Publications of Erwan Kerrien

Publications HAL de kerrien de la structure shacra;mimesis

2017

Journal articles

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.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01390923/file/medima_20161008.pdf BibTex

Conference papers

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.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01545693/file/HSMR17_paper_58.pdf BibTex

2015

Journal articles

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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.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01136728/file/haouchineTVCG2014-low.pdf BibTex

2014

Conference papers

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.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01059892/file/final_paper_6p.pdf BibTex
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.
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-00988767/file/rfia2014_submission_89.pdf BibTex
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.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01003262/file/output.pdf BibTex

2013

Conference papers

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.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00842855/file/ISMAR13-Haouchine.pdf BibTex

2012

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.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00768362/file/paper1028_final.pdf BibTex
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.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00741307/file/miccai2012.pdf BibTex
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.
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00642003/file/spie2012.pdf BibTex

Book sections

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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
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00736865/file/InTech-A_near_real_time_simulation_method_of_aneurysm_coil_embolization.pdf BibTex

2011

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.
Accès au bibtex
BibTex
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.
Accès au texte intégral et bibtex
https://hal.inria.fr/inria-00579814/file/orasis2011.pdf BibTex

2009

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.
Accès au texte intégral et bibtex
https://hal.inria.fr/inria-00430867/file/dequidt_et_al-MICCAI09.pdf BibTex

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.
Accès au texte intégral et bibtex
https://hal.inria.fr/inria-00432289/file/WFITN_poster.pdf BibTex

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.
Accès au texte intégral et bibtex
https://hal.inria.fr/inria-00321550/file/AMI-ARCS08_kerrien_etal.pdf BibTex
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.
Accès au texte intégral et bibtex
https://hal.inria.fr/inria-00336907/file/MICCAI2008_Dequidt_etal.pdf BibTex