Bibliography

Major publications by the team in recent years

[1]

N. Ayache (editor)
Computational Models for the Human Body, Handbook of Numerical Analysis (Ph. Ciarlet series editor), Elsevier, 2004.

[2]

N. Ayache, H. Delingette (editors)
Proceedings of the International Symposium on Surgery Simulation and Soft Tissue Modeling, Lecture Notes in Computer Science, Springer-Verlag, Juan-les-Pins, France, June 2003, vol. LNCS 2673.

[3]

V. Arsigny, P. Fillard, X. Pennec, N. Ayache.
Log-Euclidean Metrics for Fast and Simple Calculus on Diffusion Tensors, in: Magnetic Resonance in Medicine, August 2006, vol. 56, n^o 2, p. 411-421
ftp://ftp-sop.inria.fr/epidaure/Publications/Arsigny/arsigny_mrm_2006.pdf, PMID: 16788917.

[4]

N. Ayache.
Epidaure: a Research Project in Medical Image Analysis, Simulation and Robotics at INRIA, in: IEEE Trans. on Medical Imaging, October 2003, vol. 22, n^o 10, p. 1185–1201
ftp://ftp-sop.inria.fr/epidaure/Publications/Ayache/Ayache-editorial-ieee-tmi.pdf.

[5]

N. Ayache.
L'analyse automatique des images medicales, etat de l'art et perspectives, in: Annales de l'Institut Pasteur, avril-juin 1998, vol. 9, n^o 1, p. 13-21, Numero special sur les progres recents de l'imagerie medicale.

[6]

N. Ayache, O. Clatz, H. Delingette, G. Malandain, X. Pennec, M. Sermesant.
Asclepios: a Research Project-Team at INRIA for the Analysis and Simulation of Biomedical Images, in: From semantics to computer science: essays in honor of Gilles Kahn, Y. Bertot, G. Huet, J.-J. Lévy, G. Plotkin (editors), Cambridge University Press, 2009
http://www.inria.fr/sophia/asclepios/Publications/Nicholas.Ayache/Colloquium-Gilles-Kahn-NA-2007-v5.pdf.

[7]

C. Blondel, R. Vaillant, G. Malandain, N. Ayache.
3-D tomographic reconstruction of coronary arteries using a precomputed 4-D motion field, in: Physics in Medicine and Biology, 2004, vol. 49, n^o 11, p. 2197–2208
ftp://ftp-sop.inria.fr/epidaure/Publications/Malandain/blondel-pmb-2004.pdf.

[8]

P. Cachier, É. Bardinet, D. Dormont, X. Pennec, N. Ayache.
Iconic Feature Based Nonrigid Registration: The PASHA Algorithm, in: CVIU — Special Issue on Nonrigid Registration, Feb.-march 2003, vol. 89, n^o 2-3, p. 272–298
ftp://ftp-sop.inria.fr/epidaure/Publications/Cachier/Cachier_CVIU_2003.pdf.

[9]

O. Clatz, M. Sermesant, P.-Y. Bondiau, H. Delingette, S. K. Warfield, G. Malandain, N. Ayache.
Realistic Simulation of the 3D Growth of Brain Tumors in MR Images Coupling Diffusion with Mass Effect, in: IEEE Transactions on Medical Imaging, October 2005, vol. 24, n^o 10, p. 1334-1346
ftp://ftp-sop.inria.fr/epidaure/Publications/Clatz/TMI_GBM_clatz.pdf.

[10]

H. Delingette, N. Ayache.
Soft Tissue Modeling for Surgery Simulation, in: Computational Models for the Human Body, N. Ayache (editor), Handbook of Numerical Analysis (Ed : Ph. Ciarlet), Elsevier, 2004
ftp://ftp-sop.inria.fr/epidaure/Publications/Delingette/hna-delingette.pdf.

[11]

H. Delingette.
General Object Reconstruction based on Simplex Meshes, in: International Journal of Computer Vision, 1999, vol. 32, n^o 2, p. 111-146.

[12]

J. Duncan, N. Ayache.
Medical Image Analysis: Progress over two decades and the challenges ahead, in: IEEE Transactions on Pattern Analysis and Machine Intelligence, 2000, vol. 22, n^o 1, p. 85-106.

[13]

M. Á. González Ballester, X. Pennec, M. G. Linguraru, N. Ayache.
Generalized Image Models and Their Application as Statistical Models of Images, in: Medical Image Analysis, September 2004, vol. 8, n^o 3, p. 361–369
ftp://ftp-sop.inria.fr/epidaure/Publications/Gonzalez/Gonzalez:MedIA:2004.pdf, MICCAI 2003 Special Issue.

[14]

K. Krissian, G. Malandain, N. Ayache, R. Vaillant, Y. Trousset.
Model-Based Detection of Tubular Structures in 3D Images, in: Computer Vision and Image Understanding, 2000, vol. 80, n^o 2, p. 130–171
ftp://ftp-sop.inria.fr/epidaure/Publications/Malandain/krissian-cviu-2000.pdf.

[15]

G. Malandain, É. Bardinet, K. Nelissen, W. Vanduffel.
Fusion of autoradiographs with an MR volume using 2-D and 3-D linear transformations, in: NeuroImage, September 2004, vol. 23, n^o 1, p. 111–127
ftp://ftp-sop.inria.fr/epidaure/Publications/Malandain/malandain-neuroimage-2004.pdf.

[16]

J. Montagnat, H. Delingette.
4D Deformable Models with temporal constraints : application to 4D cardiac image segmentation, in: Medical Image Analysis, February 2005, vol. 9, n^o 1, p. 87–100
ftp://ftp-sop.inria.fr/epidaure/Publications/Delingette/montagnat-Media04.pdf.

[17]

X. Pennec, N. Ayache, J.-P. Thirion.
Landmark-based registration using features identified through differential geometry, in: Handbook of Medical Imaging, I. Bankman (editor), Academic Press, September 2000, chap. 31, p. 499-513
ftp://ftp-sop/epidaure/Publications/Pennec/Pennec.HMIP.pdf.

[18]

X. Pennec, P. Cachier, N. Ayache.
Tracking Brain Deformations in Time-Sequences of 3D US Images, in: Pattern Recognition Letters - Special Issue on Ultrasonic Image Processing and Analysis, February 2003, vol. 24, n^o 4-5, p. 801–813
ftp://ftp-sop.inria.fr/epidaure/Publications/Pennec/Pennec.Cachier.Ayache.PattRecLetters02.pdf.

[19]

G. Picinbono, H. Delingette, N. Ayache.
Non-Linear Anisotropic Elasticity for Real-Time Surgery Simulation, in: Graphical Models, September 2003, vol. 65, n^o 5, p. 305–321
ftp://ftp-sop.inria.fr/epidaure/Publications/Delingette/Picinbono-GM03.pdf.

[20]

S. Prima, S. Ourselin, N. Ayache.
Computation of the Mid-Sagittal Plane in 3D Brain Images, in: IEEE Transaction on Medical Imaging, February 2002, vol. 21, n^o 2, p. 122–138
ftp://ftp-sop.inria.fr/epidaure/Publications/Prima/tmi.final.pdf.

[21]

D. Rey, G. Subsol, H. Delingette, N. Ayache.
Automatic Detection and Segmentation of Evolving Processes in 3D Medical Images: Application to Multiple Sclerosis, in: Medical Image Analysis, June 2002, vol. 6, n^o 2, p. 163-179
ftp://ftp-sop.inria.fr/epidaure/Publications/Rey/rey-media-2002.pdf.

[22]

A. Roche, G. Malandain, N. Ayache.
Unifying Maximum Likelihood Approaches in Medical Image Registration, in: International Journal of Imaging Systems and Technology: Special Issue on 3D Imaging, 2000, vol. 11, n^o 1, p. 71–80
ftp://ftp-sop.inria.fr/epidaure/Publications/Roche/ijist00.pdf.

[23]

A. Roche, X. Pennec, G. Malandain, N. Ayache.
Rigid Registration of 3D Ultrasound with MR Images: a New Approach Combining Intensity and Gradient Information, in: IEEE Transactions on Medical Imaging, October 2001, vol. 20, n^o 10, p. 1038–1049
ftp://ftp-sop.inria.fr/epidaure/Publications/Roche/Roche_MR_US_TMI_2001.pdf.

[24]

M. Sermesant, H. Delingette, N. Ayache.
An Electromechanical Model of the Heart for Image Analysis and Simulation, in: IEEE Transactions in Medical Imaging, 2007, vol. 25, n^o 5, p. 612–625
ftp://ftp-sop.inria.fr/asclepios/Publications/Maxime.Sermesant/TMI2006Sermesant.pdf.

[25]

M. Sermesant, C. Forest, X. Pennec, H. Delingette, N. Ayache.
Deformable biomechanical models: Application to 4D cardiac image analysis, in: Medical Image Analysis, December 2003, vol. 7, n^o 4, p. 475–488
http://authors.elsevier.com/sd/article/S1361841503000689.

Publications of the year

Doctoral Dissertations and Habilitation Theses

[26]

E. Konukoglu.
Modeling Glioma Growth and Personalizing Growth Models in Medical Images, Université Nice Sophia-Antipolis, February 2009
http://www.inria.fr/sophia/asclepios/Publications/Ender.Konukoglu/konukoglu_thesis.pdf, PhD Thesis.

[27]

J.-M. Peyrat.
Comparison of Cardiac Anatomy and Function: Statistics on Fibre Architecture from DT-MRI and Registration of 4D CT Images, Nice Sophia Antipolis University, November 2009
http://www.inria.fr/sophia/asclepios/Publications/Jean-Marc.Peyrat/Peyrat_2009_PhDThesis.pdf, PhD Thesis.

[28]

J.-C. Souplet.
Évaluation de l'atrophie et de la charge lésionnelle sur des séquences IRM de patients atteints de sclérose en plaques, Université de Nice – Sophia-Antipolis, January 2009
http://www.inria.fr/sophia/asclepios/Publications/Jean-Christophe.Souplet/Souplet_PhDThesis.pdf, Thèse de sciences (PhD Thesis).

Articles in International Peer-Reviewed Journal

[29]

V. Arsigny, O. Commowick, N. Ayache, X. Pennec.
A Fast and Log-Euclidean Polyaffine Framework for Locally Linear Registration, in: J. of Math. Imaging and Vision (JMIV), 2009, vol. 33, n^o 2, p. 222-238
http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Arsigny_JMIV_polyaffine.

[30]

É. Bardinet, M. Bhattacharjee, D. Dormont, B. Pidoux, G. Malandain, M. Schupbach, N. Ayache, P. Cornu, Y. Agid, J. Yelnik.
A three-dimensional histological atlas of the human basal ganglia. II. Atlas deformation strategy and evaluation in deep brain stimulation for Parkinson disease., in: Journal of neurosurgery, February 2009, vol. 110, n^o 2, p. 208-19
http://www.inria.fr/sophia/asclepios/Publications/Bardinet/bardinet-jn-2008.pdf.

[31]

C. Brun, N. Lepore, X. Pennec, A. D. Lee, M. Barysheva, S. K. Madsen, C. Avedissian, Y.-Y. Chou, G. I. de Zubicaray, K. McMahon, M. Wright, A. W. Toga, P. M. Thompson.
Mapping the Regional Influence of Genetics on Brain Structure Variability - A Tensor-Based Morphometry Study, in: NeuroImage, October 2009, vol. 48, n^o 1, p. 37-49.

[32]

S. Durrleman, X. Pennec, A. Trouvé, N. Ayache.
Statistical Models on Sets of Curves and Surfaces based on Currents, in: Medical Image Analysis, October 2009, vol. 13, n^o 5, p. 793-808
http://www.inria.fr/sophia/asclepios/Publications/Stanley.Durrleman/Durrleman_MedIA_09.pdf.

[33]

P. Fillard, X. Pennec, P. M. Thompson, N. Ayache.
Evaluating Brain Anatomical Correlations via Canonical Correlation Analysis of Sulcal Lines, in: NeuroImage, 2009
http://www.inria.fr/sophia/asclepios/Publications/Pierre.Fillard/Fillard.Neuroimage.2008.pdf, Accepted for publication.

[34]

H. Hufnagel, J. Ehrhardt, X. Pennec, N. Ayache, H. Handels.
Computation of a Probabilistic Statistical Shape Model in a Maximum-a-posteriori Framework, in: Methods of Information in Medicine, 2009, vol. 48, n^o 4, p. 314-319
http://www.inria.fr/sophia/asclepios/Publications/Heike.Hufnagel/Hufnagel_MIM09.pdf.

[35]

A. Klein, J. Andersson, B. A. Ardekani, J. Ashburner, B. Avants, M.-C. Chiang, G. E. Christensen, D. L. Collins, P. Hellier, J. H. Song, M. Jenkinson, C. Lepage, D. Rueckert, P. M. Thompson, T. Vercauteren, R. P. Woods, J. J. Mann, R. V. Parsey.
Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration, in: NeuroImage, July 2009, vol. 46, n^o 3, p. 786–802
http://www.mindboggle.info/papers/, PMID: 19195496.

[36]

E. Konukoglu, O. Clatz, P.-Y. Bondiau, H. Delingette, N. Ayache.
Extrapolating Glioma Invasion Margin in Brain Magnetic Resonance Images: Suggesting New Irradiation Margins, in: Medical Image Analysis, 2009
http://www.inria.fr/sophia/asclepios/Publications/Ender.Konukoglu/MEDIA2009_konukoglu_extrapolation.pdf, In Press.

[37]

E. Konukoglu, O. Clatz, B. H. Menze, M.-A. Weber, B. Stieltjes, E. Mandonnet, H. Delingette, N. Ayache.
Image Guided Personalization of Reaction-Diffusion Type Tumor Growth Models Using Modified Anisotropic Eikonal Equations, in: IEEE Transactions on Medical Imaging, 2009
http://www.inria.fr/sophia/asclepios/Publications/Ender.Konukoglu/TMI2009_konukoglu_InverseProblem.pdf, In Press.

[38]

S. Nicolau, X. Pennec, L. Soler, X. Buy, A. Gangi, N. Ayache, J. Marescaux.
An Augmented Reality System for Liver Thermal Ablation: Design and Evaluation on Clinical Cases, in: Medical Image Analysis, June 2009, vol. 13, n^o 3, p. 494–506
http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Nicolau_MEDIA_09.pdf.

[39]

J.-M. Peyrat, H. Delingette, M. Sermesant, C. Xu, N. Ayache.
Registration of 4D Cardiac CT Sequences Under Trajectory Constraints With Multichannel Diffeomorphic Demons, in: IEEE Transactions on Medical Imaging, In Press 2009
http://www.inria.fr/sophia/asclepios/Publications/Jean-Marc.Peyrat/Peyrat_2009_TMI.pdf.

[40]

M. Pop, M. Sermesant, D. Lepiller, M. V. Truong, E. McVeigh, E. Crystal, A. Dick, H. Delingette, N. Ayache, G. Wright.
Fusion of optical imaging and MRI for the evaluation and adjustment of macroscopic models of cardiac electrophysiology: A feasibility study, in: Medical Image Analysis, April 2009, vol. 13, n^o 2, p. 370-80
http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/MEDIA2008Pop.pdf.

[41]

R. Sims, A. Isambert, V. Gregoire, F. Bidault, L. Fresco, J. Sage, J. Mills, J. Bourhis, D. Lefkopoulos, O. Commowick, M. Benkebil, G. Malandain.
A pre-clinical assessment of an atlas-based automatic segmentation tool for the head and neck, in: Radiother Oncol, December 2009, vol. 93, n^o 3, p. 474-8
http://www.inria.fr/sophia/asclepios/Publications/Gregoire.Malandain/sims-ro-2009.pdf.

[42]

T. Vercauteren, X. Pennec, A. Perchant, N. Ayache.
Diffeomorphic Demons: Efficient Non-parametric Image Registration, in: NeuroImage, March 2009, vol. 45, n^o 1, Supp.1, p. S61-S72
http://www.inria.fr/sophia/asclepios/Publications/Tom.Vercauteren/DiffeoDemons-NeuroImage08-Vercauteren.pdf, PMID: 19041946.

[43]

B. T. T. Yeo, M. Sabuncu, T. Vercauteren, N. Ayache, B. Fischl, P. Golland.
Spherical Demons: Fast Diffeomorphic Landmark-Free Surface Registration, in: IEEE Transactions on Medical Imaging, August 2009
http://sites.google.com/site/yeoyeo02/software/sphericaldemonsrelease.

[44]

B. T. T. Yeo, T. Vercauteren, P. Fillard, J.-M. Peyrat, X. Pennec, P. Golland, N. Ayache, O. Clatz.
DT-REFinD: Diffusion Tensor Registration with Exact Finite-Strain Differential, in: IEEE Transactions on Medical Imaging, December 2009, vol. 28, n^o 12, p. 1914–1928
http://sites.google.com/site/yeoyeo02/software/dt-refindcode.

Articles in National Peer-Reviewed Journal

[45]

J.-C. Souplet, C. Lebrun, S. Chanalet, N. Ayache, G. Malandain.
Revue des approches de segmentation des lésions de sclérose en plaques dans les séquences conventionnelles IRM, in: Revue Neurologique, 2009, vol. 165, n^o 1, p. 7–14
http://www.inria.fr/sophia/asclepios/Publications/Jean-Christophe.Souplet/souplet-rn-2009.pdf, In french.

International Peer-Reviewed Conference/Proceedings

[46]

B. André, T. Vercauteren, A. Perchant, M. B. Wallace, A. M. Buchner, N. Ayache.
Endomicroscopic image retrieval and classification using invariant visual features, in: Proceedings of the Sixth IEEE International Symposium on Biomedical Imaging 2009 (ISBI'09), Boston, MA, IEEE, July 2009, p. 346-349
http://www.inria.fr/sophia/asclepios/Publications/Barbara.Andre/andre09ISBI.pdf.

[47]

B. André, T. Vercauteren, A. Perchant, M. B. Wallace, A. M. Buchner, N. Ayache.
Introducing space and time in local feature-based endomicroscopic image retrieval, in: Proceedings of the MICCAI Workshop - Medical Content-based Retrieval for Clinical Decision (MCBR-CDS'09), September 2009
http://www-sop.inria.fr/asclepios/Publications/Barbara.Andre/Barbara_MCBR-CDS_09.pdf.

[48]

F. Billet, M. Sermesant, H. Delingette, N. Ayache.
Cardiac Motion Recovery and Boundary Conditions Estimation by Coupling an Electromechanical Model and Cine-MRI Data, in: Proceedings of Functional Imaging and Modeling of the Heart 2009 (FIMH'09), LNCS, 3-5 June 2009, vol. 5528, p. 376-385
http://www.inria.fr/sophia/asclepios/Publications/Florence.Billet/fimh09-CardiacMotionRecovery.pdf.

[49]

F. Chung, H. Delingette.
Multimodal Prior Appearance Models based on Regional Clustering of Intensity Profiles, in: Medical Image Computing and Computer-Assisted Intervention (MICCAI'09), Part II, London, UK, G.-Z. Yang, D. Hawkes, D. Rueckert, A. Noble, C. Taylor (editors), Lecture Notes in Computer Science, Springer, September 2009, vol. 5762, p. 1051–1058
http://www.inria.fr/sophia/asclepios/Publications/Francois.Chung/multimodal_prior_appearance_models_based_on_regional_clustering_of_intensity_profiles.pdf.

[50]

O. Commowick, S. K. Warfield, G. Malandain.
Using Frankenstein's Creature Paradigm to Build a Patient Specific Atlas, in: Medical Image Computing and Computer-Assisted Intervention (MICCAI'09), Part II, London, UK, G.-Z. Yang, D. Hawkes, D. Rueckert, A. Noble, C. Taylor (editors), Lecture Notes in Computer Science, Springer, September 2009, vol. 5762, p. 993–1000
http://www.inria.fr/sophia/asclepios/Publications/Olivier.Commowick/CommowickMiccai2009.pdf.

[51]

S. Durrleman, P. Fillard, X. Pennec, A. Trouvé, N. Ayache.
A Statistical Model of White Matter Fiber Bundles based on Currents, in: Proceedings of Information Processing in Medical Imaging (IPMI'09), J. L. Prince, D. L. Pham, K. J. Myers (editors), LNCS, 2009, vol. 5636, p. 114-125
http://www.inria.fr/sophia/asclepios/Publications/Stanley.Durrleman/DurrlemanIPMI09.pdf, PMID: 19694257.

[52]

S. Durrleman, X. Pennec, A. Trouvé, G. Gerig, N. Ayache.
Spatiotemporal Atlas Estimation for Developmental Delay Detection in Longitudinal Datasets, in: Medical Image Computing and Computer-Assisted Intervention (MICCAI'09), Part I, London, UK, G.-Z. Yang, D. Hawkes, D. Rueckert, A. Noble, C. Taylor (editors), Lecture Notes in Computer Science, Springer, September 2009, vol. 5761, p. 297–304
http://www.inria.fr/sophia/asclepios/Publications/Stanley.Durrleman/MICCAI09_Durrleman.pdf.

[53]

V. Gorbunova, S. Durrleman, P. Lo, X. Pennec, M. de Bruijne.
Curve- and surface-based registration of lung CT images via currents, in: Proc. of Second International Workshop on Pulmonary Image Analysis, London United Kingdom, M. Brown, M. de Bruijne, B. van Ginneken, A. Kiraly, J. Kuhnigk, C. Lorenz, J. McClelland, K. Mori, A. Reeves, J. Reinhardt (editors), 2009, p. 15–25
http://www.lungworkshop.org/2009/proc2009/15.pdf.

[54]

T. Heimann, F. Chung, H. Lamecker, H. Delingette.
Subject-Specific Ligament Models: Towards Real-Time Simulation of the Knee Joint, in: Computational Biomechanics for Medicine IV Workshop 2009, September 2009
ftp://ftp-sop.inria.fr/asclepios/Publications/Herve.Delingette/Heimann-BiomechanicsWorkshop09.pdf.

[55]

H. Hufnagel, J. Ehrhardt, X. Pennec, A. Schmidt-Richberg, H. Handels.
Level Set Segmentation Using a Point-Based Statistical Shape Model Relying on Correspondence Probabilities, in: Proc. of MICCAI Workshop Probabilistic Model for Medical Image Analysis (PMMIA'09), 2009
http://www.inria.fr/sophia/asclepios/Publications/Heike.Hufnagel/Hufnagel_PMMIA09.pdf.

[56]

D. Kainmüller, H. Lamecker, H. Seim, M. Zinser, S. Zachow.
Automatic Extraction of Mandibular Nerve and Bone from Cone-Beam CT Data, in: Proc. Medical Image Computing and Computer Assisted Intervention, G.-Z. Yang, D. Hawkes, D. Rueckert, A. Noble, C. Taylor (editors), Lecture Notes in Computer Science, Springer, 2009, vol. 5762, p. 76-83
http://www.springerlink.com/content/372l6n99476115h7/.

[57]

H. Lamecker, T. Mansi, J. Relan, F. Billet, M. Sermesant, N. Ayache, H. Delingette.
Adaptive Tetrahedral Meshing for Personalized Cardiac Simulations, in: MICCAI Workshop on Cardiovascular Interventional Imaging and Biophysical Modelling (CI2BM09), London United Kingdom, 2009, p. 149-158
http://hal.inria.fr/inria-00417371/en/.

[58]

T. Mansi, S. Durrleman, B. Bernhardt, M. Sermesant, H. Delingette, I. Voigt, P. Lurz, A. M. Taylor, J. Blanc, Y. Boudjemline, X. Pennec, N. Ayache.
A Statistical Model of Right Ventricle in Tetralogy of Fallot for Prediction of Remodelling and Therapy Planning, in: Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI'09), London, UK, Lecture Notes in Computer Science, Springer, September 2009, vol. 5761, p. 214-221
http://www.inria.fr/sophia/asclepios/Publications/Tommaso.Mansi/mansi09MICCAI.pdf.

[59]

T. Mansi, J.-M. Peyrat, M. Sermesant, H. Delingette, J. Blanc, Y. Boudjemline, N. Ayache.
Physically-Constrained Diffeomorphic Demons for the Estimation of 3D Myocardium Strain from Cine-MRI, in: Proceedings of Functional Imaging and Modeling of the Heart 2009 (FIMH'09), LNCS, 3-5 June 2009, vol. 5528, p. 201-210
http://www.inria.fr/sophia/asclepios/Publications/Tommaso.Mansi/mansi09FIMH.pdf.

[60]

M. Pop, M. Sermesant, T. Mansi, E. Crystal, J. Detsky, Y. Yang, P. Fefer, E. McVeigh, A. Dick, N. Ayache, G. Wright.
Characterization of Post-infarct Scars in a Porcine Model - a Combined Experimental and Theoretical Study, in: Proceedings of Functional Imaging and Modeling of the Heart 2009 (FIMH'09), LNCS, 3-5 June 2009, vol. 5528, p. 1-10
http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/pop09-FIMH.pdf.

[61]

L. Ramus, G. Malandain.
Using consensus measures for atlas construction, in: Proceedings of the Sixth IEEE International Symposium on Biomedical Imaging 2009 (ISBI'09), Boston, MA, July 2009
http://www.inria.fr/sophia/asclepios/Publications/Liliane.Ramus/isbi09_lramus.pdf.

[62]

J. Relan, M. Sermesant, H. Delingette, M. Pop, G. Wright, N. Ayache.
Quantitative comparison of two cardiac electrophysiology models using personalisation to optical and MR data, in: IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'09), Boston Massachussets, U.S.A., 28 2009-July 1 2009, p. 1027-1030
http://www.inria.fr/sophia/asclepios/Publications/Jatin.Relan/relan_ISBI.pdf.

[63]

J. Relan, M. Sermesant, M. Pop, H. Delingette, M. Sorine, G. Wright, N. Ayache.
Parameter Estimation of a 3D Cardiac Electrophysiology Model Including the Restitution Curve Using Optical and MR Data, in: World Congress on Medical Physics and Biomedical Engineering, September 7 - 12, 2009, Munich, Germany, O. Dössel, W. C. Schlegel (editors), IFMBE Proceedings, Springer, 2009, vol. 25/IV, p. 1716–1719
http://www.inria.fr/sophia/asclepios/Publications/Jatin.Relan/relan_WorldCongress09.pdf.

[64]

J. Relan, M. Sermesant, M. Pop, H. Delingette, M. Sorine, G. Wright, N. Ayache.
Volumetric Prediction of Cardiac Electrophysiology using a Heart Model Personalised to Surface Data, in: MICCAI Workshop on Cardiovascular Interventional Imaging and Biophysical Modelling - CI2BM09, London UK, 2009, p. 19–27
http://hal.inria.fr/inria-00418471/en/.

[65]

M. Sabuncu, B. T. T. Yeo, T. Vercauteren, K. Van Leemput, P. Golland.
Asymmetric Image-Template Registration, in: Medical Image Computing and Computer-Assisted Intervention (MICCAI'09), Part I, London, UK, G.-Z. Yang, D. Hawkes, D. Rueckert, A. Noble, C. Taylor (editors), Lecture Notes in Computer Science, Springer, September 2009, vol. 5761, p. 565–573
http://people.csail.mit.edu/msabuncu/Sabuncu_AsymmetricRegistration_Miccai09.pdf.

[66]

M. Sermesant, F. Billet, R. Chabiniok, T. Mansi, P. Chinchapatnam, P. Moireau, J.-M. Peyrat, K. Rhode, M. Ginks, P. Lambiase, S. Arridge, H. Delingette, M. Sorine, A. Rinaldi, D. Chapelle, R. Razavi, N. Ayache.
Personalised Electromechanical Model of the Heart for the Prediction of the Acute Effects of Cardiac Resynchronisation Therapy, in: Proceedings of Functional Imaging and Modeling of the Heart 2009 (FIMH'09), LNCS, 3-5 June 2009, vol. 5528, p. 239-248
http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/sermesant09-FIMH.pdf.

National Peer-Reviewed Conference/Proceedings

[67]

F. Chung, J. Schmid, O. Clatz, N. Magnenat-Thalmann, H. Delingette.
Reconstruction 3D des structures anatomiques des membres inférieurs, in: ORASIS'09, June 2009
http://www.inria.fr/sophia/asclepios/Publications/Francois.Chung/reconstruction_3d_des_structures_anatomiques_des_membres_inferieurs.pdf.

Workshops without Proceedings

[68]

H. Hufnagel, J. Ehrhardt, X. Pennec, H. Handels.
Application of a Probabilistic Statistical Shape Model to Automatic Segmentation, in: World Congress on Medical Physics and Biomedical Engineering, WC 2009, München, 2009
http://www.inria.fr/sophia/asclepios/Publications/Heike.Hufnagel/Hufnagel_WC09.pdf.

Scientific Books (or Scientific Book chapters)

[69]

N. Ayache, O. Clatz, H. Delingette, G. Malandain, X. Pennec, M. Sermesant.
Asclepios: a Research Project-Team at INRIA for the Analysis and Simulation of Biomedical Images, in: From semantics to computer science: essays in honor of Gilles Kahn, Y. Bertot, G. Huet, J.-J. Lévy, G. Plotkin (editors), Cambridge University Press, 2009, p. 415-436
http://www.cambridge.org/catalogue/catalogue.asp?isbn=9780521518253.

[70]

C. Germain-Renaud, V. Breton, P. Clarysse, B. Delhay, Y. Gaudeau, T. Glatard, E. Jannot, Y. Legré, J. Montagnat, J.-M. Moureau, A. Osorio, X. Pennec, J. Schaerer, R. Texier.
Ch.19 - Grid Analysis of Radiological Data, in: Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare, Cannataro, 2009
http://www.igi-global.com/reference/details.asp?id=34292.

[71]

T. Mansi, B. André, M. Lynch, M. Sermesant, H. Delingette, Y. Boudjemline, N. Ayache.
Virtual Pulmonary Valve Replacement Interventions with a Personalised Cardiac Electromechanical Model, in: Recent Advances in the 3D Physiological Human, Springer, 2009
http://www.inria.fr/sophia/asclepios/Publications/Tommaso.Mansi/mansi093DPH.pdf, In press.

[72]

X. Pennec, P. Fillard.
Statistical computing on non-linear spaces for computational anatomy, in: Biomedical Image Analysis: Methodologies and Applications, N. Paragios, J. Duncan, N. Ayache (editors), Springer, 2009
http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/ComputationalAnatomy.pdf, To appear.

[73]

J. Schmid, A. Sandholm, F. Chung, D. Thalmann, H. Delingette, N. Magnenat-Thalmann.
Musculoskeletal simulation model generation from MRI datasets and motion capture data, in: Recent Advances in the 3D Physiological Human, Springer, 2009, p. 3-19
http://www.inria.fr/sophia/asclepios/Publications/Francois.Chung/musculoskeletal_simulation_model_generation_from_mri_datasets_and_motion_capture_data.pdf.

Books or Proceedings Editing

[74]

N. Ayache, H. Delingette, M. Sermesant (editors)
Functional Imaging and Modeling of the Heart - FIMH 2009, LNCS, Springer, Nice, France, June 2009, vol. 5528.

Internal Reports

[75]

S. Durrleman, X. Pennec, G. Gerig, A. Trouvé, N. Ayache.
Spatiotemporal Atlas Estimation for Developmental Delay Detection in Longitudinal Datasets, INRIA, 2009, n^o RR-6952
http://hal.inria.fr/inria-00408293/en/, Research Report.

Other Publications

[76]

B. André, T. Vercauteren, A. Perchant, M. B. Wallace, A. M. Buchner, N. Ayache.
Endomicroscopic image retrieval and classification using invariant visual features, July 2009
http://www-sop.inria.fr/asclepios/Publications/Barbara.Andre/Andre_ICVSS09_Poster.pdf, The third edition of the International Computer Vision Summer School 2009 (ICVSS'09).

[77]

F. Dru, T. Vercauteren.
An ITK Implementation of the Symmetric Log-Domain Diffeomorphic Demons Algorithm, May 2009
http://hdl.handle.net/10380/3060, Insight Journal – 2009 January - June.

[78]

T. Mansi, B. André, M. Sermesant, H. Delingette, N. Ayache, Y. Boudjemline.
Simulation personnalisée de replacements valvulaires pulmonaires grâce à l'utilisation d'un modèle mathématique du cœur, June 2009, Archives de Pédiatrie - Congrès des Sociétés Françaises Médico-chirurgicales Pédiatriques.

References in notes

[79]

N. Ayache, J. Duncan (editors)
Medical Image Analysis, Elsevier.

[80]

International Symposium on Biomedical Imaging: From Nano to Macro, IEEE, Boston, 2009.

[81]

R. H. Taylor, S. Lavallée, G. S. Burdea, R. Mösges (editors)
Computer-Integrated Surgery: Technology and Clinical Applications, MIT Press, 1995.

[82]

W. Vannier, M. A. Viergever (editors)
Transactions on Medical Imaging, IEEE.

[83]

S. Webb (editor)
The Physics of Medical Imaging, Institute of Physics Publishing, 1988.

[84]

G.-Z. Yang, D. Hawkes, D. Rueckert, A. Noble, C. Taylor (editors)
Medical Image Computing and Computer-Assisted Intervention (MICCAI'09), Part I, Lecture Notes in Computer Science, Springer, London, UK, September 2009, vol. 5761.

[85]

G.-Z. Yang, D. Hawkes, D. Rueckert, A. Noble, C. Taylor (editors)
Medical Image Computing and Computer-Assisted Intervention (MICCAI'09), Part II, Lecture Notes in Computer Science, Springer, London, UK, September 2009, vol. 5762.

[86]

The international journal of Medical Robotics + Computer Assisted Surgery, Wiley.

[87]

R. Acharya, R. Wasserman, J. Stevens, C. Hinojosa.
Biomedical Imaging modalities: a tutorial, in: Computerized Medical Imaging and Graphics, 1995, vol. 19, n^o 1, p. 3–25.

[88]

P. Allen.
Brain Atlas Project, 2003
http://brain-map.org/welcome.do;jsessionid=1DB51DDFDE6BEC143CE5005682B62003.

[89]

L. Axel, A. Montillo, D. Kim.
Tagged magnetic resonance imaging of the heart: a survey, in: Medical Image Analysis, 2005, vol. 9, n^o 4, p. 376–393.

[90]

N. Ayache.
L'analyse automatique des images médicales, état de l'art et perspectives, in: Annales de l'Institut Pasteur, avril–juin 1998, vol. 9, n^o 1, p. 13–21, numéro spécial sur les progrès récents de l'imagerie médicale.

[91]

M. Belik, T. Usyk, A. McCulloch.
Computational Methods for Cardiac Electrophysiology, in: Computational Models for the Human Body, N. Ayache (editor), Elsevier, 2004, p. 129–187.

[92]

I. L. Dryden, K. V. Mardia.
Statistical Shape Analysis, John Wiley and Sons, 1998.

[93]

J. Duncan, N. Ayache.
Medical Image Analysis: Progress over two decades and the challenges ahead, in: IEEE Transactions on Pattern Analysis and Machine Intelligence, 2000, vol. 22, n^o 1, p. 85–106.

[94]

N. C. Fox, J. M. Schott.
Imaging cerebral atrophy: normal ageing to Alzheimer's disease, in: Lancet, 2004, vol. 363, n^o 9406.

[95]

A. F. Frangi, W. J. Niessen, M. A. Viergever.
Three-dimensional modeling for functional analysis of cardiac images: a review, in: IEEE Trans Med Imaging, January 2001, vol. 20, n^o 1, p. 2-25.

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P. C. Franzone, L. Guerri, M. Pennachio, B. Taccardi.
Spread of excitation in 3-D models of the anisotropic cardiac tissue, in: Mathematical Biosciences, 1988, vol. 151, p. 51–98.

[97]

P. Hunter, T. Borg.
Integration from proteins to organs: the Physiome project, in: Nature Reviews - Molecular Cell Biology, 2003, vol. 4, p. 237–243.

[98]

P. Hunter.
Computational Physiology and the Physiome Project, 2004.

[99]

E. Konukoglu, W. Wells, S. Novellas, N. Ayache, R. Kikinis, P. Black, K. Pohl.
Monitoring Slowly Evolving Tumors, in: In Proceedings of the IEEE Internation Symposium on Biomedical Imaging: From Nano to Macro (ISBI'08), Paris, France, May 2008
http://www.inria.fr/sophia/asclepios/Publications/Ender.Konukoglu/isbi08.pdf.

[100]

C. MacAulay, P. Lane, R. Richards-Kortum.
In vivo pathology: microendoscopy as a new endoscopic imaging modality, in: Gastrointestinal Endoscopy Clinics of North America, 2004, vol. 14, p. 595–620.

[101]

D. Metaxas, J. Kayes, F. Primanio.
A 3-D virtual environment for modeling mechanical cardiopulmonary interactions, in: Medical Image Analysis, 1997, vol. 3, n^o 1, p. 1–26.

[102]

M. I. Miller.
Computational anatomy: shape, growth, and atrophy comparison via diffeomorphisms, in: NeuroImage, 2004, vol. 23, n^o Supplement 1, p. S19–S33, Special Issue : Mathematics in Brain Imaging.

[103]

V. Moreau-Villéger, H. Delingette, M. Sermesant, O. Faris, E. McVeigh, N. Ayache.
Global and Local Parameter Estimation of a Model of the Electrical Activity of the Heart, INRIA, July 2004, n^o 5269
http://hal.inria.fr/inria-00070729, Research Report.

[104]

S. Nicolau, A. Garcia, X. Pennec, L. Soler, N. Ayache.
An augmented reality system to guide radio-frequency tumour ablation, in: Computer Animation and Virtual World (previously the Journal of Visualization & Computer Animation), 2005, vol. 16, n^o 1, p. 1–10
ftp://ftp-sop.inria.fr/epidaure/Publications/Pennec/Nicolau.CAVW.pdf.

[105]

S. Nicolau, X. Pennec, L. Soler, N. Ayache.
A complete Augmented Reality Guidance System for Liver Punctures: First Clinical Evaluation, in: Proceedings of the 8th Int. Conf. on Medical Image Computing and Computer-Assisted Intervention - MICCAI 2005, Part I, Palm Springs, CA, USA, October 26-29, J. Duncan, G. Gerig (editors), LNCS, Springer Verlag, 2005, vol. 3749, p. 539–547
http://springerlink.metapress.com/openurl.asp?genre=article&issn=0302-9743&volume=3749&spage=539.

[106]

NIH.
Alzheimer's Disease Neuroimaging Initiative, 2004.

[107]

D. Noble.
Modeling the Heart, from genes to cells to the whole organ, in: Science, 2002, vol. 295, p. 1678–1682.

[108]

J. Olivo-Marin.
Image Formation and Analysis in Microscopy, june 2004, Invited Session at Int. Symp. on Biomedical Imaging (ISBI).

[109]

A. Quarteroni, L. Formaggia.
Mathematical Modeling and Numerical Simulation of the Cardiovascular System, in: Computational Models for the Human Body, N. Ayache (editor), Elsevier, 2004, p. 3–128.

[110]

M. Sermesant, O. Faris, F. Evans, E. McVeigh, Y. Coudière, H. Delingette, N. Ayache.
Preliminary validation using in vivo measures of a macroscopic electrical model of the heart, in: International Symposium on Surgery Simulation and Soft Tissue Modeling (IS4TM'03), Juan-les-Pins, France, N. Ayache, H. Delingette (editors), Lecture Notes in Computer Science, Springer-Verlag, INRIA Sophia Antipolis, 2003, vol. 2673, p. 230–243
ftp://ftp-sop.inria.fr/epidaure/Publications/Sermesant/IS4TM2003Sermesant.pdf.

[111]

P. M. Thompson, K. Hayashi, E. Sowell, N. Gogtay, J. Giedd, J. Rapoport, G. I. de Zubicaray, A. Janke, S. Rose, J. Semple, D. Doddrell, Y. Wang, T. van Erp, T. Cannon, A. W. Toga.
Mapping Cortical Change in Alzheimer's Disease, Brain Development, and Schizophrenia, in: NeuroImage, 2004, vol. 23, n^o supplement 1, p. S2–S18, Special Issue : Mathematics in Brain Imaging.

[112]

P. M. Thompson, M. I. Miller, J. T. Ratnanather, R. A. Poldrack, T. E. Nichols.
Guest Editorial, in: NeuroImage, 2004, vol. 23, n^o Supplement 1, p. S1–S1, Special Issue : Mathematics in Brain Imaging.

[113]

D. W. Thompson.
On Growth and Form, Cambridge Univ. Pr., 1917.

[114]

N. Toussaint, T. Mansi, H. Delingette, N. Ayache, M. Sermesant.
An Integrated Platform for Dynamic Cardiac Simulation and Image Processing: Application to Personalised Tetralogy of Fallot Simulation, in: Proc. Eurographics Workshop on Visual Computing for Biomedicine (VCBM), Delft, The Netherlands, 2008
http://www.inria.fr/sophia/asclepios/Publications/Nicolas.Toussaint/Toussaint.VCBM08.pdf.

[115]

N. Toussaint, M. Sermesant, P. Fillard.
vtkINRIA3D: A VTK Extension for Spatiotemporal Data Synchronization, Visualization and Management, in: Proc. of Workshop on Open Source and Open Data for MICCAI, Brisbane, Australia, October 2007
http://www.inria.fr/sophia/asclepios/Publications/Pierre.Fillard/Fillard.MICCAI07.OpenWorkshop.pdf.

[116]

N. Toussaint, J.-C. Souplet, P. Fillard.
MedINRIA: Medical Image Navigation and Research Tool by INRIA, in: Proc. of MICCAI'07 Workshop on Interaction in medical image analysis and visualization, Brisbane, Australia, 2007
http://www.inria.fr/sophia/asclepios/Publications/Pierre.Fillard/Fillard.MICCAI07.InteractionWorkshop.pdf.

[117]

K. Van Leemput, F. Maes, D. Vandermeulen, P. Suetens.
A unifying framework for partial volume segmentation of brain MR images, in: IEEE Trans Med Imaging, January 2003, vol. 22, n^o 1, p. 105-19.

[118]

T. Vercauteren, X. Pennec, A. Perchant, N. Ayache.
Symmetric Log-Domain Diffeomorphic Registration: A Demons-based Approach, in: Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI'08), Part I, New York, USA, D. Metaxas, L. Axel, G. Fichtinger, G. Székely (editors), Lecture Notes in Computer Science, Springer-Verlag, September 2008, vol. 5241, p. 754–761
http://www.inria.fr/sophia/asclepios/Publications/Tom.Vercauteren/SymLogDemons-MICCAI08-Vercauteren.pdf, PMID: 18979814.

[119]

R. Weissleder, U. Mahmood.
Molecular Imaging, in: Radiology, 2001, vol. 219, p. 316–333, Special Review.

[120]

B. T. T. Yeo, M. Sabuncu, T. Vercauteren, N. Ayache, B. Fischl, P. Golland.
Spherical Demons: Fast Surface Registration, in: Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI'08), New York, USA, D. Metaxas, L. Axel, G. Fichtinger, G. Székely (editors), Lecture Notes in Computer Science, Springer-Verlag, September 2008, vol. 5241, p. 745-753
http://www.inria.fr/sophia/asclepios/Publications/Tom.Vercauteren/SphericalDemons-MICCAI08-Yeo.pdf, PMID: 18979813. Source code found <a href="http://yeoyeo02.googlepages.com/sphericaldemonsrelease">here</a>.

[121]

B. T. T. Yeo, T. Vercauteren, P. Fillard, X. Pennec, P. Golland, N. Ayache, O. Clatz.
DTI Registration with Exact Finite-Strain Differential, in: Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'08), Paris, France, IEEE, May 2008
http://www.inria.fr/sophia/asclepios/Publications/Olivier.Clatz/DTIDiffeomorphicDemons-ISBI08-Yeo.pdf.