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

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. Methods The 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. Results Efficient mapping of the TLED algorithm to parallel hardware results in very high computational performance, far exceeding that available in commercial packages. Conclusion The 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

Patient-specific simulation environment for surgical planning and preoperative rehearsal

Surgical simulation is common practice in the fields of surgical education and training. Numerous surgical simulators are available from commercial and academic organisations for the generic modelling of surgical tasks. However, a simulation platform is still yet to be found that fulfils the key requirements expected for patient-specific surgical simulation of soft tissue, with an effective translation into clinical practice. Patient-specific modelling is possible, but to date has been time-consuming, and consequently costly, because data preparation can be technically demanding. This motivated the research developed herein, which addresses the main challenges of biomechanical modelling for patient-specific surgical simulation. A novel implementation of soft tissue deformation and estimation of the patient-specific intraoperative environment is achieved using a position-based dynamics approach. This modelling approach overcomes the limitations derived from traditional physically-based approaches, by providing a simulation for patient-specific models with visual and physical accuracy, stability and real-time interaction. As a geometrically- based method, a calibration of the simulation parameters is performed and the simulation framework is successfully validated through experimental studies. The capabilities of the simulation platform are demonstrated by the integration of different surgical planning applications that are found relevant in the context of kidney cancer surgery. The simulation of pneumoperitoneum facilitates trocar placement planning and intraoperative surgical navigation. The implementation of deformable ultrasound simulation can assist surgeons in improving their scanning technique and definition of an optimal procedural strategy. Furthermore, the simulation framework has the potential to support the development and assessment of hypotheses that cannot be tested in vivo. Specifically, the evaluation of feedback modalities, as a response to user-model interaction, demonstrates improved performance and justifies the need to integrate a feedback framework in the robot-assisted surgical setting.Open Acces

Biomechanical modelling of probe to tissue interaction during ultrasound scanning

Purpose: Biomechanical simulation of anatomical deformations caused by ultrasound probe pressure is of outstanding importance for several applications, from the testing of robotic acquisition systems to multi-modal image fusion and development of ultrasound training platforms. Different approaches can be exploited for modelling the probe-tissue interaction, each achieving different trade-offs among accuracy, computation time and stability. Methods: We assess the performances of different strategies based on the finite element method for modelling the interaction between the rigid probe and soft tissues. Probe\u2013tissue contact is modelled using (i) penalty forces, (ii) constraint forces, and (iii) by prescribing the displacement of the mesh surface nodes. These methods are tested in the challenging context of ultrasound scanning of the breast, an organ undergoing large nonlinear deformations during the procedure. Results: The obtained results are evaluated against those of a non-physically based method. While all methods achieve similar accuracy, performance in terms of stability and speed shows high variability, especially for those methods modelling the contacts explicitly. Overall, prescribing surface displacements is the approach with best performances, but it requires prior knowledge of the contact area and probe trajectory. Conclusions: In this work, we present different strategies for modelling probe\u2013tissue interaction, each able to achieve different compromises among accuracy, speed and stability. The choice of the preferred approach highly depends on the requirements of the specific clinical application. Since the presented methodologies can be applied to describe general tool\u2013tissue interactions, this work can be seen as a reference for researchers seeking the most appropriate strategy to model anatomical deformation induced by the interaction with medical tools

Research on real-time physics-based deformation for haptic-enabled medical simulation

This study developed a multiple effective visuo-haptic surgical engine to handle a variety of surgical manipulations in real-time. Soft tissue models are based on biomechanical experiment and continuum mechanics for greater accuracy. Such models will increase the realism of future training systems and the VR/AR/MR implementations for the operating room

NOViSE: a virtual natural orifice transluminal endoscopic surgery simulator

Purpose: Natural Orifice Transluminal Endoscopic Surgery (NOTES) is a novel technique in minimally invasive surgery whereby a flexible endoscope is inserted via a natural orifice to gain access to the abdominal cavity, leaving no external scars. This innovative use of flexible endoscopy creates many new challenges and is associated with a steep learning curve for clinicians. Methods: We developed NOViSE - the first force-feedback enabled virtual reality simulator for NOTES training supporting a flexible endoscope. The haptic device is custom built and the behaviour of the virtual flexible endoscope is based on an established theoretical framework – the Cosserat Theory of Elastic Rods. Results: We present the application of NOViSE to the simulation of a hybrid trans-gastric cholecystectomy procedure. Preliminary results of face, content and construct validation have previously shown that NOViSE delivers the required level of realism for training of endoscopic manipulation skills specific to NOTES Conclusions: VR simulation of NOTES procedures can contribute to surgical training and improve the educational experience without putting patients at risk, raising ethical issues or requiring expensive animal or cadaver facilities. In the context of an experimental technique, NOViSE could potentially facilitate NOTES development and contribute to its wider use by keeping practitioners up to date with this novel surgical technique. NOViSE is a first prototype and the initial results indicate that it provides promising foundations for further development

Prostate Motion Modelling Using Biomechanically-Trained Deep Neural Networks on Unstructured Nodes

In this paper, we propose to train deep neural networks with biomechanical simulations, to predict the prostate motion encountered during ultrasound-guided interventions. In this application, unstructured points are sampled from segmented pre-operative MR images to represent the anatomical regions of interest. The point sets are then assigned with point-specific material properties and displacement loads, forming the un-ordered input feature vectors. An adapted PointNet can be trained to predict the nodal displacements, using finite element (FE) simulations as ground-truth data. Furthermore, a versatile bootstrap aggregating mechanism is validated to accommodate the variable number of feature vectors due to different patient geometries, comprised of a training-time bootstrap sampling and a model averaging inference. This results in a fast and accurate approximation to the FE solutions without requiring subject-specific solid meshing. Based on 160,000 nonlinear FE simulations on clinical imaging data from 320 patients, we demonstrate that the trained networks generalise to unstructured point sets sampled directly from holdout patient segmentation, yielding a near real-time inference and an expected error of 0.017 mm in predicted nodal displacement