References of "Cotin, Stephane"
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See detailSOniCS: Interfacing SOFA and FEniCS for advanced constitutive models
Mazier, Arnaud UL; El Hadramy, Sidaty; Brunet, Jean-Nicolas et al

Scientific Conference (2022, August)

The Simulation Open Framework Architecture (SOFA) is a software environment for building simulations with a particular focus on real-time medical applications, e.g. surgery. Its scope is far broader than ... [more ▼]

The Simulation Open Framework Architecture (SOFA) is a software environment for building simulations with a particular focus on real-time medical applications, e.g. surgery. Its scope is far broader than the FEniCS Project, encompassing e.g. rigid body dynamics, interfacing with haptic devices, contact and visualisation. Naturally, it also includes some finite element models of soft tissue mechanics, but these capabilities are currently ‘pre-baked’ and limited to a few simple constitutive models. The goal of this work is to incorporate state-of-the-art code generation tools from the FEniCS Project into SOFA in order to hugely increase SOFA’s capabilities in terms of soft tissue mechanics. To this end we have developed a new SOFA plugin named SOniCS. For adding a new material model in SOniCS, the user describes its strain energy density function using UFL (Unified Form Language) syntax. Then, using FFCx (FEniCSx Form Compiler) we generate the C code associated with the kernels corresponding to the automatically differentiated cell-local residual and stiffness forms. Finally, we assemble these kernels in SOFA into global tensors and solve the resulting non-linear systems of equations. The result is that it is now possible to straightforwardly implement complex material models such as the Holzapfel-Ogden anisotropic model into SOFA, and to use them alongside SOFA’s existing strong feature set in medical simulation. [less ▲]

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See detailSOniCS: Develop intuition on biomechanical systems through interactive error controlled simulations
Mazier, Arnaud UL; El Hadramy, Sidaty; Brunet, Jean-Nicolas et al

E-print/Working paper (2022)

This new approach allows the user to experiment with model choices easily and quickly without requiring in-depth expertise, as constitutive models can be modified by one line of code only. This ease in ... [more ▼]

This new approach allows the user to experiment with model choices easily and quickly without requiring in-depth expertise, as constitutive models can be modified by one line of code only. This ease in building new models makes SOniCS ideal to develop surrogate, reduced order mod- els and to train machine learning algorithms for uncertainty quantification or to enable patient-specific simulations. SOniCS is thus not only a tool that facilitates the development of surgical training simulations but also, and perhaps more importantly, paves the way to increase the intuition of users or otherwise non-intuitive behaviors of (bio)mechanical systems. The plugin uses new developments of the FEniCSx project enabling au- tomatic generation with FFCx of finite element tensors such as the local residual vector and Jacobian matrix. We validate our approach with nu- merical simulations such as manufactured solutions, cantilever beams, and benchmarks provided by FEBio. We reach machine precision accuracy and demonstrate the use of the plugin for a real-time haptic simulation involv- ing a surgical tool controlled by the user in contact with a hyperelastic liver. We include complete examples showing the use of our plugin for sim- ulations involving Saint Venant-Kirchhoff, Neo-Hookean, Mooney-Rivlin, and Holzapfel Ogden anisotropic models as supplementary material. [less ▲]

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See detailDATA DRIVEN SURGICAL SIMULATIONS
Deshpande, Saurabh UL; Bordas, Stéphane UL; Beex, Lars UL et al

Scientific Conference (2020, July)

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See detailQuantifying the uncertainty in a hyperelastic soft tissue model with stochastic parameters
Hauseux, Paul UL; Hale, Jack UL; Cotin, Stéphane et al

in Applied Mathematical Modelling (2018), 62

We present a simple open-source semi-intrusive computational method to propagate uncertainties through hyperelastic models of soft tissues. The proposed method is up to two orders of magnitude faster than ... [more ▼]

We present a simple open-source semi-intrusive computational method to propagate uncertainties through hyperelastic models of soft tissues. The proposed method is up to two orders of magnitude faster than the standard Monte Carlo method. The material model of interest can be altered by adjusting few lines of (FEniCS) code. The method is able to (1) provide the user with statistical confidence intervals on quantities of practical interest, such as the displacement of a tumour or target site in an organ; (2) quantify the sensitivity of the response of the organ to the associated parameters of the material model. We exercise the approach on the determination of a confidence interval on the motion of a target in the brain. We also show that for the boundary conditions under consideration five parameters of the Ogden-Holzapfel-like model have negligible influence on the displacement of the target zone compared to the three most influential parameters. The benchmark problems and all associated data are made available as supplementary material. [less ▲]

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See detailReal-time Error Control for Surgical Simulation: Application to Percutaneous Interventions
Bui, Huu Phuoc UL; Tomar, Satyendra UL; Courtecuisse, Hadrien et al

Presentation (2017, August)

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See detailReal-time Error Control for Surgical Simulation
Phuoc Bui, Huu; Tomar, Satyendra; Courtecuisse, Hadrien et al

in IEEE Transactions on Biomedical Engineering (2017)

To present the first real-time a posteriori error-driven adaptive finite element approach for realtime simulation and to demonstrate the method on a needle insertion problem. Methods: We use corotational ... [more ▼]

To present the first real-time a posteriori error-driven adaptive finite element approach for realtime 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. 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. [less ▲]

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See detailReal-time error control for surgical simulation
Bui, Huu Phuoc UL; Tomar, Satyendra UL; Courtecuisse, Hadrien et al

Poster (2016, December 12)

Objective: To present the first real-time a posteriori error-driven adaptive finite element approach for real-time simulation and to demonstrate the method on a needle insertion problem. Methods: We use ... [more ▼]

Objective: To present the first real-time a posteriori 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 based on friction. The problem is solved using finite elements within SOFA. 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. [less ▲]

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See detailSimulating topological changes in real time for surgical assistance
Bordas, Stéphane UL; Kerfriden, Pierre; Courtecuisse, Hadrien et al

Speeches/Talks (2016)

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See detailFracture in augmented reality
Bilger, Alexandre UL; Cotin, Stephane; Dequidt, Jeremie et al

Poster (2015, August)

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See detailReal-time surgical simulation using a lattice-continuum approach
Bui, Huu Phuoc; Courtecuisse, Hadrien; Bordas, Stéphane UL et al

Presentation (2015, February 06)

Surgery is a complex practice whose positive outcome relies heavily on the experience of surgeons and therefore involves a number of risks. Computer-based simulation is a strong candidate for surgical ... [more ▼]

Surgery is a complex practice whose positive outcome relies heavily on the experience of surgeons and therefore involves a number of risks. Computer-based simulation is a strong candidate for surgical training, guidance and surgical robotics. Cutting, tearing, needle insertion and similar operations which require topological changes, contact, and whose outcome is significantly affected by the microstructure of the material (discontinuities, holes, interfaces) remain some of the most difficult surgical gestures to simulate. One of the difficulties emanates from the  requirement to handle propagating discontinuities as well as the micro or meso structure of the material being cut. We are interested in the development of a numerical tool capable of the interactive (50Hz) simulation of surgical cutting using a multi-domain lattice-continuum approach. Around the cutting region, a mesoscopic discrete lattice approach suitable for initiation of cuts and subsequent tears is used. The remaining regions can be modeled by a continuum approach or through model reduction approaches based on pre computations. The algorithms are implemented within the SOFA framework which is  targets  real-time computations, with an emphasis on medical simulation and the work is being performed in collaboration with the group of Dr Hadrien Courtecuisse and Stéphane Cotin. [less ▲]

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See detailAnticipation of brain shift in Deep Brain Stimulation automatic planning
Bilger, Alexandre UL; Cotin, Stephane; Duriez, Christian et al

in IEEE Engineering in Medicine and Biology Society (2015)

Deep Brain Stimulation is a neurosurgery procedure consisting in implanting an electrode in a deep structure of the brain. This intervention requires a preoperative planning phase, with a millimetric ... [more ▼]

Deep Brain Stimulation is a neurosurgery procedure consisting in implanting an electrode in a deep structure of the brain. This intervention requires a preoperative planning phase, with a millimetric accuracy, in which surgeons decide the best placement of the electrode depending on a set of surgical rules. However, brain tissues may deform during the surgery because of the brain shift phenomenon, leading the electrode to mistake the target, or moreover to damage a vital anatomical structure. In this paper, we present a patient-specific automatic planning approach for DBS procedures which accounts for brain deformation. Our approach couples an optimization algorithm with FEM based brain shift simulation. The system was tested successfully on a patient-specific 3D model, and was compared to a planning without considering brain shift. The obtained results point out the importance of performing planning in dynamic conditions. [less ▲]

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See detailControlling the Error on Target Motion through Real-time Mesh Adaptation: Applications to Deep Brain Stimulation
Bui, Huu Phuoc UL; Tomar, Satyendra UL; Courtecuisse, Hadrien et al

E-print/Working paper (n.d.)

We present an error-controlled mesh refinement procedure for needle insertion simulation and apply it to the simulation of electrode implantation for deep brain stimulation, including brain shift. Our ... [more ▼]

We present an error-controlled mesh refinement procedure for needle insertion simulation and apply it to the simulation of electrode implantation for deep brain stimulation, including brain shift. Our approach enables to control the error in the computation of the displacement and stress fields around the needle tip and needle shaft by suitably refining the mesh, whilst maintaining a coarser mesh in other parts of the domain. We demonstrate through academic and practical examples that our approach increases the accuracy of the displacement and stress fields around the needle without increasing the computational expense. This enables real-time simulations. The proposed methodology has direct implications to increase the accuracy and control the computational expense of the simulation of percutaneous procedures such as biopsy, brachytherapy, regional anesthesia, or cryotherapy and can be essential to the development of robotic guidance. [less ▲]

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See detailReal-time error controlled adaptive mesh refinement in surgical simulation: Application to needle insertion simulation
Bui, Huu Phuoc; Tomar, Satyendra UL; Courtecuisse, Hadrien et al

in IEEE Transactions on Biomedical Engineering (n.d.)

This paper presents the first real-time discretisation-error-driven adaptive finite element approach for corotational elasticity problems involving strain localisation. We propose a hexahedron-based ... [more ▼]

This paper presents the first real-time discretisation-error-driven adaptive finite element approach for corotational elasticity problems involving strain localisation. We propose a hexahedron-based finite element method combined with local oct-tree $h$-refinement, driven by a posteriori error estimation, for simulating soft tissue deformation. This enables to control the local error and global error level in the mechanical fields during the simulation. The local error level is used to refine the mesh only where it is needed, while maintaining a coarser mesh elsewhere. We investigate 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. [less ▲]

Detailed reference viewed: 671 (63 UL)