Biomedical subjects

N Ayache

Publications and source records attributed to N Ayache.

At least 19 recordsLinked to original sources

PubMed2005

Simulation of cardiac pathologies using an electromechanical biventricular model and XMR interventional imaging.

Simulating cardiac electromechanical activity is of great interest for a better understanding of pathologies and for therapy planning. Design and validation of such models is difficult due to the lack of clinical data. XMR systems are a new type of interventional facility in which patients can be rapidly transferred between X-ray and MR systems. Our goal is to design and validate an electromechanical model of the myocardium using XMR imaging. The proposed model is computationally fast and uses clinically observable parameters. We present the integration of anatomy, electrophysiology, and motion from patient data. Pathologies are introduced in the model and simulations are compared to measured data. Initial qualitative comparison on the two clinical cases presented is encouraging. Once fully validated, these models will make it possible to simulate different interventional strategies.

Algorithms↗

PubMed2005

A Grid service for the interactive use of a parallel non-rigid registration algorithm of medical images.

OBJECTIVE: The goal of this work is to improve the usability of a non-rigid registration software for medical images. METHOD: We have built a registration grid service in order to use the interactivity of a visualization workstation and the computing power of a cluster. On the user side, the system is composed of a graphical interface that interacts in a complex and fluid manner with the registration software running on a remote cluster. CONCLUSION: Although the transmission of images back and forth between the computer running the user interface and the cluster running the registration service adds to the total registration time, it provides a user-friendly way of using the registration software without heavy infrastructure investments in hospitals. The system exhibits good performances even if the user is connected to the grid service through a low throughput network such as a wireless network interface or ADSL.

Algorithms↗

PubMed2004

Removing tetrahedra from manifold tetrahedralisation: application to real-time surgical simulation.

This paper proposes an efficient method for removing tetrahedra from a tetrahedral mesh while keeping its manifold property. We first define precisely the notion of manifold tetrahedral mesh and stress its relevance in the context of real-time surgery simulation. We then provide a method for removing a tetrahedron that complies with the manifold definition. This removal may require in some cases the removal of neighboring tetrahedra. After providing an exhaustive description of the tetrahedron removal algorithm, its efficiency is evaluated for different mesh configurations. This algorithm is currently used in the context of real-time surgery simulation where the action of an ultrasonic lancet can be simulated by the removal of small set of tetrahedra from a tetrahedralisation.

Algorithms↗

PubMed2004

[Image processing and radiotherapy].

Medical images are of great importance in radiotherapy, which became a privileged application field for image processing techniques. Moreover, because of the progression of the computers' performances, these techniques are also in full expansion. Today, the recent developments of the radiotherapy (3DCR, IMRT) offer a huge place to them. Effectively, they can potentially answer to the precision requirements of the modern radiotherapy, and may then contribute to improve the delivered treatments. The purpose of this article is to present the different image processing techniques that are currently used in radiotherapy (including image matching and segmentation) as they are described in the literature.

Algorithms↗

PubMed2004

[The contribution of automatic anatomical matching of sequential brain MRI scans in the monitoring of multiple sclerosis lesions].

INTRODUCTION: Magnetic resonance imaging (MRI) has transformed management of patients with multiple sclerosis. The exact contribution of brain MRI remains a subject of debate, but it is generally considered to provide a more specific and more sensitive outcome measure for monitoring purposes and for testing new therapies. The choice of MRI techniques, and measurement reproducibility for multiple sclerosis brain lesions are not defined with precision for routine practice. There are many sources of error when comparing successive images which can be overcome to some extent with repositioning and image processing techniques. METHODS: We evaluated the impact of image repositioning on treatment decision-making for twelve relapsing remitting patients. Brain MRIs were performed every three months for a one-year period. Two neurologists interpreted the non-repositioned and repositioned images giving their analysis of changes in the lesions visualized on the T2 sequences and their therapeutic decisions. RESULTS: For the first neurologist, analysis of the non-repositioned images yielded six patients whose lesions had worsened while for the repositioned images there were only three. For the second neurologist, four patients had more lesions with the non-repositioned images and only three with repositioning. The subjective interpretations were the same for the two neurologists when they used repositioned images. CONCLUSIONS: Comparison by two neurologists of non-repositioned and repositioned MRI, with no other image processing, affected the analysis and in certain cases propositions for treatment.

Adolescent↗

PubMed2003

Deformable biomechanical models: application to 4D cardiac image analysis.

This article describes a methodology for creating a generic volumetric biomechanical model from different image modalities and segmenting time series of medical images using this model. The construction of such a generic model consists of three stages: geometric meshing, non-rigid deformation of the mesh in images of various modalities, and image-to-mesh information mapping through rasterization. The non-rigid deformation stage, which relies on a combination of global and local deformations, can then be used to segment time series of images, e.g. cine MRI or gated SPECT cardiac images. We believe that this type of deformable biomechanical model can play an important role in the extraction of useful quantitative local parameters of cardiac function. The biomechanical model of the heart will be coupled with an electrical model of another collaborative project in order to simulate and analyze a larger class of pathologies.

Algorithms↗

PubMed2003

Retrospective evaluation of intersubject brain registration.

Although numerous methods to register brains of different individuals have been proposed, no work has been done, as far as we know, to evaluate and objectively compare the performances of different nonrigid (or elastic) registration methods on the same database of subjects. In this paper, we propose an evaluation framework, based on global and local measures of the relevance of the registration. We have chosen to focus more particularly on the matching of cortical areas, since intersubject registration methods are dedicated to anatomical and functional normalization, and also because other groups have shown the relevance of such registration methods for deep brain structures. Experiments were conducted using 6 methods on a database of 18 subjects. The global measures used show that the quality of the registration is directly related to the transformation's degrees of freedom. More surprisingly, local measures based on the matching of cortical sulci did not show significant differences between rigid and non rigid methods.

Adult↗

PubMed2002

Expression of TGF-betas and their receptors is differentially modulated by reactive oxygen species and nitric oxide in human articular chondrocytes.

OBJECTIVES: To study the effects exerted by two antioxidants, N-monomethyl-L-arginine (L-NMMA), as an inhibitor of nitric oxide (NO) synthesis, and N-acetylcysteine (NAC), a reactive oxygen species (ROS) scavenger, on the expression of the major growth factor involved in cartilage repair, TGF-beta, under the three isoforms beta1, beta2 and beta3, and the receptors I and II of this factor, using lipopolysaccharide (LPS)-treated human chondrocytes in culture. METHODS: Suspension cultures of human chondrocytes derived from the knee of osteoarthritic patients were treated for 48 h with lipopolysaccharide (LPS) (10 microg/ml), L-NMMA (0.5 mM) or NAC (1 mM). Nitrite levels were assayed on the culture media using the Griess spectrophotometric method. After total RNA extraction, the expression of inducible NO synthase (iNOS), TGF-beta1, TGF-beta2, TGF-beta3, TGF-beta receptors I and II, was determined by semi-quantitative polymerase chain-reaction (RT-PCR). RESULTS: LPS induced a dramatic increase of both NO production and iNOS mRNA level. The addition of L-NMMA (0.5 mM) abolished NO production without affecting iNOS mRNA levels. In contrast NAC (1 mM) strongly synergized with LPS to stimulate NO synthesis. LPS treatment did not significantly alter TGF-beta1 expression whereas L-NMMA inhibited its production. TGF-beta2 mRNA level was decreased by LPS and was not changed in the presence of L-NMMA. On the other hand, NAC was capable of counteracting the LPS-induced inhibition of TGF-beta2 expression. TGFbeta3 mRNA level was markedly reduced by LPS alone, or with both L-NMMA and NAC. Finally, the expression of TGF-betaRI was slightly increased in the presence of combined LPS and L-NMMA or NAC whereas that of TGFbeta-RII was reduced in the same conditions. CONCLUSIONS: The modulation of TGF-beta system was found to be differentially controlled by NO and ROS productions. Indeed, the control exerted on TGF-beta expression varied according to the isoform: TGF-beta1 mRNA level depends on NO whereas that of TGF-beta2 is regulated by ROS and TGF-beta3 seems to be unaffected by both of them. The expression of TGF-beta receptors appeared to be modulated by NO and ROS levels. The relevance of the present findings to osteoarthritis (OA) physiopathology and the potential use of antioxidant therapy to treat this disease are discussed.

Acetylcysteine↗

PubMed2002

Regulation by reactive oxygen species of interleukin-1beta, nitric oxide and prostaglandin E(2) production by human chondrocytes.

OBJECTIVES: To determine the effects of two drugs, N-monomethyl-L-arginine (L-NMMA) and N-acetylcysteine (NAC), on interleukin-1beta (IL-1beta), nitric oxide (NO) and prostaglandin E(2) (PGE(2)) production by human chondrocytes. The effect of aceclofenac (ACECLO), a non-steroidal antiinflammatory drug (NSAID), was also examined. METHODS: Human chondrocytes were enzymatically isolated from osteoarthritic knee cartilage and then maintained in culture in suspension for 48h in the absence or in the presence of lipopolysaccharide (LPS) (10 microg/ml), L-NMMA (0.5mM), NAC (1mM) or ACECLO (6.10(-6)M). IL-1beta and PGE(2) productions were quantified by specific immunoassays. Nitrite was measured in the culture supernatants by a spectrophotometric method based upon the Griess reaction. Cyclooxygenase-2 (COX-2), inducible NO synthase (iNOS) and IL-1beta gene expressions were quantified by transcription of mRNA followed by real time and quantitative polymerase chain reaction. COX-2 protein expression was analysed by Western blot. RESULTS: LPS markedly increased the expression of IL-1beta, iNOS and COX-2 genes. In parallel, NO(2) and PGE(2) amounts found in the culture supernatants were significantly enhanced whereas IL-1beta was immunologically undetectable. The addition of L-NMMA (0.5mM) fully blocked LPS-induced NO production but greatly increased PGE(2) production, suggesting a negative effect of NO on PGE(2) synthesis. Inversely, NO production was stimulated by NAC while PGE(2) production was not affected. Interestingly, NAC increased the IL-1beta and iNOS mRNA levels but did not significantly modify COX-2 mRNA expression. L-NMMA did not significantly affect the expression of IL-1beta, iNOS and COX-2. The amount of COX-2 protein did not change in the presence of the antioxidants. Finally, ACECLO fully blocked the production of PGE(2) by chondrocytes without affecting the levels of COX-2 mRNA. CONCLUSIONS: The stimulation of IL-1beta, NO and PGE(2) production by LPS is differentially controlled by reactive oxygen species (ROS). In fact, L-NMMA and NAC have different mechanisms of action on the regulation of NO and PGE(2) productions. L-NMMA fully inhibits NO but increases PGE(2) production whereas NAC up-regulates NO but does not modify PGE(2) synthesis. The stimulating effect of L-NMMA on PGE(2) production is not controlled at the transcriptional level. These findings suggest that antioxidant therapy could have different effects according to the oxygen radical species targeted.

Anti-Inflammatory Agents, Non-Steroidal↗

PubMed2001

Fully automatic anatomical, pathological, and functional segmentation from CT scans for hepatic surgery.

OBJECTIVE: To improve the planning of hepatic surgery, we have developed a fully automatic anatomical, pathological, and functional segmentation of the liver derived from a spiral CT scan. MATERIALS AND METHODS: From a 2 mm-thick enhanced spiral CT scan, the first stage automatically delineates skin, bones, lungs, kidneys, and spleen by combining the use of thresholding, mathematical morphology, and distance maps. Next, a reference 3D model is immersed in the image and automatically deformed to the liver contours. Then an automatic Gaussian fitting on the imaging histogram estimates the intensities of parenchyma, vessels, and lesions. This first result is next improved through an original topological and geometrical analysis, providing an automatic delineation of lesions and veins. Finally, a topological and geometrical analysis based on medical knowledge provides hepatic functional information that is invisible in medical imaging: portal vein labeling and hepatic anatomical segmentation according to the Couinaud classification. RESULTS: Clinical validation performed on more than 30 patients shows that delineation of anatomical structures by this method is often more sensitive and more specific than manual delineation by a radiologist. CONCLUSION: This study describes the methodology used to create the automatic segmentation of the liver with delineation of important anatomical, pathological, and functional structures from a routine CT scan. Using the methods proposed in this study, we have confirmed the accuracy and utility of the creation of a 3D liver model compared with the conventional reading of the CT scan by a radiologist. This work may allow improved preoperative planning of hepatic surgery by more precisely delineating liver pathology and its relationship to normal hepatic structures. In the future, this data may be integrated with computer-assisted surgery and thus represents a first step towards the development of an augmented-reality surgical system.

Humans↗

PubMed2001

Three-dimensional multimodal brain warping using the demons algorithm and adaptive intensity corrections.

This paper presents an original method for three-dimensional elastic registration of multimodal images. We propose to make use of a scheme that iterates between correcting for intensity differences between images and performing standard monomodal registration. The core of our contribution resides in providing a method that finds the transformation that maps the intensities of one image to those of another. It makes the assumption that there are at most two functional dependencies between the intensities of structures present in the images to register, and relies on robust estimation techniques to evaluate these functions. We provide results showing successful registration between several imaging modalities involving segmentations, T1 magnetic resonance (MR), T2 MR, proton density (PD) MR and computed tomography (CT). We also argue that our intensity modeling may be more appropriate than mutual information (MI) in the context of evaluating high-dimensional deformations, as it puts more constraints on the parameters to be estimated and, thus, permits a better search of the parameter space.

Algorithms↗

PubMed2001

Rigid registration of 3-D ultrasound with MR images: a new approach combining intensity and gradient information.

We present a new image-based technique to rigidly register intraoperative three-dimensional ultrasound (US) with preoperative magnetic resonance (MR) images. Automatic registration is achieved by maximization of a similarity measure which generalizes the correlation ratio, and whose novelty is to incorporate multivariate information from the MR data (intensity and gradient). In addition, the similarity measure is built upon a robust intensity-based distance measure, which makes it possible to handle a variety of US artifacts. A cross-validation study has been carried out using a number of phantom and clinical data. This indicates that the method is quite robust and that the worst registration errors are of the order of the MR image resolution.

Algorithms↗

PubMed2000

An automatic virtual patient reconstruction from CT-scans for hepatic surgical planning.

UNLABELLED: PROBLEM/BACKGROUND: In order to help hepatic surgical planning we perfected automatic 3D reconstruction of patients from conventional CT-scan, and interactive visualization and virtual resection tools. TOOLS AND METHODS: From a conventional abdominal CT-scan, we have developed several methods allowing the automatic 3D reconstruction of skin, bones, kidneys, lung, liver, hepatic lesions, and vessels. These methods are based on deformable modeling or thresholding algorithms followed by the application of mathematical morphological operators. From these anatomical and pathological models, we have developed a new framework for translating anatomical knowledge into geometrical and topological constraints. More precisely, our approach allows to automatically delineate the hepatic and portal veins but also to label the portal vein and finally to build an anatomical segmentation of the liver based on Couinaud definition which is currently used by surgeons all over the world. Finally, we have developed a user friendly interface for the 3D visualization of anatomical and pathological structures, the accurate evaluation of volumes and distances and for the virtual hepatic resection along a user-defined cutting plane. RESULTS: A validation study on a 30 patients database gives 2 mm of precision for liver delineation and less than 1 mm for all other anatomical and pathological structures delineation. An in vivo validation performed during surgery also showed that anatomical segmentation is more precise than the delineation performed by a surgeon based on external landmarks. This surgery planning system has been routinely used by our medical partner, and this has resulted in an improvement of the planning and performance of hepatic surgery procedures. CONCLUSION: We have developed new tools for hepatic surgical planning allowing a better surgery through an automatic delineation and visualization of anatomical and pathological structures. These tools represent a first step towards the development of an augmented reality system combined with computer assisted tele-robotical surgery.

Computer Graphics↗

PubMed1999

Efficient linear elastic models of soft tissues for real-time surgery simulation.

In this paper, we describe the basic components of a surgery simulator prototype developed at INRIA. We present two physical models which are well suited for surgery simulation. These models are based on linear elasticity theory and finite elements modeling. The former model can deforme large tetrahedral meshes in real-time but does not allow any topological changes. On the contrary, the latter biomechanical model can simulate the cutting and tearing of soft tissue but must have a limited number of vertices to run in real-time. We propose a method for combining these two approaches into a hybrid model which may allow real time deformations and cuttings of large enough anatomical structures.

Biomechanical Phenomena↗

PubMed1998

[A new concept in surgery of the digestive tract: surgical procedure assisted by computer, from virtual reality to telemanipulation].

Surgical simulation increasingly appears to be an essential aspect of tomorrow's surgery. The development of a hepatic surgery simulator is an advanced concept calling for a new writing system which will transform the medical world: virtual reality. Virtual reality extends the perception of our five senses by representing more than the real state of things by the means of computer sciences and robotics. It consists of three concepts: immersion, navigation and interaction. Three reasons have led us to develop this simulator: the first is to provide the surgeon with a comprehensive visualisation of the organ. The second reasons is to allow for planning and surgical simulation that could be compared with the detailed flight-plan for a commercial jet pilot. The third lies in the fact that virtual reality is an integrated part of the concept of computer assisted surgical procedure. The project consists of a sophisticated simulator which must include five requirements: a) visual fidelity, b) interactivity, c) physical properties, d) physiological properties, e) sensory input and output. In this report we describe how to obtain a realistic 3D model of the liver from bi-dimensional 2D medical images for anatomical and surgical training. The introduction of a tumor and the consequent planning and virtual resection is also described, as are force feedback and real-time interaction.

Anatomy, Cross-Sectional↗

PubMed1998

A scheme for automatically building three-dimensional morphometric anatomical atlases: application to a skull atlas.

We present a general scheme for automatically building a morphometric anatomical atlas. We detail each stage of the method, including the non-rigid registration algorithm, three-dimensional line averaging and statistical processes. We apply the method to obtain a quantitative atlas of skull crest lines. Finally, we use the resulting atlas to study a craniofacial disease; we show how we can obtain qualitative and quantitative results by contrasting a skull affected by a mandible deformation with the atlas.

Algorithms↗

PubMed1998

Definition of a four-dimensional continuous planispheric transformation for the tracking and the analysis of left-ventricle motion.

Cardiologists assume that analysis of the motion of the heart (especially the left ventricle) can provide useful information about the health of the myocardium. A 4-D polar transformation is defined to describe the left-ventricle (LV) motion and a method is presented to estimate it from sequences of 3-D images. The transformation is defined in 3-D planispheric coordinates (3PC) by a small number of parameters involved in a set of simple linear equations. It is continuous and regular in time and space, and periodicity in time can be imposed. The local motion can be easily decomposed into a few canonical motions (radial motion, rotation around the long-axis, elevation). To recover the motion from original data, the 4-D polar transformation is calculated using an adaptation of the iterative closest-point algorithm. We present the mathematical framework and a demonstration of its feasability on a series of gated SPECT sequences.

Humans↗

PubMed1998

A geometric algorithm to find small but highly similar 3D substructures in proteins.

MOTIVATION: Most biological actions of proteins depend on some typical parts of their three-dimensional structure, called 3D motifs. It is desirable to find automatically common geometric substructures between proteins to discover similarities in new structures or to model precisely a particular motif. Most algorithms for structural comparison of proteins deal with large (fold) similarities. Here, we focus on small but precise similarities. RESULTS: We propose a new 3D substructure matching algorithm based on geometric hashing techniques. The key feature of the method is the introduction of a 3D reference frame attached to each residue. This allows us to reduce drastically the complexity of the recognition. Our experimental results confirm the validity of the approach and allow us to find smaller similarities than previous methods. AVAILABILITY: The program uses commercial libraries and thus cannot be completely freely distributed. It can be found at ftp://www.inria.fr in the directory epidaure/Outgoing/xpennec/Prospect, but it requires a key to be run, available by request to xavier.pennec@sophia.inria.fr CONTACT: Xavier.Pennec@sophia.inria.fr; Nicholas.Ayache@sophia.inria.fr

Algorithms↗