Efficient Nonlinear FEM for Soft Tissue Modelling and Its GPU Implementation within the Open Source Framework SOFA

Comas, Olivier; Taylor, Zeike A.; Allard, Jérémie; Ourselin, Sébastien; Cotin, Stéphane; Passenger, Josh

doi:10.1007/978-3-540-70521-5_4

Cited by 58 publications

(38 citation statements)

References 8 publications

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“…Initial publications on the topic (Comas et al, 2008;Joldes et al, 2009) do not utilize double-precision (fp64) computation, as Nvidia CPUs did not support it. With the release of Compute Capability 1.3 devices in late 2008, fp64 computation is supported, but is still largely absent in literature.…”

Section: Gpu-accelerated Explicit Fe Analysismentioning

confidence: 99%

See 1 more Smart Citation

Rupture risk in abdominal aortic aneurysms: A realistic assessment of the explicit GPU approach

Štrbac

Pierce

Rodríguez-Vila

et al. 2017

Journal of Biomechanics

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Accurate estimation of peak wall stress (PWS) is the crux of biomechanically motivated rupture risk assessment for abdominal aortic aneurysms aimed to improve clinical outcomes. Such assessments often use the finite element (FE) method to obtain PWS, albeit at a high computational cost, motivating simplifications in material or element formulations. These simplifications, while useful, come at a cost of reliability and accuracy. We achieve research-standard accuracy and maintain clinically applicable speeds by using novel computational technologies. We present a solution using our custom finite element code based on graphics processing unit (GPU) technology that is able to account for added complexities involved with more physiologically relevant solutions, e.g. strong anisotropy and heterogeneity. We present solutions up to 17x faster relative to an established finite element code using state-of-the-art nonlinear, anisotropic and nearly-incompressible material descriptions. We show a realistic assessment of the explicit GPU FE approach by using complex problem geometry, biofidelic material law, doubleprecision floating point computation and full element integration. Due to the increased solution speed without loss of accuracy, shown on five clinical cases of abdominal aortic aneurysms, the method shows promise for clinical use in determining rupture risk of abdominal aortic aneurysms.

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Section: Gpu-accelerated Explicit Fe Analysismentioning

confidence: 99%

“…Further, benchmarking reports on GPU performance use simple or ideal (Bartezzaghi et al, 2015;Comas et al, 2008;Strbac et al, 2015) geometries. Meshing of complex geometries often requires misshaped elements (that limit usable step sizes in explicit analysis), also detailed further in Section 2.3.1.…”

Section: Gpu-accelerated Explicit Fe Analysismentioning

confidence: 99%

Rupture risk in abdominal aortic aneurysms: A realistic assessment of the explicit GPU approach

Štrbac

Pierce

Rodríguez-Vila

et al. 2017

Journal of Biomechanics

View full text Add to dashboard Cite

show abstract

“…See, e.g., de Farias et al [2008] and Comas et al [2008] for parallel computation of deformable bodies (without skeletons) where they achieved a few tens of speedup, and as far as we know, there is no previous work on parallel computing for skeleton-driven deformable body simulation.…”

Section: Parallel Computingmentioning

confidence: 99%

Fast simulation of skeleton-driven deformable body characters

Kim

Pollard

2011

ACM Trans. Graph.

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We propose a fast physically based simulation system for skeleton-driven deformable body characters. Our system can generate realistic motions of self-propelled deformable body characters by considering the two-way interactions among the skeleton, the deformable body, and the environment in the dynamic simulation. It can also compute the passive jiggling behavior of a deformable body driven by a kinematic skeletal motion. We show that a well-coordinated combination of (1) a reduced deformable body model with nonlinear finite elements, (2) a linear-time algorithm for skeleton dynamics, and (3) explicit integration can boost simulation speed to orders of magnitude faster than existing methods, while preserving modeling accuracy as much as possible. Parallel computation on the GPU has also been implemented to obtain an additional speedup for complicated characters. Detailed discussions of our engineering decisions for speed and accuracy of the simulation system are presented in the paper. We tested our approach with a variety of skeleton-driven deformable body characters, and the tested characters were simulated in real-time or near real-time.

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“…There exists a large body of research in the area of soft tissue simulation [4,5,6,7,8]. Due to the complexity of soft biological tissue, it is extremely challenging to simulate their natural behaviour accurately, especially when subject to interventions with surgical instruments.…”

Section: Related Workmentioning

confidence: 99%

Modelling Rod-Like Flexible Biological Tissues for Medical Training

Chang

Zhang

2009

Modelling the Physiological Human

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Abstract. This paper outlines a framework for the modelling of slender rod-like biological tissue structures in both global and local scales. Volumetric discretization of a rod-like structure is expensive in computation and therefore is not ideal for applications where real-time performance is essential. In our approach, the Cosserat rod model is introduced to capture the global shape changes, which models the structure as a one-dimensional entity, while the local deformation is handled separately. In this way a good balance in accuracy and efficiency is achieved. These advantages make our method appropriate for the modelling of soft tissues for medical training applications.Keywords: Medical training, surgery simulation, deformation, Cosserat rod, computer animation IntroductionVirtual simulation can replicate the teledisplay and instrumentation of laparoscopic surgery and is attracting increasing attention from both the research community and the medical practitioners. As a training methodology it can reduce the costs and risks and has been adopted widely by the surgical community. A training system based on virtual simulation provides the trainees with flexible access to training sessions, whereas traditionally the training sessions are limited by the availability of patients and training posts. The most essential element of such a system is to model the behaviour of the tissues in a proper manner in order to produce convincing visual and haptic feedback to the user. Slender shapes represent a group of organs and tissues in the human body. Efficient simulation of such structures provides a useful framework which lays the foundation for virtual surgery applications involving such objects. Our work discussed in this paper focuses on modelling slender biological tissues which can be presented with a simple rod model. In the human body, many tissues are of long, thin, rod-like shapes, and we can take the advantage of modelling them as one-dimensional entities to efficiently simulate their behaviours. Examples of such tissues include blood vessels, muscle fibres, small intestines, rectum, ligaments, tendons, and hair. Though the one

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Efficient Nonlinear FEM for Soft Tissue Modelling and Its GPU Implementation within the Open Source Framework SOFA

Cited by 58 publications

References 8 publications

Rupture risk in abdominal aortic aneurysms: A realistic assessment of the explicit GPU approach

Rupture risk in abdominal aortic aneurysms: A realistic assessment of the explicit GPU approach

Fast simulation of skeleton-driven deformable body characters

Modelling Rod-Like Flexible Biological Tissues for Medical Training

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