NiftySim: A GPU-based nonlinear finite element package for simulation of soft tissue biomechanics.

Stian F Johnsen,Yipeng Hu,Lianghao Han,John Hipwell,David J Hawkes,Zeike A Taylor,Sebastien Ourselin,Thomy Mertzanidou,Matthew J Clarkson,Bjoern Eiben,Marc Modat

doi:10.1007/s11548-014-1118-5

Abstract

Purpose NiftySim, an open-source finite element toolkit, has been designed to allow incorporation of high-performance soft tissue simulation capabilities into biomedical applications. The toolkit provides the option of execution on fast graphics processing unit (GPU) hardware, numerous constitutive models and solid-element options, membrane and shell elements, and contact modelling facilities, in a simple to use library.MethodsThe toolkit is founded on the total Lagrangian explicit dynamics (TLEDs) algorithm, which has been shown to be efficient and accurate for simulation of soft tissues. The base code is written in C++, and GPU execution is achieved using the nVidia CUDA framework. In most cases, interaction with the underlying solvers can be achieved through a single Simulator class, which may be embedded directly in third-party applications such as, surgical guidance systems. Advanced capabilities such as contact modelling and nonlinear constitutive models are also provided, as are more experimental technologies like reduced order modelling. A consistent description of the underlying solution algorithm, its implementation with a focus on GPU execution, and examples of the toolkit’s usage in biomedical applications are provided.ResultsEfficient mapping of the TLED algorithm to parallel hardware results in very high computational performance, far exceeding that available in commercial packages.ConclusionThe NiftySim toolkit provides high-performance soft tissue simulation capabilities using GPU technology for biomechanical simulation research applications in medical image computing, surgical simulation, and surgical guidance applications.

Highlights

We describe the development and features of the open-source finite element (FE) toolkit, NiftySim
Our goal is not to compete with end-to-end toolkits like SOFA1 that provide their own tools for graphical simulation definition and interaction, or general-purpose finite element analysis suites like Abaqus FEA.2
The NiftySim toolkit has been designed to enable efficient integration of simulation technology into applications in medical image computing and computer-assisted interventions. This integration is facilitated by both a command line program capable of executing simulations in a stand-alone fashion, and a library which enables simple embedding of the simulation code in third-party software

Summary

Introduction

We describe the development and features of the open-source finite element (FE) toolkit, NiftySim. While the solver may be used for the analysis of any solid materials, it has been designed and optimised for simulation of soft tissues. The motivation for its development is the growing need for robust soft tissue modelling capabilities in medical imaging and surgical simulation applications, and in particular, in time-critical applications. The latter include, for example, interactive simulation systems where real-time computation is required [5,19,24], and intra-operative image registration and image guidance systems [2,3,7] for which rapid, if not real-time, computation is necessary.

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