Notes in Computer Science 11712 of Proceedings of Geometric Science of Information, Toulouse, France, pages 484-493, August 2019. Springer. Keyword(s): Information geometry, Dually flat connections, SPD matrices. [bibtex-entry]



16. Yann Thanwerdas and Xavier Pennec. Is affine invariance well defined on SPD matrices? A principled continuum of metrics. In International Conference on Geometric Science of Information, volume Lecture Notes in Computer Science 11712 of Proceedings of Geometric Science of Information, Toulouse, France, pages 502-510, August 2019. Springer. Keyword(s): SPD matrices, Riemannian symmetric spaces. [bibtex-entry]



17. Shuman Jia, Antoine Despinasse, Zihao Wang, Hervé Delingette, Xavier Pennec, Pierre Jaïs, Hubert Cochet, and Maxime Sermesant. Automatically Segmenting the Left Atrium from Cardiac Images Using Successive 3D U-Nets and a Contour Loss. In LNCS, volume 11395 of LNCS, Granada, Spain, pages 221-229, September 2018. Keyword(s): deep learning, segmentation, left atrium, contour loss, loss function, ensemble prediction, 3D U-Net, distance map. [bibtex-entry]



18. Shuman Jia, Nicolas Duchateau, Pamela Moceri, Maxime Sermesant, and Xavier Pennec. Parallel Transport of Surface Deformations from Pole Ladder to Symmetrical Extension. In LNCS, volume 11167 of LNCS, Granada, Spain, pages 116-124, September 2018. Springer. [bibtex-entry]



19. Loïc Devilliers, Xavier Pennec, and Stéphanie Allassonnière. Inconsistency of Template Estimation with the Fréchet mean in Quotient Space. In LNCS, volume 10265 of LNCS, Boone, United States, pages 16-27, June 2017. Martin Styner and Marc Niethammer and Dinggang Shen and Stephen Aylward and Ipek Oguz and Hongtu Zhu. [bibtex-entry]



20. Shuman Jia, Claudia Camaioni, Marc-Michel Rohé, Pierre Jaïs, Xavier Pennec, Hubert Cochet, and Maxime Sermesant. Prediction of Post-Ablation Outcome in Atrial Fibrillation Using Shape Parameterization and Partial Least Squares Regression. In Lecture Notes in Computer Science, volume 10263 of Lecture Notes in Computer Science, Toronto, Canada, pages 314 - 321, June 2017. Keyword(s): regression, partial least squares, statistical shape analysis, left atrial remodeling, post-ablation outcome, catheter ablation, atrial fibrillation. [bibtex-entry]



21. Kristin Mcleod, Maxime Sermesant, and Xavier Pennec. Improving Understanding of Long-Term Cardiac Functional Remodelling via Cross-Sectional Analysis of Polyaffine Motion Parameters. In Lecture Notes in Computer Science, volume 10263 of Lecture Notes in Computer Science, Toronto, Canada, pages 51 - 59, June 2017. Springer. [bibtex-entry]



22. Roch Molléro, Hervé Delingette, Manasi Datar, Tobias Heimann, Jakob Hauser, Dilveer Panesar, Alexander Jones, Andrew Taylor, Marcus Kelm, Titus Kuehne, Marcello Chinali, Gabriele Rinelli, Nicholas Ayache, Xavier Pennec, and Maxime Sermesant. Longitudinal Analysis using Personalised 3D Cardiac Models with Population-Based Priors: Application to Paediatric Cardiomyopathies. In Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2017, Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2017, Québec City, Canada, pages 350-358, September 2017. Springer International Publishing. [bibtex-entry]



23. Roch Molléro, Jakob Hauser, Xavier Pennec, Manasi Datar, Hervé Delingette, Alexander Jones, Nicholas Ayache, Tobias Heimann, and Maxime Sermesant. Longitudinal Parameter Estimation in 3D Electromechanical Models: Application to Cardiovascular Changes in Digestion. In Functional Imaging and Modelling of the Heart, Functional Imaging and Modelling of the Heart, Toronto, Canada, pages 432-440, June 2017. Springer International Publishing. [bibtex-entry]



24. Xavier Pennec. Sample-limited L p Barycentric Subspace Analysis on Constant Curvature Spaces. In Lecture Notes in Computer Science (LNCS), Geometric Science of Information, Paris, France, pages 20-28, November 2017. Springer International Publishing. [bibtex-entry]



25. Marc-Michel Rohé, Manasi Datar, Tobias Heimann, Maxime Sermesant, and Xavier Pennec. SVF-Net: Learning Deformable Image Registration Using Shape Matching. In Medical Image Computing and Computer Assisted Intervention -- MICCAI 2017, Medical Image Computing and Computer Assisted Intervention -- MICCAI 2017, Québec, Canada, pages 266-274, September 2017. Springer International Publishing. Keyword(s): Registration, Cardiac Imaging, Deep Learning. [bibtex-entry]



26. Marc-Michel Rohé, Maxime Sermesant, and Xavier Pennec. Automatic Multi-Atlas Segmentation of Myocardium with SVF-Net. In LNCS, volume 10663 of LNCS, Québec, Canada, pages 170-177, September 2017. [bibtex-entry]



27. Jan L. Bruse, Kristin Mcleod, Elena Cervi, Giovanni Biglino, T.-y Hsia, Maxime Sermesant, Xavier Pennec, Andrew Taylor, and Silvia Schievano. Discovering clusters in pathologic cardiac morphology: MR-based hierarchical 3D shape clustering of surgically repaired aortic arches. In Computer Assisted Radiology, 30th International Congress and Exhibition, Heidelberg, Germany, June 2016. [bibtex-entry]



28. Roch Molléro, Xavier Pennec, Hervé Delingette, Nicholas Ayache, and Maxime Sermesant. A Multiscale Cardiac Model for Fast Personalisation and Exploitation. In MICCAI 2016, Lecture Notes in Computer Science, volume 9902 of MICCAI 2016, Lecture Notes in Computer Science, Athens, Greece, pages 174-182, October 2016. [bibtex-entry]



29. Marc-Michel Rohé, Roch Molléro, Maxime Sermesant, and Xavier Pennec. Highly Reduced Model of the Cardiac Function for Fast Simulation. In Image, Video, and Multidimensional Signal Processing Workshop (IVMSP), 2016 IEEE 12th, Image, Video, and Multidimensional Signal Processing Workshop (IVMSP), 2016 IEEE 12th, Bordeaux, France, pages 5, July 2016. IEEE. Keyword(s): Simulation 3D, Biomechanical Model, Reduction Order Model. [bibtex-entry]



30. Marc-Michel Rohé, Maxime Sermesant, and Xavier Pennec. Barycentric Subspace Analysis: a new Symmetric Group-wise Paradigm for Cardiac Motion Tracking. In MICCAI 2016, Lecture Notes in Computer Science, volume 9902 of MICCAI 2016, Lecture Notes in Computer Science, Athens, Greece, pages 300-307, October 2016. Keyword(s): Medical Image Analysis, Atlas Framework, Registration, Manifold atlas. [bibtex-entry]



31. Stéphanie Allassonnière, Loïc Devilliers, and Xavier Pennec. Estimating the Template in the Total Space with the Fréchet Mean on Quotient Spaces may have a Bias: a Case Study on Vector Spaces Quotiented by the Group of Translations. In Proceedings of the fifth international workshop on Mathematical Foundation sof Computational Anatomy (MFCA'15), Proceedings of the fifth international workshop on Mathematical Foundation sof Computational Anatomy (MFCA'15), Munich, Germany, pages 131-142, October 2015. [bibtex-entry]



32. Jan L. Bruse, Kristin Mcleod, Giovanni Biglino, Hopewell N. Ntsinjana, Claudio Capelli, Tain-Yen Hsia, Maxime Sermesant, Xavier Pennec, Andrew Taylor, and Silvia Schievano. A Non-parametric Statistical Shape Model for Assessment of the Surgically Repaired Aortic Arch in Coarctation of the Aorta: How Normal is Abnormal?. In Lecture Notes in Computer Science, volume 9534 of Lecture Notes in Computer Science, Munich, Germany, October 2015. Springer. [bibtex-entry]



33. Vikash Gupta, Grégoire Malandain, Nicholas Ayache, and Xavier Pennec. A framework for creating population specific multimodal brain atlas using clinical T1 and diffusion tensor images. In Computational Diffusion MRI, Computational Diffusion MRI, Munich, Germany, pages 99-108, October 2015. Keyword(s): DTI-T1 brain template, HIV, Probabilistic white matter parcel-lation map, Multimodal brain atlas. [bibtex-entry]



34. Bishesh Khanal, Marco Lorenzi, Nicholas Ayache, and Xavier Pennec. Simulating Patient Specific Multiple Time-point MRIs From a Biophysical Model of Brain Deformation in Alzheimer's Disease. In Computational Biomechanics for Medicine: Imaging, Modeling and Computing, Computational Biomechanics for Medicine: Imaging, Modeling and Computing, Munich, France, pages 167-176, October 2015. Springer International Publishing. Keyword(s): biophysical modeling, Alzheimer's disease, biomechanical simulation, MRI, longitudinal MRI. [bibtex-entry]



35. Kristin Mcleod, Maxime Sermesant, Philipp Beerbaum, and Xavier Pennec. Descriptive and Intuitive Population-Based Cardiac Motion Analysis via Sparsity Constrained Tensor Decomposition. In Lecture notes in computer science (LNCS), volume 9351 of Lecture notes in computer science (LNCS), Munich, Germany, pages 419-426, October 2015. [bibtex-entry]



36. Nina Miolane and Xavier Pennec. A survey of mathematical structures for extending 2D neurogeometry to 3D image processing. In LNCS, volume 9601 of LNCS, Munich, Germany, pages 155-167, October 2015. Keyword(s): Image processing, neurogeometry, sub-Riemannian geometry. [bibtex-entry]



37. Nina Miolane and Xavier Pennec. Biased estimators on Quotient spaces. In Lecture notes in computer science (LNCS), volume 9389 of Lecture notes in computer science (LNCS), Palaiseau, France, pages 130-139, October 2015. Springer. [bibtex-entry]



38. Roch Molléro, Dominik Neumann, Marc-Michel Rohé, Manasi Datar, Herve Lombaert, Nicholas Ayache, Dorin Comaniciu, Olivier Ecabert, Marcello Chinali, Gabriele Rinelli, Xavier Pennec, Maxime Sermesant, and Tommaso Mansi. Propagation of Myocardial Fibre Architecture Uncertainty on Electromechanical Model Parameter Estimation: A Case Study. In 8th International Conference, FIMH 2015, Maastricht, The Netherlands, June 25-27, 2015. Proceedings, 8th International Conference, FIMH 2015, Maastricht, The Netherlands, June 25-27, 2015. Proceedings, Maastricht, Netherlands, pages 448-456, June 2015. [bibtex-entry]



39. Xavier Pennec. Barycentric Subspaces Analysis on Spheres. In Proceedings of the fifth international workshop on Mathematical Foundation sof Computational Anatomy (MFCA'15), Proceedings of the fifth international workshop on Mathematical Foundation sof Computational Anatomy (MFCA'15), Munich, Germany, pages 71-82, October 2015. [bibtex-entry]



40. Xavier Pennec. Barycentric Subspaces and Affine Spans in Manifolds. In Lecture Notes in Compuer Science, volume 9389 of Lecture Notes in Compuer Science, Palaiseau, France, pages 12-21, October 2015. [bibtex-entry]



41. Marc-Michel Rohé, Nicolas Duchateau, Maxime Sermesant, and Xavier Pennec. Combination of Polyaffine Transformations and Supervised Learning for the Automatic Diagnosis of LV Infarct. In LNCS, volume 9534 of LNCS, Munich, Germany, pages 190-198, 2015. Springer. Keyword(s): Machine Learning, Cardiac Motion, Medical Imaging. [bibtex-entry]



42. Hugo Darmanté, Benoit Bugnas, Regis Bernard De Dompsure, Laurent Barresi, Nina Miolane, Xavier Pennec, Fernand de Peretti, and Nicolas Bronsard. Analyse biométrique de l'anneau pelvien en 3 dimensions - à propos de 100 scanners. In Revue de Chirurgie Orthopédique et Traumatologique, volume 100 of Revue de Chirurgie Orthopédique et Traumatologique, Paris, France, November 2014. [bibtex-entry]



43. Bishesh Khanal, Marco Lorenzi, Nicholas Ayache, and Xavier Pennec. A Biophysical Model of Shape Changes due to Atrophy in the Brain with Alzheimer's Disease. In P. GOLLAND, N. HATA, C. BARILLOT, J. HORNEGGER, and R. HOWE, editors, LNCS - Lecture Notes in Computer Science, Springer, volume 8674 of LNCS - Lecture Notes in Computer Science, Springer, Boston, United States, pages 41-48, September 2014. Springer. Keyword(s): Longitudinal modeling, Atrophy simulation, Atrophy model, Biophysical model, Alzheimer's disease. [bibtex-entry]



44. Marco Lorenzi, Xavier Pennec, Nicholas Ayache, and (adni) For The Alzheimer'S Disease Neuroimaging Initiative. Regional flux analysis of longitudinal atrophy in Alzheimer's disease. In Alzheimer's Association International Conference, Copenhagen, Denmark, July 2014. Note: Oral podium presentation. [bibtex-entry]



45. Nina Miolane and Xavier Pennec. Statistics on Lie groups : a need to go beyond the pseudo-Riemannian framework. In AIP Conference Proceedings, volume 1641 of AIP Conference Proceedings, Amboise, France, pages 59-66, September 2014. AIP Proceedings. Keyword(s): pseudo-Riemannian, Statistics, computational anatomy, Lie group, exponential barycenter, metric, manifold. [bibtex-entry]



46. Vikash Gupta, Nicholas Ayache, and Xavier Pennec. Improving DTI Resolution from a Single Clinical Acquisition: A Statistical Approach using Spatial Prior. In Kensaku Mori, Ichiro Sakuma, Yoshinobu Sato, Christian Barillot, and Nassir Navab, editors, Medical Image Computing and Computer-Assisted Intervention - MICCAI 2013 - Part III, volume 8151 of Medical Image Computing and Computer-Assisted Intervention - MICCAI 2013 - Part III, Nagoya, Japan, pages 477-484, September 2013. Springer. Keyword(s): DTI, Super-resolution, Partial volume effect, Diffusion Tensor Imaging, Clinical Medical Imaging. [bibtex-entry]



47. Marco Lorenzi, Martina Bochetta, Nicholas Ayache, Xavier Pennec, and Giovanni B. Frisoni. Conversion to MCI in healthy individuals with abnormal CSF Ab42 levels is associated with specific longitudinal morphological changes. In Alzheimer's & Dementia: The Journal of the Alzheimer's Association, volume 9, issue 4 (supplement) of Alzheimer's & Dementia: The Journal of the Alzheimer's Association, Boston, United States, pages P596, July 2013. [bibtex-entry]



48. Marco Lorenzi, Bjoern H. Menze, Marc Niethammer, Nicholas Ayache, and Xavier Pennec. Sparse Scale-Space Decomposition of Volume Changes in Deformations Fields. In Kensaku Mori, Ichiro Sakuma, Yoshinobu Sato, Christian Barillot, and Nassir Navab, editors, Medical Image Computing and Computer-Assisted Intervention - MICCAI 2013 - Part II, volume 8150 of Medical Image Computing and Computer-Assisted Intervention - MICCAI 2013 - Part II, Nagoya, Japan, pages 328-335, September 2013. Springer. Keyword(s): Scale-space decomposition, non-rigid registration, longitudinal analysis, stationary velocity fields. [bibtex-entry]



49. Marco Lorenzi and Xavier Pennec. Parallel Transport with Pole Ladder: Application to Deformations of time Series of Images. In Nielsen, Frank, Barbaresco, and F., editors, Geometric Science of Information, volume 8085 of Geometric Science of Information, Paris, France, pages 68-75, August 2013. Springer. [bibtex-entry]



50. Kristin Mcleod, Christof Seiler, Maxime Sermesant, and Xavier Pennec. Spatio-Temporal Dimension Reduction of Cardiac Motion for Group-Wise Analysis and Statistical Testing. In Kensaku Mori, Ichiro Sakuma, Yoshinobu Sato, Christian Barillot, and Nassir Navab, editors, Medical Image Computing and Computer-Assisted Intervention - MICCAI 2013 - Part II, volume 8150 of Medical Image Computing and Computer-Assisted Intervention - MICCAI 2013 - Part II, Nagoya, Japan, pages 501-508, 2013. Springer, Heidelberg. [bibtex-entry]



51. Kristin Mcleod, Christof Seiler, Nicolas Toussaint, Maxime Sermesant, and Xavier Pennec. Regional Analysis of Left Ventricle Function using a Cardiac-Specific Polyaffine Motion Model. In Sébastien Ourselin, Daniel Rueckert, and Nicolas Smith, editors, Functional Imaging and Modeling of the Heart, volume 7945 of Functional Imaging and Modeling of the Heart, London, United Kingdom, pages 483-490, June 2013. Springer. [bibtex-entry]



52. Xavier Pennec. Bi-invariant means on Lie groups with Cartan-Schouten connections. In Nielsen, Frank, Barbaresco, and F., editors, Geometric Science of Information, volume 8085 of Geometric Science of Information, Paris, France, pages 59-67, August 2013. Springer. [bibtex-entry]



53. Christof Seiler, Xavier Pennec, and Susan Holmes. Random Spatial Structure of Geometric Deformations and Bayesian Nonparametrics. In Geometric Science of Information, volume 8085 of Geometric Science of Information, Paris, France, pages 120-127, August 2013. Springer. [bibtex-entry]



54. Birkan Tunç, Alex Smith, Demian Wasserman, Xavier Pennec, William M. Wells, Ragini Verma, and Kilian M. Pohl. Multinomial Probabilistic Fiber Representation for Connectivity Driven Clustering. In Gee, J. C., Joshi, Sarang, Pohl, Kilian M., Wells, William M., Zollei, and L., editors, LNCS, volume 7917 of LNCS, Asilomar, United States, pages 730-741, June 2013. Springer. [bibtex-entry]



55. Nicolas Duchateau, Mathieu De Craene, Xavier Pennec, Beatriz Merino, Marta Sitges, and Bart Bijnens. Which Reorientation Framework for the Atlas-Based Comparison of Motion from Cardiac Image Sequences?. In Proc. of STIA 2012 (Spatio-=Temporal Image Analysis for Longitudinal and Time-Series Image Data, volume 7570 of LNCS, pages 25-37, October 2012. Springer, Heidelberg. [bibtex-entry]



56. Hervé Lombaert, Leo Grady, Xavier Pennec, Nicholas Ayache, and Farida Cheriet. Spectral Demons - Image Registration via Global Spectral Correspondence. In Proc. of ECCV (2), number 7573 of LNCS, pages 30-44, 2012. [bibtex-entry]



57. Hervé Lombaert, Leo Grady, Xavier Pennec, Jean-Marc Peyrat, Nicholas Ayache, and Farida Cheriet. Groupwise Spectral Log-Demons Framework for Atlas Construction. In Medical Computer Vision (MCV'12) MICCAI workshop, 2012. Note: Best paper award. [bibtex-entry]



58. Marco Lorenzi, Nicholas Ayache, and Xavier Pennec. Disentangling the normal aging from the pathological Alzheimer's disease progression on cross-sectional structural MR images. In MICCAI workshop on Novel Imaging Biomarkers for Alzheimer's Disease and Related Disorders (NIBAD'12), pages 145-154, October 2012. ISBN: 9781479261994. [bibtex-entry]



59. Marco Lorenzi, Nicholas Ayache, and Xavier Pennec. Regional flux analysis of longitudinal atrophy in Alzheimer's disease. In Proceedings of Medical Image Computing and Computer Assisted Intervention 2012 (MICCAI), volume 7510 of LNCS, pages 739-746, October 2012. Springer, Heidelberg. ISBN: 978-3-642-33414-6. [bibtex-entry]



60. Marco Lorenzi, Giovanni B. Frisoni, Nicholas Ayache, and Xavier Pennec. Probabilistic Flux Analysis of Cerebral Longitudinal Atrophy. In MICCAI workshop on Novel Imaging Biomarkers for Alzheimer's Disease and Related Disorders (NIBAD'12), pages 256-265, October 2012. ISBN: 9781479261994. [bibtex-entry]



61. Kristin McLeod, Adityo Prakosa, Tommaso Mansi, Maxime Sermesant, and Xavier Pennec. An Incompressible Log-Domain Demons Algorithm for Tracking Heart Tissue. In Proc. MICCAI Workshop on Statistical Atlases and Computational Models of the Heart: Mapping Structure and Function (STACOM11), number 7085 of LNCS, Toronto, pages 55-67, September 2012. Springer. [bibtex-entry]



62. Kristin McLeod, Christof Seiler, Maxime Sermesant, and Xavier Pennec. A Near-Incompressible Poly-Affine Motion Model for Cardiac Function Analysis. In Proc. MICCAI Workshop on Statistical Atlases and Computational Models of the Heart: Mapping Structure and Function + a Cardiac Electrophysiological Simulation Challenge (STACOM+CESC'12), LNCS, Nice, October 2012. Springer. [bibtex-entry]



63. Adityo Prakosa, Kristin McLeod, Maxime Sermesant, and Xavier Pennec. Evaluation of iLogDemons Algorithm for Cardiac Motion Tracking in Synthetic Ultrasound Sequence. In Proc. MICCAI Workshop on Statistical Atlases and Computational Models of the Heart: Imaging and Modelling Challenge (STACOM12), LNCS, October 2012. Springer. [bibtex-entry]



64. Christof Seiler, Xavier Pennec, and Mauricio Reyes. Simultaneous Multiscale Polyaffine Registration by Incorporating Deformation Statistics. In Proceedings of Medical Image Computing and Computer Assisted Intervention 2012 (MICCAI), volume 7511 of LNCS, pages 130-137, October 2012. Springer, Heidelberg. ISBN: 978-3-642-33417-7. [bibtex-entry]



65. Stefan Sommer, Mads Nielsen, and Xavier Pennec. Sparsity and Scale: Compact Representations of Deformation for Diffeomorphic Registration. In IEEE Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA 2012), Breckenridge, Colorado, USA, January 2012. [Abstract] [bibtex-entry]



66. B. Gibaud, F. Ahmad, C. Barillot, F. Michel, B. Wali, B. Batrancourt, M. Dojat, P. Girard, A. Gaignard, D. Lingrand, J. Montagnat, J. Rojas Balderrama, G. Malandain, X. Pennec, D. Godard, G. Kassel, and M. Pélégrini-Issac. A federated system for sharing and reuse of images and image processing tools in neuroimaging. In Proc. of Computer Assisted Radiology and Surgery 2011 (CARS 2011), June 2011. [bibtex-entry]



67. Marco Lorenzi, Nicholas Ayache, Giovanni B. Frisoni, and Xavier Pennec. Mapping the effects of A$\beta_{1-42}$ levels on the longitudinal changes in healthy aging: hierarchical modeling based on stationary velocity fields. In Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI), volume 6892 of LNCS, pages 663-670, 2011. Springer. [bibtex-entry]



68. Marco Lorenzi, Nicholas Ayache, and Xavier Pennec. Schilds Ladder for the parallel transport of deformations in time series of images. In G. Szekely and H. Hahn, editors, Proceedings of Information Processing in Medical Imaging (IPMI'11), volume 6801 of LNCS, pages 463-474, 2011. Note: Honorable Mention (runner-up) for the Erbsmann Award. [bibtex-entry]



69. Marco Lorenzi and Xavier Pennec. Geodesics, parallel transport & one-parameter subgroups. In 3rd MICCAI workshop on Mathematical Foundations of Computational Anatomy Workshop, September 2011. [bibtex-entry]



70. Marco Lorenzi, Xavier Pennec, and Giovanni B. Frisoni. Monitoring the brain's longitudinal changes in clinical trials for Alzheimers disease: a robust and reliable non-rigid registration framework. In Alzheimer's Association 2011 International Conference on Alzheimer's Disease (AAICAD), 2011. [bibtex-entry]



71. Xavier Pennec and Marco Lorenzi. Which parallel transport for the statistical analysis of longitudinal deformations?. In Colloque GRETSI '11, September 2011. [bibtex-entry]



72. Christof Seiler, Xavier Pennec, and Mauricio Reyes. Geometry-Aware Multiscale Image Registration Via OBBTree-Based Polyaffine Log-Demons. In Proceedings of Medical Image Computing and Computer Assisted Intervention 2011 (MICCAI), volume 6892 of LNCS, pages 631-638, September 2011. Springer, Heidelberg. Note: Young Scientist Award. [bibtex-entry]



73. Christof Seiler, Xavier Pennec, Lucas Ritacco, and Mauricio Reyes. Femur Specific Polyaffine Model to Regularize the Log-Domain Demons Registration. In Benoit M. Dawant and David R. Haynor, editors, Proceedings of SPIE Medical Imaging '11, volume 7962, pages Paper 7962-15, January 2011. SPIE Publishing. ISBN: 9780819485045. [bibtex-entry]



74. Viviana Siless, Pamela Guevara, Xavier Pennec, and Pierre Fillard. Joint T1 and Brain Fiber Diffeomorphic Registration Using the Demons. In Tianming Liu, Dinggang Shen, Luis Ibanez, and Xiaodong Tao, editors, Multimodal Brain Image Analysis (First Int. MICCAI Workshop on), volume 7012 of Lecture Notes in Computer Science, pages 10-18, 2011. Springer.