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Publications of year 2006

Books and proceedings

  1. Hervé Delingette and Alejandro Frangi, editors. Proceedings of the MICCAI Workshop - From Statistical Atlases to Personalized Models: Understanding Complex Diseases in Populations and Individuals, 2006.
    @proceedings{Delingette:MICCAIworkshop:06,
    editor = {Herv\'e Delingette and Alejandro Frangi},
    title = {Proceedings of the MICCAI Workshop - From Statistical Atlases to Personalized Models: Understanding Complex Diseases in Populations and Individuals},
    url-hal = {https://hal.inria.fr/inria-00614988},
    year = {2006} 
    }
    


  2. 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.
    @proceedings{Pennec:MFCAProcs:06,
    address = {Copenhagen, Denmark},
    editor = {Xavier Pennec and Sarang Joshi},
    month = {October},
    title = {Proceedings of the First International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Modelling Biological Shape Variability},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/MFCA06.pdf},
    url-hal = {https://hal.inria.fr/hal-00813806},
    year = {2006} 
    }
    


Thesis

  1. Vincent Arsigny. Processing Data in Lie Groups: An Algebraic Approach. Application to Non-Linear Registration and Diffusion Tensor MRI. Thèse de sciences (PhD Thesis), École polytechnique, November 2006. Keyword(s): DT-MRI, Tensors, Riemannian geometry, Lie groups, interpolation, Log-Euclidean metrics, Polyaffine transformations, Diffeomorphisms, Non-rigid registration, Multi-affine registration, Magnetic Resonance Imaging, Bi-invariant means, Fréchet means, Statistics.
    @phdthesis{Arsigny:PhD:2006,
    author = {Vincent Arsigny},
    keywords = {DT-MRI, Tensors, Riemannian geometry, Lie groups, interpolation, Log-Euclidean metrics, Polyaffine transformations, Diffeomorphisms, Non-rigid registration, Multi-affine registration, Magnetic Resonance Imaging, Bi-invariant means, Fr\'echet means, Statistics},
    month = {November},
    school = {\'Ecole polytechnique},
    title = {Processing Data in {L}ie Groups: An Algebraic Approach. Application to Non-Linear Registration and Diffusion Tensor MRI},
    type = {Th\`ese de sciences (PhD Thesis)},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Arsigny/arsigny_phd.pdf},
    url-hal = {https://pastel.archives-ouvertes.fr/tel-00121162},
    year = {2006} 
    }
    


  2. Olivier Clatz. Modèles biomécaniques et physio-pathologiques pour l'analyse d'images cérébrales. Thèse de sciences, École des Mines de Paris, February 2006.
    @phdthesis{Clatz:these:2006,
    author = {Olivier Clatz},
    hal-identifiant = {pastel-00003951},
    month = {February},
    school = {\'Ecole des Mines de Paris},
    title = {Mod\`eles biom\'ecaniques et physio-pathologiques pour l'analyse d'images c\'er\'ebrales},
    type = {Th\`ese de sciences},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Clatz/These_clatz.pdf},
    url-hal = {http://hal.inria.fr/pastel-00003951/en/},
    year = {2006} 
    }
    


  3. Hervé Delingette. Modélisation de structures déformables. Habilitation à diriger des recherches, Université Nice Sophia-Antipolis, March 2006.
    @phdthesis{Delingette:HDR:2006,
    author = {Herv\'e Delingette},
    month = {March},
    school = {Universit\'e Nice Sophia-Antipolis},
    title = {Mod\'elisation de structures d\'eformables},
    type = {Habilitation \`a diriger des recherches},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Herve.Delingette/hdr.pdf},
    year = {2006} 
    }
    


  4. Guillaume Dugas-Phocion. Segmentation d'IRM Cérébrales Multi-Séquences et Application à la Sclérose en Plaques. Thèse de sciences, École des Mines de Paris, March 2006.
    @phdthesis{dugas:these:2006,
    author = {Guillaume Dugas-Phocion},
    month = {March},
    school = {\'Ecole des Mines de Paris},
    title = {Segmentation d'IRM C\'er\'ebrales Multi-S\'equences et Application \`a la Scl\'erose en Plaques},
    type = {Th\`ese de sciences},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Misc/dugas-phd.pdf},
    year = {2006} 
    }
    


  5. Grégoire Malandain. Les mesures de similarité pour le recalage des images médicales. Habilitation à diriger des recherches, Université Nice Sophia-Antipolis, March 2006.
    @phdthesis{malandain:hdr:2006,
    author = {Gr\'egoire Malandain},
    month = {March},
    school = {Universit\'e Nice Sophia-Antipolis},
    title = {Les mesures de similarit\'e pour le recalage des images m\'edicales},
    type = {Habilitation \`a diriger des recherches},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Gregoire.Malandain/malandain-hdr-2006.pdf},
    year = {2006} 
    }
    


  6. 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.
    @phdthesis{Pennec:HDR:2006,
    author = {Xavier Pennec},
    keywords = {Tensors, regularization, PDE, geometry, Riemannian geometry, Registration, statistics, manifolds},
    month = {December},
    school = {Universit\'e Nice Sophia-Antipolis},
    title = {Statistical Computing on Manifolds for Computational Anatomy},
    type = {Habilitation \`a diriger des recherches},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Pennec_HDR.pdf},
    url-hal = {https://tel.archives-ouvertes.fr/tel-00633163},
    year = {2006} 
    }
    


Articles in journal, book chapters

  1. Vincent Arsigny, Pierre Fillard, Xavier Pennec, and Nicholas Ayache. Log-Euclidean Metrics for Fast and Simple Calculus on Diffusion Tensors. Magnetic Resonance in Medicine, 56(2):411-421, August 2006. Keyword(s): DT-MRI, Tensors, Riemannian geometry, Lie groups, interpolation, Log-Euclidean metrics.
    @article{Arsigny:MRM:06,
    author = {Vincent Arsigny and Pierre Fillard and Xavier Pennec and Nicholas Ayache},
    doi = {10.1002/mrm.20965},
    hal-identifiant = {inria-00502678},
    journal = {Magnetic Resonance in Medicine},
    keywords = {DT-MRI, Tensors, Riemannian geometry, Lie groups, interpolation, Log-Euclidean metrics},
    month = {August},
    number = {2},
    pages = {411-421},
    pmid = {16788917},
    title = {Log-{Euclidean} Metrics for Fast and Simple Calculus on Diffusion Tensors},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Arsigny/arsigny_mrm_2006.pdf},
    url-hal = {http://hal.inria.fr/inria-00502678/en/},
    volume = {56},
    year = {2006} 
    }
    


  2. C Bensa, C Bertogliati, S Chanalet, G Malandain, P Bedoucha, and C Lebrun. Early detection of cognitive impairment in relapsing-remitting multiple sclerosis: functional-anatomical correlations and longitudinal follow-up. Revue Neurologique, 162(12):1221-31, December 2006. Note: [In French].
    Abstract:
    Introduction. Cognitive impairment is frequent in relapsing remitting Multiple Sclerosis and is often diagnosed after disruption of occupational and social relations. METHODS: We studied at baseline a homogeneous population of 32 RRMS patients, diagnosed for less than 5 years, with spontaneous memory complaints, and 20 controls. Sixteen patients were followed for 2 years, combining physical examination, neuropsychological tests, and brain MRI. Neuropsychological tests used evaluated memory capacities, attentional capacities, executive functions, language, and visuo-constructive praxis. Lesion load on brain MRI was measured with semi-automatic segmentation procedures and manual control. RESULTS: Eighty percent of patients presented cognitive impairment, and this proportion was higher than that found in the literature. These disorders were more marked for verbal episodic memory, attention, and executive functions. Patients with brain MRI that initially fulfilled the Barkhof criteria and those with callous lesions had more memory disorders. No link between global T1 and T2 lesion loads and neuropsychological scores was found. A statistical link between posterior fossa lesions and attentional disorders was shown. In the longitudinal follow-up, patients had better performances in memory and attentional domains, and a lower number of cognitive domains with dysfunction for each patient. This improvement on neuropsychological tests, whereas EDSS levels were stable, underlined a possible test-retest effect. CONCLUSION: During the initial phase of the disease, most of the relapsing remitting patients present a mild cognitive impairment. Early detection, therapeutic propositions, and recognition of disorders are necessary.

    @article{bensa:rn:2006,
    abstract = {Introduction. Cognitive impairment is frequent in relapsing remitting Multiple Sclerosis and is often diagnosed after disruption of occupational and social relations. METHODS: We studied at baseline a homogeneous population of 32 RRMS patients, diagnosed for less than 5 years, with spontaneous memory complaints, and 20 controls. Sixteen patients were followed for 2 years, combining physical examination, neuropsychological tests, and brain MRI. Neuropsychological tests used evaluated memory capacities, attentional capacities, executive functions, language, and visuo-constructive praxis. Lesion load on brain MRI was measured with semi-automatic segmentation procedures and manual control. RESULTS: Eighty percent of patients presented cognitive impairment, and this proportion was higher than that found in the literature. These disorders were more marked for verbal episodic memory, attention, and executive functions. Patients with brain MRI that initially fulfilled the Barkhof criteria and those with callous lesions had more memory disorders. No link between global T1 and T2 lesion loads and neuropsychological scores was found. A statistical link between posterior fossa lesions and attentional disorders was shown. In the longitudinal follow-up, patients had better performances in memory and attentional domains, and a lower number of cognitive domains with dysfunction for each patient. This improvement on neuropsychological tests, whereas EDSS levels were stable, underlined a possible test-retest effect. CONCLUSION: During the initial phase of the disease, most of the relapsing remitting patients present a mild cognitive impairment. Early detection, therapeutic propositions, and recognition of disorders are necessary.},
    author = {C Bensa and C Bertogliati and S Chanalet and G Malandain and P Bedoucha and C Lebrun},
    journal = {Revue Neurologique},
    month = {December},
    note = {[In French]},
    number = {12},
    pages = {1221-31},
    title = {Early detection of cognitive impairment in relapsing-remitting multiple sclerosis: functional-anatomical correlations and longitudinal follow-up},
    url-hal = {https://hal.inria.fr/inria-00615002},
    volume = {162},
    year = {2006} 
    }
    


  3. Christophe Blondel, Grégoire Malandain, Régis Vaillant, and Nicholas Ayache. Reconstruction of Coronary Arteries from a Single Rotational X-Ray Projection Sequence. IEEE Transactions on Medical Imaging, 25(5):653-663, May 2006. Keyword(s): Angiocardiography, Coronarography, Image Motion Analysis, Image Reconstruction, Tomography.
    Abstract:
    Cardiovascular diseases remain the primary cause of death in developed countries. In most cases, exploration of possibly underlying coronary artery pathologies is performed using X-ray coronary angiography. Current clinical routine in coronary angiography is directly conducted in 2-D projection images from several static viewing angles. However, for diagnosis and treatment purposes, coronary artery reconstruction is highly suitable. The purpose of this study is to provide physicians with a 3-D model of coronary arteries, e.g. for absolute three-dimensional measures for lesion assessment, instead of direct projective measures deduced from the images, which are highly dependent on the viewing angle. In this article, we propose a novel method to reconstruct coronary arteries from one single rotational X-ray projection sequence. As a side result, we also obtain an estimation of the coronary artery motion. Our method consists of 3 main consecutive steps: (1) 3-D reconstruction of coronary artery centerlines, including respiratory motion compensation, (2) coronary artery 4-D motion computation, and (3) 3-D tomographic reconstruction of coronary arteries, involving compensation for respiratory and cardiac motions. We present some experiments on clinical datasets, and the feasibility of a true 3-D Quantitative Coronary Analysis is demonstrated.

    @article{blondel:tmi:2006,
    abstract = {Cardiovascular diseases remain the primary cause of death in developed countries. In most cases, exploration of possibly underlying coronary artery pathologies is performed using X-ray coronary angiography. Current clinical routine in coronary angiography is directly conducted in 2-D projection images from several static viewing angles. However, for diagnosis and treatment purposes, coronary artery reconstruction is highly suitable. The purpose of this study is to provide physicians with a 3-D model of coronary arteries, e.g. for absolute three-dimensional measures for lesion assessment, instead of direct projective measures deduced from the images, which are highly dependent on the viewing angle. In this article, we propose a novel method to reconstruct coronary arteries from one single rotational X-ray projection sequence. As a side result, we also obtain an estimation of the coronary artery motion. Our method consists of 3 main consecutive steps: (1) 3-D reconstruction of coronary artery centerlines, including respiratory motion compensation, (2) coronary artery 4-D motion computation, and (3) 3-D tomographic reconstruction of coronary arteries, involving compensation for respiratory and cardiac motions. We present some experiments on clinical datasets, and the feasibility of a true 3-D Quantitative Coronary Analysis is demonstrated.},
    author = {Christophe Blondel and Gr\'egoire Malandain and R\'egis Vaillant and Nicholas Ayache},
    doi = {10.1109/TMI.2006.873224},
    journal = {IEEE Transactions on Medical Imaging},
    keywords = {Angiocardiography, Coronarography, Image Motion Analysis, Image Reconstruction, Tomography},
    month = {May},
    number = {5},
    pages = {653--663},
    title = {Reconstruction of Coronary Arteries from a Single Rotational X-Ray Projection Sequence},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Gregoire.Malandain/blondel-tmi-2006.pdf},
    url-hal = {https://hal.inria.fr/inria-00614993},
    volume = {25},
    year = {2006} 
    }
    


  4. Francis Cassot, Frederic Lauwers, Céline Fouard, Steffen Prohaska, and Valerie Lauwers-Cances. A novel three-dimensional computer-assisted method for a quantitative study of microvascular networks of the human cerebral cortex. Microcirculation, 13(1):1-18, January 2006.
    Abstract:
    OBJECTIVE: Detailed information on microvascular network anatomy is a requirement for understanding several aspects of microcirculation, including oxygen transport, distributions of pressure, and wall shear stress in microvessels, regulation of blood flow, and interpretation of hemodynamically based functional imaging methods, but very few quantitative data on the human brain microcirculation are available. The main objective of this study is to propose a new method to analyze this microcirculation. METHODS: From thick sections of india ink-injected human brain, using confocal laser microscopy, the authors developed algorithms adapted to very large data sets to automatically extract and analyze center lines together with diameters of thousands of brain microvessels within a large cortex area. RESULTS: Direct comparison between the original data and the processed vascular skeletons demonstrated the high reliability of this method and its capability to manage a large amount of data, from which morphometry and topology of the cerebral microcirculation could be derived. CONCLUSIONS: Among the many parameters that can be analyzed by this method, the capillary size, the frequency distributions of diameters and lengths, the fractal nature of these networks, and the depth-related density of vessels are all vital features for an adequate model of cerebral microcirculation.

    @article{cassot:microcirculation:2006,
    abstract = {OBJECTIVE: Detailed information on microvascular network anatomy is a requirement for understanding several aspects of microcirculation, including oxygen transport, distributions of pressure, and wall shear stress in microvessels, regulation of blood flow, and interpretation of hemodynamically based functional imaging methods, but very few quantitative data on the human brain microcirculation are available. The main objective of this study is to propose a new method to analyze this microcirculation. METHODS: From thick sections of india ink-injected human brain, using confocal laser microscopy, the authors developed algorithms adapted to very large data sets to automatically extract and analyze center lines together with diameters of thousands of brain microvessels within a large cortex area. RESULTS: Direct comparison between the original data and the processed vascular skeletons demonstrated the high reliability of this method and its capability to manage a large amount of data, from which morphometry and topology of the cerebral microcirculation could be derived. CONCLUSIONS: Among the many parameters that can be analyzed by this method, the capillary size, the frequency distributions of diameters and lengths, the fractal nature of these networks, and the depth-related density of vessels are all vital features for an adequate model of cerebral microcirculation.},
    author = {Francis Cassot and Frederic Lauwers and C\'eline Fouard and Steffen Prohaska and Valerie Lauwers-Cances},
    hal-identifiant = {hal-00308888},
    journal = {Microcirculation},
    month = {January},
    number = {1},
    pages = {1-18},
    title = {A novel three-dimensional computer-assisted method for a quantitative study of microvascular networks of the human cerebral cortex},
    url-hal = {http://hal.inria.fr/hal-00308888/en/},
    volume = {13},
    year = {2006} 
    }
    


  5. Olivier Clatz, Emmanuel Mandonnet, Stéphane Chanalet, Christine Lebrun, Ender Konukoglu, Hervé Delingette, Nicholas Ayache, and Pierre-Yves Bondiau. Modèles Biomathématiques de Croissance Des Gliomes : Recherche en Informatique et Perspectives en Neuro-oncologie. Neurologies, 9(93):665-667, 2006.
    @article{clatz:neurologies:06,
    author = {Olivier Clatz and Emmanuel Mandonnet and St\'ephane Chanalet and Christine Lebrun and Ender Konukoglu and Herv\'e Delingette and Nicholas Ayache and Pierre-Yves Bondiau},
    journal = {Neurologies},
    number = {93},
    pages = {665-667},
    title = {Mod\`eles Biomath\'ematiques de Croissance Des Gliomes : Recherche en Informatique et Perspectives en Neuro-oncologie},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Clatz/clatz_neurologies.pdf},
    url-hal = {https://hal.inria.fr/inria-00614999},
    volume = {9},
    year = {2006} 
    }
    


  6. O. Colliot, T. Mansi, N. Bernasconi, V. Naessens, D. Klironomos, and A. Bernasconi. Segmentation of focal cortical dysplasia lesions on MRI using level set evolution. NeuroImage, 32(4):1621-1630, October 2006.
    Abstract:
    Focal cortical dysplasia (FCD) is the most frequent malformation of cortical development in patients with medically intractable epilepsy. On MRI, FCD lesions are not easily differentiable from the normal cortex and defining their spatial extent is challenging. In this paper, we introduce a method to segment FCD lesions on T1-weighted MRI. It relies on two successive three-dimensional deformable models, whose evolutions are based on the level set framework. The first deformable model is driven by probability maps obtained from three MRI features: cortical thickness, relative intensity and gradient. These features correspond to the visual characteristics of FCD and allow discriminating lesions and normal tissues. In a second stage, the previous result is expanded towards the underlying and overlying cortical boundaries, throughout the whole cortical section. The method was quantitatively evaluated by comparison with manually traced labels in 18 patients with FCD. The automated segmentations achieved a strong agreement with the manuals labels, demonstrating the applicability of the method to assist the delineation of FCD lesions on MRI. This new approach may become a useful tool for the presurgical evaluation of patients with intractable epilepsy related to cortical dysplasia.

    @article{colliot:2006:neuroimage,
    abstract = {Focal cortical dysplasia (FCD) is the most frequent malformation of cortical development in patients with medically intractable epilepsy. On MRI, FCD lesions are not easily differentiable from the normal cortex and defining their spatial extent is challenging. In this paper, we introduce a method to segment FCD lesions on T1-weighted MRI. It relies on two successive three-dimensional deformable models, whose evolutions are based on the level set framework. The first deformable model is driven by probability maps obtained from three MRI features: cortical thickness, relative intensity and gradient. These features correspond to the visual characteristics of FCD and allow discriminating lesions and normal tissues. In a second stage, the previous result is expanded towards the underlying and overlying cortical boundaries, throughout the whole cortical section. The method was quantitatively evaluated by comparison with manually traced labels in 18 patients with FCD. The automated segmentations achieved a strong agreement with the manuals labels, demonstrating the applicability of the method to assist the delineation of FCD lesions on MRI. This new approach may become a useful tool for the presurgical evaluation of patients with intractable epilepsy related to cortical dysplasia.},
    author = {O. Colliot and T. Mansi and N. Bernasconi and V. Naessens and D. Klironomos and A. Bernasconi},
    doi = {10.1016/j.neuroimage.2006.04.225},
    journal = {NeuroImage},
    month = {October},
    number = {4},
    pages = {1621-1630},
    title = {Segmentation of focal cortical dysplasia lesions on MRI using level set evolution},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Tommaso.Mansi/colliot06.pdf},
    url-hal = {https://hal.inria.fr/inria-00614998},
    url-publisher = {http://www.sciencedirect.com/science/article/B6WNP-4KJDWX2-1/2/5e566226c5ecf099e5aed67c4cdb7c16},
    volume = {32},
    year = {2006} 
    }
    


  7. Hervé Delingette and Nicholas Ayache. La simulation de Chirurgie Hépatique. Pour la science, 52(52):106-109, July 2006. Keyword(s): Simulation.
    @article{Delingette:PLS:06,
    author = {Herv\'e Delingette and Nicholas Ayache},
    journal = {Pour la science},
    keywords = {Simulation},
    month = {July},
    number = {52},
    pages = {106-109},
    title = {La simulation de Chirurgie H\'epatique},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Herve.Delingette/Simulation-Pour-La-Science.pdf},
    volume = {52},
    year = {2006} 
    }
    


  8. Hervé Delingette, Xavier Pennec, Luc Soler, Jacques Marescaux, and Nicholas Ayache. Computational Models for Image Guided, Robot-Assisted and Simulated Medical Interventions. Proceedings of the IEEE, 94(9):1678- 1688, September 2006.
    @article{Delingette:IEEEProc:06,
    author = {Herv\'e Delingette and Xavier Pennec and Luc Soler and Jacques Marescaux and Nicholas Ayache},
    doi = {10.1109/JPROC.2006.880718},
    journal = {Proceedings of the IEEE},
    month = {September},
    number = {9},
    pages = {1678- 1688},
    title = {Computational Models for Image Guided, Robot-Assisted and Simulated Medical Interventions},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Herve.Delingette/IEEE-proceedings-Robotics.pdf},
    url-hal = {https://hal.inria.fr/inria-00615001},
    volume = {94},
    year = {2006} 
    }
    


  9. Denis Ducreux, Frédéric Dhermain, and Pierre Fillard. [Functional MRI in brain tumours]. Cancer radiothérapie, 10(6-7):330-3, November 2006. Note: [In French]. Keyword(s): Brain, anatomy & histology, Brain Mapping, Brain Neoplasms, pathology, Humans, Magnetic Resonance Imaging, methods, Prognosis.
    Abstract:
    Functional MRI is a technique of imaging which is developing fast as it allows non-aggressive evaluation of brain functions. Diffusion, perfusion and activation are each used to study brain responsiveness to a given task. As a pretherapeutic routine investigation, in brain tumours, it can be helpful as an additional tool to morphological MRI in evaluating the prognosis of patients.

    @article{Ducreux:CancerRadiotherapy:06,
    abstract = {Functional MRI is a technique of imaging which is developing fast as it allows non-aggressive evaluation of brain functions. Diffusion, perfusion and activation are each used to study brain responsiveness to a given task. As a pretherapeutic routine investigation, in brain tumours, it can be helpful as an additional tool to morphological MRI in evaluating the prognosis of patients.},
    author = {Denis Ducreux and Fr\'ed\'eric Dhermain and Pierre Fillard},
    hal-identifiant = {inria-00502605},
    journal = {Cancer radioth\'erapie},
    keywords = {Brain, anatomy & histology, Brain Mapping, Brain Neoplasms, pathology, Humans, Magnetic Resonance Imaging, methods, Prognosis},
    month = {November},
    note = {[In French]},
    number = {6-7},
    pages = {330-3},
    title = {[Functional MRI in brain tumours]},
    url-hal = {https://hal.inria.fr/inria-00502605},
    volume = {10},
    year = {2006} 
    }
    


  10. Denis Ducreux, Jean-Francois Lepeintre, Pierre Fillard, C. Loureiro, Marc Tadié, and Pierre Lasjaunias. MR diffusion tensor imaging and fiber tracking in 5 spinal cord astrocytomas. AJNR. American journal of neuroradiology, 27(1):214-6, January 2006. Keyword(s): Adult, Astrocytoma, diagnosis, Diffusion Magnetic Resonance Imaging, Female, Humans, Image Processing Computer-Assisted, Imaging Three-Dimensional, Male, Nerve Fibers, pathology, Spinal Cord, pathology, Spinal Cord Neoplasms, diagnosis.
    Abstract:
    Spinal cord astrocytomas are rare neoplasms that can result in alteration of the spinal cord structural integrity, which can be assessed by using diffusion tensor imaging methods. Our objective was to visualize the deformation of the posterior spinal cord lemniscal and corticospinal tracts in 5 patients with low-grade astrocytomas compared with 10 healthy volunteers by using 3D fiber-tracking reconstructions.

    @article{Ducreux:AJNR:06,
    abstract = {Spinal cord astrocytomas are rare neoplasms that can result in alteration of the spinal cord structural integrity, which can be assessed by using diffusion tensor imaging methods. Our objective was to visualize the deformation of the posterior spinal cord lemniscal and corticospinal tracts in 5 patients with low-grade astrocytomas compared with 10 healthy volunteers by using 3D fiber-tracking reconstructions.},
    author = {Denis Ducreux and Jean-Francois Lepeintre and Pierre Fillard and C. Loureiro and Marc Tadi\'e and Pierre Lasjaunias},
    hal-identifiant = {inria-00502663},
    journal = {AJNR. American journal of neuroradiology},
    keywords = {Adult, Astrocytoma, diagnosis, Diffusion Magnetic Resonance Imaging, Female, Humans, Image Processing Computer-Assisted, Imaging Three-Dimensional, Male, Nerve Fibers, pathology, Spinal Cord, pathology, Spinal Cord Neoplasms, diagnosis},
    month = {January},
    number = {1},
    pages = {214-6},
    title = {MR diffusion tensor imaging and fiber tracking in 5 spinal cord astrocytomas},
    url-hal = {https://hal.inria.fr/inria-00502663},
    volume = {27},
    year = {2006} 
    }
    


  11. Céline Fouard, Grégoire Malandain, Steffen Prohaska, and Malte Westerhoff. Blockwise Processing Applied to Brain Microvascular Network Study. IEEE Transactions on Medical Imaging, 25(10):1319-1328, 2006.
    Abstract:
    The study of cerebral microvascular networks requires high-resolution images. However, to obtain statistically relevant results, a large area of the brain (several square millimeters) must be analyzed. This leads us to consider huge images, too large to be loaded and processed at once in the memory of a standard computer. To consider a large area, a compact representation of the vessels is required. The medial axis is the preferred tool for this application. To extract it, a dedicated skeletonization algorithm is proposed. Numerous approaches already exist which focus on computational efficiency. However, they all implicitly assume that the image can be completely processed in the computer memory, which is not realistic with the large images considered here. We present in this paper a skeletonization algorithm that processes data locally (in subimages) while preserving global properties (i.e., homotopy). We then show some results obtained on a mosaic of three-dimensional images acquired by confocal microscopy.

    @article{fouard:tmi:2006,
    abstract = {The study of cerebral microvascular networks requires high-resolution images. However, to obtain statistically relevant results, a large area of the brain (several square millimeters) must be analyzed. This leads us to consider huge images, too large to be loaded and processed at once in the memory of a standard computer. To consider a large area, a compact representation of the vessels is required. The medial axis is the preferred tool for this application. To extract it, a dedicated skeletonization algorithm is proposed. Numerous approaches already exist which focus on computational efficiency. However, they all implicitly assume that the image can be completely processed in the computer memory, which is not realistic with the large images considered here. We present in this paper a skeletonization algorithm that processes data locally (in subimages) while preserving global properties (i.e., homotopy). We then show some results obtained on a mosaic of three-dimensional images acquired by confocal microscopy.},
    author = {C\'eline Fouard and Gr\'egoire Malandain and Steffen Prohaska and Malte Westerhoff},
    doi = {10.1109/TMI.2006.880670},
    hal-identifiant = {hal-00308887},
    journal = {IEEE Transactions on Medical Imaging},
    number = {10},
    pages = {1319-1328},
    title = {Blockwise Processing Applied to Brain Microvascular Network Study},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Gregoire.Malandain/fouard-tmi-2006.pdf},
    url-hal = {http://hal.inria.fr/hal-00308887/en/},
    volume = {25},
    year = {2006} 
    }
    


  12. M. Liberatore, C. Denier, Pierre Fillard, M.C. Petit-Lacour, F. Benoudiba, Pierre Lasjaunias, and Denis Ducreux. [Diffusion tensor imaging and tractography of central pontine myelinolysis]. J Neuroradiol, 33(3):189-193, June 2006. Note: [In French]. Keyword(s): Adult, Anorexia, complications, Diffusion Magnetic Resonance Imaging, Female, Humans, Myelinolysis Central Pontine, diagnosis, Pyramidal Tracts, pathology.
    Abstract:
    OBJECTIVES: To illustrate the value of diffusion tensor imaging and tractography in the diagnosis and follow-up of central pontine myelinolysis. CASE REPORT: We report a case of central pontine myelinolysis in a 29 year old woman, also anorexic, studied using MR Diffusion Tensor Imaging (DTI) and Fibre Tracking (FT) focused on the pons, and compared with the studies of 5 normal volunteers. Tractography showed a swollen aspect of the right corticospinal fiber tract correlating with mild left lower extremity deficit at clinical evaluation. The pontine fibers were posteriorly displaced but intact. The sensory tracts were also intact. Apparent Diffusion Coefficient values were increased and Fractional Anisotropy was decreased in the lesions. Follow up imaging showed persistent abnormal ADC and FA values in the pons although the left cortico-spinal tract returned to normal, consistent with the clinical outcome. CONCLUSION: Diffusion Tensor Imaging MR and Fiber tractography are a new method to analyse white matter tracts. It can be used to prospectively evaluate the location of white matter tract lesions at the acute phase of central pontine myelinolysis and follow up.

    @article{Liberatore:JNeuroradiology:06,
    abstract = {OBJECTIVES: To illustrate the value of diffusion tensor imaging and tractography in the diagnosis and follow-up of central pontine myelinolysis. CASE REPORT: We report a case of central pontine myelinolysis in a 29 year old woman, also anorexic, studied using MR Diffusion Tensor Imaging (DTI) and Fibre Tracking (FT) focused on the pons, and compared with the studies of 5 normal volunteers. Tractography showed a swollen aspect of the right corticospinal fiber tract correlating with mild left lower extremity deficit at clinical evaluation. The pontine fibers were posteriorly displaced but intact. The sensory tracts were also intact. Apparent Diffusion Coefficient values were increased and Fractional Anisotropy was decreased in the lesions. Follow up imaging showed persistent abnormal ADC and FA values in the pons although the left cortico-spinal tract returned to normal, consistent with the clinical outcome. CONCLUSION: Diffusion Tensor Imaging MR and Fiber tractography are a new method to analyse white matter tracts. It can be used to prospectively evaluate the location of white matter tract lesions at the acute phase of central pontine myelinolysis and follow up.},
    author = {M. Liberatore and C. Denier and Pierre Fillard and M.C. Petit-Lacour and F. Benoudiba and Pierre Lasjaunias and Denis Ducreux},
    hal-identifiant = {inria-00502681},
    journal = {J Neuroradiol},
    keywords = {Adult, Anorexia, complications, Diffusion Magnetic Resonance Imaging, Female, Humans, Myelinolysis Central Pontine, diagnosis, Pyramidal Tracts, pathology},
    month = {June},
    note = {[In French]},
    number = {3},
    pages = {189-193},
    title = {[Diffusion tensor imaging and tractography of central pontine myelinolysis]},
    url-hal = {https://hal.inria.fr/inria-00502681},
    volume = {33},
    year = {2006} 
    }
    


  13. M.G. Linguraru, N. Ayache, E. Bardinet, M.A. González Ballester, D. Galanaud, S. Haïk, B.A. Faucheux, J.J. Hauw, P. Cozzone, D. Dormont, and J.P. Brandel. Differentiation of sCJD and vCJD Forms by Automated Analysis of Basal Ganglia Intensity Distribution in Multisequence MRI of the Brain - Definition and Evaluation of New MRI-based Ratios. IEEE Transactions on Medical Imaging, 25(8):1052-1067, 2006.
    @article{Linguraru:TMI:2006,
    author = {M.G. Linguraru and N. Ayache and E. Bardinet and M.A. Gonz\'alez Ballester and D. Galanaud and S. Ha\"ik and B.A. Faucheux and J.J. Hauw and P. Cozzone and D. Dormont and J.P. Brandel},
    hal-identifiant = {hal-00092290},
    journal = {IEEE Transactions on Medical Imaging},
    number = {8},
    pages = {1052-1067},
    title = {Differentiation of sCJD and vCJD Forms by Automated Analysis of Basal Ganglia Intensity Distribution in Multisequence MRI of the Brain - Definition and Evaluation of New MRI-based Ratios},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Linguraru/Linguraru_TMI_2006.pdf},
    url-hal = {http://hal.inria.fr/hal-00092290/en/},
    volume = {25},
    year = {2006} 
    }
    


  14. M.G. Linguraru, K. Marias, R. English, and J.M. Brady. A Biologically Inspired Algorithm for Microcalcification Cluster Detection. Medical Image Analysis, 10(6), 2006.
    @article{Linguraru:MedIA:2006,
    author = {M.G. Linguraru and K. Marias and R. English and J.M. Brady},
    journal = {Medical Image Analysis},
    number = {6},
    publisher = {Elsevier},
    title = {A Biologically Inspired Algorithm for Microcalcification Cluster Detection},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Linguraru/Linguraru_MEDIA_2006.pdf},
    volume = {10},
    year = {2006} 
    }
    


  15. Valérie Moreau-Villéger, Hervé Delingette, Maxime Sermesant, Hiroshi Ashikaga, Elliot McVeigh, and Nicholas Ayache. Building Maps of Local Apparent Conductivity of the Epicardium with a 2D Electrophysiological Model of the Heart. IEEE Transactions on Bio-Medical Engineering, 53(8):1457-1466, August 2006.
    @article{moreau:ieeetbme06,
    author = {Val\'erie Moreau-Vill\'eger and Herv\'e Delingette and Maxime Sermesant and Hiroshi Ashikaga and Elliot McVeigh and Nicholas Ayache},
    journal = {IEEE Transactions on Bio-Medical Engineering},
    month = {August},
    number = {8},
    pages = {1457-1466},
    title = {Building Maps of Local Apparent Conductivity of the Epicardium with a 2D Electrophysiological Model of the Heart},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Moreau/moreauIEEETBME05.pdf},
    url-hal = {https://hal.inria.fr/inria-00614992},
    volume = {53},
    year = {2006} 
    }
    


  16. Xavier Pennec. Intrinsic Statistics on Riemannian Manifolds: Basic Tools for Geometric Measurements. Journal of Mathematical Imaging and Vision, 25(1):127-154, July 2006. Note: A preliminary appeared as INRIA RR-5093, January 2004. Keyword(s): Fréchet means, Statistics, Lie groups, Riemannian geometry.
    @article{Pennec:JMIV:06,
    author = {Xavier Pennec},
    doi = {10.1007/s10851-006-6228-4},
    journal = {Journal of Mathematical Imaging and Vision},
    keywords = {Fr\'echet means, Statistics, Lie groups, Riemannian geometry},
    month = {July},
    note = {A preliminary appeared as INRIA RR-5093, January 2004.},
    number = {1},
    pages = {127-154},
    title = {Intrinsic Statistics on {R}iemannian Manifolds: Basic Tools for Geometric Measurements},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Pennec.JMIV06.pdf},
    url-hal = {https://hal.inria.fr/inria-00614994},
    volume = {25},
    year = {2006} 
    }
    


  17. Xavier Pennec, Pierre Fillard, and Nicholas Ayache. A Riemannian Framework for Tensor Computing. International Journal of Computer Vision, 66(1):41-66, January 2006. Note: A preliminary version appeared as INRIA Research Report 5255, July 2004. Keyword(s): Tensors, regularization, PDE, geometry, Riemannian geometry.
    Abstract:
    Tensors are nowadays a common source of geometric information. In this paper, we propose to endow the tensor space with an affine-invariant Riemannian metric. We demonstrate that it leads to strong theoretical properties: the cone of positive definite symmetric matrices is replaced by a regular and complete manifold without boundaries (null eigenvalues are at the infinity), the geodesic between two tensors and the mean of a set of tensors are uniquely defined, etc. We have previously shown that the Riemannian metric provides a powerful framework for generalizing statistics to manifolds. In this paper, we show that it is also possible to generalize to tensor fields many important geometric data processing algorithms such as interpolation, filtering, diffusion and restoration of missing data. For instance, most interpolation and Gaussian filtering schemes can be tackled efficiently through a weighted mean computation. Linear and anisotropic diffusion schemes can be adapted to our Riemannian framework, through partial differential evolution equations, provided that the metric of the tensor space is taken into account. For that purpose, we provide intrinsic numerical schemes to compute the gradient and Laplace-Beltrami operators. Finally, to enforce the fidelity to the data (either sparsely distributed tensors or complete tensors fields) we propose least-squares criteria based on our invariant Riemannian distance which are particularly simple and efficient to solve.

    @article{Pennec:IJCV:06,
    abstract = { Tensors are nowadays a common source of geometric information. In this paper, we propose to endow the tensor space with an affine-invariant Riemannian metric. We demonstrate that it leads to strong theoretical properties: the cone of positive definite symmetric matrices is replaced by a regular and complete manifold without boundaries (null eigenvalues are at the infinity), the geodesic between two tensors and the mean of a set of tensors are uniquely defined, etc. We have previously shown that the Riemannian metric provides a powerful framework for generalizing statistics to manifolds. In this paper, we show that it is also possible to generalize to tensor fields many important geometric data processing algorithms such as interpolation, filtering, diffusion and restoration of missing data. For instance, most interpolation and Gaussian filtering schemes can be tackled efficiently through a weighted mean computation. Linear and anisotropic diffusion schemes can be adapted to our Riemannian framework, through partial differential evolution equations, provided that the metric of the tensor space is taken into account. For that purpose, we provide intrinsic numerical schemes to compute the gradient and Laplace-Beltrami operators. Finally, to enforce the fidelity to the data (either sparsely distributed tensors or complete tensors fields) we propose least-squares criteria based on our invariant Riemannian distance which are particularly simple and efficient to solve.},
    author = {Xavier Pennec and Pierre Fillard and Nicholas Ayache},
    doi = {10.1007/s11263-005-3222-z},
    journal = {International Journal of Computer Vision},
    keywords = {Tensors, regularization, PDE, geometry, Riemannian geometry},
    month = {January},
    note = {A preliminary version appeared as INRIA Research Report 5255, July 2004.},
    number = {1},
    pages = {41--66},
    title = {A {R}iemannian Framework for Tensor Computing},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Pennec.IJCV05.pdf},
    url-hal = {https://hal.inria.fr/inria-00614990},
    url-publisher = {http://springerlink.metapress.com/openurl.asp?genre=article&issn=0920-5691&volume=66&issue=1&spage=41},
    volume = {66},
    year = {2006} 
    }
    


  18. Alain Pitiot, Eric Bardinet, Paul M. Thompson, and Grégoire Malandain. Piecewise Affine Registration of Biological Images for Volume Reconstruction. Medical Image Analysis, 10(3):465-483, June 2006. Keyword(s): registration, clustering, reconstruction, histology, MRI.
    Abstract:
    This manuscript tackles the reconstruction of 3D volumes via mono-modal registration of series of 2D biological images (histological sections, autoradiographs, cryosections, etc.). The process of acquiring these images typically induces composite transformations that we model as a number of rigid or affine local transformations embedded in an elastic one. We propose a registration approach closely derived from this model. Given a pair of input images, we first compute a dense similarity field between them with a block matching algorithm. We use as a similarity measure an extension of the classical correlation coefficient that improves the consistency of the field. A hierarchical clustering algorithm then automatically partitions the field into a number of classes from which we extract independent pairs of sub-images. Our clustering algorithm relies on the Earth mover's distribution metric and is additionally guided by robust least-square estimation of the transformations associated with each cluster. Finally, the pairs of sub-images are, independently, affinely registered and a hybrid affine/non-linear interpolation scheme is used to compose the output registered image. We investigate the behavior of our approach on several batches of histological data and discuss its sensitivity to parameters and noise.

    @article{pitiot:media:2006,
    abstract = {This manuscript tackles the reconstruction of 3D volumes via mono-modal registration of series of 2D biological images (histological sections, autoradiographs, cryosections, etc.). The process of acquiring these images typically induces composite transformations that we model as a number of rigid or affine local transformations embedded in an elastic one. We propose a registration approach closely derived from this model. Given a pair of input images, we first compute a dense similarity field between them with a block matching algorithm. We use as a similarity measure an extension of the classical correlation coefficient that improves the consistency of the field. A hierarchical clustering algorithm then automatically partitions the field into a number of classes from which we extract independent pairs of sub-images. Our clustering algorithm relies on the Earth mover's distribution metric and is additionally guided by robust least-square estimation of the transformations associated with each cluster. Finally, the pairs of sub-images are, independently, affinely registered and a hybrid affine/non-linear interpolation scheme is used to compose the output registered image. We investigate the behavior of our approach on several batches of histological data and discuss its sensitivity to parameters and noise.},
    author = {Alain Pitiot and Eric Bardinet and Paul M. Thompson and Gr\'egoire Malandain},
    journal = {Medical Image Analysis},
    keywords = {registration, clustering, reconstruction, histology, MRI},
    month = {June},
    number = {3},
    pages = {465--483},
    title = {Piecewise Affine Registration of Biological Images for Volume Reconstruction},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Gregoire.Malandain/MedIA-WBIR-pitiot-etal.pdf},
    volume = {10},
    year = {2006} 
    }
    


  19. J Renoux, D Facon, P Fillard, I Huynh, P Lasjaunias, and D Ducreux. MR diffusion tensor imaging and fiber tracking in inflammatory diseases of the spinal cord. AJNR. American journal of neuroradiology, 27(9):1947-51, October 2006. Keyword(s): Adult, Anisotropy, Diagnosis Differential, Diffusion Magnetic Resonance Imaging, Female, Humans, Image Enhancement, Image Processing Computer-Assisted, Male, Middle Aged, Multiple Sclerosis, diagnosis, Myelitis, diagnosis, Myelitis Transverse, diagnosis, Nerve Fibers, pathology, Neurologic Examination, Prospective Studies, Reference Values, Sarcoidosis, diagnosis, Spinal Cord, pathology.
    Abstract:
    PURPOSE: Our aim was to study the fractional anisotropy (FA) variations and the fiber tracking (FT) patterns observed in patients with myelitis. MATERIAL AND METHODS: Fifteen patients with symptomatic myelitis and 11 healthy subjects were prospectively selected. We performed T2-weighted and diffusion tensor imaging on a 1.5T MR scanner. FA and apparent diffusion coefficient maps were computed in both healthy subjects and patients. In each patient, we performed FT to study pathologic aspects on this imaging method. FA data were analyzed by using z-scores. RESULTS: For the healthy subjects, averaged FA values ranged from 0.745 to 0.751. All abnormal areas seen on T2-weighted imaging had a significantly decreased FA value. In 9 patients (60%), FA maps showed decreased FA areas, whereas T2-weighted imaging findings were normal. These areas matched the neurologic deficit in 33%. Eighty percent of patients had multiple decreased FA areas. Five patients (33%) had increased FA values in normal T2-weighted areas. CONCLUSION: We observed specific FA and FT pattern variations in patients with myelitis.

    @article{renoux:aajn:2006,
    abstract = {PURPOSE: Our aim was to study the fractional anisotropy (FA) variations and the fiber tracking (FT) patterns observed in patients with myelitis. MATERIAL AND METHODS: Fifteen patients with symptomatic myelitis and 11 healthy subjects were prospectively selected. We performed T2-weighted and diffusion tensor imaging on a 1.5T MR scanner. FA and apparent diffusion coefficient maps were computed in both healthy subjects and patients. In each patient, we performed FT to study pathologic aspects on this imaging method. FA data were analyzed by using z-scores. RESULTS: For the healthy subjects, averaged FA values ranged from 0.745 to 0.751. All abnormal areas seen on T2-weighted imaging had a significantly decreased FA value. In 9 patients (60%), FA maps showed decreased FA areas, whereas T2-weighted imaging findings were normal. These areas matched the neurologic deficit in 33%. Eighty percent of patients had multiple decreased FA areas. Five patients (33%) had increased FA values in normal T2-weighted areas. CONCLUSION: We observed specific FA and FT pattern variations in patients with myelitis.},
    author = {J Renoux and D Facon and P Fillard and I Huynh and P Lasjaunias and D Ducreux},
    hal-identifiant = {inria-00502684},
    journal = {AJNR. American journal of neuroradiology},
    keywords = {Adult, Anisotropy, Diagnosis Differential, Diffusion Magnetic Resonance Imaging, Female, Humans, Image Enhancement, Image Processing Computer-Assisted, Male, Middle Aged, Multiple Sclerosis, diagnosis, Myelitis, diagnosis, Myelitis Transverse, diagnosis, Nerve Fibers, pathology, Neurologic Examination, Prospective Studies, Reference Values, Sarcoidosis, diagnosis, Spinal Cord, pathology},
    month = {October},
    number = {9},
    pages = {1947-51},
    title = {MR diffusion tensor imaging and fiber tracking in inflammatory diseases of the spinal cord},
    url-hal = {https://hal.inria.fr/inria-00502684},
    volume = {27},
    year = {2006} 
    }
    


  20. Gilles Scarella, Olivier Clatz, Stéphane Lanteri, Grégory Beaume, Steve Oudot, Jean-Philippe Pons, Serge Piperno, Patrick Joly, and Joe Wiart. Realistic numerical modelling of human head tissue exposure to electromagnetic waves from cellular phones. Comptes Rendus de l'Académie des Sciences - Physics, 7(5):501-508, June 2006.
    Abstract:
    The ever-rising diffusion of cellular phones has brought about an increased concern for the possible consequences of electromagnetic radiation on human health. Possible thermal effects have been investigated, via experimentation or simulation, by several research projects in the last decade. Concerning numerical modeling, the power absorption in a user's head is generally computed using discretized models built from clinical MRI data. The vast majority of such numerical studies have been conducted using Finite Differences Time Domain methods, although strong limitations of their accuracy are due to heterogeneity, poor definition of the detailed structures of head tissues (staircasing effects), etc. In order to propose numerical modeling using Finite Element or Discontinuous Galerkin Time Domain methods, reliable automated tools for the unstructured discretization of human heads are also needed. Results presented in this article aim at filling the gap between human head MRI images and the accurate numerical modeling of wave propagation in biological tissues and its thermal effects.

    @article{Scarella:CRAS:06,
    abstract = {The ever-rising diffusion of cellular phones has brought about an increased concern for the possible consequences of electromagnetic radiation on human health. Possible thermal effects have been investigated, via experimentation or simulation, by several research projects in the last decade. Concerning numerical modeling, the power absorption in a user's head is generally computed using discretized models built from clinical MRI data. The vast majority of such numerical studies have been conducted using Finite Differences Time Domain methods, although strong limitations of their accuracy are due to heterogeneity, poor definition of the detailed structures of head tissues (staircasing effects), etc. In order to propose numerical modeling using Finite Element or Discontinuous Galerkin Time Domain methods, reliable automated tools for the unstructured discretization of human heads are also needed. Results presented in this article aim at filling the gap between human head MRI images and the accurate numerical modeling of wave propagation in biological tissues and its thermal effects.},
    author = {Gilles Scarella and Olivier Clatz and St\'ephane Lanteri and Gr\'egory Beaume and Steve Oudot and Jean-Philippe Pons and Serge Piperno and Patrick Joly and Joe Wiart},
    hal-identifiant = {hal-00607719},
    journal = {Comptes Rendus de l'Acad\'emie des Sciences - Physics},
    month = {June},
    number = {5},
    pages = {501-508},
    title = {Realistic numerical modelling of human head tissue exposure to electromagnetic waves from cellular phones},
    url = {http://cermics.enpc.fr/~piper/perso/papers/2005-CRAS-HEADEXP.pdf},
    url-hal = {https://hal-enpc.archives-ouvertes.fr/hal-00607719},
    volume = {7},
    year = {2006} 
    }
    


  21. Maxime Sermesant, Hervé Delingette, and Nicholas Ayache. An Electromechanical Model of the Heart for Image Analysis and Simulation. IEEE Transactions on Medical Imaging, 25(5):612-625, 2006.
    @article{Sermesant:TMI:06,
    author = {Maxime Sermesant and Herv\'e Delingette and Nicholas Ayache},
    journal = {IEEE Transactions on Medical Imaging},
    number = {5},
    pages = {612--625},
    title = {An Electromechanical Model of the Heart for Image Analysis and Simulation},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/TMI2006Sermesant.pdf},
    url-hal = {https://hal.inria.fr/inria-00614991},
    volume = {25},
    year = {2006} 
    }
    


  22. Maxime Sermesant, Philippe Moireau, Oscar Camara, Jacques Sainte-Marie, Rado Andriantsimiavona, Robert Cimrman, Derek L. Hill, Dominique Chapelle, and Reza Razavi. Cardiac function estimation from MRI using a heart model and data assimilation: Advances and difficulties. Medical Image Analysis, 10(4):642-656, 2006.
    @article{Sermesant:MEDIA:06,
    author = {Maxime Sermesant and Philippe Moireau and Oscar Camara and Jacques Sainte-Marie and Rado Andriantsimiavona and Robert Cimrman and Derek L. Hill and Dominique Chapelle and Reza Razavi},
    journal = {Medical Image Analysis},
    number = {4},
    pages = {642--656},
    title = {Cardiac function estimation from MRI using a heart model and data assimilation: Advances and difficulties},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/MEDIA2006Sermesant.pdf},
    url-hal = {https://hal.inria.fr/inria-00614997},
    volume = {10},
    year = {2006} 
    }
    


  23. Arjan W Simonetti, Vedat A Elezi, Regine Farion, Gregoire Malandain, Christoph Segebarth, Chantal Remy, and Emmanuel L Barbier. A low temperature embedding and section registration strategy for 3D image reconstruction of the rat brain from autoradiographic sections. Journal of Neuroscience Methods, 158(2):242-50, December 2006.
    Abstract:
    In studies on animal models of human brain pathologies, three-dimensional reconstruction from histological sections is particularly useful when assessing the morphologic, functional and biochemical changes induced by pathology. It allows assessing lesion heterogeneity in planes different from the cutting plane and allows correlating the histology with images obtained in vivo, such as by means of magnetic resonance imaging. To create a 3D volume from autoradiographic sections with minimal distortion, both cryosectioning as well as section registration need to be optimal. This paper describes a strategy whereby four external fiducial markers are positioned outside the rat brain with the use of a low temperature brain embedding procedure. The fiducial markers proposed here can be rapidly added to any frozen tissue block with no impact on the subsequent histological operations. Since embedding is performed at a low temperature, no tissue degradation occurs due to sample heating. The markers enable robust and almost error free registration, even in the presence of missing sections and poor image quality. Furthermore, the markers may be used to partially correct for global distortions.

    @article{simonetti:jnm:2006,
    abstract = {In studies on animal models of human brain pathologies, three-dimensional reconstruction from histological sections is particularly useful when assessing the morphologic, functional and biochemical changes induced by pathology. It allows assessing lesion heterogeneity in planes different from the cutting plane and allows correlating the histology with images obtained in vivo, such as by means of magnetic resonance imaging. To create a 3D volume from autoradiographic sections with minimal distortion, both cryosectioning as well as section registration need to be optimal. This paper describes a strategy whereby four external fiducial markers are positioned outside the rat brain with the use of a low temperature brain embedding procedure. The fiducial markers proposed here can be rapidly added to any frozen tissue block with no impact on the subsequent histological operations. Since embedding is performed at a low temperature, no tissue degradation occurs due to sample heating. The markers enable robust and almost error free registration, even in the presence of missing sections and poor image quality. Furthermore, the markers may be used to partially correct for global distortions.},
    author = {Arjan W Simonetti and Vedat A Elezi and Regine Farion and Gregoire Malandain and Christoph Segebarth and Chantal Remy and Emmanuel L Barbier},
    hal-identifiant = {inserm-00388981},
    journal = {Journal of Neuroscience Methods},
    month = {December},
    number = {2},
    pages = {242-50},
    title = {A low temperature embedding and section registration strategy for 3D image reconstruction of the rat brain from autoradiographic sections},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Gregoire.Malandain/simonetti-jnm-2006.pdf},
    url-hal = {http://hal.inria.fr/inserm-00388981/en/},
    volume = {158},
    year = {2006} 
    }
    


  24. Tom Vercauteren, Aymeric Perchant, Grégoire Malandain, Xavier Pennec, and Nicholas Ayache. Robust Mosaicing with Correction of Motion Distortions and Tissue Deformation for In Vivo Fibered Microscopy. Medical Image Analysis, 10(5):673-692, October 2006. Note: Annual Medical Image Analysis (MedIA) Best Paper Award 2006. PMID: 16887375.
    @article{Vercauteren:Media:06,
    author = {Tom Vercauteren and Aymeric Perchant and Gr\'egoire Malandain and Xavier Pennec and Nicholas Ayache},
    doi = {10.1016/j.media.2006.06.006},
    hal-identifiant = {inria-00163961},
    journal = {Medical Image Analysis},
    month = {October},
    note = {Annual Medical Image Analysis (MedIA) Best Paper Award 2006. PMID: 16887375},
    number = {5},
    pages = {673--692},
    title = {Robust Mosaicing with Correction of Motion Distortions and Tissue Deformation for In Vivo Fibered Microscopy},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Tom.Vercauteren/RobustMosaicingMotionDistoTissueDefInVivoFCM-MedIA06-Vercauteren.pdf},
    url-hal = {https://hal.inria.fr/inria-00163961},
    volume = {10},
    year = {2006} 
    }
    


Conference articles

  1. Vincent Arsigny, Olivier Commowick, Xavier Pennec, and Nicholas Ayache. A Log-Euclidean Framework for Statistics on Diffeomorphisms. In Proc. of the 9th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI'06), Part I, number 4190 of LNCS, pages 924-931, 2-4 October 2006. Keyword(s): Non-rigid registration, Lie groups, Diffeomorphisms, Log-Euclidean metrics, Magnetic Resonance Imaging.
    @inproceedings{Arsigny:MICCAI:06,
    author = {Vincent Arsigny and Olivier Commowick and Xavier Pennec and Nicholas Ayache},
    booktitle = {Proc. of the 9th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI'06), Part I},
    doi = {10.1007/11866565_113},
    keywords = {Non-rigid registration, Lie groups, Diffeomorphisms, Log-Euclidean metrics, Magnetic Resonance Imaging},
    month = {2-4 October},
    number = {4190},
    pages = {924--931},
    pmid = {17354979},
    series = {LNCS},
    title = {A Log-{Euclidean} Framework for Statistics on Diffeomorphisms},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Arsigny/arsigny_miccai06.pdf},
    url-hal = {https://hal.inria.fr/inria-00615594},
    x-editorial-board = {yes},
    x-international-audience = {yes},
    x-proceedings = {yes},
    year = {2006} 
    }
    


  2. Vincent Arsigny, Olivier Commowick, Xavier Pennec, and Nicholas Ayache. A Log-Euclidean Polyaffine Framework for Locally Rigid or Affine Registration. In J.P.W. Pluim, B. Likar, and F.A. Gerritsen, editors, Proceedings of the Third International Workshop on Biomedical Image Registration (WBIR'06), volume 4057 of LNCS, Utrecht, The Netherlands, pages 120-127, 9 - 11 July 2006. Springer. Keyword(s): Polyaffine transformations, Diffeomorphisms, Non-rigid registration, Multi-affine registration, Lie groups, Log-Euclidean metrics, Magnetic Resonance Imaging.
    @inproceedings{Arsigny:Wbir:06,
    address = {Utrecht, The Netherlands},
    author = {Vincent Arsigny and Olivier Commowick and Xavier Pennec and Nicholas Ayache},
    booktitle = {Proceedings of the Third International Workshop on Biomedical Image Registration (WBIR'06)},
    doi = {10.1007/11784012_15},
    editor = {J.P.W. Pluim and B. Likar and F.A. Gerritsen},
    keywords = {Polyaffine transformations, Diffeomorphisms, Non-rigid registration, Multi-affine registration, Lie groups, Log-Euclidean metrics, Magnetic Resonance Imaging},
    month = {9 - 11 July},
    pages = {120-127},
    publisher = {Springer},
    series = {LNCS},
    title = {A Log-{Euclidean} Polyaffine Framework for Locally Rigid or Affine Registration},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Arsigny/arsigny_wbir.pdf},
    url-hal = {https://hal.inria.fr/inria-00615607},
    volume = {4057},
    year = {2006} 
    }
    


  3. Vincent Arsigny, Olivier Commowick, Xavier Pennec, and Nicholas Ayache. Statistics on Diffeomorphisms in A Log-Euclidean Framework. In X. Pennec and S. Joshi, editors, Proc. of the International Workshop on the Mathematical Foundations of Computational Anatomy (MFCA-2006), pages 16-17, 1st of October 2006. Keyword(s): Non-rigid registration, Lie groups, Diffeomorphisms, Log-Euclidean metrics, Magnetic Resonance Imaging.
    @inproceedings{Arsigny:MFCA:06,
    author = {Vincent Arsigny and Olivier Commowick and Xavier Pennec and Nicholas Ayache},
    booktitle = {Proc. of the International Workshop on the Mathematical Foundations of Computational Anatomy (MFCA-2006)},
    editor = {X. Pennec and S. Joshi},
    keywords = {Non-rigid registration, Lie groups, Diffeomorphisms, Log-Euclidean metrics, Magnetic Resonance Imaging},
    month = {1st of October},
    pages = {16-17},
    title = {Statistics on Diffeomorphisms in A Log-{Euclidean} Framework},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Arsigny/arsigny_mfca.pdf},
    x-international-audience = {yes},
    x-proceedings = {no},
    year = {2006} 
    }
    


  4. M. A. Audette, H. Delingette, A. Fuchs, O. Burgert, and K. Chinzei. A topologically faithful, tissue-guided, spatially varying meshing strategy for computing patient-specific head models for endoscopic pituitary surgery simulation. In Studies in health technology and informatics, Medicine Meets Virtual Reality (MMVR), pages 22-27, 2006.
    @inproceedings{Audette:mmvr:2006,
    author = {M. A. Audette and H. Delingette and A. Fuchs and O. Burgert and K. Chinzei},
    booktitle = {Studies in health technology and informatics, Medicine Meets Virtual Reality (MMVR)},
    pages = {22--27},
    title = {A topologically faithful, tissue-guided, spatially varying meshing strategy for computing patient-specific head models for endoscopic pituitary surgery simulation},
    url-hal = {https://hal.inria.fr/inria-00615611},
    year = {2006} 
    }
    


  5. Nicholas Ayache, Tom Vercauteren, Grégoire Malandain, Fabien Oberrietter, Nicolas Savoire, and Aymeric Perchant. Processing and Mosaicing of Fibered Confocal Images. In MICCAI Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB'06), October 2006. Note: Invited.
    @inproceedings{Ayache:MIAAB:06,
    author = {Nicholas Ayache and Tom Vercauteren and Gr\'egoire Malandain and Fabien Oberrietter and Nicolas Savoire and Aymeric Perchant},
    booktitle = {MICCAI Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB'06)},
    month = {October},
    note = {Invited},
    title = {Processing and Mosaicing of Fibered Confocal Images},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Ayache/ExAbstractMIIAB06-Ayache-light.pdf},
    url-hal = {https://hal.inria.fr/inria-00615589},
    year = {2006} 
    }
    


  6. Antoine Azar, Chenyang Xu, Xavier Pennec, and Nicholas Ayache. An interactive Intensity- and Feature-Based Non-Rigid Registration Framework for 3D Medical Images. In Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI 2006), Crystal Gateway Marriott, Arlington, Virginia, USA, pages 824-827, April 2006. Keyword(s): Spine, variability model, Riemannian geometry.
    @inproceedings{Azar:ISBI:06,
    address = {Crystal Gateway Marriott, Arlington, Virginia, USA},
    author = {Antoine Azar and Chenyang Xu and Xavier Pennec and Nicholas Ayache},
    booktitle = {Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI 2006)},
    doi = {10.1109/ISBI.2006.1625045},
    keywords = {Spine, variability model, Riemannian geometry},
    month = {April},
    pages = {824--827},
    title = {An interactive Intensity- and Feature-Based Non-Rigid Registration Framework for 3D Medical Images},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Azar.ISBI06.pdf},
    url-hal = {https://hal.inria.fr/inria-00615601},
    year = {2006} 
    }
    


  7. Jonathan Boisvert, Farida Cheriet, Xavier Pennec, Nicholas Ayache, and Hubert Labelle. A Novel Framework for the 3D Analysis of Spine Deformation Modes. In Research into Spinal Deformities, volume 123 of Studies in Health Technology and Informatics, pages 176-182, 2006.
    @inproceedings{Boisvert:IRSSD_model:06,
    author = {Jonathan Boisvert and Farida Cheriet and Xavier Pennec and Nicholas Ayache and Hubert Labelle},
    booktitle = {Research into Spinal Deformities},
    pages = {176--182},
    pmid = {17108423},
    series = {Studies in Health Technology and Informatics},
    title = {A Novel Framework for the 3D Analysis of Spine Deformation Modes},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Boisvert.IRSSD_spine.pdf},
    url-publisher = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=3635},
    volume = {123},
    year = {2006} 
    }
    


  8. Jonathan Boisvert, Farida Cheriet, Xavier Pennec, Nicholas Ayache, and Hubert Labelle. Assessment of Brace Local Action on Vertebrae Relative Poses. In Research into Spinal Deformities, volume 123 of Studies in Health Technology and Informatics, pages 372-378, 2006.
    @inproceedings{Boisvert:IRSSD_brace:06,
    author = {Jonathan Boisvert and Farida Cheriet and Xavier Pennec and Nicholas Ayache and Hubert Labelle},
    booktitle = {Research into Spinal Deformities},
    pages = {372--378},
    pmid = {17108454},
    series = {Studies in Health Technology and Informatics},
    title = {Assessment of Brace Local Action on Vertebrae Relative Poses},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Boisvert.IRSSD_brace.pdf},
    url-hal = {https://hal.inria.fr/inria-00615609},
    url-publisher = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=3670},
    volume = {123},
    year = {2006} 
    }
    


  9. Jonathan Boisvert, Xavier Pennec, Nicholas Ayache, Hubert Labelle, and Farida Cheriet. 3D Anatomic Variability Assesment of the Scoliotic Spine Using Statistics on Lie Groups. In Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI 2006), Crystal Gateway Marriott, Arlington, Virginia, USA, pages 750-753, April 2006. IEEE. Keyword(s): Spine, variability model, Riemannian geometry.
    @inproceedings{Boisvert:ISBI:06,
    address = {Crystal Gateway Marriott, Arlington, Virginia, USA},
    author = {Jonathan Boisvert and Xavier Pennec and Nicholas Ayache and Hubert Labelle and Farida Cheriet},
    booktitle = {Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI 2006)},
    doi = {10.1109/ISBI.2006.1625025},
    keywords = {Spine, variability model, Riemannian geometry},
    month = {April},
    pages = {750--753},
    publisher = {IEEE},
    title = {3{D} Anatomic Variability Assesment of the Scoliotic Spine Using Statistics on {L}ie Groups},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Boisvert.ISBI06.pdf},
    url-hal = {https://hal.inria.fr/inria-00615602},
    year = {2006} 
    }
    


  10. Jonathan Boisvert, Xavier Pennec, Hubert Labelle, Farida Cheriet, and Nicholas Ayache. Principal Spine Shape Deformation Modes Using Riemannian Geometry and Articulated Models. In Proc of the IV Conference on Articulated Motion and Deformable Objects, Andratx, Mallorca, Spain, 11-14 July, volume 4069 of LNCS, pages 346-355, 2006. Springer. Note: AMDO best paper award 2006.
    @inproceedings{Boisvert:AMDO:06,
    author = {Jonathan Boisvert and Xavier Pennec and Hubert Labelle and Farida Cheriet and Nicholas Ayache},
    booktitle = {Proc of the IV Conference on Articulated Motion and Deformable Objects, Andratx, Mallorca, Spain, 11-14 July},
    doi = {10.1007/11789239_36},
    note = {AMDO best paper award 2006},
    pages = {346--355},
    publisher = {Springer},
    series = {LNCS},
    title = {Principal Spine Shape Deformation Modes Using {R}iemannian Geometry and Articulated Models},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Boisvert.AMDO06.pdf},
    url-hal = {https://hal.inria.fr/inria-00615592},
    volume = {4069},
    year = {2006} 
    }
    


  11. Nikos Chrisochoides, Andriy Fedorov, Andriy Kot, Neculai Archip, Peter Black, Olivier Clatz, Alexandra Golby, Ron Kikinis, and Simon K. Warfield. Toward Real-Time, Image Guided Neurosurgery Using Distributed and Grid Computing. In SuperComputing06, Tampa, Florida, USA, November 2006.
    @inproceedings{Chrisochoides:SC:06,
    address = {Tampa, Florida, USA},
    author = {Nikos Chrisochoides and Andriy Fedorov and Andriy Kot and Neculai Archip and Peter Black and Olivier Clatz and Alexandra Golby and Ron Kikinis and Simon K. Warfield},
    booktitle = {SuperComputing06},
    month = {November},
    title = {Toward Real-Time, Image Guided Neurosurgery Using Distributed and Grid Computing},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Olivier.Clatz/chrisochoides_SC_06.pdf},
    url-hal = {https://hal.inria.fr/inria-00615612},
    year = {2006} 
    }
    


  12. Desmond Chung, Mihaela Pop, Maxime Sermesant, and Graham Wright. Stereo Reconstruction of the Epicardium for Optical Fluorescence Imaging. In MICCAI Workshop on Biophotonics Imaging for Diagnostics and Treatment, pages 33-40, 2006.
    @inproceedings{Chung:MICCAI:06,
    author = {Desmond Chung and Mihaela Pop and Maxime Sermesant and Graham Wright},
    booktitle = {MICCAI Workshop on Biophotonics Imaging for Diagnostics and Treatment},
    pages = {33-40},
    title = {Stereo Reconstruction of the Epicardium for Optical Fluorescence Imaging},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Maxime.Sermesant/MICCAI2006Chung.pdf},
    url-hal = {https://hal.inria.fr/inria-00615588},
    year = {2006} 
    }
    


  13. Olivier Clatz, Stéphane Lanteri, and Serge Piperno. Unstructured mesh solvers for the simulation of electromagnetic wave propagation and induced temperature elevation in living tissues. In 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering, 2006.
    @inproceedings{Clatz:CMBBE:06,
    author = {Olivier Clatz and St\'ephane Lanteri and Serge Piperno},
    booktitle = {7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering},
    title = {Unstructured mesh solvers for the simulation of electromagnetic wave propagation and induced temperature elevation in living tissues},
    url-hal = {https://hal.inria.fr/inria-00615586},
    year = {2006} 
    }
    


  14. O. Colliot, T. Mansi, P. Besson, N. Bernasconi, and A. Bernasconi. Improved segmentation of focal cortical dysplasia lesions on MRI using expansion towards cortical boundaries. In 3rd IEEE International Symposium on Biomedical Imaging: Nano to Macro (ISBI), pages 323-326, 2006.
    Abstract:
    Focal cortical dysplasia (FCD), a malformation of cortical development, is an important cause of intractable epilepsy. On magnetic resonance images (MRI), FCD lesions are difficult to distinguish from healthy cortex and defining their spatial extent is challenging. We previously introduced a method to segment FCD lesions on MRI, relying on a 3D deformable model driven by MR features of FCD. In the present paper, we propose to improve our approach by adding a second evolution step which expands the result towards the cortical boundaries. A quantitative evaluation was performed in 18 FCD patients by comparison with manually traced lesion labels. The proposed approach achieved a strong agreement with the manual labels and substantially improved the results obtained with our previous method.

    @inproceedings{colliot06:ISBI,
    abstract = {Focal cortical dysplasia (FCD), a malformation of cortical development, is an important cause of intractable epilepsy. On magnetic resonance images (MRI), FCD lesions are difficult to distinguish from healthy cortex and defining their spatial extent is challenging. We previously introduced a method to segment FCD lesions on MRI, relying on a 3D deformable model driven by MR features of FCD. In the present paper, we propose to improve our approach by adding a second evolution step which expands the result towards the cortical boundaries. A quantitative evaluation was performed in 18 FCD patients by comparison with manually traced lesion labels. The proposed approach achieved a strong agreement with the manual labels and substantially improved the results obtained with our previous method.},
    author = {O. Colliot and T. Mansi and P. Besson and N. Bernasconi and A. Bernasconi},
    booktitle = {3rd IEEE International Symposium on Biomedical Imaging: Nano to Macro (ISBI)},
    pages = {323-326},
    title = {Improved segmentation of focal cortical dysplasia lesions on MRI using expansion towards cortical boundaries},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Tommaso.Mansi/colliot06ISBI.pdf},
    url-hal = {https://hal.inria.fr/inria-00615584},
    url-publisher = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1624918},
    year = {2006} 
    }
    


  15. Olivier Commowick, Vincent Arsigny, Jimena Costa, Nicholas Ayache, and Grégoire Malandain. An Efficient Locally Affine Framework for the Registration of Anatomical Structures. In Proceedings of the Third IEEE International Symposium on Biomedical Imaging (ISBI 2006), Crystal Gateway Marriott, Arlington, Virginia, USA, pages 478-481, April 2006. Keyword(s): Non-rigid registration, Multi-affine registration, Magnetic Resonance Imaging, Polyaffine transformations, Log-Euclidean metrics, Diffeomorphisms.
    @inproceedings{Commowick:ISBI:06,
    address = {Crystal Gateway Marriott, Arlington, Virginia, USA},
    author = {Olivier Commowick and Vincent Arsigny and Jimena Costa and Nicholas Ayache and Gr\'egoire Malandain},
    booktitle = {Proceedings of the Third IEEE International Symposium on Biomedical Imaging (ISBI 2006)},
    keywords = {Non-rigid registration, Multi-affine registration, Magnetic Resonance Imaging, Polyaffine transformations, Log-Euclidean metrics, Diffeomorphisms},
    month = {April},
    pages = {478-481},
    title = {An Efficient Locally Affine Framework for the Registration of Anatomical Structures},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Commowick/CommowickIsbi2006.pdf},
    url-hal = {https://hal.inria.fr/inria-00615606},
    year = {2006} 
    }
    


  16. Olivier Commowick and Grégoire Malandain. Evaluation of Atlas Construction Strategies in the Context of Radiotherapy Planning. In Proceedings of the SA2PM Workshop (From Statistical Atlases to Personalized Models), Copenhagen, October 2006. Note: Held in conjunction with MICCAI 2006. Keyword(s): Non-rigid registration, Atlas, Head And Neck.
    @inproceedings{Commowick:SA2PM:06,
    address = {Copenhagen},
    author = {Olivier Commowick and Gr\'egoire Malandain},
    booktitle = {Proceedings of the SA2PM Workshop (From Statistical Atlases to Personalized Models)},
    keywords = {Non-rigid registration, Atlas, Head And Neck},
    month = {October},
    note = {held in conjunction with MICCAI 2006},
    title = {Evaluation of Atlas Construction Strategies in the Context of Radiotherapy Planning},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Commowick/CommowickMiccai2006.pdf},
    url-hal = {https://hal.inria.fr/inria-00615605},
    year = {2006} 
    }
    


  17. Pierre Fillard, Vincent Arsigny, Xavier Pennec, and Nicholas Ayache. Clinical DT-MRI estimation, smoothing and fiber tracking with log-Euclidean metrics. In Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI 2006), Crystal Gateway Marriott, Arlington, Virginia, USA, pages 786-789, April 2006. Keyword(s): DT-MRI, tensor estimation, Riemannian geometry, Log-Euclidean metrics.
    @inproceedings{Fillard:ISBI:06,
    address = {Crystal Gateway Marriott, Arlington, Virginia, USA},
    author = {Pierre Fillard and Vincent Arsigny and Xavier Pennec and Nicholas Ayache},
    booktitle = {Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI 2006)},
    doi = {10.1109/ISBI.2006.1625034},
    keywords = {DT-MRI, tensor estimation, Riemannian geometry, Log-Euclidean metrics},
    month = {April},
    pages = {786-789},
    title = {Clinical {DT-MRI} estimation, smoothing and fiber tracking with log-{Euclidean} metrics},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Fillard/Fillard.ISBI.06.pdf},
    url-hal = {https://hal.inria.fr/inria-00615579},
    year = {2006} 
    }
    


  18. J. Freund, D. Comaniciu, Y. Ioannis, P. Liu, R. McClatchey, E. Moley-Fletcher, X. Pennec, G. Pongiglione, and X.S. Zhou. Health-e-Child: An Integrated Biomedical Platform for Grid-Based Pediatrics. In Proc of Health-Grid 2006, volume 120 of Studies in Health Technology and Informatics, Valancia, Spain, pages 259-270, 2006.
    @inproceedings{HeC:HealthGrid:06,
    address = {Valancia, Spain},
    author = {J. Freund and D. Comaniciu and Y. Ioannis and P. Liu and R. McClatchey and E. Moley-Fletcher and X. Pennec and G. Pongiglione and X.S. Zhou},
    booktitle = {Proc of Health-Grid 2006},
    pages = {259-270},
    pmid = {16823144},
    series = {Studies in Health Technology and Informatics},
    title = {Health-e-Child: An Integrated Biomedical Platform for Grid-Based Pediatrics},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Health-e-Child_HG06.pdf},
    url-hal = {https://hal.inria.fr/inria-00615591},
    volume = {120},
    year = {2006} 
    }
    


  19. Tristan Glatard, David Emsellem, and Johan Montagnat. Generic web service wrapper for efficient embedding of legacy codes in service-based workflows. In Grid-Enabling Legacy Applications and Supporting End Users Workshop (GELA'06), Paris, France, June 19-23, 2006.
    @inproceedings{Glatard:GELA:06,
    author = {Tristan Glatard and David Emsellem and Johan Montagnat},
    booktitle = {Grid-Enabling Legacy Applications and Supporting End Users Workshop (GELA'06), Paris, France, June 19-23},
    title = {Generic web service wrapper for efficient embedding of legacy codes in service-based workflows},
    url = {http://www.i3s.unice.fr/~johan/publis/GELA06.pdf},
    url-hal = {https://hal.archives-ouvertes.fr/hal-00683196},
    year = {2006} 
    }
    


  20. Tristan Glatard, Johan Montagnat, and Xavier Pennec. An experimental comparison of Grid5000 clusters and the EGEE grid. In Proc of the Workshop on Experimental Grid testbeds for the assessment of large-scale distributed applications and tools (EXPGRID'06), Paris, France, June 19-23, 2006.
    @inproceedings{Glatard:EXPGRID:06,
    author = {Tristan Glatard and Johan Montagnat and Xavier Pennec},
    booktitle = {Proc of the Workshop on Experimental Grid testbeds for the assessment of large-scale distributed applications and tools (EXPGRID'06), Paris, France, June 19-23},
    title = {An experimental comparison of Grid5000 clusters and the EGEE grid},
    url = {http://www.i3s.unice.fr/~johan/publis/EXPGRID06.pdf},
    url-hal = {https://hal.archives-ouvertes.fr/hal-00683199},
    year = {2006} 
    }
    


  21. Tristan Glatard, Johan Montagnat, and Xavier Pennec. Efficient services composition for grid-enabled data-intensive applications. In IEEE, editor, Proceedings of the IEEE International Symposium on High Performance Distributed Computing (HPDC'06), Paris, France, June 19, pages 333-334, June 2006. IEEE.
    @inproceedings{Glatard:HPDC:06,
    author = {Tristan Glatard and Johan Montagnat and Xavier Pennec},
    booktitle = {Proceedings of the IEEE International Symposium on High Performance Distributed Computing (HPDC'06), Paris, France, June 19},
    doi = {10.1109/HPDC.2006.1652170},
    editor = { IEEE},
    month = {June},
    organization = {IEEE},
    pages = {333--334},
    title = {Efficient services composition for grid-enabled data-intensive applications},
    url = {http://www.i3s.unice.fr/~johan/publis/HPDC06.pdf},
    url-hal = {https://hal.archives-ouvertes.fr/hal-00683201},
    year = {2006} 
    }
    


  22. Tristan Glatard, Johan Montagnat, and Xavier Pennec. Medical image registration algorithms assessment: Bronze Standard application enactment on grids using the MOTEUR workflow engine. In Proc. of the HealthGrid conference (HealthGrid'06), Valencia, Spain, June 7-9, volume 120 of Studies in Health Technology and Informatics, pages 93-103, 2006.
    @inproceedings{Glatard:HealthGrid:06,
    author = {Tristan Glatard and Johan Montagnat and Xavier Pennec},
    booktitle = {Proc. of the HealthGrid conference (HealthGrid'06), Valencia, Spain, June 7-9},
    pages = {93--103},
    pmid = {16823126},
    series = {Studies in Health Technology and Informatics},
    title = {Medical image registration algorithms assessment: Bronze Standard application enactment on grids using the MOTEUR workflow engine},
    url = {http://www.i3s.unice.fr/~johan/publis/HealthGrid06b.pdf},
    url-hal = {https://hal.archives-ouvertes.fr/hal-00683188},
    volume = {120},
    year = {2006} 
    }
    


  23. Tristan Glatard, Johan Montagnat, and Xavier Pennec. Probabilistic and dynamic optimization of job partitioning on a grid infrastructure. In 14th euromicro conference on Parallel, Distributed and network-based Processing (PDP06), Montbéliard-Sochaux, pages 231-238, February 2006. IEEE.
    @inproceedings{Glatard:PDP:2006,
    address = {Montb\'eliard-Sochaux},
    author = {Tristan Glatard and Johan Montagnat and Xavier Pennec},
    booktitle = {14th euromicro conference on Parallel, Distributed and network-based Processing (PDP06)},
    doi = {10.1109/PDP.2006.61},
    month = {February},
    pages = {231-238},
    publisher = {IEEE},
    title = {Probabilistic and dynamic optimization of job partitioning on a grid infrastructure},
    url = {http://www.i3s.unice.fr/~johan/publis/PDP06.pdf},
    url-hal = {https://hal.archives-ouvertes.fr/hal-00683203},
    year = {2006} 
    }
    


  24. Tristan Glatard, Xavier Pennec, and Johan Montagnat. Performance evaluation of grid-enabled registration algorithms using bronze-standards. In Proc. of the 9th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI'06), Part II, volume 4191 of LNCS, pages 152-160, 2-4 October 2006. Springer.
    @inproceedings{Glatard:MICCAI:06,
    author = {Tristan Glatard and Xavier Pennec and Johan Montagnat},
    booktitle = {Proc. of the 9th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI'06), Part II},
    doi = {10.1007/11866763_19},
    month = {2-4 October},
    pages = {152--160},
    pmid = {17354767},
    publisher = {Springer},
    series = {LNCS},
    title = {Performance evaluation of grid-enabled registration algorithms using bronze-standards},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Xavier.Pennec/Glatard.MICCAI06.pdf},
    url-hal = {https://hal.archives-ouvertes.fr/hal-00683176},
    volume = {4191},
    year = {2006} 
    }
    


  25. Ender Konukoglu, Olivier Clatz, Pierre-Yves Bondiau, Hervé Delingette, and Nicholas Ayache. Extrapolating Tumor Invasion Margins for Physiologically Determined Radiotherapy Regions. In Proc. of the 9th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI'06), Part I, number 4190 of LNCS, pages 338-346, 2-4 October 2006. Keyword(s): Tumor growth modeling, Glioma, brain tumors, radiotherapy, hamilton jacobi, DT-MRI, DTI, Diffusion Tensor, fisher kolmogorov, F-KPP.
    @inproceedings{Konukoglu:MICCAI:06,
    author = {Ender Konukoglu and Olivier Clatz and Pierre-Yves Bondiau and Herv\'e Delingette and Nicholas Ayache},
    booktitle = {Proc. of the 9th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI'06), Part I},
    keywords = {Tumor growth modeling, Glioma, brain tumors, radiotherapy, hamilton jacobi, DT-MRI, DTI, Diffusion Tensor, fisher kolmogorov, F-KPP},
    month = {2-4 October},
    number = {4190},
    pages = {338--346},
    series = {LNCS},
    title = {Extrapolating Tumor Invasion Margins for Physiologically Determined Radiotherapy Regions},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Ender.Konukoglu/41900338.pdf},
    url-hal = {https://hal.inria.fr/inria-00615595},
    year = {2006} 
    }
    


  26. M.G. Linguraru and R.D. Howe. Texture-based Segmentation of Instruments in 3D Ultrasound. In E.L. Siegel, E. Krupinski, and M. Sonka, editors, SPIE Medical Imaging '06, 2006. SPIE Publishing.
    @inproceedings{Linguraru:SPIE:06,
    author = {M.G. Linguraru and R.D. Howe},
    booktitle = {SPIE Medical Imaging '06},
    editor = {E.L. Siegel and E. Krupinski and M. Sonka},
    publisher = {SPIE Publishing},
    title = {Texture-based Segmentation of Instruments in 3D Ultrasound},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Linguraru/Linguraru_SPIE_2006.pdf},
    year = {2006} 
    }
    


  27. M.G. Linguraru, N.V. Vasilyev, P.J. del Nido, and R.D. Howe. Atrial Septal Defect Tracking in 3D Cardiac Ultrasound. In R. Larsen, M. Nielsen, and M. Sporring, editors, Medical Image Computing and Computer-Assisted Intervention - MICCAI'06, volume 4190 of LNCS, pages 596-603, 2006. Springer.
    @inproceedings{Linguraru:MICCAI:2006,
    author = {M.G. Linguraru and N.V. Vasilyev and del Nido, P.J. and R.D. Howe},
    booktitle = {Medical Image Computing and Computer-Assisted Intervention - MICCAI'06},
    editor = {R. Larsen and M. Nielsen and M. Sporring},
    pages = {596-603},
    publisher = {Springer},
    series = {LNCS},
    title = {Atrial Septal Defect Tracking in 3D Cardiac Ultrasound},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Linguraru/Linguraru_MICCAI_2006.pdf},
    volume = {4190},
    year = {2006} 
    }
    


  28. Johan Montagnat, Tristan Glatard, and Diane Lingrand. Data composition patterns in service-based workflows. In Workshop on Workflows in Support of Large-Scale Science (WORKS'06), Paris, France, June 2006.
    @inproceedings{Montagnat:WORKS:06,
    address = {Paris, France},
    author = {Johan Montagnat and Tristan Glatard and Diane Lingrand},
    booktitle = {Workshop on Workflows in Support of Large-Scale Science (WORKS'06)},
    month = {June},
    title = {Data composition patterns in service-based workflows},
    url = {http://www.i3s.unice.fr/~johan/publis/WORKS06.pdf},
    url-hal = {https://hal.archives-ouvertes.fr/hal-00683193},
    year = {2006} 
    }
    


  29. Xavier Pennec. Left-Invariant Riemannian Elasticity: a distance on shape diffeomorphisms ?. In Xavier Pennec and Sarang Joshi, editors, 1st MICCAI Workshop on Mathematical Foundations of Computational Anatomy: Geometrical, Statistical and Registration Methods for Modeling Biological Shape Variability, Copenhagen, Danemark, pages 1-13, October 2006.
    Abstract:
    In inter-subject registration, one often lacks a good model of the transformation variability to choose the optimal regularization. Some works attempt to model the variability in a statistical way, but the re-introduction in a registration algorithm is not easy. In [1], we interpreted the elastic energy as the distance of the Green-St Venant strain tensor to the identity. By changing the Euclidean metric for a more suitable Riemannian one, we defined a consistent statistical framework to quantify the amount of deformation. In particular, the mean and the covariance matrix of the strain tensor could be efficiently computed from a population of non-linear transformations and introduced as parameters in a Mahalanobis distance to measure the statistical deviation from the observed variability. This statistical Riemannian elasticity was able to handle anisotropic deformations but its isotropic stationary version was locally inverse-consistent. In this paper, we investigate how to modify the Riemannian elasticity to make it globally inverse consistent. This allows to define a left-invariant "distance" between shape diffeomorphisms that we call the left-invariant Riemannian elasticity. Such a closed form energy on diffeomorphisms can optimize it directly without relying on a time and memory consuming numerical optimization of the geodesic path.

    @inproceedings{Pennec:MFCA:06,
    abstract = {{In inter-subject registration, one often lacks a good model of the transformation variability to choose the optimal regularization. Some works attempt to model the variability in a statistical way, but the re-introduction in a registration algorithm is not easy. In [1], we interpreted the elastic energy as the distance of the Green-St Venant strain tensor to the identity. By changing the Euclidean metric for a more suitable Riemannian one, we defined a consistent statistical framework to quantify the amount of deformation. In particular, the mean and the covariance matrix of the strain tensor could be efficiently computed from a population of non-linear transformations and introduced as parameters in a Mahalanobis distance to measure the statistical deviation from the observed variability. This statistical Riemannian elasticity was able to handle anisotropic deformations but its isotropic stationary version was locally inverse-consistent. In this paper, we investigate how to modify the Riemannian elasticity to make it globally inverse consistent. This allows to define a left-invariant "distance" between shape diffeomorphisms that we call the left-invariant Riemannian elasticity. Such a closed form energy on diffeomorphisms can optimize it directly without relying on a time and memory consuming numerical optimization of the geodesic path.}},
    address = {Copenhagen, Danemark},
    affiliation = {ASCLEPIOS - INRIA Sophia Antipolis},
    audience = {internationale },
    author = {Pennec, Xavier},
    booktitle = {{1st MICCAI Workshop on Mathematical Foundations of Computational Anatomy: Geometrical, Statistical and Registration Methods for Modeling Biological Shape Variability}},
    collaboration = {Session 01 : Statistics on diffeomorphisms },
    editor = {Xavier Pennec and Sarang Joshi },
    hal_id = {inria-00634098},
    language = {Anglais},
    month = {October},
    pages = {1-13},
    pdf = {http://hal.inria.fr/inria-00634098/PDF/Pennec\_MFCA06.pdf},
    title = {{Left-Invariant Riemannian Elasticity: a distance on shape diffeomorphisms ?}},
    url-hal = {http://hal.inria.fr/inria-00634098},
    year = {2006} 
    }
    


  30. Jean-Marc Peyrat, Maxime Sermesant, Hervé Delingette, Xavier Pennec, Chenyang Xu, Elliot McVeigh, and Nicholas Ayache. Towards a Statistical Atlas of Cardiac Fiber Structure. In Proc. of the 9th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI'06), Part I, volume 4190 of LNCS, pages 297-304, 2-4 October 2006. Springer. Keyword(s): DT-MRI, DTI, Diffusion Tensor, Log-Euclidean, Cardiac Fiber, Heart, Myocardium, Atlas.
    @inproceedings{Peyrat:MICCAI:06,
    author = {Jean-Marc Peyrat and Maxime Sermesant and Herv\'e Delingette and Xavier Pennec and Chenyang Xu and Elliot McVeigh and Nicholas Ayache},
    booktitle = {Proc. of the 9th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI'06), Part I},
    doi = {10.1007/11866565_37},
    keywords = {DT-MRI, DTI, Diffusion Tensor, Log-Euclidean, Cardiac Fiber, Heart, Myocardium, Atlas},
    month = {2-4 October},
    pages = {297--304},
    pmid = {17354903},
    publisher = {Springer},
    series = {LNCS},
    title = {Towards a Statistical Atlas of Cardiac Fiber Structure},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Peyrat/Peyrat_MICCAI_2006.pdf},
    url-hal = {https://hal.inria.fr/inria-00615596},
    volume = {4190},
    year = {2006} 
    }
    


  31. Mihaela Pop, Maxime Sermesant, Yves Coudière, J. Graham, M. Bronskill, A. Dick, and Graham Wright. A theoretical model of ventricular reentry and its radiofrequency ablation therapy. In 3rd IEEE International Symposium on Biomedical Imaging: Macro to Nano (ISBI'06), pages 33-36, 2006.
    @inproceedings{Pop:ISBI:06,
    author = {Mihaela Pop and Maxime Sermesant and Yves Coudi\`ere and J. Graham and M. Bronskill and A. Dick and Graham Wright},
    booktitle = {3rd IEEE International Symposium on Biomedical Imaging: Macro to Nano (ISBI'06)},
    pages = {33-36},
    title = {A theoretical model of ventricular reentry and its radiofrequency ablation therapy},
    url-hal = {https://hal.inria.fr/inria-00615583},
    year = {2006} 
    }
    


  32. Mihaela Pop, Maxime Sermesant, Alexander Dick, John Graham, Yves Coudière, and Graham Wright. Aid of Computer Modelling to Identify Ventricular Reentries due to Infarct Scars. In 15th World Congress in Cardiac Electrophysiology and Cardiac Techniques (Cardiostim'06), 2006.
    @inproceedings{Pop:Cardiostim:06a,
    author = {Mihaela Pop and Maxime Sermesant and Alexander Dick and John Graham and Yves Coudi\`ere and Graham Wright},
    booktitle = {15th World Congress in Cardiac Electrophysiology and Cardiac Techniques (Cardiostim'06)},
    title = {Aid of Computer Modelling to Identify Ventricular Reentries due to Infarct Scars},
    url-hal = {https://hal.inria.fr/inria-00615581},
    year = {2006} 
    }
    


  33. Mihaela Pop, Maxime Sermesant, Alexander Dick, John Graham, Yves Coudière, and Graham Wright. Assessment of Radio-frequency Ablation of Ventricular Arrhythmias Via Magnetic Resonance Imaging and Computer Modelling. In 15th World Congress in Cardiac Electrophysiology and Cardiac Techniques (Cardiostim'06), 2006.
    @inproceedings{Pop:Cardiostim:06b,
    author = {Mihaela Pop and Maxime Sermesant and Alexander Dick and John Graham and Yves Coudi\`ere and Graham Wright},
    booktitle = {15th World Congress in Cardiac Electrophysiology and Cardiac Techniques (Cardiostim'06)},
    title = {Assessment of Radio-frequency Ablation of Ventricular Arrhythmias Via Magnetic Resonance Imaging and Computer Modelling},
    url-hal = {https://hal.inria.fr/inria-00615582},
    year = {2006} 
    }
    


Internal reports

  1. Vincent Arsigny, Olivier Commowick, Xavier Pennec, and Nicholas Ayache. A Fast and Log-Euclidean Polyaffine Framework for Locally Affine Registration. Research report RR-5865, INRIA Sophia-Antipolis, March 2006. Keyword(s): Polyaffine transformations, Diffeomorphisms, Non-rigid registration, Multi-affine registration, Lie groups, Log-Euclidean metrics, Magnetic Resonance Imaging.
    @techreport{Arsigny:RRPolyaffine:06,
    author = {Vincent Arsigny and Olivier Commowick and Xavier Pennec and Nicholas Ayache},
    hal-identifiant = {inria-00070161},
    institution = {INRIA Sophia-Antipolis},
    keywords = {Polyaffine transformations, Diffeomorphisms, Non-rigid registration, Multi-affine registration, Lie groups, Log-Euclidean metrics, Magnetic Resonance Imaging},
    month = {March},
    number = {RR-5865},
    title = {A Fast and Log-{Euclidean} Polyaffine Framework for Locally Affine Registration},
    type = {Research report},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Arsigny/arsigny_rr_polyaffine.pdf},
    url-hal = {https://hal.inria.fr/inria-00070161},
    url-publisher = {http://www.inria.fr/rrrt/rr-5865.html},
    year = {2006} 
    }
    


  2. Vincent Arsigny, Xavier Pennec, and Nicholas Ayache. Bi-invariant Means in Lie Groups. Application to Left-invariant Polyaffine Transformations. Research report RR-5885, INRIA Sophia-Antipolis, April 2006. Keyword(s): Bi-invariant means, Fréchet means, Statistics, Lie groups, Riemannian geometry, Polyaffine transformations, Diffeomorphisms.
    @techreport{Arsigny:RRBiinvariantMean:06,
    author = {Vincent Arsigny and Xavier Pennec and Nicholas Ayache},
    hal-identifiant = {inria-00071383},
    institution = {INRIA Sophia-Antipolis},
    keywords = {Bi-invariant means, Fr\'echet means, Statistics, Lie groups, Riemannian geometry, Polyaffine transformations, Diffeomorphisms},
    month = {April},
    number = {RR-5885},
    title = {Bi-invariant Means in {L}ie Groups. Application to Left-invariant Polyaffine Transformations},
    type = {Research report},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Arsigny/arsigny_rr_biinvariant_mean.pdf},
    url-hal = {http://hal.inria.fr/inria-00071383/en/},
    year = {2006} 
    }
    


  3. 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. Research report RR-5887, INRIA, April 2006.
    @techreport{Fillard:RR:06,
    author = {Pierre Fillard and Vincent Arsigny and Xavier Pennec and Kiralee M. Hayashi and Paul M. Thompson and Nicholas Ayache},
    hal-identifiant = {inria-00071381},
    institution = {INRIA},
    month = {April},
    number = {RR-5887},
    title = {Measuring Brain Variability by Extrapolating Sparse Tensor Fields Measured on Sulcal Lines},
    type = {Research report},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Fillard/Fillard.RR.06.pdf},
    url-hal = {https://hal.inria.fr/inria-00071381},
    url-publisher = {http://www.inria.fr/rrrt/rr-5887.html},
    year = {2006} 
    }
    


  4. Tristan Glatard, Johan Montagnat, and Xavier Pennec. Optimizing jobs timeouts on clusters and production grids. Technical report I3S/RR-2006-35-FR, I3S, 2006.
    @techreport{Glatard:RRTimeout:06,
    author = {Tristan Glatard and Johan Montagnat and Xavier Pennec},
    institution = {I3S},
    number = {I3S/RR-2006-35-FR},
    title = {Optimizing jobs timeouts on clusters and production grids},
    url = {http://www.i3s.unice.fr/~mh/RR/2006/RR-06.35-T.GLATARD.pdf},
    url-hal = {https://hal.archives-ouvertes.fr/hal-00683172},
    year = {2006} 
    }
    


  5. Tristan Glatard, Johan Montagnat, Xavier Pennec, David Emsellem, and Diane Lingrand. MOTEUR: a data-intensive service-based workflow manager. Technical report I3S/RR-2006-07-FR, I3S RAINBOW team, Univ. Nice-Sophia-Antipolis, March 2006.
    @techreport{Glatard:RRMoteur:06,
    author = {Tristan Glatard and Johan Montagnat and Xavier Pennec and David Emsellem and Diane Lingrand},
    institution = {I3S RAINBOW team, Univ. Nice-Sophia-Antipolis},
    month = {March},
    number = {I3S/RR-2006-07-FR},
    title = {MOTEUR: a data-intensive service-based workflow manager},
    url = {http://www.i3s.unice.fr/~mh/RR/2006/RR-06.07-T.GLATARMoteurD.pdf},
    year = {2006} 
    }
    


  6. Martin Huber, Xavier Pennec, Alessandro Verri, Harry Dimitropoulos, Maxime Sermesant, Cristian Mircean, Sonja Zilner, Homer Metaxas, Michael Lynch, Ender Konukoglu, Maria-Luisa Garre, Anna Charisi, Curzio Basso, and Elise Arnaud. State of the art report on disease models, decision support systems and knwoledge discovery for pediatric oncology, cardiology and rheumatology. Deliverables 11.1, 12.1, 13.1, European project Health-e-Child (IST-2004-027749), June 2006.
    @techreport{Health-e-Child:A6:06,
    author = {Martin Huber and Xavier Pennec and Alessandro Verri and Harry Dimitropoulos and Maxime Sermesant and Cristian Mircean and Sonja Zilner and Homer Metaxas and Michael Lynch and Ender Konukoglu and Maria-Luisa Garre and Anna Charisi and Curzio Basso and Elise Arnaud},
    institution = {European project Health-e-Child (IST-2004-027749)},
    month = {June},
    title = {State of the art report on disease models, decision support systems and knwoledge discovery for pediatric oncology, cardiology and rheumatology},
    type = {Deliverables 11.1, 12.1, 13.1},
    year = {2006} 
    }
    


  7. Jean-Marc Peyrat, Maxime Sermesant, Hervé Delingette, Xavier Pennec, Chenyang Xu, Elliot McVeigh, and Nicholas Ayache. Towards a Statistical Atlas of Cardiac Fiber Architecture. Research report RR-5906, INRIA, May 2006. Keyword(s): DT-MRI, DTI, Diffusion Tensor, Log-Euclidean, Cardiac Fiber, Heart, Myocardium, Atlas.
    @techreport{Peyrat:RR:06,
    author = {Jean-Marc Peyrat and Maxime Sermesant and Herv\'e Delingette and Xavier Pennec and Chenyang Xu and Elliot McVeigh and Nicholas Ayache},
    hal-identifiant = {inria-00071359},
    institution = {INRIA},
    keywords = {DT-MRI, DTI, Diffusion Tensor, Log-Euclidean, Cardiac Fiber, Heart, Myocardium, Atlas},
    month = {May},
    number = {RR-5906},
    postscript = {ftp://ftp.inria.fr/INRIA/publication/publi-ps-gz/RR/RR-5906.ps.gz},
    title = {Towards a Statistical Atlas of Cardiac Fiber Architecture},
    type = {Research report},
    url = {ftp://ftp.inria.fr/INRIA/publication/publi-pdf/RR/RR-5906.pdf},
    url-hal = {https://hal.inria.fr/inria-00071359},
    url-publisher = {http://www.inria.fr/rrrt/rr-5906.html},
    year = {2006} 
    }
    


Patents, standards

  1. Vincent Arsigny, Xavier Pennec, Pierre Fillard, and Nicholas Ayache. Device for processing raw images or tensor images. US patent US 2008/0170802 (filed 07.04.2006, published 17.07.2008, July 2006.
    @patent{Arsigny:Patent:US:06,
    address = {},
    author = {Vincent Arsigny and Xavier Pennec and Pierre Fillard and Nicholas Ayache},
    month = {July},
    note = {},
    number = {US patent US 2008/0170802 (filed 07.04.2006, published 17.07.2008},
    optabstract = {},
    optdoi = {},
    opthal-date-depot = {},
    opthal-identifiant = {},
    opthal-version = {},
    optisbn = {},
    optissn = {},
    optkeywords = {},
    opturl = {},
    opturl-publisher = {},
    optx-scientific-popularization = {},
    title = {Device for processing raw images or tensor images},
    url-hal = {https://hal.inria.fr/hal-00875690},
    x-language = {},
    x-pays = {},
    year = {2006} 
    }
    


Miscellaneous

  1. Romain Vauchelles. Mise en place d'un programme d'analyse d'images en wound healing et mise en évidence du rôle de l'activation de Arf 1 par le GEF ARNO dans la migration cellulaire. Master's thesis, Master Imagerie pour la Biologie, Université de Rouen, 2006.
    @mastersthesis{vauchelles:master:2006,
    author = {Romain Vauchelles},
    school = {Master Imagerie pour la Biologie, Universit\'e de Rouen},
    title = {Mise en place d'un programme d'analyse d'images en wound healing et mise en \'evidence du r\^ole de l'activation de Arf 1 par le GEF ARNO dans la migration cellulaire},
    type = {Master's thesis},
    year = {2006} 
    }
    


  2. Nicholas Ayache, Jean-Pierre Boissel, Soren Brunak, Gordon Clapworthy, Guy Lonsdale, Jochen Fingberg, Alejandro Frangi, Gustavo Deco, Peter Hunter, Poul Nielsen, Matt Halstead, Rod Hose, Isabelle Magnin, Fernando Martin-Sanchez, Peter Sloot, Jaap Kaandorp, Alfons Hoekstra, Serge Van Sint Jan, and Marco Viceconti. Towards Virtual Physiological Human: Multilevel Modelling and Simulation of the Human Anatomy and Physiology. Virtual Physiological Human: White paper, EC - DG INFSO and DG JRC, 2006.
    @misc{VPH:2006,
    author = {Nicholas Ayache and Jean-Pierre Boissel and Soren Brunak and Gordon Clapworthy and Guy Lonsdale and Jochen Fingberg and Alejandro Frangi and Gustavo Deco and Peter Hunter and Poul Nielsen and Matt Halstead and Rod Hose and Isabelle Magnin and Fernando Martin-Sanchez and Peter Sloot and Jaap Kaandorp and Alfons Hoekstra and Van Sint Jan, Serge and Marco Viceconti},
    howpublished = {Virtual Physiological Human: White paper, EC - DG INFSO and DG JRC},
    title = {Towards Virtual Physiological Human: Multilevel Modelling and Simulation of the Human Anatomy and Physiology},
    url = {http://europa.eu.int/information_society/activities/health/docs/events/barcelona2005/ec-vph-white-paper2005nov.pdf},
    year = {2006} 
    }
    


  3. N. Bernasconi, P. Besson, T. Mansi, and A. Bernasconi. MRI Texture Analysis Enhances the Visibility of Cortical Tubers in Tuberous Sclerosis. Annual Meeting of the American Epilepsy Society AES 2006 (abstracts), 2006.
    @misc{bernasconi06:AES,
    author = {N. Bernasconi and P. Besson and T. Mansi and A. Bernasconi},
    howpublished = {Annual Meeting of the American Epilepsy Society AES 2006 (abstracts)},
    title = {MRI Texture Analysis Enhances the Visibility of Cortical Tubers in Tuberous Sclerosis},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Tommaso.Mansi/bernasconi06AES.pdf},
    year = {2006} 
    }
    


  4. Pierre Fillard, Nicolas Toussaint, and Xavier Pennec. MedINRIA: DT-MRI Processing and Visualization Software, November 2006. Note: Guest paper at the Similar Tensor Workshop, Las Palmas, Spain.
    @misc{Fillard:TensorWorkshop:06,
    author = {Pierre Fillard and Nicolas Toussaint and Xavier Pennec},
    month = {November},
    note = {Guest paper at the Similar Tensor Workshop, Las Palmas, Spain.},
    title = {{MedINRIA: DT-MRI} Processing and Visualization Software},
    url = {http://www.inria.fr/sophia/asclepios/Publications/Pierre.Fillard/Fillard.TensorWorkshop.06.pdf},
    year = {2006} 
    }
    


  5. Aurélie Isambert, Guillaume Bonniaud, R. Lery, R. Comtat, Jean-Christophe Diaz, Grégoire Malandain, and Dimitri Lefkopoulos. Evaluation sur fantôme d'un logiciel de recalage d'images multimodales automatique pour la radiothérapie. 17e Congrès de la Société Française de Radiothérapie Oncologique (SFRO), November 2006. Note: Cancer radiothérapie 10(6-7):507, 2006.
    @misc{isambert:sfro:2006,
    author = {Aur\'elie Isambert and Guillaume Bonniaud and R. Lery and R. Comtat and Jean-Christophe Diaz and Gr\'egoire Malandain and Dimitri Lefkopoulos},
    howpublished = {17e Congr\`es de la Soci\'et\'e Fran\c{c}aise de Radioth\'erapie Oncologique (SFRO)},
    month = {November},
    note = {Cancer radioth\'erapie 10(6-7):507, 2006},
    title = {Evaluation sur fant\^ome d'un logiciel de recalage d'images multimodales automatique pour la radioth\'erapie},
    year = {2006} 
    }
    


  6. Aurélie Isambert, Frédéric Dhermain, F. Bidault, Guillaume Bonniaud, R. Lery, Grégoire Malandain, Olivier Commowick, Jean-Christophe Diaz, Jean Bourhis, and Dimitri Lefkopoulos. Evaluation of Multimodality Image Registration Software and Atlas-based Automatic Segmentation for Delineation of Organs at Risk (OAR) in the Brain in Conformal Radiotherapy (CRT). 48th Annual Meeting of the American Society for Therapeutic Radiology and Oncology (ASTRO), November 2006. Keyword(s): Multimodality image registration, atlas-based automatic segmentation, radiation therapy.
    @misc{isambert:astro:2006,
    address = {Philadelphia, Pennsylvania},
    author = {Aur\'elie Isambert and Fr\'ed\'eric Dhermain and F. Bidault and Guillaume Bonniaud and R. Lery and Gr\'egoire Malandain and Olivier Commowick and Jean-Christophe Diaz and Jean Bourhis and Dimitri Lefkopoulos},
    howpublished = {48th Annual Meeting of the American Society for Therapeutic Radiology and Oncology (ASTRO)},
    keywords = {Multimodality image registration, atlas-based automatic segmentation, radiation therapy},
    month = {November},
    title = {Evaluation of Multimodality Image Registration Software and Atlas-based Automatic Segmentation for Delineation of Organs at Risk (OAR) in the Brain in Conformal Radiotherapy (CRT)},
    year = {2006} 
    }
    


  7. Aurélie Isambert, Frédéric Dhermain, Guillaume Bonniaud, F. Bidault, A. Beaudre, Grégoire Malandain, Olivier Commowick, Jean-Christophe Diaz, M. Ricard, Jean Bourhis, and Dimitri Lefkopoulos. Evaluation d'un logiciel de recalage d'images multimodal et d'un outil de segmentation automatique des organes à risque (OAR) intra-crâniens en situation clinique d'une radiothérapie conformationnelle 3D (RTC3D). Congrès annuel de la Société Française des Physiciens Médicaux (SFPM), June 2006.
    @misc{isambert:sfpm:2006,
    author = {Aur\'elie Isambert and Fr\'ed\'eric Dhermain and Guillaume Bonniaud and F. Bidault and A. Beaudre and Gr\'egoire Malandain and Olivier Commowick and Jean-Christophe Diaz and M. Ricard and Jean Bourhis and Dimitri Lefkopoulos},
    howpublished = {Congr\`es annuel de la Soci\'et\'e Fran\c{c}aise des Physiciens M\'edicaux (SFPM)},
    month = {June},
    title = {Evaluation d'un logiciel de recalage d'images multimodal et d'un outil de segmentation automatique des organes \`a risque (OAR) intra-cr\^aniens en situation clinique d'une radioth\'erapie conformationnelle 3D (RTC3D)},
    year = {2006} 
    }
    


  8. Ender Konukoglu, Olivier Clatz, Pierre-Yves Bondiau, Hervé Delingette, and Nicholas Ayache. Extrapolating tumor invasion margins for physiologically determined radiotherapy regions. Presented in DIMACS Workshop: Computational Tumor Modeling, 2006.
    @misc{Konukoglu:DIMACS:2006,
    author = {Ender Konukoglu and Olivier Clatz and Pierre-Yves Bondiau and Herv\'e Delingette and Nicholas Ayache},
    howpublished = {Presented in DIMACS Workshop: Computational Tumor Modeling},
    title = {Extrapolating tumor invasion margins for physiologically determined radiotherapy regions},
    year = {2006} 
    }
    


  9. Xavier Pennec. A European paediatric platform. INédit 56, p.4, November 2006.
    @misc{Pennec:Inedit:06,
    author = {Xavier Pennec},
    howpublished = {IN\'edit 56, p.4},
    month = {November},
    title = {A European paediatric platform},
    url-obsolete = {http://www.inria.fr/actualites/inedit/pdf/inedit56.en.pdf},
    url-publisher = {http://www.inria.fr/actualites/inedit/inedit56_indusa.en.html},
    year = {2006} 
    }
    


  10. Aymeric Perchant, Tom Vercauteren, Charlotte Cavé, and Sacha Loiseau. Mosaicing of Confocal Microscopic In Vivo Soft Tissue Video Sequences Improves Multimodality Approach. Proc. Radiological Society of North America (RSNA'06), December 2006. Note: Abstract only.
    @misc{Vercauteren:RSNA:06,
    address = {Chicago, Illinois},
    author = {Aymeric Perchant and Tom Vercauteren and Charlotte Cav\'e and Sacha Loiseau},
    howpublished = {Proc. Radiological Society of North America (RSNA'06)},
    month = {December},
    note = {Abstract only},
    title = {Mosaicing of Confocal Microscopic In Vivo Soft Tissue Video Sequences Improves Multimodality Approach},
    year = {2006} 
    }
    



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