Construction and Validation of a Hybrid Lumbar Spine Model For the Fast Evaluation of Intradiscal Pressure and Mobility

International audienceA novel hybrid model of the lumbar spine, allowing fast static and dynamic simulations of the disc pressure and the spine mobility, is introduced in this work. Our contribution is to combine rigid bodies, deformable finite elements, articular constraints, and springs into a unique model of the spine. Each vertebra is represented by a rigid body controlling a surface mesh to model contacts on the facet joints and the spinous process. The discs are modeled using a heterogeneous tetrahedral finite element model. The facet joints are represented as elastic joints with six degrees of freedom, while the ligaments are modeled using non-linear one-dimensional elastic elements. The challenge we tackle is to make these different models efficiently interact while respecting the principles of Anatomy and Mechanics. The mobility, the intradiscal pressure, the facet joint force and the instantaneous center of rotation of the lumbar spine are validated against the experimental and theoretical results of the literature on flexion, extension, lateral bending as well as axial rotation. Our hybrid model greatly simplifies the modeling task and dramatically accelerates the simulation of pressure within the discs, as well as the evaluation of the range of motion and the instantaneous centers of rotation, without penalizing precision. These results suggest that for some types of biomechanical simulations, simplified models allow far easier modeling and faster simulations compared to usual full-FEM approaches without any loss of accuracy

Anatomy Transfer

Characters with precise internal anatomy are important in film and visual effects, as well as in medical applications. We propose the first semi-automatic method for creating anatomical structures, such as bones, muscles, viscera and fat tissues. This is done by transferring a reference anatomical model from an input template to an arbitrary target character, only defined by its boundary representation (skin). The fat distribution of the target character needs to be specified. We can either infer this information from MRI data, or allow the users to express their creative intent through a new editing tool. The rest of our method runs automatically: it first transfers the bones to the target character, while maintaining their structure as much as possible. The bone layer, along with the target skin eroded using the fat thickness information, are then used to define a volume where we map the internal anatomy of the source model using harmonic (Laplacian) deformation. This way, we are able to quickly generate anatomical models for a large range of target characters, while maintaining anatomical constraints

From Generic to Specic Musculoskeletal Simulations using an Ontology-based Modeling Pipeline

International audienceWe present a novel pipeline for the construction of biomechanical simulations by combining generic anatomical knowledge with specic data. Based on functional descriptors supplied by the user, the list of the involved anatomical entities (currently bones and muscles) is generated using formal knowledge stored in ontologies, as well as a physical model based on reference geometry and mechanical parameters. This simulation-ready model can then be registered to subject-speci c geometry to perform customized simulations. The user can provide additional speci c geometry, such as a simulation mesh, to assemble with the reference geometry. Subject-specic information can also be used to individualize each functional model. The model can then be visualized and animated. This pipeline dramatically eases the creation of biomechanical models. We detail an example of a musculoskeletal simulation of knee flexion and extension and hip flexion and abduction, based on rigid bones and the Hill muscle model, with subject-specic 3D meshes non-rigidly attached to the simulated bone

Living Book of Anatomy Project: See your Insides in Motion!

International audienceThe complexity of human anatomy makes learning and understanding it a difficult task.We present the Living Book of Anatomy (LBA) project, an augmented reality system for teaching anatomy. Using a Kinect, we superimpose our 3d highly-detailed anatomical model onto the user's color map and we animate it. By showing our work, we hope to have interesting feedback from Emerging Technologies attendees.See more at http://lba.inrialpes.fr

Qualitative behavioral reasoning from components' interfaces to components' functions for DMU adaption to FE analyses

International audienceA digital mock-up (DMU), with its B-Rep model of product components, is a standard industrial representation that lacks geometric information about interfaces between components. Component shapes reflect common engineering practices that influence component interfaces with interferences and not only contacts. The proposed approach builds upon relationships between function, behavior, and shape to derive functional information from the geometry of component interfaces. Among these concepts, the concept of behavior is more difficult to set up and connect to the geometry of interfaces and functions. Indeed, states and design rules are introduced to express the behavior of components through a qualitative reasoning process. This reasoning process, in turn, takes advantage of domain knowledge rules and facts, checking the validity of certain hypotheses that must hold true all along a specific state of the product's lifecycle, such as operational, stand-by or relaxed states. Eliminating configurations that contradict one or more of those hypotheses in their corresponding reference state reduces ambiguity, subsequently producing functional information in a bottom-up manner. This bottom-up process starts with the generation of a conventional interfaces graph (CIG) with components as nodes, and conventional interfaces (CIs) as arcs. A CI is initially defined by a geometric interaction that can be a contact or an interference between two components. CIs are then populated with functional interpretations (FIs) according to their geometric properties, producing potentially many combinations. A first step of the reasoning process, the validation against reference states, reduces the number of FIs per CI. Domain knowledge rules are then applied again to group semantics of component interfaces into one functional designation per component to connect together geometric entities of its boundary with its function

My Corporis Fabrica: Making Anatomy Easy

International audienceCharacters with precise internal anatomy are important in film and visual effects, as well as in medical applications. However, setting up detailed anatomical models has been a difficult task, especially for simulation. We demonstrate MyCorporisFabrica(MyCF), the first assistant tool for modeling and simulating anatomical structures such as bones, muscles, viscera and fat tissues. This is done by transferring a reference anatomical model from an input template to an arbitrary target character, only defined by its skin. Given the target character in a similar pose as the reference anatomy, and optionally a distribution of fat, the method runs automatically. This allows to quickly generate anatomical models for a large range of target characters, while maintaining anatomical constraints. Moreover, the tool includes a novel anatomy knowledge base designed to help selecting anatomical entities based on their contribution to physiological functions. Finally, the knowledge base contains mechanical data used to set up different mechanical models of the selected entities, which we export to a simulator. This dramatically eases biomechanical modeling and makes it possible for non-expert users to enter that field. The application works in a web browser. In this 20 minute talk, we demonstrate this technology and detail a practical example

OntoSIDES: Ontology-based student progress monitoring on the national evaluation system of French Medical Schools

International audienceWe introduce OntoSIDES, the core of an ontology-based learning management system in Medicine, in which theeducational content, the traces of students’ activities and the correction of exams are linked and related to itemsof an official reference program in a unified RDF data model. OntoSIDES is an RDF knowledge base comprised ofa lightweight domain ontology that serves as a pivot high-level vocabulary of the query interface with users, andof a dataset made of factual statements relating individual entities to classes and properties of the ontology.Thanks to an automatic mapping-based data materialization and rule-based data saturation, OntoSIDES containsaround 8 millions triples to date, and provides an integrated access to useful information for student progressmonitoring, using a powerful query language (namely SPARQL) allowing users to express their specific needs ofdata exploration and analysis. Since we do not expect end-users to master the raw syntax of SPARQL and toexpress directly complex queries in SPARQL, we have designed a set of parametrized queries that users caninstantiate through a user-friendly interface

Brain-shift compensation using intraoperative ultrasound and constraint-based biomechanical simulation

International audiencePurpose. 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

Vessel-based brain-shift compensation using elastic registration driven by a patient-specific finite element model

International audienceDuring 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

My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development

International audienceBackground: Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physically based modeling are used to assist the visualization and the simulation of virtual humans for numerous domains such as surgical simulation and learning. On the other side, the ontology-based approach applied to knowledge representation is more and more successfully adopted in the life-science domains to formalize biological entities and phenomena, thanks to a declarative approach for expressing and reasoning over symbolic information. 3D models and ontologies are two complementary ways to describe biological entities that remain largely separated. Indeed, while many ontologies providing a unified formalization of anatomy and embryology exist, they remain only descriptive and make the access to anatomical content of complex 3D embryology models and simulations difficult. Results: In this work, we present a novel ontology describing the development of the human embryology deforming 3D models. Beyond describing how organs and structures are composed, our ontology integrates a procedural description of their 3D representations, temporal deformation and relations with respect to their developments. We also created inferences rules to express complex connections between entities. It results in a unified description of both the knowledge of the organs deformation and their 3D representations enabling to visualize dynamically the embryo deformation during the Carnegie stages. Through a simplified ontology, containing representative entities which are linked to spatial position and temporal process information, we illustrate the added-value of such a declarative approach for interactive simulation and visualization of 3D embryos.Conclusions: Combining ontologies and 3D models enables a declarative description of different embryological models that capture the complexity of human developmental anatomy. Visualizing embryos with 3D geometric models and their animated deformations perhaps paves the way towards some kind of hypothesis-driven application. These can also be used to assist the learning process of this complex knowledge.Availability: http://www.mycorporisfabrica.org