Publications of Hadrien Courtecuisse

Publications HAL de courtecuisse de la structure shacra;mimesis

2017

Journal articles

titre
Real-time Error Control for Surgical Simulation
auteur
Huu Phuoc Bui, Satyendra Tomar, Hadrien Courtecuisse, Stéphane Cotin, Stéphane Bordas
article
IEEE Transactions on Biomedical Engineering, Institute of Electrical and Electronics Engineers, 2017, pp.12
resume
Objective: To present the first real-time a poste-riori error-driven adaptive finite element approach for real-time simulation and to demonstrate the method on a needle insertion problem. Methods: We use corotational elasticity and a frictional needle/tissue interaction model. The problem is solved using finite elements within SOFA 1. The refinement strategy relies upon a hexahedron-based finite element method, combined with a posteriori error estimation driven local h-refinement, for simulating soft tissue deformation. Results: We control the local and global error level in the mechanical fields (e.g. displacement or stresses) during the simulation. We show the convergence of the algorithm on academic examples, and demonstrate its practical usability on a percutaneous procedure involving needle insertion in a liver. For the latter case, we compare the force displacement curves obtained from the proposed adaptive algorithm with that obtained from a uniform refinement approach. Conclusions: Error control guarantees that a tolerable error level is not exceeded during the simulations. Local mesh refinement accelerates simulations. Significance: Our work provides a first step to discriminate between discretization error and modeling error by providing a robust quantification of discretization error during simulations. Index Terms—Finite element method, real-time error estimate, adaptive refinement, constraint-based interaction.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01514621/file/TBME_2017_error_controlled_refinement_final.pdf BibTex
titre
Brain-shift compensation using intraoperative ultrasound and constraint-based biomechanical simulation
auteur
Fanny Morin, Hadrien Courtecuisse, Ingerid Reinertsen, Florian Le Lann, Olivier Palombi, Yohan Payan, Matthieu Chabanas
article
Medical Image Analysis, Elsevier, 2017, 40, pp.133 – 153. <10.1016/j.media.2017.06.003>
resume
Purpose. During brain tumor surgery, planning and guidance are based on pre-operative images which do not account for brain-shift. However, this deformation is a major source of error in image-guided neurosurgery and affects the accuracy of the procedure. In this paper, we present a constraint-based biome-chanical simulation method to compensate for craniotomy-induced brain-shift that integrates the deformations of the blood vessels and cortical surface, using a single intraoperative ultrasound acquisition. Methods. Prior to surgery, a patient-specific biomechanical model is built from preoperative images, accounting for the vascular tree in the tumor region and brain soft tissues. Intraoperatively, a navigated ultrasound acquisition is performed directly in contact with the organ. Doppler and B-mode images are recorded simultaneously, enabling the extraction of the blood vessels and probe footprint respectively. A constraint-based simulation is then executed to register the pre-and intraoperative vascular trees as well as the cortical surface with the probe footprint. Finally, preoperative images are updated to provide the surgeon with images corresponding to the current brain shape for navigation. Results. The robustness of our method is first assessed using sparse and noisy synthetic data. In addition, quantitative results for five clinical cases are provided , first using landmarks set on blood vessels, then based on anatomical structures delineated in medical images. The average distances between paired vessels landmarks ranged from 3.51 to 7.32 (in mm) before compensation. With our method, on average 67% of the brain-shift is corrected (range [1.26; 2.33]) against 57% using one of the closest existing works (range [1.71; 2.84]). Finally, our method is proven to be fully compatible with a surgical workflow in terms of execution times and user interactions. Conclusion. In this paper, a new constraint-based biomechanical simulation method is proposed to compensate for craniotomy-induced brain-shift. While being efficient to correct this deformation, the method is fully integrable in a clinical process.
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01560157/file/MEDIMA_1264.pdf BibTex

Conference papers

titre
Real-time Error Control for Surgical Simulation
auteur
Huu Phuoc Bui, Satyendra Tomar, Hadrien Courtecuisse, Stéphane Cotin, Stéphane Bordas
article
BIOMECHANICS AND COMPUTER ASSISTED SURGERY MEETS MEDICAL REALITY, Aug 2017, Lille, France. 2017, <http://595.euromech.org/>
resume
Real-time simulations are becoming increasingly common for various applications, from geometric design to medical simulation. Two of the main factors concurrently involved in defining the accuracy of surgical simulations are: the modeling error and the discretization error. Most work in the area has been looking at the above sources of error as a compounded, lumped, overall error. Little or no work has been done to discriminate between modeling error (e.g. needle-tissue interaction, choice of constitutive models) and discretization error (use of approximation methods like FEM). However, it is impossible to validate the complete surgical simulation approach and, more importantly, to understand the sources of error, without evaluating both the discretization error and the modeling error. Our objective is thus to devise a robust and fast approach to measure the discretization error via a posteriori error estimates, which are then used for local remeshing in surgical simulations. To ensure that the approach can be used in clinical practice, the method should be robust enough to deal, as realistically as possible, with the interaction of surgical tools with the organ, and fast enough for real-time simulations. The approach should also lead to an improved convergence so that an economical mesh is obtained at each time step. The final goal is to achieve optimal convergence and the most economical mesh, which will be studied in our future work.
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01571194/file/euromech595_2017_Bui_et_al.pdf BibTex

2016

Conference papers

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titre
Inverse real-time Finite Element simulation for robotic control of flexible needle insertion in deformable tissues
auteur
Yinoussa Adagolodjo, Laurent Goffin, Michel De Mathelin, Hadrien Courtecuisse
article
IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2016) , Oct 2016, Daejeon, South Korea. <http://www.iros2016.org/>
resume
This paper introduces a new method for automatic robotic needle steering in deformable tissues. The main contribution relies on the use of an inverse Finite Element (FE) simulation to control an articulated robot interacting with deformable structures. In this work we consider a flexible needle, embedded in the end effector of a 6 arm Mitsubishi RV1A robot, and its insertion into a silicone phantom. Given a trajectory on the rest configuration of the silicone phantom, our method provides in real-time the displacements of the articulated robot which guarantee the permanence of the needle within the predefined path, taking into account any undergoing deformation on both the needle and the trajectory itself. A forward simulation combines i) a kinematic model of the robot, ii) FE models of the needle and phantom gel iii) an interaction model allowing the simulation of friction and puncture force. A Newton-type method is then used to provide the displacement of the robot to minimize the distance between the needle’s tip and the desired trajectory. We validate our approach with a simulation in which a virtual robot can successfully perform the insertion while both the needle and the trajectory undergo significant deformations.
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01353925/file/iros2016.pdf BibTex
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titre
Vessel-based brain-shift compensation using elastic registration driven by a patient-specific finite element model
auteur
Fanny Morin, Ingerid Reinertsen, Hadrien Courtecuisse, Olivier Palombi, Bodil Munkvold, Hans Kristian Bø, Yohan Payan, Matthieu Chabanas
article
International Conference on Information Processing in Computer-Assisted Interventions (IPCAI), Jun 2016, Heidelberg, Germany
resume
During brain tumor surgery, planning and guidance are based on pre-operative images which do not account for brain-shift. However, this shift is a major source of error in neuro-navigation systems and affects the accuracy of the procedure. The vascular tree is extracted from pre-operative Magnetic Resonance Angiography and from intra-operative Doppler ultrasound images, which provides sparse information on brain deformations. The pre-operative images are then updated based on an elastic registration of the blood vessels, driven by a patient-specific biomechanical model. This biomechanical model is used to extrapolate the deformation to the surrounding soft tissues. Quantitative results on a single surgical case are provided, with an evaluation of the execution time for each processing step. Our method is proved to be efficient to compensate for brain deformation while being compatible with a surgical process.
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01331713/file/revised_paper_bis.pdf BibTex
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titre
3D Physics-Based Registration of 2D Dynamic MRI Data
auteur
Raffaella Trivisonne, Igor Peterlik, Stéphane Cotin, Hadrien Courtecuisse
article
MMVR – Medicine Meets Virtual Reality, Apr 2016, Los Angeles, United States. 2016
resume
We present a method allowing for intra-operative targeting of a specific anatomical feature. The method is based on a registration of 3D pre-operative data to 2D intra-operative images. Such registration is performed using an elastic model reconstructed from the 3D images, in combination with sliding constraints imposed via Lagrange multipliers. We register the pre-operative data, where the feature is clearly detectable, to intra-operative dynamic images where such feature is no more visible. Despite the lack of visibility on the 2D MRI images, we are able both to determine the location of the target as well as follow its displacement due to respiratory motion.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01254388/file/Trivisonne_R.pdf BibTex

2015

Journal articles

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titre
Rest shape computation for highly deformable model of brain.
auteur
Fanny Morin, Hadrien Courtecuisse, Matthieu Chabanas, Yohan Payan
article
Computer Methods in Biomechanics and Biomedical Engineering, London : Informa Healthcare, 2015, 18 Suppl 1, pp.2006-2007. <10.1080/10255842.2015.1070591>
resume
In medical simulations, finite element (FE) models are often extracted from medical images. This initial geometry usually corresponds to a state of the model at equilibrium between external and internal forces. Therefore, an important issue in biomechanics is to estimate the initial stress of FE model before running a simulation. this paper introduces a biomechanical model of the brain that will be used to model brain-shift during surgery. The initial stress is estimated for this model by taking into account gravity.
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https://hal.archives-ouvertes.fr/hal-01217673/file/CMBBE%202015%20Morin.pdf BibTex
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titre
Virtual Cutting of Deformable Objects based on Efficient Topological Operations
auteur
Christoph Paulus, Lionel Untereiner, Hadrien Courtecuisse, Stephane Cotin, David Cazier
article
Visual Computer, Springer Verlag, 2015, 31 (6-8), pp.831-841. <10.1007/s00371-015-1123-x>
resume
Virtual cutting of deformable objects is at the core of many applications in interactive simulation and especially in computational medicine. The ability to simulate surgical cuts, dissection, soft tissue tearing ormicro-fractures is essential for augmenting the capabilities of existing or future simulation systems. To support such features,we combine a new remeshing algorithm with a fast finite element approach. The proposed method is generic enough to support a large variety of applications. We show the benefits of our approach evaluating the impact of cuts on the number of nodes and the numerical quality of the mesh. These points are crucial to ensure accurate and stable real-time simulations.
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01162099/file/2015CGI.pdf BibTex

Conference papers

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titre
Haptic Rendering of Hyperelastic Models with Friction
auteur
Hadrien Courtecuisse, Yinoussa Adagolodjo, Hervé Delingette, Christian Duriez
article
2015 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), Sep 2015, Hamburg, Germany. IEEE, pp.591-596, 2015, <10.1109/IROS.2015.7353432>
resume
— This paper presents an original method for inter-actions’ haptic rendering when treating hyperelastic materials. Such simulations are known to be difficult due to the non-linear behavior of hyperelastic bodies; furthermore, haptic constraints enjoin contact forces to be refreshed at least at 1000 updates per second. To enforce the stability of simulations of generic objects of any range of stiffness, this method relies on implicit time integration. Soft tissues dynamics is simulated in real time (20 to 100 Hz) using the Multiplicative Jacobian Energy Decomposition (MJED) method. An asynchronous preconditioner, updated at low rates (1 to 10 Hz), is used to obtain a close approximation of the mechanical coupling of interactions. Finally, the contact problem is linearized and, using a specific-loop, it is updated at typical haptic rates (around 1000 Hz) allowing this way new simulations of prompt stiff-contacts and providing a continuous haptic feedback as well.
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01184113/file/IROS15_1122_FI.pdf BibTex
titre
Virtual Cutting of Deformable Objects based on Efficient Topological Operations
auteur
Christoph Paulus, Lionel Untereiner, Hadrien Courtecuisse, Stéphane Cotin, David Cazier
article
Computer Graphics International, 2015, Strasbourg, France. 2015
resume
Virtual cutting of deformable objects is at the core of many applications in interactive simulation and especially in computational medicine. The ability to simulate surgical cuts, dissection, soft tissue tearing ormicro-fractures is essential for augmenting the capabilities of existing or future simulation systems. To support such features,we combine a new remeshing algorithm with a fast finite element approach. The proposed method is generic enough to support a large variety of applications. We show the benefits of our approach evaluating the impact of cuts on the number of nodes and the numerical quality of the mesh. These points are crucial to ensure accurate and stable real-time simulations.
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BibTex

2014

Journal articles

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titre
Real-time simulation of contact and cutting of heterogeneous soft-tissues
auteur
Hadrien Courtecuisse, Jeremie Allard, Pierre Kerfriden, Stephane Pierre-Alain Bordas, Stephane Cotin, Christian Duriez
article
Medical Image Analysis, Elsevier, 2014, 18 (2), pp.394-410. <10.1016/j.media.2013.11.001>
resume
This paper presents a numerical method for interactive (real-time) simulations, which considerably improves the accuracy of the response of heterogeneous soft-tissue models undergoing contact, cutting and other topological changes. We provide an integrated methodology able to deal both with the ill-conditioning issues associated with material heterogeneities, contact boundary conditions which are one of the main sources of inaccuracies, and cutting which is one of the most challenging issues in interactive simulations. Our approach is based on an implicit time integration of a non-linear finite element model. To enable real-time computations, we propose a new preconditioning technique, based on an asynchronous update at low frequency. The preconditioner is not only used to improve the computation of the deformation of the tissues, but also to simulate the contact response of homogeneous and heterogeneous bodies with the same accuracy. We also address the problem of cutting the heterogeneous structures and propose a method to update the preconditioner according to the topological modifications. Finally, we apply our approach to three challenging demonstrators: i) a simulation of cataract surgery ii) a simulation of laparoscopic hepatectomy iii) a brain tumor surgery.
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BibTex

Conference papers

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titre
Atlas-based Transfer of Boundary Conditions for Biomechanical Simulation
auteur
Rosalie Plantefeve, Igor Peterlik, Hadrien Courtecuisse, Raffaella Trivisonne, Jean-Pierre Radoux, Stéphane Cotin
article
MICCAI – 17th International Conference on Medical Image Computing and Computer Assisted Intervention, Sep 2014, Boston, United States. 2014
resume
An environment composed of different types of living tissues (such as the abdominal cavity) reveals a high complexity of boundary conditions, which are the attachments (e.g. connective tissues, ligaments) connecting different anatomical structures. Together with the material properties, the boundary conditions have a significant influence on the mechanical response of the organs, however corresponding correct me- chanical modeling remains a challenging task, as the connective struc- tures are difficult to identify in certain standard imaging modalities. In this paper, we present a method for automatic modeling of boundary con- ditions in deformable anatomical structures, which is an important step in patient-specific biomechanical simulations. The method is based on a statistical atlas which gathers data defining the connective structures at- tached to the organ of interest. In order to transfer the information stored in the atlas to a specific patient, the atlas is registered to the patient data using a physics-based technique and the resulting boundary conditions are defined according to the mean position and variance available in the atlas. The method is evaluated using abdominal scans of ten patients. The results show that the atlas provides a sufficient information about the boundary conditions which can be reliably transferred to a specific patient. The boundary conditions obtained by the atlas-based transfer show a good match both with actual segmented boundary conditions and in terms of mechanical response of deformable organs.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01070339/file/paper_1071.pdf BibTex
ipcai-peterlik.jpg
titre
Model-Based Identification of Anatomical Boundary Conditions in Living Tissues
auteur
Igor Peterlik, Hadrien Courtecuisse, Christian Duriez, Stéphane Cotin
article
Information Processing in Computer Assisted Interventions, Jun 2014, Fukuoka, Japan. 2014, <10.1007/978-3-319-07521-1_21>
resume
In this paper, we present a novel method dealing with the identification of boundary conditions of a deformable organ, a particularly important step for the creation of patient-specific biomechani-cal models of the anatomy. As an input, the method requires a set of scans acquired in different body positions. Using constraint-based finite element simulation, the method registers the two data sets by solving an optimization problem minimizing the energy of the deformable body while satisfying the constraints located on the surface of the registered organ. Once the equilibrium of the simulation is attained (i.e. the organ registration is computed), the surface forces needed to satisfy the constraints provide a reliable estimation of location, direction and magnitude of boundary conditions applied to the object in the deformed position. The method is evaluated on two abdominal CT scans of a pig acquired in flank and supine positions. We demonstrate that while computing a physically admissible registration of the liver, the resulting constraint forces applied to the surface of the liver strongly correlate with the location of the anatomical boundary conditions (such as contacts with bones and other organs) that are visually identified in the CT images.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01264434/file/Peterlik_PDFProof.pdf BibTex
titre
Haptic Rendering on Deformable Anatomical Tissues with Strong Heterogeneities
auteur
Guillaume Kazmitcheff, Hadrien Courtecuisse, Yann Nguyen, Mathieu Miroir, Alexis Bozorg-Grayeli, Stéphane Cotin, Olivier Sterkers, Christian Duriez
article
Eurohaptics 2014, Jun 2014, Versailles, France. Springer, 2014
resume
This paper is focus on the development of a haptic rendering method to simulate interactions with heterogeneous deformable materials, such as anatomical components. Indeed, the strong heterogeneities of the biological tissues involves numerical and real-time issues to simulate the deformations and the mechanical interactions between the organs and the surgical tools. In this paper, we propose a new haptic algorithm adapted to the modeling of heterogeneous biological tissues, based on non-linear finite element model. The central contribution is the use of a triple asynchronous approach: one loop at low rate, which computes a preconditionner that solves the numerical conditioning problems; a second at intermediate rate, to update the model of the biological simulation; and the haptic loop which provides the feedback to the user at high rate. Despite of the desynchronization, we show that the calculation of haptic forces remains accurate compared to the model. We apply our method to a challenging microsurgical intervention of the human middle ear. This surgery requires a delicate gesture in order to master the applied forces.
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titre
Constraint-Based Simulation for Non-Rigid Real-Time Registration
auteur
Hadrien Courtecuisse, Igor Peterlik, Raffaella Trivisonne, Christian Duriez, Stéphane Cotin
article
Medicine Meets Virtual Reality, Feb 2014, Manhattan Beach, California., United States. 2014
resume
In this paper we propose a method to address the problem of non-rigid registration in real-time. We use Lagrange multipliers and soft sliding constraints to combine data acquired from dynamic image sequence and a biomechanical model of the structure of interest. The biomechanical model plays a role of regulariza-tion to improve the robustness and the flexibility of the registration. We apply our method to a pre-operative 3D CT scan of a porcine liver that is registered to a sequence of 2D dynamic MRI slices during the respiratory motion. The finite element simulation provides a full 3D representation (including heterogeneities such as vessels, tumor,. . .) of the anatomical structure in real-time.
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https://hal.inria.fr/hal-01160739/file/MMVR14.pdf BibTex

2013

Journal articles

titre
Computer-based training system for cataract surgery
auteur
Jérémie Dequidt, Hadrien Courtecuisse, Olivier Comas, Jérémie Allard, Christian Duriez, Stéphane Cotin, Elodie Dumortier, Olivier Wavreille, Jean-Francois Rouland
article
Transactions of the Society for Modeling and Simulation International, SAGE, 2013, <http://is.gd/2Mihj1>. <10.1177/0037549713495753>
resume
This paper describes a single simulation framework to perform interactive cataract surgery simulations. Contributions includes advanced bio-mechanical models and intensive use of modern graphics hard- ware to provide fast computation times. Surgical de- vices are replicated and located in a real-time thanks to infra-red tracking. Combination of a high-fidelity simulation and actual surgical tools are able to im- prove surgeon immersion while training. Preliminary tests have been performed by experienced ophthal- mologists to qualitatively assess the face-validity of the simulator and the faithfulness of the behavior of the anatomical structures as well as the interactions with the surgical tools.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00855821/file/cataractChapter.pdf BibTex

2012

Conference papers

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titre
Towards Real-Time Computation of Cardiac Electrophysiology for Training Simulator
auteur
Hugo Talbot, Christian Duriez, Hadrien Courtecuisse, Jatin Relan, Maxime Sermesant, Stéphane Cotin, Hervé Delingette
article
Statistical Atlases and Computational Models of the Heart – STACOM 2012 in the 15th International Conference on Medical Image Computing and Computer Assisted Intervention – MICCAI 2012, Oct 2012, Nice, France. Springer, 2012, Lecture Notes in Computer Science
resume
This work aims at developing a training simulator for interventional radiology and thermo-ablation of cardiac arrhythmias. To achieve this, a real-time model of the cardiac electrophysiology is needed, which is very challenging due to the stiff equations involved. In this paper, we detail our contributions in order to obtain efficient cardiac electrophysiology simulations. First, an adaptive parametrisation of the Mitchell-Schaeffer model as well as numerical optimizations are proposed. An accurate computation of both conduction velocity and action potential is ensured, even with relatively coarse meshes. Second, a GPU implementation of the electrophysiology was realised in order to decrease the computation time. We evaluate our results by comparison with an accurate reference simulation using model parameters, personalized on patient data. We demonstrate that a fast simulation (close to real-time) can be obtained while keeping a precise description of the phenomena.
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https://hal.inria.fr/hal-00750835/file/SimulationOfCardiacAblation-STACOM2012.pdf BibTex
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titre
Interactive Electromechanical Model of the Heart for Patient-Specific Therapy Planning and Training using SOFA
auteur
Hugo Talbot, Stéphanie Marchesseau, Christian Duriez, Hadrien Courtecuisse, Jatin Relan, Maxime Sermesant, Stéphane Cotin, Hervé Delingette
article
VPH 2012, Sep 2012, Londres, United Kingdom. 2012
resume
The contributions of this work are twofold. First, we developed an electrophysiological training simulator in SOFA which tackles the interactive issue in the context of cardiac arrhythmias. Coupled with this electrophysiology, we developed a mechanical model of the heart that can be personalized from MRI datasets. Our simulations are based on the SOFA platform. SOFA is an open-source framework targeted at real-time simulation with an emphasis on medical simulation, mainly developed at Inria. A large choice of efficient solvers, hyperelastic or viscous material laws are already implemented in SOFA. Moreover, it enables interactivity during the simulation (pacing, surgery planning, …) and gives a good trade-off between accuracy and computational efficiency.
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https://hal.inria.fr/hal-00751537/file/VPH2012.pdf BibTex

Book sections

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titre
SOFA: A Multi-Model Framework for Interactive Physical Simulation
auteur
François Faure, Christian Duriez, Hervé Delingette, Jérémie Allard, Benjamin Gilles, Stéphanie Marchesseau, Hugo Talbot, Hadrien Courtecuisse, Guillaume Bousquet, Igor Peterlik, Stéphane Cotin
article
Yohan Payan. Soft Tissue Biomechanical Modeling for Computer Assisted Surgery, 11, Springer, pp.283-321, 2012, Studies in Mechanobiology, Tissue Engineering and Biomaterials, 978-3-642-29013-8. <10.1007/8415_2012_125>
resume
SOFA (Simulation Open Framework Architecture) is an open-source C++ library primarily targeted at interactive computational medical simulation. SOFA facilitates collaborations between specialists from various domains, by decomposing complex simulators into components designed independently and organized in a scenegraph data structure. Each component encapsulates one of the aspects of a simulation, such as the degrees of freedom, the forces and constraints, the differential equations, the main loop algorithms, the linear solvers, the collision detection algorithms or the interaction devices. The simulated objects can be represented using several models, each of them optimized for a different task such as the computation of internal forces, collision detection, haptics or visual display. These models are synchronized during the simulation using a mapping mechanism. CPU and GPU implementations can be transparently combined to exploit the computational power of modern hardware architectures. Thanks to this flexible yet efficient architecture, \sofa{} can be used as a test-bed to compare models and algorithms, or as a basis for the development of complex, high-performance simulators.
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https://hal.inria.fr/hal-00681539/file/main.pdf BibTex

2011

Conference papers

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titre
Preconditioner-Based Contact Response and Application to Cataract Surgery
auteur
Hadrien Courtecuisse, Jérémie Allard, Christian Duriez, Stéphane Cotin
article
G. Fichtinger and A. Martel and T. Peters. MICCAI – 14th International Conference on Medical Image Computing and Computer Assisted Intervention – 2011, Sep 2011, Toronto, Canada. Springer, 6891, pp.315-322, 2011, Lecture Notes in Computer Science; MICCAI 2011, Part 1. <10.1007/978-3-642-23623-5_40>
resume
In this paper we introduce a new method to compute, in real-time, the physical behavior of several colliding soft-tissues in a surgical simulation. The numerical approach is based on finite element modeling and allows for a fast update of a large number of tetrahedral elements. The speed-up is obtained by the use of a specific preconditioner that is updated at low frequency. The preconditioning enables an optimized computation of both large deformations and precise contact response. Moreover, homogeneous and inhomogeneous tissues are simulated with the same accuracy. Finally, we illustrate our method in a simulation of one step in a cataract surgery procedure, which require to handle contacts with non homogeneous objects precisely.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00685593/file/miccai2011-preconditioner.pdf BibTex
sig11talk-gpu.jpg
titre
Implicit FEM and Fluid Coupling on GPU for Interactive Multiphysics Simulation
auteur
Jérémie Allard, Hadrien Courtecuisse, François Faure
article
Mark Elendt. SIGGRAPH Talks, Aug 2011, Vancouver, Canada. ACM, pp.Article No. 52, 2011, <10.1145/2037826.2037895>
resume
We present a method to implement on the GPU an implicit FEM solver which is fast and stable enough to handle interactions and collisions. We combine this method with GPU-based fluids and collision detection to achieve interactive multiphysics simulations entirely running on the GPU.
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https://hal.inria.fr/inria-00589203/file/sig11talk-gpu.pdf BibTex

Book sections

titre
Implicit FEM Solver on GPU for Interactive Deformation Simulation
auteur
Jérémie Allard, Hadrien Courtecuisse, François Faure
article
Wen-mei W. Hwu. GPU Computing Gems Jade Edition, Elsevier, pp.281-294, 2011, Applications of GPU Computing Series, 9780123859631. <10.1016/B978-0-12-385963-1.00021-6>
resume
We present a set of methods to implement an implicit Finite Element solver on the GPU. In contrast to previous FEM implementations on the GPU which only address explicit time integration, our method allows large time steps for arbitrarily stiff objects. Unlike previous GPU-based sparse solvers, we avoid the assembly of the system matrix, and parallelize the matrix op- erations directly on the original object mesh. This considerably reduces the number of operations required, and more importantly the consumed band- width, enabling the method to be fast enough for highly complex interactive stiff body simulations. The presented methods can be applied in game and visual effects simulations, as well as medical and physics applications, where FEM is well established but currently limited by its computational cost. The core of the method can also be applied to many other scientific appli- cations where a large irregular sparse system of equations is solved using an iterative method.
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Theses

titre
Nouvelles architectures parallèles pour simulations interactives médicales
auteur
Hadrien Courtecuisse
article
Calcul parallèle, distribué et partagé [cs.DC]. Université des Sciences et Technologie de Lille – Lille I, 2011. Français
resume
Cette thèse apporte des solutions pour exploiter efficacement les nouvelles architectures hautement parallèles, dans le contexte des simulations d’objets déformables en temps réel. Les premières contributions de ce document, se concentrent sur le calcul de la déformation des objets. Pour cela nous proposerons des solutions de parallélisations de solveurs linéaires, couplées à des techniques de preconditionnement asynchrone. Le second ensemble de contributions, repose sur le processeur graphique pour produire une nouvelle méthode de détection des collisions, basée sur le volume d’intersection entre les objets déformables. Enfin les derniers travaux apportent des solutions pour produire une réponse précise aux contacts, et compatible avec le temps réel. Nous aborderons notamment les problèmes liés à la découpe des organes, et à la prise en compte du couplage mécanique entre les contacts. Pour terminer, nous illustrerons nos contributions dans un ensemble d’applications médicales, qui tirent parti des contributions de ce document.
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https://tel.archives-ouvertes.fr/tel-00772312/file/These.pdf BibTex

2010

Journal articles

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titre
GPU-based Real-Time Soft Tissue Deformation with Cutting and Haptic Feedback
auteur
Hadrien Courtecuisse, Hoeryong Jung, Jérémie Allard, Christian Duriez, Doo Yong Lee, Stéphane Cotin
article
Progress in Biophysics and Molecular Biology, Elsevier, 2010, Special Issue on Biomechanical Modelling of Soft Tissue Motion, 103 (2-3), pp.159-168. <10.1016/j.pbiomolbio.2010.09.016>
resume
This article describes a series of contributions in the field of real-time simulation of soft tissue biomechanics. These contributions address various requirements for interactive simulation of complex surgical procedures. In particular, this article presents results in the areas of soft tissue deformation, contact modelling, simulation of cutting, and haptic rendering, which are all relevant to a variety of medical interventions. The contributions described in this article share a common underlying model of deformation and rely on GPU implementations to significantly improve computation times. This consistency in the modelling technique and computational approach ensures coherent results as well as efficient, robust and flexible solutions.
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https://hal.inria.fr/hal-00686056/file/pbmb10-fem-cutting.pdf BibTex
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titre
Volume Contact Constraints at Arbitrary Resolution
auteur
Jérémie Allard, François Faure, Hadrien Courtecuisse, Florent Falipou, Christian Duriez, Paul Kry
article
ACM Transactions on Graphics, Association for Computing Machinery, 2010, Proceedings of SIGGRAPH 2010, 29 (3), pp.Article No. 82. <10.1145/1778765.1778819>
resume
We introduce a new method for simulating frictional contact between volumetric objects using interpenetration volume constraints. When applied to complex geometries, our formulation results in dramatically simpler systems of equations than those of traditional mesh contact models. Contact between highly detailed meshes can be simplified to a single unilateral constraint equation, or accurately processed at arbitrary geometry-independent resolution with simultaneous sticking and sliding across contact patches. We exploit fast GPU methods for computing layered depth images, which provides us with the intersection volumes and gradients necessary to formulate the contact equations as linear complementarity problems. Straightforward and popular numerical methods, such as projected Gauss-Seidel, can be used to solve the system. We demonstrate our method in a number of scenarios and present results involving both rigid and deformable objects at interactive rates.
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https://hal.inria.fr/inria-00502446/file/sig10ldi-preprint.pdf BibTex

Conference papers

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titre
Asynchronous Preconditioners for Efficient Solving of Non-linear Deformations
auteur
Hadrien Courtecuisse, Jérémie Allard, Christian Duriez, Stéphane Cotin
article
VRIPHYS – Virtual Reality Interaction and Physical Simulation, Nov 2010, Copenhagen, Denmark. Eurographics Association, pp.59-68, 2010, <10.2312/PE/vriphys/vriphys10/059-068>
resume
In this paper, we present a set of methods to improve numerical solvers, as used in real-time non-linear deformable models based on implicit integration schemes. The proposed approach is particularly beneficial to simulate nonhomogeneous objects or ill-conditioned problem at high frequency. The first contribution is to desynchronize the computation of a preconditioner from the simulation loop.We also exploit today’s heterogeneous parallel architectures: the graphic processor performs the mechanical computations whereas the CPU produces efficient preconditioners for the simulation. Moreover, we propose to take advantage of a warping method to limit the divergence of the preconditioner over time. Finally, we validate our work with several preconditioners on different deformable models. In typical scenarios, our method improves significantly the performances of the perconditioned version of the conjugate gradient.
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https://hal.inria.fr/hal-00688865/file/vriphys2010.pdf BibTex

2009

Conference papers

titre
Parallel dense gauss-seidel algorithm on many-core processors
auteur
Hadrien Courtecuisse, Jérémie Allard
article
HPCC’09 – 11th IEEE International Conference on High Performance Computing and Communications – 2009, Jun 2009, Seoul, South Korea. IEEE, pp.139–147, 2009, <10.1109/HPCC.2009.51>
resume
The Gauss-Seidel method is very efficient for solving problems such as tightly-coupled constraints with possible redundancies. However, the underlying algorithm is inherently sequential. Previous works have exploited sparsity in the system matrix to extract parallelism. In this paper, we propose to study several parallelization schemes for fully-coupled systems, unable to be parallelized by existing methods, taking advantage of recent many-cores architectures offering fast synchronization primitives. Experimental results on both multi-core CPUs and recent GPUs show that our proposed method is able to fully exploit the available units, whereas trivial parallel algorithms often fail. This method is illustrated by an application in medical intervention planning, where it is used to solve a linear complementary problem (LCP) expressing the contacts applied to a deformable body.
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BibTex