# Publications

Publications HAL 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.
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titre
Multiorgan Motion Tracking in Dynamic Magnetic Resonance Imaging for Evaluation of Pelvic System Mobility and Shear Strain
auteur
Zhifan Jiang, Jean-François Witz, Pauline Lecomte-Grosbras, Jeremie Dequidt, Stéphane Cotin, Christelle Rubod, Christian Duriez, Mathias Brieu
article
Strain, Wiley-Blackwell, 2017, 53 (2), <10.1111/str.12224 >
resume
Female pelvic disorders have a large social impact, the diagnosis of which relies on a key indication: pelvic mobility. The normal mobility is present in a healthy patient, meanwhile the hypermobility can be a sign of female pelvic prolapse and the hypomobility for endometriosis. The evaluation of pelvic mobility is based on medical image analysis. However, the latter does not provide precise values of these indicators directly. Moreover, suspension devices play an important role in pelvic organ function, but can hardly be observed on medical images. Our objective is to propose an image-based analysis tool for the quantitative evaluation of pelvic mobility and the shear strain which has an impact on suspension devices. Hence, this paper introduces a such tool based on an e cient and semi-automatic motion tracking of multiple pelvic organs: the bladder, vagina and rectum presented in dynamic magnetic resonance imaging sequences. The method was validated on prototypical images and applied to di↵erent mobility cases. The computed displacement and shear strain fields provide important information on the quality of suspension devices between organs for a fine diagnosis in the clinical context, for example the early diagnosis of female pelvic prolapse and the localization of possible lesion areas before surgery. Meanwhile, the predicted mobility can be used to compare with the finite element model for numerical simulation.
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titre
Blood vessel modeling for interactive simulation of interventional neuroradiology procedures
auteur
Erwan Kerrien, Ahmed Yureidini, Jeremie Dequidt, Christian Duriez, René Anxionnat, Stéphane Cotin
article
Medical Image Analysis, Elsevier, 2017, 35, pp.685 – 698. <10.1016/j.media.2016.10.003>
resume
Endovascular interventions can benefit from interactive simulation in their training phase but also during pre-operative and intra-operative phases if simulation scenarios are based on patient data. A key feature in this context is the ability to extract, from patient images, models of blood vessels that impede neither the realism nor the performance of simulation. This paper addresses both the segmentation and reconstruction of the vasculature from 3D Rotational Angiography data, and adapted to simulation: An original tracking algorithm is proposed to segment the vessel tree while filtering points extracted at the vessel surface in the vicinity of each point on the centerline; then an automatic procedure is described to reconstruct each local unstructured point set as a skeleton-based implicit surface (blobby model). The output of successively applying both algorithms is a new model of vasculature as a tree of local implicit models. The segmentation algorithm is compared with Multiple Hypothesis Testing (MHT) algorithm (Friman et al, 2010) on patient data, showing its greater ability to track blood vessels. The reconstruction algorithm is evaluated on both synthetic and patient data and demonstrates its ability to fit points with a subvoxel precision. Various tests are also reported where our model is used to simulate catheter navigation in interventional neuroradiology. An excellent realism, and much lower computational costs are reported when compared to triangular mesh surface models.
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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.
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Conference papers

titre
DejaVu: Intra-operative Simulation for Surgical Gesture Rehearsal
auteur
Nazim Haouchine, Danail Stoyanov, Frederick Roy, Stéphane Cotin
article
Medical Image Computing and Computer Assisted Interventions Conference MICCAI 2017, Oct 2017, Quebec City, Canada
resume
Advances in surgical simulation and surgical augmented reality have changed the way surgeons prepare for practice and conduct medical procedures. Despite considerable interest from surgeons, the use of simulation is still predominantly confined to pre-operative training of surgical tasks and the lack of robustness of surgical augmented reality means that it is seldom used for surgical guidance. In this paper, we present DejaVu, a novel surgical simulation approach for intra-operative surgical gesture rehearsal. With DejaVu we aim at bridging the gap between pre-operative surgical simulation and crucial but not yet robust intra-operative surgical augmented reality. By exploiting intra-operative images we produce a simulation that faithfully matches the actual procedure without visual discrepancies and with an underlying physical modelling that performs real-time deformation of organs and surrounding tissues, surgeons can interact with the targeted organs through grasping, pulling or cutting to immediately rehearse their next gesture. We present results on different in vivo surgical procedures and demonstrate the feasibility of practical use of our system.
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titre
Image-driven Stochastic Identification of Boundary Conditions for Predictive Simulation
auteur
Igor Peterlik, Nazim Haouchine, Lukáš Ručka, Stéphane Cotin
article
20th International Conference on Medical Image Computing and Computer Assisted Intervention, Sep 2017, Québec, Canada. 2017
resume
In computer-aided interventions, biomechanical models reconstructed from the pre-operative data are used via augmented reality to facilitate the intra-operative navigation. The predictive power of such models highly depends on the knowledge of boundary conditions. However , in the context of patient-specific modeling, neither the pre-operative nor the intra-operative modalities provide a reliable information about the location and mechanical properties of the organ attachments. We present a novel image-driven method for fast identification of boundary conditions which are modelled as stochastic parameters. The method employs the reduced-order unscented Kalman filter to transform in real-time the probability distributions of the parameters, given observations extracted from intra-operative images. The method is evaluated using synthetic, phantom and real data acquired in vivo on a porcine liver. A quantitative assessment is presented and it is shown that the method significantly increases the predictive power of the biomechanical model.
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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.
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titre
Template-based Monocular 3D Recovery of Elastic Shapes using Lagrangian Multipliers
auteur
Nazim Haouchine, Stéphane Cotin
article
Computer Vision and Pattern Recognition (CVPR), Jul 2017, Honolulu, Hawai, United States
resume
We present in this paper an efficient template-based method for 3D recovery of elastic shapes from a fixed monocular camera. By exploiting the object’s elasticity, in contrast to isometric methods that use inextensibility constraints , a large range of deformations can be handled. Our method is expressed as a saddle point problem using La-grangian multipliers resulting in a linear system which unifies both mechanical and optical constraints and integrates Dirichlet boundary conditions, whether they are fixed or free. We experimentally show that no prior knowledge on material properties is needed, which exhibit the generic usability of our method with elastic and inelastic objects with different kinds of materials. Comparisons with existing techniques are conducted on synthetic and real elastic objects with strains ranging from 25% to 130% resulting to low errors.
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titre
Augmented 3D Catheter Navigation using Constrained Shape from Template
auteur
Raffaella Trivisonne, Erwan Kerrien, Stéphane Cotin
article
Hamlyn Symposium, Jun 2017, London, United Kingdom
resume
In order to overcome the lack of depth perception in fluoroscopic images of endovascolar procedures, we propose a method to retrieve the 3D catheter navigation only having 2D information from x-rays images. The method is based only on image features and real-time constraint-based mechanical simulation.
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titre
Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Motile Cells with Growing Filopodia
auteur
Dmitry Sorokin, Igor Peterlik, Vladimír Ulman, David Svoboda, Martin Maška
article
International Symposium on Biomedical Imaging, Apr 2017, Melbourne, Australia
resume
The existence of benchmark datasets is essential to objectively evaluate various image analysis methods. Nevertheless, manual annotations of fluorescence microscopy image data are very laborious and not often practicable, especially in the case of 3D+t experiments. In this work, we propose a simulation system capable of generating 3D time-lapse sequences of single motile cells with filopodial protrusions, accompanied by inherently generated ground truth. The system consists of three globally synchronized modules, each responsible for a separate task: the evolution of filopodia on a molecular level, linear elastic deformation of the entire cell with filopodia, and generation of realistic, time-coherent cell texture. The capability of our system is demonstrated by generating a synthetic 3D time-lapse sequence of a single lung cancer cell with two growing filopodia, visually resembling its real counterpart acquired using a confocal fluorescence microscope.
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titre
Fast reconstruction of image deformation field using radial basis function
auteur
Lukáš Ručka, Igor Peterlík
article
ISBI2017 – International Symposium on Biomedical Imaging, Apr 2017, Melbourne, Australia. Proceedings of International Symposium on Biomedical Imaging
resume
Fast and accurate registration of image data is a key component of computer-aided medical image analysis. Instead of performing the registration directly on the input images, many algorithms compute the transformation using a sparse representation extracted from the original data. However, in order to apply the resulting transformation onto the original images, a dense deformation field has to be reconstructed using a suitable inter-/extra-polation technique. In this paper, we employ the radial basis function (RBF) to reconstruct the dense deformation field from a sparse transformation computed by a model-based registration. Various kernels are tested using different scenario. The dense deformation field is used to warp the source image and compare it quantitatively to the target image using two different metrics. Moreover, the influence of the number and distribution of the control points required by the RBF is studied via two different scenarios. Beside the accuracy, the performance of the method accelerated using a GPU is reported.
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titre
Face-based Smoothed Finite Element Method for Real-time Simulation of soft tissue
auteur
Andrea Mendizabal, Rémi Duparc, Huu Phuoc Bui, Christoph Paulus, Igor Peterlik, Stéphane Cotin
article
SPIE Medical Imaging, Feb 2017, Orlando, United States. SPIE Medical Imaging
resume
In soft tissue surgery, a tumor and other anatomical structures are usually located using the preoperative CT or MR images. However, due to the deformation of the concerned tissues, this information suffers from inaccuracy when employed directly during the surgery. In order to account for these deformations in the planning process, the use of a bio-mechanical model of the tissues is needed. Such models are often designed using the finite element method (FEM), which is, however, computationally expensive, in particular when a high accuracy of the simulation is required. In our work, we propose to use a smoothed finite element method (S-FEM) in the context of modeling of the soft tissue deformation. This numerical technique has been introduced recently to overcome the overly stiff behavior of the standard FEM and to improve the solution accuracy and the convergence rate in solid mechanics problems. In this paper, a face-based smoothed finite element method (FS-FEM) using 4-node tetrahedral elements is presented. We show that in some cases, the method allows for reducing the number of degrees of freedom, while preserving the accuracy of the discretization. The method is evaluated on a simulation of a cantilever beam loaded at the free end and on a simulation of a 3D cube under traction and compression forces. Further, it is applied to the simulation of the brain shift and of the kidney’s deformation. The results demonstrate that the method outperforms the standard FEM in a bending scenario and that has similar accuracy as the standard FEM in the simulations of brain shift and kidney deformation.
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Theses

titre
Topological Changes in Simulations of Deformable Objects
auteur
Christoph Paulus
article
Modeling and Simulation. University of Strasbourg, 2017. English
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, soft tissue tearing or fractures, is essential for augmenting the capabilities of existing or future simulation systems. In this thesis, we present a new remeshing algorithm based on the finite element method. For tetrahedral elements with linear shape functions, we combined remeshing algorithm with the movement of the nodes to the cutting surface, called snapping in the literature. Our approach shows benefits when evaluating the impact of cuts on the number of nodes and the numerical quality of the mesh. When applying our remeshing algorithm to quadratic shape functions, we observe similar results. Due to the curved surfaces of the elements, when using quadratic shape functions, the snapping of nodes entails higher challenges. Thus, to investigate into the snapping, experience has been gathered on triangular shell elements, simulating fractures. Beyond the simulation of fractures, our remeshing approach for tetrahedral elements is generic enough to support a large variety of applications. In this work, we are the first to present results on the detection of topological changes, such as fractures, tearing and cutting, from a monocular video stream. Ex amples with highly elastic silicone bands, in-vivo livers and ex-vivo kidneys show the robustness of our detection algorithm, which is combined with the remeshing approach, in different scenarios. Finally, the augmentation of internal organ structures highlights the clinical potential and importance of the conducted work.
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2016

Journal articles

titre
Robust Augmented Reality registration method for Localization of Solid Organs’ Tumors Using CT-derived Virtual Biomechanical Model and Fluorescent Fiducials
auteur
Seong-Ho Kong, Nazim Haouchine, Renato Soares, Andrey S Klymchenko, Bohdan Andreiuk, Bruno Marques, Galyna Shabat, Thierry Piéchaud, Michele Diana, Stéphane Cotin, Jacques Marescaux
article
Surgical Endoscopy, Springer Verlag (Germany), 2016, <10.1007/s00464-016-5297-8>
resume
Accurate localization of solid organs tumors is crucial to ensure both radicality and organ function preservation. Augmented Reality (AR) is the fusion of computer-generated and real-time images. AR can be used in surgery as a navigation tool, by creating a patient-specific virtual model through 3D software manipulation of DICOM imaging (e.g. CT-scan). The virtual model can be superimposed to the real-time images to obtain the enhanced real-time localization. However, the 3D virtual model is rigid, and does not take into account inner structures’ deformations. We present a concept of automated navigation system, enabling transparency visualization of internal anatomy and tumor’s margins, while the organs undergo deformation during breathing or surgical manipulation.
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titre
Handling Topological Changes during Elastic Registration: Application to Augmented Reality in Laparoscopic Surgery
auteur
Christoph Joachim Paulus, Nazim Haouchine, Seong-Ho Kong, Renato Vianna Soares, David Cazier, Stéphane Cotin
article
International Journal of Computer Assisted Radiology and Surgery (IJCARS), Springer, 2016
resume
Purpose: Locating the internal structures of an organ is a critical aspect of many surgical procedures. Minimally invasive surgery, associated with augmented reality techniques, offers the potential to visualize inner structures, allowing for improved analysis, depth perception or for supporting planning and decision systems. Methods: Most of the current methods dealing with rigid or non-rigid augmented reality make the assumption that the topology of the organ is not modified. As surgery relies essentially on cutting and dissection of anatomical structures, such methods are limited to the early stages of the surgery. We solve this shortcoming with the introduction of a method for physics-based elastic registration using a single view from a monocular camera. Singularities caused by topological changes are detected and propagated to the pre-operative model. This significantly improves the coherence between the actual laparoscopic view and the model, and provides added value in terms of navigation and decision-making, e.g. by overlaying the internal structures of an organ on the laparoscopic view. Results: Our real time augmentation method is assessed on several scenarios, using synthetic objects and real organs. In all cases, the impact of our approach is demonstrated, both qualitatively and quantitatively. Conclusion: The presented approach tackles the challenge of localizing internal structures throughout a complete surgical procedure, even after surgical cuts. This information is crucial for surgeons to improve the outcome for their surgical procedure and avoid complications.
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Conference papers

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.
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titre
Using Contours as Boundary Conditions for Elastic Registration during Minimally Invasive Hepatic Surgery
auteur
Nazim Haouchine, Frederick Roy, Lionel Untereiner, Stéphane Cotin
article
International Conference on Intelligent Robots and Systems, Oct 2016, Daejeon, South Korea
resume
We address in this paper the ill-posed problem of initial alignment of pre-operative to intra-operative data for augmented reality during minimally invasive hepatic surgery. This problem consists of finding the rigid transformation that relates the scanning reference and the endoscopic camera pose, and the non-rigid transformation undergone by the liver w.r.t its scanned state. Most of the state-of-the-art methods assume a known initial registration. Here, we propose a method that permits to recover the deformation undergone by the liver while simultaneously finding the rotational and translational parts of the transformation. Our formulation considers the boundaries of the liver with its surrounding tissues as hard constraints directly encoded in an energy minimization process. We performed experiments on real in-vivo data of human hepatic surgery and synthetic data, and compared our method with related works.
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titre
Simultaneous Pose Estimation and Augmentation of Elastic Surfaces from a Moving Monocular Camera
auteur
Nazim Haouchine, Marie-Odile Berger, Stephane Cotin
article
International Symposium on Mixed and Augmented Reality, Sep 2016, Merida, Mexico
resume
We present in this paper an original method to estimate the pose of a monocular camera while simultaneously modeling and capturing the elastic deformation of the object to be augmented. Our method tackles a challenging problem where ambiguities between rigid motion and non-rigid deformation are present. This issue represents a major lock for the establishment of an efficient surgical augmented reality where endoscopic camera moves and organs deform. Using an underlying physical model to estimate the low stressed regions our algorithm separates the rigid body motion from the elastic deformations using polar decomposition of the strain tensor. Following this decomposition, a constrained minimization, that encodes both the optical and the physical constraints, is resolved at each frame. Results on real and simulated data are exposed to show the effectiveness of our approach.
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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.
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titre
Segmentation and Labelling of Intra-operative Laparoscopic Images using Structure from Point Cloud
auteur
Nazim Haouchine, Stephane Cotin
article
International Symposium on Biomedical Imaging : “From Nano to Macro” (ISBI 2016), Apr 2016, Prague, Czech Republic
resume
We present in this paper an automatic method for segmenting and labelling of liver its surrounding tissues in intra-operative laparoscopic images. The goal is to be able to distinguished between the different structure that compose a common intra-operative hepatic surgery scene. This will permits to improve the registration between pre-operative data and intra-operative images for task such as Augmented Reality. Our segmentation method consider the scene as a 3D structured point cloud instead of a laparoscopic images in order to exploit powerful informations such as curvature and normals, in addition to visual cues that permits to efficiently classify the scene. Our approach works well on sparse and noisy point clouds, thanks to a surface approximation stage, and unlike existing approaches, is independent of organs texture in the image. Experiements performed on challenging human hepatic surgery confirm that accurate segmentation and labelling are possible using 3D structure information and appropriate visual cues.
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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.
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Theses

titre
Augmented Reality and Numerical Simulations for Hepatic Tumors Resection
auteur
Rosalie Plantefève
article
Modeling and Simulation. Université Lille 1 Sciences et Technologies, 2016. English
resume
Liver cancer is the 2nd most common cause of cancer death worldwide, with more than 745,000 deaths from liver cancer in 2012. When including deaths from liver cirrhosis, the toll reaches nearly 2 million people worldwide. Today, surgical tumors ablation remains the best treatment for liver cancer. To localize the hepatic tumors and to define the resection planes, clinicians rely on pre-operative medical images (obtained with computed tomography scanner or magnetic resonance imaging). However, the liver lesions and vascular system are difficult to localize during surgery. This may lead to incomplete tumor resection or haemorrhage. The purpose of this thesis work is to provide surgeons with an augmented view of the liver and its internal structures during surgery to help them to optimally resect the tumors while limiting the risk of vascular lesion. Therefore, an elastic registration method to align the pre-operative and intra-operative data has been developed. This method, which uses a biomechanical model and anatomical landmarks, was designed to limit its impact on the clinical workflow and reaches a registration accuracy below the resection margin even when the liver is strongly deformed between its pre-operative and intra-operative state. This registration algorithm has been integrated into a software, sofaOR, to conduct the first clinical tests.
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2015

Journal articles

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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titre
Patient-specific Biomechanical Modeling for Guidance during Minimally-invasive Hepatic Surgery
auteur
Rosalie Plantefève, Igor Peterlik, Nazim Haouchine, Stéphane Cotin
article
Annals of Biomedical Engineering, Springer Verlag, 2015
resume
During the minimally-invasive liver surgery, only the partial surface view of the liver is usually provided to the surgeon via the laparoscopic camera. Therefore, it is necessary to estimate the actual position of the internal structures such as tumors and vessels from the pre-operative images. Nevertheless, such task can be highly challenging since during the intervention, the abdominal organs undergo important deformations due to the pneumoperitoneum, respiratory and cardiac motion and the interaction with the surgical tools. Therefore, a reliable automatic system for intra-operative guidance requires fast and reliable registration of the pre- and intra-operative data. In this paper we present a complete pipeline for the registration of pre-operative patient-specific image data to the sparse and incomplete intra-operative data. While the intra-operative data is represented by a point cloud extracted from the stereo-endoscopic images, the pre-operative data is used to reconstruct a biomechanical model which is necessary for accurate estimation of the position of the internal structures, considering the actual deformations. This model takes into account the patient-specific liver anatomy composed of parenchyma, vascularization and capsule, and is enriched with anatomical boundary conditions transferred from an atlas. The registration process employs the iterative closest point technique together with a penalty-based method. We perform a quantitative assessment based on the evaluation of the target registration error on synthetic data as well as a qualitative assessment on real patient data. We demonstrate that the proposed registration method provides good results in terms of both accuracy and robustness w. r. t. the quality of the intra-operative data.
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titre
B-spline Based Multi-organ Detection in Magnetic Resonance Imaging
auteur
Zhifan Jiang, Jean-Francois Witz, M Lecomte-Grosbras, Jeremie Dequidt, Christian Duriez, Michel Cosson, Stéphane Cotin, M Brieu
article
Strain, Wiley-Blackwell, 2015, 51, pp.235 – 247. <10.1111/str.12136>
resume
In the context of the female pelvic medicine, non-invasive Magnetic Resonance Imaging (MRI) is widely used for the diagnosis of pelvic floor disorders. Nowadays in the clinical routine, diagnoses rely largely on human interpretation of medical images, on the experience of physicians, with sometimes subjective interpretations. Hence, image correlation methods would be an alternative way to assist physicians to provide more objective analyses with standard procedures and parametrization for patient-specific cases. Moreover, the main symptoms of pelvic system pathologies are abnormal mobilities. The FEM (Finite Element Model) simulation is a powerful tool for understanding such mobilities. Both the patient-specific simulation and the image analysis require accurate and smooth geometries of the pelvic organs. This paper introduces a new method that can be classified as a model-to-image correlation approach. The method performs fast semi-automatic detection of the bladder, vagina and rectum from MR images for geometries reconstruction and further study of the mobilities. The approach consists of fitting a B-spline model to the organ shapes in real images via a generated virtual image. We provided efficient, adaptive and consistent segmentation on a dataset of 19 patient images (healthy and pathological).
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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.
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titre
CPH: a compact representation for hierarchical meshes generated by primal refinement
auteur
Lionel Untereiner, Pierre Kraemer, David Cazier, Dominique Bechmann
article
Computer Graphics Forum, Wiley, 2015, 34 (8), pp.155-166. <10.1111/cgf.12667>
resume
We present CPH (Compact Primal Hierarchy): a compact representation of the hierarchical connectivity of surface and volume manifold meshes generated through primal subdivision refinements. CPH is consistently defined in several dimensions and supports multiple kinds of tessellations and refinements, whether regular or adaptive. The basic idea is to store only the finest mesh, encoded in a classical monoresolution structure that is enriched with a minimal set of labels. These labels allow traversal of any intermediate level of the mesh concurrently without having to extract it in an additional structure. Our structure allows attributes to be stored on the cells not only on the finest level, but also on any intermediate level. We study the trade-off between the memory cost of this compact representation and the time complexity of mesh traversals at any resolution level.
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titre
Preoperative trajectory planning for percutaneous procedures in deformable environments
auteur
Noura Hamzé, Igor Peterlík, Stéphane Cotin, Caroline Essert
article
Computerized Medical Imaging and Graphics, Elsevier, 2015, 47, <10.1016/j.compmedimag.2015.10.002>
resume
In image-guided percutaneous interventions, a precise planning of the needle path is a key factor to a successful intervention. In this paper we propose a novel method for computing a patient-specific optimal path for such interventions, accounting for both the deformation of the needle and soft tissues due to the insertion of the needle in the body. To achieve this objective, we propose an optimization method for estimating preoperatively a curved trajectory allowing to reach a target even in the case of tissue motion and needle bending. Needle insertions are simulated and regarded as evaluations of the objective function by the iterative planning process. In order to test the planning algorithm, it is coupled with a fast needle insertion simulation involving a flexible needle model and soft tissue finite element modeling, and experimented on the use-case of thermal ablation of liver tumors. Our algorithm has been successfully tested on twelve datasets of patient-specific geometries. Fast convergence to the actual optimal solution has been shown. This method is designed to be adapted to a wide range of percutaneous interventions.
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titre
Monocular 3D Reconstruction and Augmentation of Elastic Surfaces with Self-occlusion Handling
auteur
Nazim Haouchine, Jeremie Dequidt, Marie-Odile Berger, Stephane Cotin
article
IEEE Transactions on Visualization and Computer Graphics, Institute of Electrical and Electronics Engineers, 2015, pp.14. <10.1109/TVCG.2015.2452905>
resume
This paper focuses on the 3D shape recovery and augmented reality on elastic objects with self-occlusions handling, using only single view images. Shape recovery from a monocular video sequence is an underconstrained problem and many approaches have been proposed to enforce constraints and resolve the ambiguities. State-of-the art solutions enforce smoothness or geometric constraints, consider specific deformation properties such as inextensibility or resort to shading constraints. However, few of them can handle properly large elastic deformations. We propose in this paper a real-time method that uses a mechanical model and able to handle highly elastic objects. The problem is formulated as an energy minimization problem accounting for a non-linear elastic model constrained by external image points acquired from a monocular camera. This method prevents us from formulating restrictive assumptions and specific constraint terms in the minimization. In addition, we propose to handle self-occluded regions thanks to the ability of mechanical models to provide appropriate predictions of the shape. Our method is compared to existing techniques with experiments conducted on computer-generated and real data that show the effectiveness of recovering and augmenting 3D elastic objects. Additionally, experiments in the context of minimally invasive liver surgery are also provided and results on deformations with the presence of self-occlusions are exposed.
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titre
Impact of Soft Tissue Heterogeneity on Augmented Reality for Liver Surgery
auteur
Nazim Haouchine, Stephane Cotin, Igor Peterlik, Jeremie Dequidt, Mario Sanz-Lopez, Erwan Kerrien, Marie-Odile Berger
article
IEEE Transactions on Visualization and Computer Graphics, Institute of Electrical and Electronics Engineers, 2015, 21 (5), pp.584 – 597. <10.1109/TVCG.2014.2377772>
resume
This paper presents a method for real-time augmented reality of internal liver structures during minimally invasive hepatic surgery. Vessels and tumors computed from pre-operative CT scans can be overlaid onto the laparoscopic view for surgery guidance. Compared to current methods, our method is able to locate the in-depth positions of the tumors based on partial three-dimensional liver tissue motion using a real-time biomechanical model. This model permits to properly handle the motion of internal structures even in the case of anisotropic or heterogeneous tissues, as it is the case for the liver and many anatomical structures. Experimentations conducted on phantom liver permits to measure the accuracy of the augmentation while real-time augmentation on in vivo human liver during real surgery shows the benefits of such an approach for minimally invasive surgery.
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Conference papers

titre
Framework for augmented reality in Minimally Invasive laparoscopic surgery
auteur
Bruno Marques, Rosalie Plantefeve, Frédérick Roy, Nazim Haouchine, Emmanuel Jeanvoine, Igor Peterlik, Stéphane Cotin
article
HealthCom 2015, Oct 2015, Boston, United States. 2015 17th International Conference on E-health Networking, Application & Services (HealthCom) 2015, <10.1109/HealthCom.2015.7454467>
resume
This article presents a framework for fusing pre-operative data and intra-operative data for surgery guidance. This framework is employed in the context of Minimally Invasive Surgery (MIS) of the liver. From stereoscopic images a three dimensional point cloud is reconstructed in real-time. This point cloud is then used to register a patient-specific biomechanical model derived from Computed Tomography images onto the laparoscopic view. In this way internal structures such as vessels and tumors can be visualized to help the surgeon during the procedure. This is particularly relevant since abdominal organs undergo large deformations in the course of the surgery, making it difficult for surgeons to correlate the laparoscopic view with the pre-operative images. Our method has the potential to reduce the duration of the operation as the biomechanical model makes it possible to estimate the in-depth position of tumors and vessels at any time of the surgery, which is essential to the surgical decision process. Results show that our method can be successfully applied during laparoscopic procedure without interfering with the surgical work flow.
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titre
Surgical Augmented Reality with Topological Changes
auteur
Christoph Paulus, Nazim Haouchine, David Cazier, Stéphane Cotin
article
Medical Image Computing and Computer Assisted Interventions, Oct 2015, München, Germany. <http://miccai2015.org/>
resume
The visualization of internal structures of organs in minimally invasive surgery is an important avenue for improving the perception of the surgeon, or for supporting planning and decision systems. However, current methods dealing with non-rigid augmented reality only provide augmentation when the topology of the organ is not modified. In this paper we solve this shortcoming by introducing a method for physics-based non-rigid augmented reality. Singularities caused by topo-logical changes are detected and propagated to the pre-operative model. This significantly improves the coherence between the actual laparascopic view and the model, and provides added value in terms of navigation and decision making. Our real time augmentation algorithm is assessed on a video showing the cut of a porcine liver’s lobe in minimal invasive surgery.
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titre
Augmented Reality during Cutting and Tearing of Deformable Objects
auteur
Christoph Paulus, Nazim Haouchine, David Cazier, Stephane Cotin
article
The 14th IEEE International Symposium on Mixed and Augmented Reality, Sep 2015, Fukuoka, Japan. pp.6
resume
Current methods dealing with non-rigid augmented reality only provide an augmented view when the topology of the tracked object is not modified, which is an important limitation. In this paper we solve this shortcoming by introducing a method for physics-based non-rigid augmented reality. Singularities caused by topological changes are detected by analyzing the displacement field of the underlying deformable model. These topological changes are then applied to the physics-based model to approximate the real cut. All these steps, from deformation to cutting simulation, are performed in real-time. This significantly improves the coherence between the actual view and the model, and provides added value.
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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.
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titre
Anticipation of Brain Shift in Deep Brain Stimulation Automatic Planning
auteur
Noura Hamzé, Alexandre Bilger, Christian Duriez, Stéphane Cotin, Caroline Essert
article
IEEE Engineering in Medicine and Biology Society (EMBC’15), Aug 2015, Milan, Italy. IEEE, pp.3635 – 3638 2015, <10.1109/EMBC.2015.7319180>
resume
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.
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titre
Augmented Reality for Cryoablation Procedures
auteur
Hugo Talbot, Frederick Roy, Stéphane Cotin
article
SIGGRAPH 2015, Aug 2015, Los Angeles, United States
resume
Cryotherapy is a rapidly growing minimally invasive technique for the treatment of different kinds of tumors, such as breast cancer, renal and prostate cancer. Several hollow needles are percutaneously inserted in the target area under image guidance and a gas (usually argon) is then decompressed inside the needles. Based on the Thompson-Joule principle, the temperature drops drown and a ball of ice crystals forms around the tip of each needle. Radiologists rely on the geometry of this iceball (273K), visible on computer tomographic (CT) or magnetic resonance (MR) images, to assess the status of the ablation. However, cellular death only occurs when the temperature falls below 233K. The complexity of the procedure therefore resides in planning the optimal number, position and orientation of the needles required to treat the tumor, while avoiding any damage to the surrounding healthy tissues. This planning is currently done qualitatively, based on experience, and can take several hours, with a result that is often different from the expected one. To solve this important limitation of cryotherapy, a few planning systems have been proposed in the literature. Currently, commercial systems are nearly non existent, and emerging tools are limited to a visualization of the isotherms obtained for each needle in ideal conditions (usually in a gel). They do not account for any influence of the soft tissue properties, the presence of blood vessels, or the combined effect of multiple needles. As a consequence, large safety margins over 5mm are defined. To address this challenge, our method extracts information from medical images (CT or MR) and allows to assess different strategies with an augmented visualization of the resulting iceball and the associated isotherms.
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titre
Improving depth perception during surgical augmented reality
auteur
Bruno Marques, Nazim Haouchine, Rosalie Plantefeve, Stephane Cotin
article
SIGGRAPH [Poster], Aug 2015, Los Angeles, United States. pp.Article No. 24, 2015, <10.1145/2787626.2792654>
resume
This study suggests a method to compensate the loss of depth perception while enhancing organ vessels and tumors to surgeons. This method relies on a combination of contour rendering technique and adaptive alpha blending to effectively perceive the vessels and tumors depth. In addition, this technique is designed to achieve real-time to satisfy the requirements of clinical routines, and has been tested on real human surgery.
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titre
Fracture in Augmented Reality
auteur
Nazim Haouchine, Alexandre Bilger, Jeremie Dequidt, Stephane Cotin
article
SIGGRAPH [Poster], Aug 2015, Los Angeles, United States. 2015
resume
We propose in this study an image-guided mesh cutting method to handle real-time augmentation of paper tearing. This method relies on the combination of visually-based fracture tracking algorithm and a physics-based model that is dynamically superimposed on the image.
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titre
Personalization of Cardiac Electrophysiology Model using the Unscented Kalman Filtering
auteur
Hugo Talbot, Stephane Cotin, Reza Razavi, Christopher Rinaldi, Hervé Delingette
article
Computer Assisted Radiology and Surgery (CARS 2015), Jun 2015, Barcelona, Spain
resume
Cardiac electrophysiology mapping techniques now allow to record denser intra-operative electrograms (ECG). The patient-specific information extracted from these clinical recordings is extremely valuable. A growing field of research focuses on the personalization of electro-physiology models using this patient-specific information. The modeling in silico of a patient electrophysiology is needed to better understand the mechanism of cardiac arrhythmia. In the scope of ischemic cardiomyopa-thy, the predictive power of patient-specific simulations may also provide a substantial guidance in defining the optimal location of the implantable defibrillator, since all possible configurations could be tested in silico. This article describes an innovative personalization approach based on an unscented Kalman filter. Following an iterative process, the apparent conductivity is efficiently estimated in specific regions. A sensitivity analysis is performed to assess the filter parameters. With three patient cases, we finally demonstrate the accuracy and efficiency of our algorithm.
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titre
Surgery Training, Planning and Guidance Using the SOFA Framework
auteur
Hugo Talbot, Nazim Haouchine, Igor Peterlik, Jeremie Dequidt, Christian Duriez, Hervé Delingette, Stephane Cotin
article
Eurographics, May 2015, Zurich, Switzerland
resume
In recent years, an active development of novel technologies dealing with medical training, planning and guidance has become an increasingly important area of interest in both research and health-care manufacturing. A combination of advanced physical models, realistic human-computer interaction and growing computational power is bringing new solutions in order to help both medical students and experts to achieve a higher degree of accuracy and reliability in surgical interventions. In this paper, we present three different examples of medical physically-based simulations implemented in a common software platform called SOFA. Each example represents a different application: training for cardiac electrophysiology, pre-operative planning of cryosurgery and per-operative guidance for laparoscopy. The goal of this presentation is to evaluate the realism, accuracy and efficiency of the simulations, as well as to demonstrate the potential and flexibility of the SOFA platform.
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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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Theses

titre
Modélisation des interactions entre solides déformables et films fluides pour la simulation médicale temps-réel
auteur
Vincent Majorczyk
article
Modélisation et simulation. Université des Sciences et Technologies de Lille, 2015. Français
resume
Cette thèse apporte une solution pour permettre de couplage entre fluide et solide déformable dans le cadre d’applications médicales en temps-réel. Le modèle de couplage concerne le cas d’un film de fluide compris entre deux solides déformables. La première contribution de ce document concerne une méthode de fluide semi-lagrangienne. Nous proposons une modification d’une méthode existante pour pouvoir l’utiliser en tant que modèle de fluide 2.5D. La seconde contribution se concentre sur le modèle de couplage en lui-même où nous avons choisi de prédire le comportement de l’interface fluide-solide pendant le calcul du fluide. La troisième contribution repose sur des applications médicales basées sur cette approche. Elles contribuent dans les domaines de la chirurgie ophtalmologique et reconstruction chirurgicale.
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titre
Image-guided Simulation for Augmented Reality during Hepatic Surgery
auteur
Nazim Haouchine
article
Computer Science [cs]. Université de Lille1, 2015. English
resume
The main objective of this thesis is to provide surgeons with tools for pre and intra-operative decision support during minimally invasive hepatic surgery. These interventions are usually based on laparoscopic techniques or, more recently, flexible endoscopy. During such operations, the surgeon tries to remove a significant number of liver tumors while preserving the functional role of the liver. This involves defining an optimal hepatectomy, i.e. ensuring that the volume of post-operative liver is at least at 55% of the original liver and the preserving at hepatic vasculature. Although intervention planning can now be considered on the basis of preoperative patient-specific, significant movements of the liver and its deformations during surgery data make this very difficult to use planning in practice. The work proposed in this thesis aims to provide augmented reality tools to be used in intra-operative conditions in order to visualize the position of tumors and hepatic vascular networks at any time.
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Preprints, Working Papers, …

titre
Hexahedral-dominant meshing
auteur
Dmitry Sokolov, Nicolas Ray, Lionel Untereiner, Bruno Lévy
article
2015
resume
This article introduces a method that generates a hexahedral-dominant mesh from an input tetrahedral mesh. It follows a three-steps pipeline similar to the one proposed by Carrier-Baudoin et al.: (1) generate a frame field; (2) generate a pointset P that is mostly organized on a regular grid locally aligned with the frame field; and (3) generate the hexahedral-dominant mesh by recombining the tetrahedra obtained from the constrained Delaunay triangulation of P. For step (1), we use a state of the art algorithm to generate a smooth frame field. For step (2), we introduce an extension of Periodic Global Parameterization to the volumetric case. As compared with other global parameterization methods (such as CubeCover), our method relaxes some global constraints and avoids creating degenerate elements, at the expense of introducing some singularities that are meshed using non-hexahedral elements. For step (3), we build on the formalism introduced by Meshkat and Talmor, fill-in a gap in their proof and provide a complete enumeration of all the possible recombinations, as well as an algorithm that efficiently detects all the matches in a tetrahedral mesh. The method is evaluated and compared with the state of the art on a database of examples with various mesh complexities, varying from academic examples to real industrial cases. Compared with the method of Carrier-Baudoin et al., the method results in better scores for classical quality criteria of hexahedral-dominant meshes (hexahedral proportion, scaled Jacobian, etc.). The method also shows better robustness than CubeCover and its derivatives when applied to complicated industrial models.
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2014

Journal articles

titre
Modèle pour la simulation de tissus connectifs
auteur
Julien Bosman, Christian Duriez, Stéphane Cotin
article
Revue Electronique Francophone d’Informatique Graphique, Association Française d’Informatique Graphique, 2014, pp.13
resume
Dans le cadre de la simulation médicale, les récents travaux ont conduit à de réels progrès en terme de simulation d’organes. Cependant, la modélisation des tissus connectifs est très souvent ignorée malgré le rôle mécanique majeur qu’ils peuvent jouer dans l’interaction entre certains organes. Nous proposons un modèle de simulation de tissus connectifs reposant sur des méthodes sans maillage basées sur des repères. Le réalisme des simulations repose sur une formulation variationnelle des équations de la mécanique des milieux continus, proche de la méthode par éléments finis. Notre approche permet de simuler des objets déformables aux topologies diverses (volumiques, surfaciques et linéiques). Dans le soucis d’obtenir une simulation stable de la dynamique de ces corps dé-formables, nous utilisons une intégration temporelle implicite. Grâce à notre méthode, il est possible de modéliser ces tissus, sans présager de leur géométrie, permettant ainsi le couplage mécanique entre les organes.
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titre
Middle-Ear Microsurgery Simulation to Improve New Robotic Procedures
auteur
Guillaume Kazmitcheff, Yann Nguyen, Mathieu Miroir, Fabien Péan, Evelyne Ferrary, Stéphane Cotin, Olivier Sterkers, Christian Duriez
article
BioMed Research International , Hindawi Publishing Corporation, 2014, pp.10. <10.1155/2014/891742>
resume
Otological microsurgery is delicate and requires high dexterity in bad ergonomic conditions. To assist surgeons in these indications, a teleoperated system, called RobOtol, is developed. This robot enhances gesture accuracy and handiness and allows exploration of new procedures for middle ear surgery. To plan new procedures that exploit the capacities given by the robot, a surgical simulator is developed. The simulation reproduces with high fidelity the behavior of the anatomical structures and can also be used as a training tool for an easier control of the robot for surgeons. In the paper, we introduce the middle ear surgical simulation and then we perform virtually two challenging procedures with the robot. We show how interactive simulation can assist in analyzing the benefits of robotics in the case of complex manipulations or ergonomics studies and allow the development of innovative surgical procedures. New robot-based microsurgical procedures are investigated. The improvement offered by RobOtol is also evaluated and discussed.
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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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titre
Simulation virtuelle de la palpation de la chaîne des osselets: développement d’un retour de forces réaliste
auteur
Guillaume Kazmitcheff, Yann Nguyen, Mathieu Miroir, Evelyne Ferrary, Christian Duriez, Olivier Sterkers
article
Annales françaises d’Oto-rhino-laryngologie et de Pathologie Cervico-faciale, Elsevier, United States, 2014, 131 (4), pp.A77. <10.1016/j.aforl.2014.07.417>
resume
no abstract
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titre
Simulation de l’interaction entre film fluide et solides déformables
auteur
Vincent Majorczyk, Stéphane Cotin, Jérémie Allard, Christian Duriez
article
Revue Electronique Francophone d’Informatique Graphique, Association Française d’Informatique Graphique, 2014, 8 (2), pp.10
resume
Les liquides organiques sont un constituant essentiel du corps humain, aussi bien par leur volume que par leurs multiples fonctions. En dehors du sang et du liquide lymphatique, de nombreux autres fluides sont présents dans l’organisme et y ont des fonctions importantes, telles que lubrification ou d’absorption de chocs. Dans ce travail nous nous intéressons plus particulièrement aux fluides se trouvant à l’interface entre deux structures anato-miques. Nous présentons une méthode permettant de simuler les phénomènes d’interaction entre un film fluide et les surfaces entre lesquelles il est contraint. L’approche que nous proposons repose sur un modèle de fluide et son couplage mécanique avec des surfaces déformables. Selon la pression du fluide et la raideur des solides dé-formables en contact avec le fluide, différents comportements sont attendus. Nos résultats préliminaires montrent qu’il est possible de simuler les caractéristiques principales de ces comportements. De plus, les approches choi-sies pour le modèle de fluide, le modèle déformable, et le couplage entre les deux sont compatibles avec des simulations temps-réel.
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Conference papers

titre
Real-time FEM based control of soft surgical robots
auteur
Frederick Largilliere, Eulalie Coevoet, Laurent Grisoni, Christian Duriez
article
SURGETICA 2014, Dec 2014, Chambéry, France
resume
In this paper, we present a new method for the control of soft surgical robots based on the real-time inverse simulation with internal deformation computed through the use of Finite Element Method. We also consider the coupling of this method with a modified version of the same algorithm for parametrization of soft-tissue models, in order to control the navigation of the robot while gathering information on the surrounding organs.
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titre
Intra-operative Registration for Stereotactic Procedures driven by a combined Biomechanical Brain and CSF Model
auteur
Alexandre Bilger, Éric Bardinet, Sara Fernández-Vidal, Christian Duriez, Pierre Jannin, Stéphane Cotin
article
ISBMS – International Symposium on Biomedical Simulation, Oct 2014, Strasbourg, France. 2014
resume
During stereotactic neurosurgery, the brain shift could affect the accuracy of the procedure. However, this deformation of the brain is not often considered in the pre-operative planning step or intra-operatively, and may lead to surgical complications, side effects or ineffectiveness. In this paper, we present a method to update the pre-operative planning based on a physical simulation of the brain shift. Because the simulation requires unknown input parameters, the method relies on a parameter estimation process to compute the intracranial state that matches the partial data taken from intra-operative modalities. The simulation is based on a biomechanical model of the brain and the cerebro-spinal fluid. In this paper, we show on an anatomical atlas that the method is numerically sound.
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titre
Testbed for assessing the accuracy of interventional radiology simulations
auteur
Mario Sanz-Lopez, Jérémie Dequidt, Erwan Kerrien, Christian Duriez, Marie-Odile Berger, Stéphane Cotin
article
ISBMS – 6th International Symposium on Biomedical Simulation, Oct 2014, Strasbourg, France. Springer, 2014, LNCS
resume
The design of virtual reality simulators, and more specifically those dedicated to surgery training, implies to take into account numerous constraints so that simulators look realistic to trainees and train proper skills for surgical procedures. Among those constraints, the accuracy of the biophysical models remains a very hot topic since parameter estimation and experimental validation often rely on invasive protocols that are obviously not suited for living beings. In the context of Interventional Radiology the procedures involve the navigation of surgical catheter tools inside the vascular network where many contacts, sliding and friction phenomena occur. The simulation of these procedures require complex interaction models between the tools and the blood vessels for which there is no ground truth data available for parametrization and validation. This paper introduces an experimental testbed to address this issue: acquisition devices as well as a data-processing algorithms are used to record the motion of interventional radiology tools in a silicon phantom representing a vascular network. Accuracy and high acquisition rates are the key features of this testbed as it enables to capture dynamic friction of non-smooth dynamics and because it could provide extensive data to improve the accuracy of the mechanical model of the tools and the interaction model between the tools and the blood vessel.
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titre
The Role of Ligaments: Patient-Specific or Scenario-Specific ?
auteur
Julien Bosman, Nazim Haouchine, Jérémie Dequidt, Igor Peterlik, Stéphane Cotin, Christian Duriez
article
International Symposium on Biomedical Simulation ISBMS, Oct 2014, Strasbourg, France. 2014
resume
In this paper, we present a preliminary study dealing with the importance of correct modeling of connective tissues such as ligaments in laparoscopic liver surgery simulation. We show that the model of these tissues has a significant impact on the overall results of the simulation. This is demonstrated numerically using two different scenarios from the laparoscopic liver surgery, both resulting in important deformation of the liver: insufflation of the abdominal cavity with gas (pneumoperitoneum) and manipulation with the liver lobe using a surgical instrument (grasping pincers). For each scenario, a series of simulations is performed with or without modeling the deformation of the ligaments (fixed constraints or biomechanical model with the parameter of the literature). The numerical comparison shows that modeling the ligament deformations can be at least as important as the correct selection of the patient-specific parameters, nevertheless this observation depends on the simulated scenario.
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titre
Automatic Alignment of pre and intraoperative Data using Anatomical Landmarks for Augmented Laparoscopic Liver Surgery
auteur
Rosalie Plantefeve, Nazim Haouchine, Jean Pierre Radoux, Stéphane Cotin
article
International Symposium on Biomedical Simulation ISBMS, Oct 2014, Strasbourg, France. 2014
resume
Each year in Europe 50,000 new liver cancer cases are diagnosed for which hepatic surgery combined to chemotherapy is the most common treatment. In particular the number of laparoscopic liver surgeries has increased significantly over the past years. This type of minimally invasive procedure which presents many benefits for the patient is challenging for the surgeons due to the limited field of view. Recently new augmented reality techniques which merge preoperative data and intraoperative images and permit to visualize internal structures have been proposed to help surgeons during this type of surgery. One of the difficulties is to align preoperative data with the intraoperative images. We propose in this paper a semi-automatic approach for solving the ill-posed problem of initial alignment for Augmented Reality systems during liver surgery. Our registration method relies on anatomical landmarks extracted from both the laparoscopic images and three-dimensional model, using an image-based soft-tissue reconstruction technique and an atlas-based approach, respectively. The registration evolves automatically from a quasi-rigid to a non-rigid registration. Furthermore, the surface-driven deformation is induced in the volume via a patient specific biomechanical model. The experiments conducted on both synthetic and in vivo data show promising results with a registration error of 2 mm when dealing with a visible surface of 30% of the whole liver.
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titre
Interactive Training System for Interventional Electrocardiology Procedures
auteur
H Talbot, F Spadoni, Christian Duriez, M Sermesant, Stéphane Cotin, Hervé Delingette
article
6th International Symposium on Biomedical Simulation – ISBMS 2014, Oct 2014, Strabsourg, France. pp.11 – 19, 2014, <10.1007/978-3-319-12057-7_2>
resume
Recent progress in cardiac catheterization and devices al-lowed to develop new therapies for severe cardiac diseases like arrhyth-mias and heart failure. The skills required for such interventions are still very challenging to learn, and typically acquired over several years. Vir-tual reality simulators can reduce this burden by allowing to practice such procedures without consequences on patients. In this paper, we propose the first training system dedicated to cardiac electrophysiology, includ-ing pacing and ablation procedures. Our framework involves an efficient GPU-based electrophysiological model. Thanks to an innovative mul-tithreading approach, we reach high computational performances that allow to account for user interactions in real-time. Based on a scenario of cardiac arrhythmia, we demonstrate the ability of the user-guided simulator to navigate inside vessels and cardiac cavities with a catheter and to reproduce an ablation procedure involving: extra-cellular poten-tial measurements, endocardial surface reconstruction, electrophysiology mapping, radio-frequency (RF) ablation, as well as electrical stimulation. This works is a step towards computerized medical learning curriculum.
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titre
Interactive Training System for Interventional Electrocardiology Procedures
auteur
Hugo Talbot, Federico Spadoni, Christian Duriez, Maxime Sermesant, Stéphane Cotin, Hervé Delingette
article
Biomedical Simulation: 6th International Symposium, ISBMS 2014, Strasbourg, France, October 16-17, 2014. Proceedings, Oct 2014, Strasbourg, France. Lecture Notes in Computer Science (LNCS), 8789, pp.11-19, 2016, <10.1007/978-3-319-12057-7_2>
resume
Recent progress in cardiac catheterization and devices has allowed the development of new therapies for severe cardiac diseases like arrhythmias and heart failure. The skills required for such interventions are very challenging to learn, and are typically acquired over several years. Virtual reality simulators may reduce this burden by allowing trainees to practice such procedures without risk to patients. In this paper, we propose the first training system dedicated to cardiac electrophysiology, including pacing and ablation procedures. Our framework involves the simulation of a catheter navigation that reproduces issues intrinsic to intra-cardiac catheterization, and a graphics processing unit (GPU)-based electrophysiological model. A multi-threading approach is proposed to compute both physical simulations (navigation and electrophysiology) asynchronously. With this method, we reach computational performances that account for user interactions in real-time. Based on a scenario of cardiac arrhythmia, we demonstrate the ability of the user-guided simulator to navigate inside vessels and cardiac cavities with a catheter and to reproduce an ablation procedure involving: extra-cellular potential measurements, endocardial surface reconstruction, electrophysiol-ogy mapping, radio-frequency (RF) ablation, as well as electrical stimulation. A clinical evaluation assessing the different aspects of the simulation is presented. This works is a step towards computerized medical learning curriculum.
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titre
Introducing interactive inverse FEM simulation and its application for adaptive radiotherapy
auteur
Eulalie Coevoet, Nick Reynaert, Eric Lartigau, Luis Schiappacasse, Jérémie Dequidt, Christian Duriez
article
MICCAI – 17th International Conference on Medical Image Computing and Computer-Assisted Intervention, Sep 2014, Boston, United States. 2014
resume
We introduce a new methodology for semi-automatic deformable registration of anatomical structures, using interactive inverse simulations. The method relies on non-linear real-time Finite Element Method (FEM) within a constraint-based framework. Given a set of few registered points provided by the user, a real-time optimization adapts the boundary conditions and(/or) some parameters of the FEM in order to obtain the adequate geometrical deformations. To dramatically fasten the process, the method relies on a projection of the model in the space of the optimization variables. In this reduced space, a quadratic programming problem is formulated and solved very quickly. The method is validated with numerical examples for retrieving Young’s modulus and some pressures on the boundaries. Then, we apply the approach for the registration of the parotid glands during the radiotherapy of the head and neck cancer. Radiotherapy treatment induces weight loss that modifi es the shape and the positions of these structures and they eventually intersect the target volume. We show how we could adapt the planning to limit the radiation of these glands.
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titre
Intra-operative Registration for Deep Brain Stimulation Procedures based on a Full Physics Head Model
auteur
Alexandre Bilger, Eric Bardinet, Sara Fernández-Vidal, Christian Duriez, Pierre Jannin, Stéphane Cotin
article
MICCAI 2014 Workshop on Deep Brain Stimulation Methodological Challenges – 2nd edition, Sep 2014, Boston, United States. 2014
resume
Brain deformation is a factor of inaccuracy during stereotactic neurosurgeries. If this phenomenon is not considered in the pre-operative planning or intra-operatively, it could lead to surgical complications, side effects or ineffectiveness. In this paper, we present a patient-specific method to update the pre-operative planning based on a physical simulation of the brain shift. A minimization process estimates parameters of the simulation in order to compute the brain tissue deformation matching the partial data taken from intra-operative modalities. The simulation is based on a patient-specific biomechanical model of the brain and the cerebro-spinal fluid. We validate the method on a patient with a post-operative MRI.
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titre
Single View Augmentation of 3D Elastic Objects
auteur
Nazim Haouchine, Jérémie Dequidt, Marie-Odile Berger, Stéphane Cotin
article
International Symposium on Mixed and Augmented Reality – ISMAR, Sep 2014, Munich, Germany. 2014
resume
This paper proposes an efficient method to capture and augment highly elastic objects from a single view. 3D shape recovery from a monocular video sequence is an underconstrained problem and many approaches have been proposed to enforce constraints and resolve the ambiguities. State-of-the art solutions enforce smoothness or geometric constraints, consider specific deformation properties such as inextensibility or ressort to shading constraints. However, few of them can handle properly large elastic deformations. We propose in this paper a real-time method which makes use of a me chanical model and is able to handle highly elastic objects. Our method is formulated as a energy minimization problem accounting for a non-linear elastic model constrained by external image points acquired from a monocular camera. This method prevents us from formulating restrictive assumptions and specific constraint terms in the minimization. The only parameter involved in the method is the Young’s modulus where we show in experiments that a rough estimate of its value is sufficient to obtain a good reconstruction. Our method is compared to existing techniques with experiments conducted on computer-generated and real data that show the effectiveness of our approach. Experiments in the context of minimally invasive liver surgery are also provided.
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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.
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titre
Réalité augmentée pour la chirurgie minimalement invasive du foie utilisant un modèle biomécanique guidé par l’image
auteur
Nazim Haouchine, Stéphane Cotin, Jérémie Dequidt, Erwan Kerrien, Marie-Odile Berger
article
Reconnaissance de Formes et Intelligence Artificielle (RFIA) 2014, Jun 2014, France. 2014
resume
Cet article présente une méthode de réalité augmentée pour la chirurgie minimalement invasive du foie. Le réseau vasculaire et les tumeurs internes reconstruites à partir des données pré-opératoires (IRM ou CT) peuvent ainsi être visualisées dans l’image laparoscopique afin de guider les gestes du chirurgien pendant l’opération. Cette méthode est capable de propager les déformations 3D de la surface du foie à ses structures internes grâce à un modèle biomécanique sous-jacent qui prend en compte l’anisotropie et l’hétérogénéité du tissu hépatique. Des résultats sont montrés sur une vidéo in-vivo d’un foie humain acquise pendant une opération et sur un foie en silicone.
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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.
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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
Towards an Accurate Tracking of Liver Tumors for Augmented Reality in Robotic Assisted Surgery
auteur
Nazim Haouchine, Jérémie Dequidt, Igor Peterlik, Erwan Kerrien, Marie-Odile Berger, Stéphane Cotin
article
International Conference on Robotics and Automation (ICRA), Jun 2014, Hong Kong, China. 2014
resume
This article introduces a method for tracking the internal structures of the liver during robot-assisted procedures. Vascular network, tumors and cut planes, computed from pre-operative data, can be overlaid onto the laparoscopic view for image-guidance, even in the case of large motion or deformation of the organ. Compared to current methods, our method is able to precisely propagate surface motion to the internal structures. This is made possible by relying on a fast yet accurate biomechanical model of the liver combined with a robust visual tracking approach designed to properly constrain the model. Augmentation results are demonstrated on in-vivo sequences of a human liver during robotic surgery, while quantitative validation is performed on an ex-vivo porcine liver experimentation. Validation results show that our approach gives an accurate surface registration with an error of less than 6mm on the position of the tumor.
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titre
Virtual Simulation of Stapedotomy Surgery
auteur
Guillaume Kazmitcheff, Yann Nguyen, Mathieu Miroir, Evelyne Ferrary, Stéphane Cotin, Christian Duriez, Olivier Sterkers
article
ARO 2014, Feb 2014, San Diego, CA, United States. 2014
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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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titre
Interactive Planning of Cryotherapy Using Physically-Based Simulation
auteur
Hugo Talbot, Myriam Lekkal, Rémi Béssard-Duparc, Stéphane Cotin
article
MMVR 21 – Medicine Meets Virtual Reality – 2014, Feb 2014, Manhattan Beach, California, United States. 2014
resume
Cryotherapy is a rapidly growing minimally invasive technique for the treatment of certain tumors. It consists in destroying cancer cells by extreme cold delivered at the tip of a needle-like probe. As the resulting iceball is often smaller than the targeted tumor, a key to the success of cryotherapy is the planning of the position and orientation of the multiple probes required to treat a tumor, while avoiding any damage to the surrounding tissues. In order to provide such a planning tool, a number of challenges need to be addressed such as fast and accurate computation of the freezing process or interactive positioning of the virtual cryoprobes in the pre-operative image volume. To address these challenges, we present an approach which relies on an advanced computational framework, and a gesture-based planning system using contact-less technology to remain compatible with a use in a sterile environment.
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titre
Computation and Visualization of Risk Assessment in Deep Brain Stimulation
auteur
Alexandre Bilger, Christian Duriez, Stéphane Cotin
article
MMVR 21 – Medicine Meets Virtual Reality, Feb 2014, Manhattan Beach, California, United States. IOS Press, 2014
resume
Deep Brain Stimulation is a neurosurgical approach for the treatment of pathologies such as Parkinson’s disease. The basic principle consists in placing a thin electrode in a deep part of the brain. To safely reach the target of interest, careful planning must be performed to ensure that no vital structure (e.g. blood vessel) will be damaged during the insertion of the electrode. Currently this planning phase is done without considering the brain shift, which occurs during the surgery once the skull is open, leading to increased risks of complications. In this paper, we propose a method to compute the motion of anatomical structures induced by the brain shift. This computation is based on a biomechanical model of the brain and the cerebro-spinal fluid. We then visualize in a intuitive way the risk of damaging vital structures with the electrode.
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Other publications

titre
Information Processing in Computer-Assisted Interventions: 4th International Conference, 2013
auteur
Dean Barratt, Pierre Jannin, Gabor Fichtinger, Stéphane Cotin
article
Information processing in computer-assisted interventions: 4th international conference, 2013. 2014
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Patents

titre
Interface de commande à distance d’un dispositif de contrôle et d’affichage d’informations dans une salle d’opération chirurgicale
auteur
Stéphane Cotin, Géry Casiez, Myriam Lekkal, Raffaella Trivisonne
article
France, N° de brevet: 14 60867. 2014
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Theses

titre
Patient-specific biomechanical simulation for deep brain stimulation
auteur
Alexandre Bilger
article
Modeling and Simulation. Université des Sciences et Technologie de Lille, 2014. English
resume
Deep brain stimulation is a neurosurgical treatment involving the permanent implantation of electrodes in the brain, to stimulate a specific deep structure. Electrical stimulation of some brain structures treats symptoms of motor or affective neurological disorders. The success of the operation relies on the electrode placement precision, which the goal is to maximize the therapeutic outcomes, and minimize the adverse effects. To do that, a pre-operative planning step determine the target coordinates to stimulate, as well as the electrode trajectory to reach it, thanks to a combination of medical images of the patient and numerical tools. However, intra-operative brain deformation, called brain shift, might invalidate the planning. The contributions of this thesis rely on a biomechanical model of brain shift which comprises a mechanical model for deformation, as well as a model of cerebrospinal fluid leak. We present a pre-operative tool, based on our model, in order to provide to the surgeon an information on the deformation risks, that he could use to select a safe trajectory for the patient, even in the case of brain shift. Moreover, we propose an intra-operative registration method based on our biomechanical model, in order to compute the new location of anatomical structures. Finally, thanks to a model of insertion of the electrode and its interaction with brain tissue, we reproduce the operating protocol in order to compute the electrode curvature due to brain shift.
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titre
Interactive Patient-Specific Simulation of Cardiac Electrophysiology
auteur
Hugo Talbot
article
Computer Science [cs]. Université des Sciences et Technologies de Lille, 2014. English
resume
As in most of the medical departments, interns in cardiac electrophysiology follow a curriculum combining an intense theoritical learning with a long clinical practice. After years of theory (mainly book learning), junior electrophysiologists start practicing on patients under the supervision of a senior cardiologist. In the last decades, the improvement of computational technologies led to the development of numerical tools dedicated to training, planning or guiding of surgical procedures. The objective of this thesis is to construct a training framework, allowing junior electrophysiologists to practice radio-frequency (RF) ablation for the treatment of ventricular arrhythmias on virtual patients. Training on in silico models can not only shorten the electrophysiology curriculum, but it can also standardize it. Yet the development of such training systems raises several challenges. The first challenge consists in simulating the cardiac electrophysiology in real-time. Through the improvement of cardiac imaging, characterization of the normal and arrhythmic electrical activity of the heart using mathematical models has been an important research topic. We focus here on a model representing the electrophysiology at the organ scale: the Mitchell-Schaeffer model. A powerful GPU implementation is proposed to reach real-time performances. Our efficient electrophysiology model is coupled with a mechanical model of the heart. A realistic left bundle branch block can be simulated, thus inducing the associated late contraction of the left ventricle. For clinical application of electrophysiological mathematics, our virtual scenario of cardiac arrhythmias needs to be personalized. This crucial step aims at adapting all model parameters in order to fit patient data, acquired intra-operatively. After a detailed state of the art of optimization methods, the unscented Kalman filter deriving from a Bayesian approach is chosen and applied on a dataset of three patients suffering from ventricular tachycardia. Relying on our GPU electrophysiology model, the optimization process is achieved in about 20~minutes, while faithfully reproducing the pathology recorded in the operation room. Lastly, the construction of the first training framework dedicated to cardiac ablation is presented. The scenario reproduces the catheter navigation inside the vascular system using a physics-based approach, and the beating heart is modeled from patient data. In addition to the cardiovascular navigation, a case of an ectopic focus in the right ventricle is modeled using our GPU implementation. An innovative multithreading approach couples both simulations, thus offering performances close to real-time. The computational efficiency allows the trainee to interact with the simulation and perform all the clinical gestures, namely electrical catheter measurements, electro-anatomical mapping, electrical stimulation and eventually RF ablation. A clinical evaluation by electrophysiologists highlights the good performances and the realism of the training framework.
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titre
Modélisation dynamique de l’oreille moyenne et des interactions outils organes pour la conception d’un simulateur appliqué à la chirurgie otologique
auteur
Guillaume Kazmitcheff
article
Informatique [cs]. L’UNIVERSITÉ DES SCIENCES ET DES TECHNOLOGIES DE LILLE 1, 2014. Français
resume
La microchirurgie de l’oreille moyenne requiert une forte dextérité en raison de la finesse et de l’extrême sensibilité des structures impliquées. L’apprentissage de cette chirurgie est délicat et est effectué en fin d’internat. Ce travail porte sur le développement d’un modèle mécanique en éléments finis des différentes structures qui composent l’oreille moyenne dans le but de concevoir un simulateur chirurgical. Les objectifs sont de fournir un outil polyvalent pour l’apprentissage et l’entraînement de la chirurgie par la chirurgie, ainsi que d’offrir la possibilité d’explorer et d’évaluer de nouvelles procédures chirurgicales liées à l’apport de nouvelles technologies telles que la robotique. Le comportement mécanique du modèle développé a été confronté avec succès aux observations réalisées sur des pièces anatomiques. Afin d’obtenir un outil de simulation qui tient compte des différences anatomiques de chaque patient, une méthode de déformation de l’atlas mécanique basée sur l’imagerie clinique a été implémentée. La simulation du fraisage de la platine de l’étrier ainsi que le placement d’une prothèse ossiculaire ont été réalisés à l’aide d’une interface haptique et d’une nouvelle approche du rendu. Ce travail constitue ainsi le premier simulateur virtuel de chirurgie de l’oreille moyenne. Enfin le robot télé-opéré, RobOtol, a été intégré au simulateur afin d’étudier de nouvelles procédures chirurgicales robotisées. La simulation permet, en outre, d’entraîner les otologistes à l’utilisation du robot. Le travail effectué porte essentiellement sur la simulation interactive réaliste des procédures chirurgicales complexes ainsi que sur la formation et la robotisation de la microchirurgie otologique.
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titre
Robust blood vessel surface reconstruction for interactive simulations from patient data
auteur
Ahmed Yureidini
article
Medical Imaging. Université des Sciences et Technologie de Lille – Lille I, 2014. English
resume
In the context of interactive simulation, the lack of patient specific geometrical models remains one of the major limitations of simulators. Current commercial simulators proposed no or a limited number of cases. However, a vast literature on the subject has been introduced in the past twenty years. Nevertheless, the proposed methods are not adapted to an interactive context, especially when dealing with vascular networks. In this work, we address the problem of blood vessel segmentation and reconstruction from 3DRA patient data. To this end, we propose two novel algorithms for segmentation and reconstruction. First, the vessel tree is built by tracking the vessel centerline. Our dedicated tracking process also extracts points on the vessel surface in a robust way. Second, those points are fitted by an implicit surface (a blobby model) that is iteratively refined. Tracking and reconstruction results are reported on synthetic and patient data. Simulations within an interventional tool navigation context showed that the resulting geometrical model complies with interactive simulation requirements: fast collision detection and prediction, topology information, smoothness and availability of differential quantities for contact response computation.
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2013

Journal articles

titre
A Combined Force and Thermal Feedback Interface for Minimally Invasive Procedures Simulation
auteur
Mohamed Guiatni, Vincent Riboulet, Christian Duriez, Abderrahmane Kheddar, Stéphane Cotin
article
IEEE/ASME Transactions on Mechatronics, Institute of Electrical and Electronics Engineers, 2013, 18 (3), pp.1170-1181. <10.1109/TMECH.2012.2197862>
resume
We present a new interface for minimally invasive surgery (MIS) training that incorporates novel broadband sensory modalities that include visual, force, and thermal technology, into the evolution of the next generation of surgical robotics and simulators. A new haptic device is designed to provide high force and torque capabilities for a better touch feedback. Part of the surgical tool is kept to be the real grasper (i.e., the handle) of the haptic interface. Yet, our main novel contribution is in integrating thermal feedback in MIS applied perspectives; indeed, thermal sensing finds particular utility in detecting and isolating unstable arterial plaque and tumors. In addition, thermal energy is used in several therapeutic procedures such as tumor ablation or tissue welding. We propose several thermal exchange models based on the Pennes’bioheat transfer equation. The overall haptic interface (force and thermal display) is interfaced with an open source virtual reality simulator (the SOFA framework). We added in SOFA the necessary models dealing with thermal simulation using built-in data structure and methods. The integration is successful, and realistic simulation scenarios combining visual, thermal, and force feedback were achieved. Results using the overall simulation are presented and evaluated
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titre
Towards an Interactive Electromechanical Model of the Heart
auteur
Hugo Talbot, Stéphanie Marchesseau, Christian Duriez, Maxime Sermesant, Stéphane Cotin, Hervé Delingette
article
Interface Focus, Royal Society publishing, 2013, The Virtual Physiological Human: Integrative Approaches to Computational Biomedicine, 3 (2), pp.4. <http://rsfs.royalsocietypublishing.org/content/3/2/20120091.full.pdf+html>. <10.1098/rsfs.2012.0091>
resume
In this work, we develop an interactive framework for rehearsal and training in the context of cardiac catheter ablation, and for planning in the context of Cardiac Resynchronization Therapy (CRT). To this end, an interactive and real-time electrophysiology model of the heart is developed to fit patient-specific data. The proposed interactive framework relies on two main contributions. An efficient implementation of cardiac electrophysiology is first proposed using latest GPU computing techniques. Second, a mechanical simulation is then coupled to the electrophysiological signals to produce realistic motion of the heart. We demonstrate that pathological mechanical and electrophysiological behaviour can be simulated.
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titre
Novel DNA polymerase mutations conferring cytomegalovirus resistance: input of BAC-recombinant phenotyping and 3D model.
auteur
Sébastien Hantz, Sébastien Cotin, Eva Borst, Anthony Couvreux, Arielle Salmier, Isabelle Garrigue, Pierre Merville, Catherine Mengelle, Michel Attal, Martin Messerle, Sophie Alain
article
Antiviral Research, Elsevier Masson, 2013, 98(1), pp.130-4. <10.1016/j.antiviral.2013.02.002>
resume
Long-term exposure to antiviral therapy in immunocompromised patients favors emergence of human cytomegalovirus (HCMV) resistance mutations. Two new UL54 DNA polymerase mutations (deletion of codon 524 and N408S substitution) identified in a kidney recipient and a bone marrow recipient respectively were characterized. Marker transfer experiment through recombination into a HCMV AD169 BAC demonstrated del524 and mutation N408S confer GCV and CDV resistance. These results suggest continued mutation of UL54 under selective antiviral pressure. Characterization of each new mutation is thus required to inform genotypic assays and to better understand the functional regions of UL54 for the development of novel antivirals.
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titre
Deformation-based Augmented Reality for Hepatic Surgery
auteur
Nazim Haouchine, Jérémie Dequidt, Marie-Odile Berger, Stéphane Cotin
article
Studies in Health Technology and Informatics, IOS Press, 2013, 184
resume
In this paper we introduce a method for augmenting the laparoscopic view during hepatic tumor resection. Using augmented reality techniques, vessels, tumors and cutting planes computed from pre-operative data can be overlaid onto the laparoscopic video. Compared to current techniques, which are limited to a rigid registration of the pre-operative liver anatomy with the intra-operative image, we propose a real-time, physics-based, non-rigid registration. The main strength of our approach is that the deformable model can also be used to regularize the data extracted from the computer vision algorithms. We show preliminary results on a video sequence which clearly highlights the interest of using physics-based model for elastic registration.
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titre
Conception d’un atlas mécanique pour la simulation de la chirurgie de l’oreille moyenne
auteur
Guillaume Kazmitcheff, Yann Nguyen, Mathieu Miroir, Evelyne Ferrary, Christian Duriez, Stéphane Cotin, Olivier Sterkers
article
Annales françaises d’Oto-rhino-laryngologie et de Pathologie Cervico-faciale, Elsevier, United States, 2013, 130 (4), pp.A76
resume
no abstract
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titre
Évaluation de techniques chirurgicales innovantes pour l’otospongiose à l’aide d’un simulateur chirurgical
auteur
Yann Nguyen, Guillaume Kazmitcheff, Mathieu Miroir, Evelyne Ferrary, Christian Duriez, Stéphane Cotin, Olivier Sterkers
article
Annales françaises d’Oto-rhino-laryngologie et de Pathologie Cervico-faciale, Elsevier, United States, 2013, 130 (4), pp.A76
resume
no abstract
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titre
Validation Method of a Middle Ear Mechanical Model to Develop a Surgical Simulator
auteur
Guillaume Kazmitcheff, Mathieu Miroir, Yann Nguyen, Evelyne Ferrary, Olivier Sterkers, Stéphane Cotin, Christian Duriez, Alexis Bozorg-Grayeli
article
Audiology and Neurotology, Karger, 2013, <10.1159/000356301>
resume
Ossicular surgery requires a high dexterity for the manipulation of the fragile and small middle ear components. Currently, the only efficient technique for training residents in otological surgery is through the use of temporal bone specimens, where any existing surgical simulator does not provide useful feedback. The objective of this study was to develop a finite-element model of the human ossicular chain dedicated to surgical simulation and to propose a method to evaluate its behavior. A model was developed based on human middle ear micromagnetic resonance imaging. The mechanical parameters were determined according to published data. To assess its performance, the middle ear transfer function was analyzed. The robustness of our model and the influence of different middle ear components were also evaluated at low frequency by static force pressure simulations. The mechanical behavior of our model in nominal and pathological conditions was in good agreement with published human temporal bone measurements. We showed that the cochlea influences the transfer function only at high frequency and could be omitted from a surgical simulator. In addition, surgeons were able to manipulate the validated middle ear model with a real-time haptic feedback. The computational efficiency of our approach allowed real-time interactions, making it suitable for use in a training simulator.
Accès au bibtex
titre
Modelling Prostate Deformation: SOFA versus Experiments
auteur
Pedro Moreira, Igor Peterlik, Herink Mark, Christian Duriez, Stéphane Cotin, Sarthak Misra
article
Mechanical Engineering Research, Canadian Center of Science and Education, 2013, 3 (2), p64. <10.5539/mer.v3n2p64>
resume
Needle insertion procedures are commonly used to treat and to diagnose prostate cancer. Surgical simulation systems can be used to estimate prostate deformation during pre- and intra-operative needle insertion planning. Such systems require a model that can accurately predict the prostate deformation in real time. In this study, we present a prostate model that incorporates the anatomy of the male pelvic region. The model is used to predict the prostate deformation during needle insertion and it is implemented in the Simulation Open Framework Architecture (SOFA). SOFA simulations are compared with experimental results for two scenarios: indentation and needle insertion. An experimental phantom is developed using anatomically accurate magnetic resonance images and populated with elasticity properties obtained from ultrasound-based Acoustic Radiation Force Impulse imaging technique. Markers are placed on the phantom surface to identify the deformation during indentation experiments. The root mean square error (RMSE) obtained in indentation experiments is 0.36 mm. During the needle insertion, the needle tip position is used to validate the model. The SOFA simulation resulted in a RMSE of 0.14 mm. The results of this study demonstrate that SOFA is a feasible option to be used in surgical simulations for pre-operative planning and training.
Accès au bibtex
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.
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Conference papers

titre
Connective Tissues Simulation on GPU
auteur
Julien Bosman, Christian Duriez, Stéphane Cotin
article
10th Workshop on Virtual Reality Interaction and Physical Simulation, Nov 2013, Lille, France. 2013
resume
Recent work in the field of medical simulation have led to real advances in the mechanical simulation of organs. However, it is important to notice that, despite the major role they may have in the interaction between organs, the connective tissues are often left out of these simulations. In this paper, we propose a model which can rely on either a mesh based or a meshless methods. To provide a realistic simulation of these tissues, our work is based on the weak form of continuum mechanics equations for hyperelastic soft materials. Furthermore, the stability of deformable objects simulation is ensured by an implicit temporal integration scheme. Our method allows to model these tissues without prior assumption on the dimension of their of their geometry (curve, surface or volume), and enables mechanical coupling between organs. To obtain an interactive frame rate, we develop a parallel version suitable for to GPU computation. Finally we demonstrate the proper convergence of our finite element scheme.
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titre
Haptic Rendering of Interacting Dynamic Deformable Objects Simulated in Real-Time at Different Frequencies
auteur
François Dervaux, Igor Peterlik, Jérémie Dequidt, Stéphane Cotin, Christian Duriez
article
IROS – IEEE/RSJ International Conference on Intelligent Robots and Systems, Nov 2013, Tokyo, Japan. IEEE, 2013
resume
The dynamic response of deformable bodies varies significantly in dependence on mechanical properties of the objects: while the dynamics of a stiff and light object (e. g. wire or needle) involves high-frequency phenomena such as vibrations, much lower frequencies are sufficient for capturing dynamic response of an object composed of a soft tissue. Yet, when simulating mechanical interactions between soft and stiff deformable models, a single time-step is usually employed to compute the time integration of dynamics of both objects. However, this can be a serious issue when haptic rendering of complex scenes composed of various bodies is considered. In this paper, we present a novel method allowing for dynamic simulation of a scene composed of colliding objects modelled at different frequencies: typically, the dynamics of soft objects are calculated at frequency about 50 Hz, while the dynamics of stiff object is modeled at 1 kHz, being directly connected to the computation of haptic force feedback. The collision response is performed at both low and high frequencies employing data structures which describe the actual constraints and are shared between the high and low frequency loops. During the simulation, the realistic behaviour of the objects according to the mechanical principles (such as non-interpenetration and action-reaction principle) is guaranteed. Examples showing the scenes involving different bodies in interaction are given, demonstrating the benefits of the proposed method.
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titre
Image-guided Simulation of Heterogeneous Tissue Deformation For Augmented Reality during Hepatic Surgery
auteur
Nazim Haouchine, Jérémie Dequidt, Igor Peterlik, Erwan Kerrien, Marie-Odile Berger, Stéphane Cotin
article
ISMAR – IEEE International Symposium on Mixed and Augmented Reality 2013, Oct 2013, Adelaide, Australia. 2013
resume
This paper presents a method for real-time augmentation of vas- cular network and tumors during minimally invasive liver surgery. Internal structures computed from pre-operative CT scans can be overlaid onto the laparoscopic view for surgery guidance. Com- pared to state-of-the-art methods, our method uses a real-time biomechanical model to compute a volumetric displacement field from partial three-dimensional liver surface motion. This permits to properly handle the motion of internal structures even in the case of anisotropic or heterogeneous tissues, as it is the case for the liver and many anatomical structures. Real-time augmentation results are presented on in vivo and ex vivo data and illustrate the benefits of such an approach for minimally invasive surgery.
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titre
Towards a better understanding of pelvic system disorders using numerical simulation
auteur
Pauline Lecomte-Grosbras, Mouhamadou Nassirou – Diallo, Jean-François Witz, Damien Marchal, Jérémie Dequidt, Stéphane Cotin, Michel Cosson, Christian Duriez, Mathias Brieu
article
Medical Image Computing and Computer Assisted Intervention, Sep 2013, Nagoya, Japan. 2013
resume
Genital prolapse is a pathologic hyper-mobility of the organs that forms the pelvic system. Although this is common condition, the pathophysiology of this disorder is not well known. In order to improve the understanding of its origins, we recreate – virtually – this biomechanical pathology using numerical simulation. The approach builds on a finite element model with parameters measured on several fresh cadavers. The meshes are created from a MRI of a healthy woman and the simulation includes the mechanical interactions between organs (contacts, ligaments, adhesion…). The model is validated through comparison of functional mobilities of the pelvic system observed on a dynamic MRI. We then propose to modify, step by step, the model and its parameters to produce a pathologic situation and have a better understanding of the process. It is not a formal proof but the numerical experiments reinforce the clinical hypothesis on the multifactorial origins of the pathology.
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titre
Simulation of Lipofilling Reconstructive Surgery using coupled Eulerian Fluid and Deformable Solid Models
auteur
Vincent Majorczyk, Stéphane Cotin, Christian Duriez, Jérémie Allard
article
Medical Image Computing and Computer Assisted Intervention Society, Sep 2013, Nagoya, Japan. Springer, 2013
resume
We present a method to simulate the outcome of reconstructive facial surgery based on fat-filling. Facial anatomy is complex: the fat is constrained between layers of tissues which behave as walls along the face; in addition, connective tissues that are present between these different layers also influence the fat-filling procedure. To simulate the end result, we propose a method which couples a 2.5D Eulerian fluid model for the fat and a finite element model for the soft tissues. The two models are coupled using the computation of the mechanical compliance matrix. Two contributions are presented in this paper: a solver for fluids which couples properties of solid tissues and fluid pressure, and an application of this solver to fat-filling surgery procedure simulation.
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titre
Registration of a Validated Mechanical Atlas of Middle Ear for Surgical Simulation
auteur
Guillaume Kazmitcheff, Christian Duriez, Mathieu Miroir, Yann Nguyen, Olivier Sterkers, Alexis Bozorg-Grayeli, Stéphane Cotin
article
MICCAI 2013, 2013, Nagoya, Japan. 2013
resume
This paper is centered on the development of a new train- ing and rehearsal simulation system for middle ear surgery. First, we have developed and validated a mechanical atlas based on finite element method of the human middle ear. The atlas is based on a microMRI. Its mechanical behavior computed in real-time has been successfully val- idated. In addition, we propose a method for the registration of the mechanical atlas on patient imagery. The simulation can be used for a rehearsal surgery with the geometrical anatomy of a given patient and with mechanical data that are validated. Moreover, this process does not necessitate a complete re-built of the model.
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titre
Control of Elastic Soft Robots based on Real-Time Finite Element Method
auteur
Christian Duriez
article
ICRA 2013 IEEE International Conference on Robotics and Automation, 2013, Karlsruhe, France. 2013
resume
In this paper, we present a new method for the control of soft robots with elastic behavior, piloted by several actuators. The central contribution of this work is the use of the Finite Element Method (FEM), computed in real-time, in the control algorithm. The FEM based simulation computes the nonlinear deformations of the robots at interactive rates. The model is completed by Lagrange multipliers at the actuation zones and at the end-effector position. A reduced compliance matrix is built in order to deal with the necessary inversion of the model. Then, an iterative algorithm uses this compliance matrix to find the contribution of the actuators (force and/or position) that will deform the structure so that the terminal end of the robot follows a given position. Additional constraints, like rigid or deformable obstacles, or the internal characteristics of the actuators are integrated in the control algorithm. We illustrate our method using simulated examples of both serial and parallel structures and we validate it on a real 3D soft robot made of silicone
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Habilitation à diriger des recherches

titre
Real-time haptic simulation of medical procedures involving deformations and device-tissue interactions
auteur
Christian Duriez
article
Modeling and Simulation. Université des Sciences et Technologie de Lille – Lille I, 2013
resume
The research work presented for the habilitation thesis aim to provide new simulation tools for medical and surgical interventions.These tools have many applications including training of physicians, planning of interventions (for rehearsal and for the validation of a therapy) or providing assistance during a real intervention. However, to obtain a realistic or even predictive simulation of the procedure, we must take into account the deformation of anatomical structures and the mechanical interactions between devices and tissues. At the same time, the simulation must be interactive and computed in real-time to keep the gesture of the physician in the loop of the simulation. The major challenge of our work is to guarantee a certain level of accuracy in the simulation while keeping a very short computation time, consistent with the real-time. First, we present an optimized formulation of the finite element method (FEM) for the deformable models and new numerical tools (preconditionner, coupling between models…) dedicated to real-time FEM computation. This approach is used to compute the biomechanics of anatomical soft-tissues, as well as flexible instruments. The second key point is the boundary conditions: the mechanical interactions between organs and/or with surgical devices are often difficult to account for. Yet, a bad modeling of these interaction can lead to a large source of errors. Our approach builds on non-smooth mechanics for modeling contact and friction between solids but also extends to other models of interaction (like needle insertion for instance). In this context, we also address the difficult problem of computing the compliance of deformable structures in real-time. Third, during some procedures, the visual feedback is far from perfect and the physician uses haptic feedback for guidance. In such case it is important to provide haptic rendering using dedicated haptic devices and simulation algorithms. In this domain, we provide a new asynchronous approach that is centered on the mechanical interactions between devices and human tissues. The method addresses the problem of high-refresh rates (1kHz) needed in the haptic loop. Finally, we present some research results on concrete application examples that we are currently developing. We present the remaining challenges to allow a large diffusion of the simulation as a clinical tool, used by physicians in the future.
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Books

titre
Information Processing in Computer-Assisted Interventions – Proceedings of the 4th International IPCAI conference, Heidelberg, June 26, 2013.
auteur
Stéphane Cotin, Pierre Jannin, Dean Barratt, Nassir Navab, Gabor Fichtinger
article
Barratt, D. and Cotin, S. and Fichtinger, G. and Jannin, P. and Navab, N. Springer, 7915, pp.111, 2013, 978-3-642-38568-1
resume
This book constitutes the proceedings of the 4th International Conference on Information Processing in Computer-Assisted Interventions IPCAI 2013, held in Heidelberg, Germany, on June 26, 2013. The 11 papers presented were carefully reviewed and selected from 20 submissions. The papers are organized in topical sections on simulation, neurosurgical interventions, ultrasound guided interventions, and image guided interventions.
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Reports

titre
Deliverable D10.4.2
auteur
Hugo Talbot, Federico Spadoni, Maxime Sermesant, Nicholas Ayache, Hervé Delingette
article
[Research Report] 2013, pp.22
resume
This deliverable describes the final status of Task 10.4 of Workpackage 10 of the euHeart project. The aim of this task is to develop a prototype of an endovascular simulator of cardiac radiofrequency ablation. More precisely, its purpose is to simulate the patient-specific catheter navigation and radiofre- quency ablation of ventricular tachycardia. Since deliverable 10.4.1, work on the simulator prototype has focused on the development of a user interface and the integration of two software compo- nents : endovascular simulation and electrophysiology simulation. The first component aims at modeling the deformation of catheters and guidewires inside vessels and to generate a realistic visualization of the vis- ible X-ray images. The second component is focused on the simulation of electrophysiology. We have chosen the Mitchell-Schaeffer phenomenological model to represent the evolution of action potential on the myocardium. The integration of those 2 software components is difficult because they should both run simultaneously in real-time. To this end, we have developed a multi-thread framework allowing to parallelize the computation of the catheter deformation and the cardiac electrophysiology while sharing a minimum num- ber of information. We have also developed a user interface that can display X-ray images, 3D view of the heart and simulated electro-physiology signals measured at the tip of the catheter. An example of simulation is provided starting from the endovascular navi- gation from the veina cava and finishing with the radiofrequency ablation of endocardial tissue inside the right ventricle.
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2012

Journal articles

titre
From conception to application of a tele-operated assistance robot for middle ear surgery
auteur
Yann Nguyen, Mathieu Miroir, Guillaume Kazmitcheff, Evelyne Ferrary, Olivier Sterkers, Alexis Bozorg-Grayeli
article
Surgical Innovation, SAGE Publications (UK and US), 2012, 19 (3), pp.241–251. <10.1177/1553350611426012>
resume
The authors’ goal was to design and evaluate a robot dedicated to middle ear surgery. Specifications for dimensions, forces, and kinematics were collected, based on the otosclerosis procedure. The robot structure has a compact geometry with 3 linear and 3 rotatory motors. It is remotely piloted via a robot-surgeon interface under operative microscope. Ability to reach anatomical targets, to perform stapedectomy, and to place prosthesis in a model of stapedotomy was evaluated by 6 surgeons. Multiple anatomical targets in the middle ear could be successfully reached without damaging surrounding structures. The robot could be used under operative microscope with minimal visual field impairment or jointly with a 4-mm endoscope through the external auditory canal to perform stapedectomy in temporal bone specimens. Prosthesis could be inserted in the stapedotomy model. The assistance robot is the first prototype with 6 degrees of freedom, a kinematic structure, and dimensions optimized for tele-operated middle ear surgery.
Accès au bibtex
titre
Friction force measurement during cochlear implant insertion: application to a force-controlled insertion tool design
auteur
Mathieu Miroir, Yann Nguyen, Guillaume Kazmitcheff, Evelyne Ferrary, Olivier Sterkers, Alexis Bozorg-Grayeli
article
Otology and Neurotology, Lippincott, Williams & Wilkins, 2012, 33 (6), pp.1092–1100. <10.1097/MAO.0b013e31825f24de>
resume
no abstract
Accès au bibtex
titre
Ear robot surgeons
auteur
Mathieu Miroir, Yann Nguyen, Guillaume Kazmitcheff, Evelyne Ferrary, Olivier Sterkers
article
Biofutur, Elsevier – Cachan : Lavoisier, 2012, pp.43–44
resume
no abstract
Accès au bibtex
titre
Des robots chirurgiens de l’oreille
auteur
Mathieu Miroir, Yann Nguyen, Guillaume Kazmitcheff, Evelyne Ferrary, Olivier Sterkers
article
Biofutur, Elsevier – Cachan : Lavoisier, 2012, 31 (337), pp.43–44
resume
Née dans les années 1980, la chirurgie assistée par ordinateur est aujourd’hui implantée dans de nombreux blocs opératoires. Son objectif n’est pas de remplacer le praticien mais de lui apporter une aide « intelligente » en améliorant son pouvoir de perception, de décision et d’action. Elle a également apporté des améliorations notables pour le patient en limitant la douleur, la taille des cicatrices et les complications post-opératoires.
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titre
Mesure des forces d’insertions durant l’implantation cochléaire: intérêt pour le chirurgien
auteur
Yann Nguyen, Mathieu Miroir, Guillaume Kazmitcheff, Evelyne Ferrary, Julie Bensimon, Olivier Sterkers, Alexis Bozorg-Grayeli
article
Annales françaises d’Oto-rhino-laryngologie et de Pathologie Cervico-faciale, Elsevier, United States, 2012, 129 (4), pp.A90
resume
no abstract
Accès au bibtex
titre
Évaluation des performances des chirurgiens pour un abord de la fenêtre ronde par des rochers artificiels
auteur
S Touhami, Yann Nguyen, Guillaume Kazmitcheff, Mathieu Miroir, Olivier Sterkers, Alexis Bozorg-Grayeli
article
Annales françaises d’Oto-rhino-laryngologie et de Pathologie Cervico-faciale, Elsevier, United States, 2012, 129 (4), pp.A45–A46. <10.1016/j.aforl.2012.07.119>
resume
no abstract
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titre
Mise au point d’un simulateur et d’un modèle mécanique de l’oreille moyenne pour la chirurgie ossiculaire
auteur
Guillaume Kazmitcheff, Mathieu Miroir, Christian Duriez, Yann Nguyen, Stéphane Mazalaigue, Evelyne Ferrary, Julie Bensimon, Olivier Sterkers, Stéphane Cotin, Alexis Bozorg-Grayeli
article
Annales françaises d’Oto-rhino-laryngologie et de Pathologie Cervico-faciale, Elsevier, United States, 2012, 129 (4), pp.A77. <10.1016/j.aforl.2012.07.204>
resume
no abstract
Accès au bibtex
titre
Cochlear implant insertion forces in microdissected human cochlea to evaluate a prototype array
auteur
Yann Nguyen, Mathieu Miroir, Guillaume Kazmitcheff, Jasmine Sutter, Morad Bensidhoum, Evelyne Ferrary, Olivier Sterkers, Alexis Bozorg Grayeli
article
Audiology and Neurotology, Karger, 2012, 17 (5), pp.290
resume
Cochlear implant array insertion forces are potentially related to cochlear trauma. We compared these forces between a standard (Digisonic SP; Neurelec, Vallauris, France) and an array prototype (Neurelec) with a smaller diameter. The arrays were inserted by a mechatronic tool in 23 dissected human cochlea specimens exposing the basilar membrane. The array progression under the basilar membrane was filmed together with dynamic force measurements. Insertion force profiles and depth of insertion were compared. The recordings showed lower insertion forces beyond 270° of insertion and deeper insertions with the thin prototype array. This will potentially allow larger cochlear coverage with less trauma.
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titre
Modeling and Real-Time Simulation of a Vascularized Liver Tissue
auteur
Igor Peterlík, Christian Duriez, Stéphane Cotin
article
Medical Image Computing and Computer-Assisted Intervention–MICCAI 2012, 2012, pp.50–57
resume
In Europe only, about 100,000 deaths per year are related to cirrhosis or liver cancer. While surgery remains the option that offers the foremost success rate against such pathologies, several limitations still hinder its widespread development. Among the limiting factors is the lack of accurate planning systems, which has been a motivation for several recent works, aiming at better resection planning and training systems, relying on pre-operative imaging, anatomical and biomechanical modelling. While the vascular network in the liver plays a key role in defining the operative strategy, its influence at a biomechanical level has not been taken into account. In the paper we propose a real-time model of vascularized organs such as the liver. The model takes into account separate constitutive laws for the parenchyma and vessels, and defines a coupling mechanism between these two entities. In the evaluation section, we present results of in vitro porcine liver experiments that indicate a significant influence of vascular structures on the mechanical behaviour of tissue. We confirm the val- ues obtained in the experiments by computer simulation using standard FEM. Finally, we show that the conventional modelling approach can be efficiently approximated with the proposed composite model capable of real-time calculations.
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Conference papers

titre
Physics-based Augmented Reality for 3D Deformable Object
auteur
Nazim Haouchine, Jérémie Dequidt, Erwan Kerrien, Marie-Odile Berger, Stéphane Cotin
article
Eurographics Workshop on Virtual Reality Interaction and Physical Simulation, Dec 2012, Darmstadt, Germany. 2012
resume
This paper introduces an original method to perform augmented or mixed reality on deformable objects. Compared to state-of-the-art techniques, our method is able to track deformations of volumetric objects and not only surfacic objects. A flexible framework that relies on the combination of a 3D motion estimation and a physics-based deformable model used as a regularization and interpolation step allows to perform a non-rigid and robust registration. Results are exposed, based on computer-generated datasets and video sequences of real environments in order to assess the relevance of our approach.
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titre
Bézier Shell Finite Element for Interactive Surgical Simulation
auteur
Tomáš Golembiovský, Christian Duriez
article
Jan Bender and Arjan Kuijper and Dieter W. Fellner and Eric Guerin. VRIPHYS 12: 9th Workshop on Virtual Reality Interactions and Physical Simulations, Dec 2012, Darmstadt, Germany. Eurographics Association, pp.107-116, 2012, <10.2312/PE/vriphys/vriphys12/107-116>
resume
There is a strong need, in surgical simulations, for physically based deformable model of thin or hollow structures. The use of shell theory allows to have a well-founded formulation resulting from continuum mechanics of thin objects. However, this formulation asks for second order spatial derivatives so requires the use of complex elements. In this paper, we present a new way of building the interpolation: First, we use the trianular cubic Bézier shell to allow for a good continuity inside and between the elements and second, we build a kinematic mapping to reduce the degrees of freedom of the element from 10 control points with 3 Degrees of Freedom ($=30$ DOFs) to only 3 nodes with 6 DOFs ($=18$ DOFs). This reduction allows for good computation performance. This new shell model description is also used to map a smooth surface (for the collision detection and response) on a coarse mechanical mesh to account for the complex contacts that take place during surgical procedures. We demonstrate the convergence and the computational efficiency of our approach as well as its use in two different simulation cases: the planning of surgery for congenital heart disease correction and a preliminary simulation of childbirth.
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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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titre
Brain-shift aware risk map for Deep Brain Stimulation Planning
auteur
Alexandre Bilger, Caroline Essert, Christian Duriez, Stéphane Cotin
article
DBSMC – MICCAI 2012 Workshop on Deep Brain Stimulation Methodological Challenges, Oct 2012, Nice, France. 2012
resume
In Deep Brain Stimulation surgery, the efficiency of the procedure heavily relies on the accuracy of the placement of the stimulating electrode. Meanwhile, the effectiveness of the placement is difficult due to brain shifts occurring during and after the procedure. We propose an approach to overcome the limitations of current planning software that ignores brain shift. In particular, we consider the motion of vascular structures in order to reduce risks of dissecting a vessel during the procedure. Facing the difficulty to produce an exact brain shift prediction, we propose to build a brain shift aware risk map which embeds the vascular motion risk. This risk map is extrapolated using simulation from clinical studies that provide statistics on the displacement of anatomical landmarks during the procedure. Risk maps can be directly integrated into automatic path planning algorithms to better predict optimal electrode trajectories. The method relies on a physics-based simulation that takes into account brain deformation, electrode placement, cerebrospinal fluid, and vascular motion. The goal is to reproduce the spread of brain shift situations that are noted in clinical studies. Preliminary results show that it is possible to compute safe electrode trajectories even in case of brain shift and yet optimal regarding the placement within the targeted area.
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titre
Local implicit modeling of blood vessels for interactive simulation
auteur
Ahmed Yureidini, Erwan Kerrien, Jérémie Dequidt, Christian Duriez, Stéphane Cotin
article
Ayache, Nicholas and Delingette, Hervé and Golland, Polina and Moria, Kensaku. MICCAI – 15th International Conference on Medical Image Computing and Computer-Assisted Intervention, Oct 2012, Nice, France. Springer, 7510, pp.553-560, 2012, Lecture Notes in Computer Science; Medical Image Computing and Computer-Assisted Intervention – MICCAI 2012. <10.1007/978-3-642-33415-3_68>
resume
In the context of computer-based simulation, contact management requires an accurate, smooth, but still efficient surface model for the blood vessels. A new implicit model is proposed, consisting of a tree of local implicit surfaces generated by skeletons ({\em blobby models}). The surface is reconstructed from data points by minimizing an energy, alternating with an original blob selection and subdivision scheme. The reconstructed models are very efficient for simulation and were shown to provide a sub-voxel approximation of the vessel surface on 5 patients.
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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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titre
A Sketch-Based Interface for Annotation of 3D Brain Vascular Reconstructions
auteur
David Selosse, Jérémie Dequidt, Laurent Grisoni
article
Computer Graphics International 2012, Jun 2012, Bournemouth, United Kingdom. 2012
resume
Within the medical imaging community, 3D models of anatomical structures are now widely used in order to establish more accurate diagnoses than those based on 2D images. Many research works focus on an automatic process to build such 3D models. However automatic reconstruction induces many artifacts if the anatomical structure exhibits tortuous and thin parts (such as vascular networks) and the correction of these artifacts involves 3D-modeling skills and times that radiologists do not have. This article presents a semi-automatic approach to build a correct topology of vascular networks from 3D medical images. The user interface is based on sketching; user strokes both defines a command and the part of geometry where the command is applied to. Moreover the user-gesture speed is taken into account to adjust the command: a slow and precise gesture will correct a local part of the topology while a fast gesture will correct a larger part of the topology. This allows to correct the anatomical aberrations or ambiguities that appear on the segmented model in a few strokes.
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titre
Robust RANSAC-based blood vessel segmentation
auteur
Ahmed Yureidini, Erwan Kerrien, Stéphane Cotin
article
Dave R. Haynor and Sébastien Ourselin. SPIE Medical Imaging, Feb 2012, San Diego, CA, United States. SPIE Press, 8314, pp.8314M, 2012, Image Processing. <10.1117/12.911670>
resume
Many vascular clinical applications require a vessel segmentation process that is able to both extract the centerline and the surface of the blood vessels. However, noise and topology issues (such as kissing vessels) prevent existing algorithms from being able to easily retrieve such a complex system as the brain vasculature. We propose here a new blood vessel tracking algorithm that 1) detect the vessel centerline; 2) provide a local radius estimate; and 3) extracts a dense set of points at the blood vessel surface. This algorithm is based on a RANSAC-based robust fitting of successive cylinders along the vessel. Our method was validated against the Multiple Hypothesis Testing (MHT) algorithm on 10 3DRA patient data of the brain vasculature. Over 30 blood vessels of various sizes were considered for each patient. Our results demonstrated a greater ability of our algorithm to track small, tortuous and touching vessels (96% success rate), compared to MHT (65% success rate). The computed centerline precision was below 1 voxel when compared to MHT. Moreover, our results were obtained with the same set of parameters for all patients and all blood vessels, except for the seed point for each vessel, also necessary for MHT. The proposed algorithm is thereafter able to extract the full intracranial vasculature with little user interaction.
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titre
Simulation of Congenital Heart Defect Corrective Surgeries Using Thin Shell Elements
auteur
Stefan Kislinskiy, Tomáš Golembiovský, Christian Duriez, Eugénie Riesenkampff, Titus Kuehne, Hans-Peter Meinzer, Tobias Heimann
article
Computational Biomechanics for Medicine, 2012, France. 12p, 2012
resume
Congenital heart defect (CHD) corrective interventions in infants are extremely challenging due to commonly complex and heterogeneous disease pat-terns. At present, cardiac surgeons can only rely on non-invasive imaging prior to surgery. Critical decisions regarding the surgical procedure of choice and its exe-cution must be made during the actual surgery and are strongly dependent on ex-perience. We want to improve surgery planning by providing a simulation system that is able to accurately predict patient-specific results for different surgical pro-cedures preoperatively. Therefore we use a sophisticated simulation model based on thin shell elements. We present a novel joining approach that allows for im-plementing all necessary surgical low-level procedures, e.g. incising and suturing, independent from the simulation model. No modifications are necessary for al-ready approved thin shell implementations and our simulation system can instan-taneously benefit from further improved simulation models in the future. By re-ducing computationally expensive simulations to a minimum during a virtual surgery we can achieve a fluent workflow for surgeons. However, a specialized mesh resampling algorithm is required to fully utilize our simulation system.
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Book sections

titre
A (Near) Real-Time Simulation Method of Aneurysm Coil Embolization
auteur
Yiyi Wei, Stéphane Cotin, Jérémie Dequidt, Christian Duriez, Jérémie Allard, Erwan Kerrien
article
Yasuo Murai. Aneurysm, InTech, pp.223-248, 2012, 978-953-51-0730-9. <10.5772/48635>
resume
A (Near) Real-Time Simulation Method of Aneurysm Coil Embolization
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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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Theses

titre
Apprentissage incrémental en ligne sur flux de données
auteur
Christophe Salperwyck
article
Apprentissage [cs.LG]. Université Charles de Gaulle – Lille III, 2012. Français. < NNT : 2012LIL30037 >
resume
L’apprentissage statistique propose un vaste ensemble de techniques capables de construire des modèles prédictifs à partir d’observations passées. Ces techniques ont montré leurs capacités à traiter des volumétries importantes de données sur des problèmes réels. Cependant, de nouvelles applications génèrent de plus en plus de données qui sont seulement visibles sous la forme d’un flux et doivent être traitées séquentiellement. Parmi ces applications on citera : la gestion de réseaux de télécommunications, la modélisation des utilisateurs au sein d’un réseau social, le web mining. L’un des défis techniques est de concevoir des algorithmes permettant l’apprentissage avec les nouvelles contraintes imposées par les flux de données. Nous proposons d’abord ce problème en proposant de nouvelles techniques de résumé de flux de données dans le cadre de l’apprentissage supervisé. Notre méthode est constituée de deux niveaux. Le premier niveau utilise des techniques incrémentales de résumé en-ligne pour les flux qui prennent en compte les ressources mémoire et processeur et possèdent des garanties en termes d’erreur. Le second niveau utilise les résumés de faible taille, issus du premier niveau, pour construire le résumé final à l’aide d’une méthode supervisée performante hors-ligne. Ces résumés constituent un prétraitement qui nous permet de proposer de nouvelles versions du classifieur bayésien naïf et des arbres de décision fonctionnant en-ligne sur flux de données. Les flux de données peuvent ne pas être stationnaires mais comporter des changements de concept. Nous proposons aussi une nouvelle technique pour détecter ces changements et mettre à jour nos classifieurs.
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2011

Journal articles

titre
Constraint-based haptic rendering of multirate compliant mechanisms
auteur
Igor Peterlik, Mourad Nouicer, Christian Duriez, Stéphane Cotin, Abderrahmane Kheddar
article
IEEE Transactions on Haptics (ToH), IEEE, 2011, 4 (3), pp.175-187. <10.1109/TOH.2011.41>
resume
The paper is dedicated to haptic rendering of complex physics-based environment in the context of surgical simulation. A new unified formalism for modeling the mechanical interactions between medical devices and anatomical structures and for computing accurately the haptic force feedback is presented. The approach deals with the mechanical interactions using appropriate force and/or motion transmission models named compliant mechanisms. These mechanisms are formulated as a constraint-based problem that is solved in two separate threads running at different frequencies. The first thread processes the whole simulation including the soft-tissue deformations, whereas the second one only deals with computer haptics. This method builds a bridge between the so-called virtual mechanisms (that were proposed for haptic rendering of rigid bodies) and intermediate representations (used for rendering of complex simulations). With this approach, it is possible to describe the specific behavior of various medical devices while relying on a unified method for solving the mechanical interactions between deformable objects and haptic rendering. The technique is demonstrated in interactive simulation of flexible needle insertion through soft anatomical structures with force feedback.
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titre
Interactive Blood-Coil Simulation in Real-time during Aneurysm Embolization
auteur
Yiyi Wei, Stéphane Cotin, Jérémie Allard, Le Fang, Chunhong Pan, Songde Ma
article
Computers and Graphics, Elsevier, 2011, Visual Computing in Biology and Medicine, 35 (2), pp.422-430. <10.1016/j.cag.2011.01.010>
resume
Over the last decade, remarkable progress has been made in the field of endovascular treatment of aneurysms. Technological advances continue to make it possible for a growing number of patients with cerebral aneurysms to be treated with a variety of endovascular strategies, essentially using detachable platinum coils. Yet, coil embolization remains a very complex medical procedure for which careful planning must be combined with advanced technical skills in order to be successful. In this paper, we describe a complete process for patient-specific simulations of coil embolization, from mesh generation with medical datasets to computation of coil-flow bilateral influence. We propose a new method for simulating the complex blood flow patterns that take place within the aneurysm, and for simulating the interaction of coils with this flow. This interaction is twofold, first involving the impact of the flow on the coil during the initial stages of its deployment, and second concerning the decrease of blood velocity within the aneurysm, as a consequence of coil packing. We also propose an approach to achieve real-time computation of coil-flow bilateral influence, necessary for interactive simulation. This in turns allows to dynamically plan coil embolization for two key steps of the procedure: choice and placement of the first coils, and assessment of the number of coils necessary to reduce aneurysmal blood velocity and wall pressure. Finally, we provide the blood flow simulation results on several aneurysms with interesting clinical characteristics both in 2D and 3D, as well as comparisons with a commercial package for validation. The coil embolization procesure is simulated within an aneurysm, and pre- and post-operative status is reported.
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titre
A025 Evaluation of insertions forces of an atraumatic array prototype in a model of micro dissected cochlea
auteur
Yann Nguyen, Mathieu Miroir, Guillaume Kazmitcheff, Evelyne Ferrary, Olivier Sterkers, Ab Grayeli
article
International Journal of Pediatric Otorhinolaryngology, Elsevier, 2011, 75 (1), pp.5. <10.1016/S0165-5876(11)70026-X>
resume
no abstract
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Conference papers

titre
Computer-based simulation for the endovascular treatment of intracranial aneurysms
auteur
Ahmed Yureidini, Jérémie Dequidt, Erwan Kerrien, Christian Duriez, Stéphane Cotin
article
LIVIM Imaging Worshop, Dec 2011, Strasbourg, France. 2011
resume
This paper describes a framework for the development of computer-based simulations of endovascular procedures. In particular, we focus on patient-specific modeling of the vascular anatomy, using an implicit formulation, which offers many benefits, both in terms of anatomical modeling and in terms of computational efficiency. Our preliminary results demonstrate a very realistic simulation in interactive times of coil embolization of intracranial aneurysms.
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titre
Evaluation of command modes of an assistance robot for middle ear surgery
auteur
Guillaume Kazmitcheff, Mathieu Miroir, Yann Nguyen, Charlotte Célérier, Stéphane Mazalaigue, Evelyne Ferrary, Olivier Sterkers, Alexis Bozorg-Grayeli
article
International Conference on Intelligent Robots and Systems (IROS), 2011 IEEE/RSJ, Sep 2011, San Francisco, United States. pp.2532–2538, 2011, <10.1109/IROS.2011.6094634>
resume
RobOtol is a micro-surgical tele operated system designed to assist middle ear surgery. A new prototype, with an improved controller system and mechanical enhancement is presented. Surgeons and engineers evaluated the robot by tasks specific to middle ear surgery with two command modes (position-velocity and position-position) and by questionnaires. There was no prevailing command mode. A human robot interface was developed to offer easy and fast intra operative adaptation of the command mode to surgeons’ preferences and specific situations.
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titre
Biomechanical Simulation of Electrode Migration for Deep Brain Stimulation
auteur
Alexandre Bilger, Jérémie Dequidt, Christian Duriez, Stéphane Cotin
article
Gabor Fichtinger and Anne Martel and Terry Peters. 14th International Conference on Medical Image Computing and Computer-Assisted Intervention – MICCAI 2011, Sep 2011, Toronto, Canada. Springer, 6891/2011, pp.339-346, 2011, Lecture Notes in Computer Science; Medical Image Computing and Computer-Assisted Intervention – MICCAI 2011. <10.1007/978-3-642-23623-5_43>
resume
Deep Brain Stimulation is a modern surgical technique for treating patients who suffer from affective or motion disorders such as Parkinson’s disease. The efficiency of the procedure relies heavily on the accuracy of the placement of a micro-electrode which sends electrical pulses to a specific part of the brain that controls motion and affective symptoms. However, targeting this small anatomical structure is rendered difficult due to a series of brain shifts that take place during and after the procedure. This paper introduces a biomechanical simulation of the intra and postoperative stages of the procedure in order to determine lead deformation and electrode migration due to brain shift. To achieve this goal, we propose a global approach, which accounts for brain deformation but also for the numerous interactions that take place during the procedure (contacts between the brain and the inner part of the skull and falx cerebri, effect of the cerebro-spinal fluid, and biomechanical interactions between the brain and the electrodes and cannula used during the procedure). Preliminary results show a good correlation between our simulations and various results reported in the literature.
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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.
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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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titre
Reconstruction robuste des vaisseaux sanguins par surfaces implicites locales
auteur
Ahmed Yureidini, Erwan Kerrien, Stéphane Cotin
article
Orasis, Jun 2011, Praz-sur-Arly, France. 2011
resume
Les simulateurs informatiques suscitent un intérêt croissant, notamment dans le domaine de la radiologie interventionnelle. Dans ce contexte, nous abordons le problème de segmentation des vaisseaux sanguins par reconstruction de surfaces implicites à partir d’acquisitions d’angiographie rotationnelle 3D. Nous proposons un nouveau modèle implicite sous forme d’un arbre de fonctions implicites locales. L’arbre est bâti grâce à un algorithme dédié de suivi. Ce faisant des points sont extraits de manière robuste sur la surface vasculaire. Chaque fonction implicite est ensuite estimée avec une méthode originale pour approximer ces points. Enfin, nous présentons des résultats de suivi sur un patient, ainsi qu’une analyse expérimentale de notre modèle sur des exemples synthétiques en 2D pour finir par des résultats préliminaires de segmentation sur des données réelles de fantôme vasculaire.
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titre
Asynchronous haptic simulation of contacting deformable objects with variable stiffness
auteur
Igor Peterlik, Christian Duriez, Stéphane Cotin
article
Intelligent Robots and Systems (IROS), 2011 IEEE/RSJ International Conference on, 2011, san francisco, United States. pp.2608–2613, 2011
resume
Abstract–This paper presents a new asynchronous approach for haptic rendering of deformable objects. When stiff nonlinear deformations take place, they introduce important and rapid variations of the force sent to the user. This problem is similar to the stiff virtual wall for which a high refresh rate is required to obtain a stable haptic feedback. However, when dealing with several interacting deformable objects, it is usually impossible to simulate all objects at high rates. To address this problem we propose a quasi-static framework that allows for stable interactions of asynchronously computed deformable objects. In the proposed approach, a deformable object can be computed at high refresh rates, while the remaining deformable virtual objects remain computed at low refresh rates. Moreover, contacts and other constraints between the different objects of the virtual environment are accurately solved using a shared Linear Complementarity Problem (LCP). Finally, we demonstrate our method on two test cases: a snap-in example involving non-linear deformations and a virtual thread interacting with a deformable object.
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titre
Realisation d’un Prototype de Simulateur Fonctionnel pour la Chirurgie de la Cataracte
auteur
Elodie Dumortier, Stephane Cotin, Jérémie Dequidt, Jean-Francois Rouland
article
117e CONGRES de la Société Française d’Ophtalmologie, 2011, paris, France. 2011
resume
no abstract
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titre
Assessment Metrics For A Prototype Of Simulation System For Cataract Surgery Training
auteur
Elodie Dumortier, Stephane Cotin, Jérémie Dequidt, Jean-Francois Rouland
article
Annual Meeting of the Association for Research in Vision and Opthalmology, 2011, Fort Lauderdale, United States. 2011
resume
no abstract
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titre
A Prototype of Simulation System for Cataract Surgery Training
auteur
Elodie Dumortier, Stephane Cotin, Jérémie Dequidt, Jean-Francois Rouland
article
European Society of Cataract & Refractive Surgeons Winter Meeting, 2011, Istanbul, Turkey. 2011
resume
no abstract
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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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Reports

titre
Deliverable D10.4.1
auteur
Hugo Talbot, Federico Spadoni, Maxime Sermesant, Nicholas Ayache, Hervé Delingette
article
[Research Report] 2011, pp.25
resume
This deliverable describes the final status of Task 10.4 of Workpackage 10 of the euHeart project. The aim of this task is to develop a prototype of an endovascular simulator of cardiac radiofrequency ablation. More precisely, its purpose is to simulate the patient-specific catheter navigation and radiofre- quency ablation of ventricular tachycardia. Since deliverable 10.4.1, work on the simulator prototype has focused on the development of a user interface and the integration of two software compo- nents : endovascular simulation and electrophysiology simulation. The first component aims at modeling the deformation of catheters and guidewires inside vessels and to generate a realistic visualization of the vis- ible X-ray images. The second component is focused on the simulation of electrophysiology. We have chosen the Mitchell-Schaeffer phenomenological model to represent the evolution of action potential on the myocardium. The integration of those 2 software components is difficult because they should both run simultaneously in real-time. To this end, we have developed a multi-thread framework allowing to parallelize the computation of the catheter deformation and the cardiac electrophysiology while sharing a minimum num- ber of information. We have also developed a user interface that can display X-ray images, 3D view of the heart and simulated electro-physiology signals measured at the tip of the catheter. An example of simulation is provided starting from the endovascular navi- gation from the veina cava and finishing with the radiofrequency ablation of endocardial tissue inside the right ventricle.
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Theses

titre
Nouvelles architectures parallèles pour simulations interactives médicales
auteur
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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2010

Journal articles

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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titre
Volumetric modeling and interactive cutting of deformable bodies
auteur
Lenka Jerabkova, Guillaume Bousquet, Sébastien Barbier, François Faure, Jérémie Allard
article
Progress in Biophysics and Molecular Biology, Elsevier, 2010, Special Issue on Biomechanical Modelling of Soft Tissue Motion, 103 (2-3), pp.217-224. <10.1016/j.pbiomolbio.2010.09.012>
resume
A new approach for the interactive simulation of viscoelastic object cutting is presented. Two synchronized geo- metrical models at different resolutions are used, both derived from medical images. In contrast with most previous approaches, the blade deforms the object, and cutting occurs once a contact pressure threshold is exceeded. Moreover, we achieve interactive simulation rates by embedding a high resolution geometry within a regular grid with arbitrary resolution. This allows to trade off accuracy for speed in the computation of deformations. The input data is a high- resolution volumetric model of the objects. The surface model of the object, used for rendering as well as collision detection and response, is a polygonal level set of the volumetric data. It is embedded in the volume model using barycentric coordinates. Cutting is performed by removing voxels at the fine level, and updating the surface and volume models accordingly. We introduce a new data structure, which we call a Dynamic Branched Grid, in order to preserve the fine level topology at the coarse level. When an element of the coarse volumetric model is cut, it is replaced by a number of superimposed elements with the same size and at the same rest position as the original one. Each new element is assigned a part of material contained in the original one, and the mass and stiffness are recomputed accordingly. The well-known problem of creating small, ill-shaped finite elements while remeshing is thus completely avoided.
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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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titre
Modularity for Large Virtual Reality Applications
auteur
Jérémie Allard, Jean-Denis Lesage, Bruno Raffin
article
Presence: Teleoperators and Virtual Environments, Massachusetts Institute of Technology Press (MIT Press), 2010, 19 (2), pp.142-161. <10.1162/pres.19.2.142>
resume
This paper focuses on the design of high performance VR applications. These applications usually involve various I/O devices and complex simulations. A parallel architecture or grid infrastructure is required to provide the necessary I/O and processing capabilities. Developing such applications faces several difficulties, two important ones being software engineering and performance issues. We argue that application modularity is a key concept to help the developer handle the complexity of these applications. We discuss how various approaches borrowed from other existing works can be combined to significantly improve the modularity of VR applications. This led to the development of the FlowVR middleware that associates a data-flow model with a hierarchical component model. Different case studies are presented to discuss the benefits of the approach proposed.
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titre
Multicamera Real-Time 3D Modeling for Telepresence and Remote Collaboration
auteur
Benjamin Petit, Jean-Denis Lesage, Clément Menier, Jérémie Allard, Jean-Sébastien Franco, Bruno Raffin, Edmond Boyer, François Faure
article
International journal of digital multimedia broadcasting, Hindawi, 2010, Advances in 3DTV: Theory and Practice, 2010, Article ID 247108, 12 p. <10.1155/2010/247108>
resume
We present a multicamera real-time 3D modeling system that aims at enabling new immersive and interactive environments. This system, called Grimage, allows to retrieve in real-time a 3D mesh of the observed scene as well as the associated textures. This information enables a strong visual presence of the user into virtual worlds. The 3D shape information is also used to compute collisions and reaction forces with virtual objects, enforcing the mechanical presence of the user in the virtual world. The innovation is a fully integrated system with both immersive and interactive capabilities. It embeds a parallel version of the EPVH modeling algorithm inside a distributed vision pipeline. It also adopts the hierarchical component approach of the FlowVR middleware to enforce software modularity and enable distributed executions. Results show high refresh rates and low latencies obtained by taking advantage of the I/O and computing resources of PC clusters. The applications we have developed demonstrate the quality of the visual and mechanical presence with a single platform and with a dual platform that allows telecollaboration.
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Conference papers

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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titre
High Fidelity Haptic Rendering for Deformable Objects Undergoing Topology Changes
auteur
Hoeryong Jung, Stéphane Cotin, Christian Duriez, Jérémie Allard, Doo Yong Lee
article
EuroHaptics – Haptics: Generating and Perceiving Tangible Sensations International Conference, Jul 2010, Amsterdam, Netherlands. Springer, 6191, pp.262-268, 2010, LNCS. <10.1007/978-3-642-14064-8_38>
resume
The relevance of haptic feedback for minimally invasive surgery has been demonstrated at numerous counts. However, the proposed methods often prove inadequate to handle correct contact computation during the complex interactions or topological changes that can be found in surgical interventions. In this paper, we introduce an approach that allows for accurate computation of contact forces even in the presence of topological changes due to the simulation of soft tissue cutting. We illustrate this approach with a simulation of cataract surgery, a typical example of microsurgery.
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titre
Six Degree-of Freedom Haptic Rendering for Dental Implantology Simulation
auteur
Cedric Syllebranque, Christian Duriez
article
Bello, Fernando; Cotin, Stéphane. International Symposium on Computational Models for Biomedical Simulation, Jan 2010, Phoenix, United States. Springer, 5958, pp.139–149, 2010, Lecture Notes in Computer Science. <10.1007/978-3-642-11615-5_15>
resume
Dental implantology procedures are among the most com- plex surgical procedures executed by dentists. During the critical part of the procedure, the jawbone is drilled at the location of the missing tooth (or the missing group of teeth). This asks for specic skills from the dentists, who need to be well trained. In this paper we present a virtual reality based training system for im- plantology and we mainly focus on the simulation of drilling. We have two main contributions: The rst one is a method for precise haptic rendering of contacts between the drilling tool and the jawbone model issued from a CT-scan. The second one is the real-time simulation of the jawbone erosion during drilling which is compatible with the haptic rendering of contacts.
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titre
A Shell Model for Real-time Simulation of intra-ocular Implant Deployment
auteur
Olivier Comas, Stéphane Cotin, Christian Duriez
article
Bello, Fernando; Cotin, Stéphane. International Symposium on Computational Models for Biomedical Simulation, Jan 2010, Phoenix, United States. Springer, 5958, pp.160–170, 2010, Lecture Notes in Computer Science. <10.1007/978-3-642-11615-5_15>
resume
With 30 million interventions a year worldwide, cataract surgery is one of the most frequently performed procedures. Yet, no tool currently allows teaching all steps of the procedure without putting pa- tients at risk. A particularly challenging stage of this surgery deals with the injection and deployment of the intra-ocular lens implant. In this paper we propose to rely on shell theory to accurately describe the com- plex deformations of the implant. Our approach extends the co-rotational method used in finite element analysis of in-plane deformations to incor- porate a bending energy. This results in a relatively simple and compu- tationally efficient approach which was applied to the simulation of the lens deployment. This simulation also accounts for the complex contacts that take place during the injection phase.
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titre
Shell Model for Reconstruction and Real-Time Simulation of Thin Anatomical Structures
auteur
Olivier Comas, Christian Duriez, Stephane Cotin
article
MICCAI, 2010, China. pp.371-379, 2010
resume
This paper presents a new modelling technique for the defor- mation of thin anatomical structures like membranes and hollow organs. We show that the behaviour of this type of surface tissue can be ab- stracted with a modelling of their elastic resistance using shell theory. In order to apply the shell theory in the context of medical simulation, our method propose to base the geometrical reconstruction of the organ on the shape functions of the shell element. Moreover, we also use these continuous shape functions to handle the contacts and the interactions with other types of deformable tissues. The technique is illustrated using several examples including the simulation of an angioplasty procedure.
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titre
Computer-Based Training System for Cataract Surgery
auteur
Elodie Dumortier, Stephane Cotin, Jérémie Dequidt, Christian Duriez, Jeremie Allard, Jean-Francois Rouland
article
International ICST Conference on Electronic Healthcare for the 21st Century, 2010, Casablanca, Morocco. 2010
resume
no abstract
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titre
Computer-Based Simulation of Cataract Surgery: Toward a New Teaching Paradigm
auteur
Nadia Boubchir, Stephane Cotin, Olivier Comas, Frederick Roy, Christian Duriez, Jérémie Dequidt, Jeremie Allard, Jean-Francois Rouland
article
Annual Meeting of the American Academy of Ophthalmology, 2010, Fort Lauderdale, United States. 2010
resume
no abstract
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titre
Super paramagnetic nanoparticles delivery through a microcatheter by solenoids
auteur
Yann Nguyen, Mathieu Miroir, Guillaume Kazmitcheff, Evelyne Ferrary, Olivier Sterkers, Ab Grayeli
article
Nano/Molecular Medicine and Engineering (NANOMED), 2010 IEEE 4th International Conference on, 2010, Unknown, Unknown or Invalid Region. pp.153–157, 2010
resume
no abstract
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Books

titre
Biomedical Simulation: 5th International Symposium, ISBMS 2010, Phoenix, Az, USA, January 23-24, 2010
auteur
Stéphane Cotin, Fernando Bello
article
Stéphane Cotin; Fernando Bello. Springer, 5958, pp.193, 2010, Lecture Notes in Computer Science, 3642116140
resume
The International Symposium on Biomedical Simulation (ISBMS) is a well-established scientific meeting that provides an international forum for researchers interested in using biomedical simulation technology for the improvement of patient care and patient safety. To celebrate its 5th edition, the symposium was organized in conjunction with the International Meeting on Simulation in Healthcare (IMSH). Already in its 10th anniversary, IMSH is the premier simulation in healthcare meeting and largest single gathering of clinicians, educators, administrators and other simulation stakeholders. This unique link up aims to bring together simulation users with those involved in its scientific and technological developments. In continuation of the spirit of previous symposia at INRIA (2003), CIMIT (2004), ETH (2006) and Imperial College (2008), ISBMS10 was held as a single track meeting to stimulate participants in sharing their latest work and discuss future trends and applications. In addition to original scientific contributions selected based on double-blinded peer review and keynote presentations, the meeting offered opportunities to present demonstration systems.
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Theses

titre
Real-time Soft Tissue Modelling on GPU for Medical Simulation
auteur
Olivier Comas
article
Modeling and Simulation. Université des Sciences et Technologie de Lille – Lille I, 2010. English
resume
Modelling the deformation of anatomical structures in real-time is a crucial problem in medical simulation. Because their shape and their constitution greatly differ, a unique model cannot deal with the variousness of the mechanical behaviours. Hence, we identified two major types of structures in human body, they can be either solid (brain, liver, prostate etc.) or hollow (colon, blood vessels, stomach etc.). Our answer to this problematic is twofold. Our first contribution is an efficient GPU implementation of a non-linear, anisotropic and viscoelastic finite element model for solid organs. Our second contribution is a framework for real-time modelling of thin anatomical structures via a parallelisable co-rotational shell finite element formulation and a method to mesh a complex surface with curved shell elements. Although the two soft tissue models are based on continuum mechanics for greater accuracy, they may both be employed to simulate the deformation of entire organs in real-time. Finally, their implementation into the open source framework SOFA will provide worldwide researchers with new models to assist in enhancing the realism of medical simulators.
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titre
Suture en chirurgie virtuelle : simulation interactive et modèles hétérogènes
auteur
Christophe Guébert
article
Modélisation et simulation. Université des Sciences et Technologie de Lille – Lille I, 2010. Français
resume
La médecine a été une grande motivation dans la recherche en informatique, et nous pensons que la simulation de procédures médicales sera un élément majeur de la médecine du 21e siècle. Pour ces applications, la simulation physique doit être interactive et proposer un comportement et un rendu visuel des objets simulés qui soient réalistes tout en faisant avec un temps de calcul limité. Dans ce travail, nous nous sommes intéressés à la simulation du geste chirurgical de la suture, faisant interagir des modèles hétérogènes (rigides, déformables 1D et 3D) dans la reproduction d’un geste complexe. Nous proposons de modéliser ces interactions par des contraintes de complémentarité, avec une méthode générique et une résolution indépendante des types de contraintes utilisées. Cette approche a permis la mise au point de contraintes spécifiques pour créer des modèles d’interaction nouveaux. Ces contraintes ont permis une simulation complète de l’insertion d’aiguille, validée par les mesures expérimentales des travaux antérieurs, qui suit les lois physiques et s’adapte à la manipulation de l’utilisateur. Enfin, une simulation interactive très réaliste a été réalisée pour l’entraînement au geste de suture dans le cadre d’opérations laparoscopiques.
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2009

Journal articles

titre
Fiber-based Fracture Model for Simulating Soft Tissue Tearing
auteur
Jérémie Allard, Maud Marchal, Stéphane Cotin
article
Studies in Health Technology and Informatics, IOS Press, 2009, Medicine Meets Virtual Reality 17, 142, pp.13-18. <10.3233/978-1-58603-964-6-13>
resume
In this paper, we propose a novel approach for simulating soft tissue tearing, using a model that takes into account the existence of fibers within the tissue. These fibers influence the deformation by introducing anisotropy, and impact the direction of propagation for the fracture during tearing. We describe our approach for simulating, in real-time, the deformation and fracture of anisotropic membranes, and we illustrate our method with the simulation of capsulorhexis, one of the critical steps of cataract surgery.
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Conference papers

titre
Towards interactive planning of coil embolization in brain aneurysms
auteur
Jérémie Dequidt, Christian Duriez, Stéphane Cotin, Erwan Kerrien
article
Yang, G.-Z. and Hawkes, D.J. and Rueckert, D. and Noble, A. and Taylor, C. Medical Image Computing and Computer Assisted Intervention – MICCAI 2009, Sep 2009, London, United Kingdom. Springer Berlin / Heidelberg, 5761, pp.377-385, 2009, Lecture Notes in Computer Science; 12th International conference on Medical Image Computing and Computer-Assisted Intervention – MICCAI 2009, part I. <10.1007/978-3-642-04268-3_47>
resume
Many vascular pathologies can now be treated in a minimally invasive way thanks to interventional radiology. Instead of open surgery, it allows to reach the lesion of the arteries with therapeutic devices through a catheter. As a particular case, intracranial aneurysms are treated by ﬁlling the localized widening of the artery with a set of coils to prevent a rupture due to the weakened arterial wall. Considering the location of the lesion, close to the brain, and its very small size, the procedure requires a combination of careful planning and excellent technical skills. An interactive and reliable simulation, adapted to the patient anatomy, would be an interesting tool for helping the interventional neuroradiologist plan and rehearse a coil embolization procedure. This paper describes an original method to perform interactive simulations of coil embolization and proposes a clinical metric to quantitatively measure how the ﬁrst coil ﬁlls the aneurysm. The simulation relies on an accurate reconstruction of the aneurysm anatomy and a real-time model of the coil for which sliding and friction contacts are taken into account. Simulation results are compared to real embolization procedure and exhibit good adequacy.
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titre
Toward Real-time Simulation of Blood-Coil Interaction during Aneurysm Embolization
auteur
Yiyi Wei, Stéphane Cotin, Le Fang, Jérémie Allard, Chunhong Pan
article
Guang-Zhong Yang and David Hawkes and Daniel Rueckert and Alison Noble and Chris Taylor. MICCAI 2009 – International Conference on Medical Image Computing and Computer Assisted Intervention, Sep 2009, London, United Kingdom. Springer, 5761, pp.198-205, 2009, Lecture Notes in Computer Science; Medical Image Computing and Computer-Assisted Intervention. <10.1007/978-3-642-04268-3_25>
resume
Over the last decade, remarkable progress has been made in the field of endovascular treatment of aneurysms. Technological advances continue to enable a growing number of patients with cerebral aneurysms to be treated with a variety of endovascular strategies, essentially using detachable platinum coils. Yet, coil embolization remains a very complex medical procedure for which careful planning must be combined with advanced technical skills in order to be successful. In this paper we propose a method for computing the complex blood flow patterns that take place within the aneurysm, and for simulating the interaction of coils with this flow. This interaction is twofold, first involving the impact of the flow on the coil during the initial stages of its deployment, and second concerning the decrease of blood velocity within the aneurysm, as a consequence of coil packing. We also propose an ap- proach to achieve real-time computation of coil-flow bilateral influence, necessary for interactive simulation. This in turns allows to dynamically plan coil embolization for two key steps of the procedure: choice and placement of the first coils, and assessment of the number of coils neces- sary to reduce aneurysmal blood velocity and wall pressure.
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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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titre
CT Scan Merging to Enhance Navigation in Interventional Radiology Simulation
auteur
Pierre-Frédéric Villard, Vincent Luboz, Paul Neumann, Stéphane Cotin, Steve Dawson
article
Medicine Meet Virtual Reality conference 17, Jan 2009, Long Beach, United States. IOS Press, 142, pp.407-412, 2009, <http://ebooks.iospress.nl/publication/12058>. <10.3233/978-1-58603-964-6-407>
resume
We present a method to merge two distinct CT scans acquired from dif- ferent patients such that the second scan can supplement the first when it is missing necessary supporting anatomy. The aim is to provide vascular intervention simula- tions with full body anatomy. Often, patient CT scans are confined to a localised region so that the patient is not exposed to more radiation than necessary and to increase scanner throughput. Unfortunately, this localised scanning region may be limiting for some applications where surrounding anatomy may be required and where approximate supporting anatomy is acceptable. The resulting merged scan can enhance body navigation simulations with X-ray rendering by providing a com- plete anatomical reference which may be useful in training and rehearsal. An ex- ample of the use of our CT scan merging technique in the field of interventional radiology is described.
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titre
Computer-Based Simulation of IOL Injection: Toward a Full Featured Cataract Surgery Training System
auteur
Nadia Boubchir, Stephane Cotin, Christian Duriez, Jérémie Dequidt, Jeremie Allard, Jean-Francois Rouland
article
Annual Meeting of the American Academy of Ophthalmology, 2009, San Diego, United States. 2009
resume
no abstract
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Poster communications

titre
Evaluation of a computer-based simulation for the endovascular treatment of intracranial aneurysms
auteur
René Anxionnat, Federico Rocca, Serge Bracard, Jérémie Dequidt, Erwan Kerrien, Christian Duriez, Marie-Odile Berger, Stéphane Cotin
article
10th congress of the World Federation of Interventional and Therapeutic Neuroradiology – WFITN 2009, Jun 2009, Montréal, Canada
resume
Purpose: Endovascular treatment (EVT) of intracranial aneurysms requires highly trained physicians and careful pre-therapeutic evaluation of the aneurysm morphology. A realistic interventional neuroradiology simulator would provide procedural and skill training for either educational purpose or pre-therapeutic simulation in complex cases. This work aims at evaluating the clinical realism of a computer-based simulator for the EVT of aneurysms. Material and Methods: A prototype computer-based EVT simulation system was developed and implemented. A silicon vascular phantom (Elastrat, Geneva, Switzerland) as well as two patient data sets were used for the evaluation. A coil adapted to the aneurysm was deployed under fluoroscopy. Then, a simulation was done with the same, as well as larger and smaller coils under the same viewing incidence and was visually assessed and compared to fluoroscopic images. The maximum of coil pressure onto the aneurysm sac was recorded during all simulations. Results: In all cases, simulation with the correct coil showed a realistic coil behaviour and aneurysm filling. As expected, full and stable coiling of the aneurysm was impossible to simulate with too small coils. Protrusions outside the sac were observed with too large coils. In this latter case, the pressure onto the aneurysm wall dramatically increased as compared with the correct coil. Conclusion: A preliminary evaluation of a computer-based EVT simulation system was made on both phantom and patient data. Our report emphasizes the clinical realism of the simulated deployment of coils, in particular with regard to potential hazards related to an inadequate choice of coil.
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2008

Conference papers

titre
Refining the 3D surface of blood vessels from a reduced set of 2D DSA images
auteur
Erwan Kerrien, Marie-Odile Berger, Jérémie Dequidt
article
AMI-ARCS 2008, Sep 2008, New York, NY, United States. pp.61-69, 2008
resume
Numerical simulations, such as blood flow or coil deployment in an intra-cranial aneurism, are very sensitive to the boundary conditions given by the surface of the vessel walls. Despite the undisputable high quality of 3D vascular imaging modalities, artifacts and noise still hamper the extraction of this surface with enough accuracy. Previous studies took the a priori that a homogeneous object was considered to make the reconstruction from the Xray images more robust. Here, an active surface approach is described, that does not depend on any particular image similarity criterion and grounds on high speed computation of the criterion derivatives. Mean square error and normalized cross-correlation are used to successfully demonstrate our algorithm on real images acquired on an anthropomorphic phantom. Preliminary results of coil deployment simulation are also given.
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titre
Interactive Simulation of Embolization Coils: Modeling and Experimental Validation
auteur
Jérémie Dequidt, Maud Marchal, Christian Duriez, Erwan Kerrien, Stéphane Cotin
article
Medical Imaging Computing and Computer Assisted Intervention -MICCAI’08, Sep 2008, New York City, United States. Springer, 5241, pp.695-702, 2008, Lecture Notes in Computer Science. <10.1007/978-3-540-85988-8_83>
resume
Coil embolization offers a new approach to treat aneurysms. This medical procedure is namely less invasive than an open-surgery as it relies on the deployment of very thin platinum-based wires with the aneurysm through the arteries. When performed intracranially, this procedure must be particularly accurate and therefore carefully planned and performed by experienced radiologists. A simulator of the coil deployment represents an interesting and helpful tool for the physician by providing information on the coil behavior. In this paper, an original modeling is proposed to obtain interactive and accurate simulations of coil deployment. The model takes into account geometric nonlinearities and uses a shape memory formulation to describe its complex geometry. An experimental validation is performed in a contact-free environment to identify the mechanical properties of the coil and to quantitatively compare the simulation with the real data. Computational performances are also measured to insure an interactive simulation.
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titre
Efficient Contact Modeling using Compliance Warping
auteur
Guillaume Saupin, Christian Duriez, Stephane Cotin, Laurent Grisoni
article
computer graphics international, 2008, Istambul, Turkey. 2008
resume
Contact handling is the key of deformable objects simulation, since without it, objects can not interact with their environment nor with the user. In this paper, we propose a novel and very efficient approach for precise computation of contact response between various types of objects commonly used in computer animation. Being constraint based, this method ensures physical correctness, and respects Singorini s law. It can be used with any deformation model, and is based on the use of the initial compliance matrix and contact warping. Thus, the contact response can be computed efficiently, and the object deformation can still be done in a physically plausible way provided the underlying model is physical.
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Book sections

titre
Efficient nonlinear FEM for soft tissue modelling and its GPU implementation within the open source framework SOFA
auteur
Olivier Comas, Zeike A Taylor, Jérémie Allard, Sébastien Ourselin, Stéphane Cotin, Josh Passenger
article
Fernando Bello, Philip J. Edwards. ISBMS 2008 – International Symposium on Biomedical Simulation – 2008, 5104, Springer Berlin Heidelberg, pp.28–39, 2008, Lecture Notes in Computer Science, 978-3-540-70521-5. <10.1007/978-3-540-70521-5_4>
resume
Accurate biomechanical modelling of soft tissue is a key aspect for achieving realistic surgical simulations. However, because medical simulation is a multi-disciplinary area, researchers do not always have sufficient resources to develop an efficient and physically rigorous model for organ deformation. We address this issue by implementing a CUDA-based nonlinear finite element model into the SOFA open source framework. The proposed model is an anisotropic visco-hyperelastic constitutive formulation implemented on a graphical processor unit (GPU). After presenting results on the model’s performance we illustrate the benefits of its integration within the SOFA framework on a simulation of cataract surgery.
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titre
Towards a framework for assessing deformable models in medical simulation
auteur
Maud Marchal, Jérémie Allard, Christian Duriez, Stéphane Cotin
article
Fernando Bello, Philip J. Edwards. ISBMS ’08 – International Symposium on Biomedical Simulation – 2008, 5104, Springer Berlin Heidelberg, pp.176–184, 2008, Lecture Notes in Computer Science, 978-3-540-70521-5. <10.1007/978-3-540-70521-5_19>
resume
Computational techniques for the analysis of mechanical problems have recently moved from traditional engineering disciplines to biomedical simulations. Thus, the number of complex models describing the mechanical behavior of medical environments have increased these last years. While the development of advanced computational tools has led to interesting modeling algorithms, the relevances of these models are often criticized due to incomplete model verification and validation. The objective of this paper is to propose a framework and a methodology for assessing deformable models. This proposal aims at providing tools for testing the behavior of new modeling algorithms proposed in the context of medical simulation. Initial validation results comparing different modeling methods are reported as a first step towards a more complete validation framework and methodology.
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titre
Contact model for haptic medical simulations
auteur
Guillaume Saupin, Christian Duriez, Stephane Cotin
article
Fernando Bello, Philip J. Edwards. ISBMS 2008 – International Symposium on Biomedical Simulation – 2008, 5104, Springer Berlin Heidelberg, pp.157–165, 2008, Lecture Notes in Computer Science, 978-3-540-70521-5. <10.1007/978-3-540-70521-5_17>
resume
In surgery simulation, precise contact modeling is essential to obtain both realistic behavior and convincing haptic feedback. When instruments create deformations on soft tissues, they modify the boundary conditions of the models and will mainly modify their behavior. Yet, most recent work has focused on the more precise modeling of soft tissues while improving efficiency; but this effort is ruined if boundary conditions are ill-defined. In this paper, we propose a novel and very efficient approach for precise computation of the interaction between organs and instruments. The method includes an estimation of the contact compliance of the concerned zones of the organ and of the instrument. This compliance is put in a buffer and is the heart of the multithreaded local model used for haptics. Contact computation is then performed in both simulation and haptic loops. It follows unilateral formulation and allows realistic interactions on non-linear models simulated with stable implicit scheme of time integration. An iterative solver, initialized with the solution found in the simulation, allows for fast computation in the haptic loop. We obtain realistic and physical results for the simulation and stable haptic rendering.
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Habilitation à diriger des recherches

titre
Computer Based Interactive Medical Simulation ￼￼
auteur
Stéphane Cotin
article
Modeling and Simulation. Université des Sciences et Technologie de Lille – Lille I, 2008
resume
Computer-based interactive medical simulation is a revolutionary technique for improving the effectiveness of medical practice while reducing risk exposure to patients. Although traditionally focused on training, such simulations could be used, in the near future, for planning and rehearsing complex interventions, or even for assisting physicians in the operating room. This manuscript presents a detailed overview of the multi-disciplinary field of medical simulation and highlights our various contributions in this area. After an overview, in Chapter I, of the many applications of medical simulation, Chapter II addresses the importance of models, from anatomical modeling (to create realistic, and potentially patient-specific, representations of the anatomy) to biomechanical modeling (to determine soft tissue characteristics, and define mathematical models of soft tissue deformation). Problems related to medical device modeling (such as flexible instruments of imaging devices) and physiological modeling (to compute blood flow for instance) are also addressed. Chapter III discusses the importance of tissue-tool interactions, which represent an essential part of medical procedures. Techniques for modeling such interactions, through efficient collision detection, and advanced contact mechanics, are presented in this chapter. In Chapter IV are presented several contributions in the area of validation, from the verification of algorithms for soft tissue deformation to the assessment of training systems. Chapter V is dedicated to the presentation of several prototypes of simulators that were developed during this research and Chapter VI presents an overview of our most recent efforts to design a framework for unifying key elements of real-time interactive simulations. This framework, called SOFA, is a multi-institutional collaborative work which has the potential to accelerate research, development and collaborations in the field of medical simulation. Finally, Chapter VII summarizes our different contributions to the field of medical simulation and presents challenging and exciting perspectives, in particular in the area of patient-specific interactive planning.
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