Grand Joldes - Academia.edu (original) (raw)
Papers by Grand Joldes
We propose an efficient numerical algorithm for computing deformations of "very" soft t... more We propose an efficient numerical algorithm for computing deformations of "very" soft tissues (such as the brain, liver, kidney etc.), with applications to real time surgical simulation. The algorithm is based on the finite element method using the Total Lagrangian formulation, where stresses and strains are measured with respect to the original configuration. This choice allows for pre-computing of most
Computers in Biology and Medicine, 2015
To enhance neuro-navigation, high quality pre-operative images must be registered onto intra-oper... more To enhance neuro-navigation, high quality pre-operative images must be registered onto intra-operative configuration of the brain. Therefore evaluation of the degree to which structures may remain misaligned after registration is critically important. We consider two Hausdorff Distance (HD)-based evaluation approaches: the edge-based HD (EBHD) metric and the Robust HD (RHD) metric as well as various commonly used intensity-based similarity metrics such as Mutual Information (MI), Normalised Mutual Information (NMI), Entropy Correlation Coefficient (ECC), Kullback-Leibler Distance (KLD) and Correlation Ratio (CR). We conducted the evaluation by applying known deformations to simple sample images and real cases of brain shift. We conclude that the intensity-based similarity metrics such as MI, NMI, ECC, KLD and CR do not correlate well with actual alignment errors, and hence are not useful for assessing misalignment. On the contrary, the EBHD and the RHD metrics correlated well with actual alignment errors; however, they have been found to underestimate the actual misalignment. We also note that it is beneficial to present HD results as a percentile-HD curve rather than a single number such as the 95-percentile HD. Percentile-HD curves present the full range of alignment errors and also facilitate the comparison of results obtained using different approaches. Furthermore, the qualities that should be possessed by an ideal evaluation metric were highlighted. Future studies could focus on developing such an evaluation metric.
Engineering Analysis with Boundary Elements, 2015
Computational Biomechanics for Medicine, 2012
ABSTRACT Biomechanical modeling has become a viable alternative to purely image-based approaches ... more ABSTRACT Biomechanical modeling has become a viable alternative to purely image-based approaches for predicting brain deformation during surgery. Most of the time, a finite element mesh is used for computing the deformation field. Although many papers discuss methods for obtaining the deformation field, there is little information on how it will be used, especially for updating images intraoperatively. In this paper, we discuss some requirements related to the use of this deformation field for warping high quality preoperative brain images. A software implementation is presented, which satisfies most of these requirements. Based on this implementation, we outline some of the difficulties in performing brain registration intraoperatively in real time and propose possible solutions.
Lecture Notes in Computer Science, 2014
Applied Mathematical Modelling, 2014
ABSTRACT The problem of finding the un-deformed configuration of an elastic body, when the deform... more ABSTRACT The problem of finding the un-deformed configuration of an elastic body, when the deformed configuration and the loads are known, occurs in many engineering applications. Standard solution methods for such problems include conservation laws based on Eshelby’s energy–momentum tensor and re-parameterization of the standard equilibrium equations. In this paper we present a different method for solving such problems, based on a re-parameterization of the nodal forces using the Total Lagrangian formulation. The obtained nonlinear system of equations describing equilibrium can be solved using either Newton–Raphson or an explicit dynamic relaxation algorithm. The solution method requires only minor modifications to similar algorithms designed for forward motion calculations. Several examples involving large deformations and different boundary conditions and loads are presented.
Computational Biomechanics for Medicine, 2014
International journal for numerical methods in biomedical engineering, 2011
Dynamic Relaxation is an explicit method that can be used for computing the steady state solution... more Dynamic Relaxation is an explicit method that can be used for computing the steady state solution for a discretised continuum mechanics problem. The convergence speed of the method depends on the accurate estimation of the parameters involved, which is especially difficult for nonlinear problems. In this paper we propose a completely adaptive Dynamic Relaxation method in which the parameters are updated during the iteration process, converging to their optimal values. We use the proposed method for computing intra-operative organ deformations using non-linear finite element models involving large deformations, nonlinear materials and contacts. The simulation results prove the accuracy and computational efficiency of the method. The proposed method is also very well suited for GPU implementation.
Acta of bioengineering and biomechanics / Wrocław University of Technology, 2010
This article presents a summary of the key-note lecture delivered at Biomechanics 10 Conference h... more This article presents a summary of the key-note lecture delivered at Biomechanics 10 Conference held in August 2010 in Warsaw. We present selected topics in the area of mathematical and numerical modelling of the brain biomechanics for neurosurgical simulation and brain image registration. These processes can reasonably be described in purely mechanical terms, such as displacements, strains and stresses and therefore can be analysed using established methods of continuum mechanics. We advocate the use of fully non-linear theory of continuum mechanics. We discuss in some detail modelling geometry, boundary conditions, loading and material properties. We consider numerical problems such as the use of hexahedral and mixed hexahedral-tetrahedral meshes as well as meshless spatial discretisation schemes. We advocate the use of Total Lagrangian Formulation of both finite element and meshless methods together with explicit time-stepping procedures. We support our recommendations and conclu...
Progress in biophysics and molecular biology, 2010
Long computation times of non-linear (i.e. accounting for geometric and material non-linearity) b... more Long computation times of non-linear (i.e. accounting for geometric and material non-linearity) biomechanical models have been regarded as one of the key factors preventing application of such models in predicting organ deformation for image-guided surgery. This contribution presents real-time patient-specific computation of the deformation field within the brain for six cases of brain shift induced by craniotomy (i.e. surgical opening of the skull) using specialised non-linear finite element procedures implemented on a graphics processing unit (GPU). In contrast to commercial finite element codes that rely on an updated Lagrangian formulation and implicit integration in time domain for steady state solutions, our procedures utilise the total Lagrangian formulation with explicit time stepping and dynamic relaxation. We used patient-specific finite element meshes consisting of hexahedral and non-locking tetrahedral elements, together with realistic material properties for the brain t...
Medical image analysis, 2009
Real time computation of soft tissue deformation is important for the use of augmented reality de... more Real time computation of soft tissue deformation is important for the use of augmented reality devices and for providing haptic feedback during operation or surgeon training. This requires algorithms that are fast, accurate and can handle material nonlinearities and large deformations. A set of such algorithms is presented in this paper, starting with the finite element formulation and the integration scheme used and addressing common problems such as hourglass control and locking. The computation examples presented prove that by using these algorithms, real time computations become possible without sacrificing the accuracy of the results. For a brain model having more than 7,000 degrees of freedom, we computed the reaction forces due to indentation with frequency of around 1,000 Hz using a standard dual core PC. Similarly, we conducted simulation of brain shift using a model with more than 50,000 degrees of freedom in less than one minute. The speed benefits of our models result fr...
Computational Biomechanics for Medicine, 2011
International Journal for Numerical Methods in Biomedical Engineering, 2012
Motivated by patient-specific computational modelling in the context of image-guided brain surger... more Motivated by patient-specific computational modelling in the context of image-guided brain surgery, we propose a new fuzzy mesh-free modelling framework. The method works directly on an unstructured cloud of points that do not form elements so that mesh generation is not required. Mechanical properties are assigned directly to each integration point based on fuzzy tissue classification membership functions without the need for image segmentation. Geometric integration is performed over an underlying uniform background grid. The verification example shows that, while requiring no hard segmentation and meshing, the proposed model gives, for all practical purposes, equivalent results to a finite element model.
We present selected topics in the area of mathematical and numerical modelling of the brain biome... more We present selected topics in the area of mathematical and numerical modelling of the brain biomechanics for brain image registration. We show how to describe registration in purely mechanical terms, such as displacements, strains and stresses and perform it using established methods of continuum mechanics. We advocate the use of fully non-linear theory of continuum mechanics. We discuss in some
Biological and Medical Physics, Biomedical Engineering, 2011
ABSTRACT During neurosurgery, the brain significantly deforms. Despite the enormous complexity of... more ABSTRACT During neurosurgery, the brain significantly deforms. Despite the enormous complexity of the brain (see Chap. 2) many aspects of its response can be reasonably described in purely mechanical terms, such as displacements, strains and stresses. They can therefore be analyzed using established methods of continuum mechanics. In this chapter, we discuss approaches to biomechanical modeling of the brain from the perspective of two distinct applications: neurosurgical simulation and neuroimage registration in image-guided surgery. These two challenging applications are described below.1
Computational Biomechanics for Medicine, 2012
Computational Biomechanics for Medicine, 2013
Computational Biomechanics for Medicine, 2010
Page 1. Chapter 6 Cortical Surface Motion Estimation for Brain Shift Prediction Grand Roman Jolde... more Page 1. Chapter 6 Cortical Surface Motion Estimation for Brain Shift Prediction Grand Roman Joldes, Adam Wittek, and Karol Miller Abstract In this chapter we present an algorithm for computing the displacement of the exposed surface of the brain during surgery. ...
International Journal for Numerical Methods in Biomedical Engineering, 2010
A method is presented for computing deformation of very soft tissue. The method is motivated by t... more A method is presented for computing deformation of very soft tissue. The method is motivated by the need for simple, automatic model creation for real-time simulation. The method is meshless in the sense that deformation is calculated at nodes that are not part of an element mesh. Node placement is almost arbitrary. Fully geometrically nonlinear Total Lagrangian formulation is used. Geometric integration is performed over a regular background grid that does not conform to the simulation geometry. Explicit time integration is used via the central difference method. As an example the simple but fully nonlinear Neo-Hookean material model is employed. The results are compared with a finite element simulation to verify the usefulness of the method.
Lecture Notes in Computer Science, 2009
Patient-specific biomechanical models implemented using specialized nonlinear (i.e. taking into a... more Patient-specific biomechanical models implemented using specialized nonlinear (i.e. taking into account material and geometric nonlinearities) finite element procedures were applied to predict the deformation field within the brain for five cases of craniotomy-induced brain shift. The procedures utilize the Total Lagrangian formulation with explicit time stepping. The loading was defined by prescribing deformations on the brain surface under the craniotomy. Application of the computed deformation fields to register the preoperative images with the intraoperative ones indicated that the models very accurately predict the intraoperative positions and deformations of the brain anatomical structures for limited information about the brain surface deformations. For each case, it took less than 40 s to compute the deformation field using a standard personal computer, and less than 4 s using a Graphics Processing Unit (GPU). The results suggest that nonlinear biomechanical models can be regarded as one possible method of complementing medical image processing techniques when conducting non-rigid registration within the real-time constraints of neurosurgery.
We propose an efficient numerical algorithm for computing deformations of "very" soft t... more We propose an efficient numerical algorithm for computing deformations of "very" soft tissues (such as the brain, liver, kidney etc.), with applications to real time surgical simulation. The algorithm is based on the finite element method using the Total Lagrangian formulation, where stresses and strains are measured with respect to the original configuration. This choice allows for pre-computing of most
Computers in Biology and Medicine, 2015
To enhance neuro-navigation, high quality pre-operative images must be registered onto intra-oper... more To enhance neuro-navigation, high quality pre-operative images must be registered onto intra-operative configuration of the brain. Therefore evaluation of the degree to which structures may remain misaligned after registration is critically important. We consider two Hausdorff Distance (HD)-based evaluation approaches: the edge-based HD (EBHD) metric and the Robust HD (RHD) metric as well as various commonly used intensity-based similarity metrics such as Mutual Information (MI), Normalised Mutual Information (NMI), Entropy Correlation Coefficient (ECC), Kullback-Leibler Distance (KLD) and Correlation Ratio (CR). We conducted the evaluation by applying known deformations to simple sample images and real cases of brain shift. We conclude that the intensity-based similarity metrics such as MI, NMI, ECC, KLD and CR do not correlate well with actual alignment errors, and hence are not useful for assessing misalignment. On the contrary, the EBHD and the RHD metrics correlated well with actual alignment errors; however, they have been found to underestimate the actual misalignment. We also note that it is beneficial to present HD results as a percentile-HD curve rather than a single number such as the 95-percentile HD. Percentile-HD curves present the full range of alignment errors and also facilitate the comparison of results obtained using different approaches. Furthermore, the qualities that should be possessed by an ideal evaluation metric were highlighted. Future studies could focus on developing such an evaluation metric.
Engineering Analysis with Boundary Elements, 2015
Computational Biomechanics for Medicine, 2012
ABSTRACT Biomechanical modeling has become a viable alternative to purely image-based approaches ... more ABSTRACT Biomechanical modeling has become a viable alternative to purely image-based approaches for predicting brain deformation during surgery. Most of the time, a finite element mesh is used for computing the deformation field. Although many papers discuss methods for obtaining the deformation field, there is little information on how it will be used, especially for updating images intraoperatively. In this paper, we discuss some requirements related to the use of this deformation field for warping high quality preoperative brain images. A software implementation is presented, which satisfies most of these requirements. Based on this implementation, we outline some of the difficulties in performing brain registration intraoperatively in real time and propose possible solutions.
Lecture Notes in Computer Science, 2014
Applied Mathematical Modelling, 2014
ABSTRACT The problem of finding the un-deformed configuration of an elastic body, when the deform... more ABSTRACT The problem of finding the un-deformed configuration of an elastic body, when the deformed configuration and the loads are known, occurs in many engineering applications. Standard solution methods for such problems include conservation laws based on Eshelby’s energy–momentum tensor and re-parameterization of the standard equilibrium equations. In this paper we present a different method for solving such problems, based on a re-parameterization of the nodal forces using the Total Lagrangian formulation. The obtained nonlinear system of equations describing equilibrium can be solved using either Newton–Raphson or an explicit dynamic relaxation algorithm. The solution method requires only minor modifications to similar algorithms designed for forward motion calculations. Several examples involving large deformations and different boundary conditions and loads are presented.
Computational Biomechanics for Medicine, 2014
International journal for numerical methods in biomedical engineering, 2011
Dynamic Relaxation is an explicit method that can be used for computing the steady state solution... more Dynamic Relaxation is an explicit method that can be used for computing the steady state solution for a discretised continuum mechanics problem. The convergence speed of the method depends on the accurate estimation of the parameters involved, which is especially difficult for nonlinear problems. In this paper we propose a completely adaptive Dynamic Relaxation method in which the parameters are updated during the iteration process, converging to their optimal values. We use the proposed method for computing intra-operative organ deformations using non-linear finite element models involving large deformations, nonlinear materials and contacts. The simulation results prove the accuracy and computational efficiency of the method. The proposed method is also very well suited for GPU implementation.
Acta of bioengineering and biomechanics / Wrocław University of Technology, 2010
This article presents a summary of the key-note lecture delivered at Biomechanics 10 Conference h... more This article presents a summary of the key-note lecture delivered at Biomechanics 10 Conference held in August 2010 in Warsaw. We present selected topics in the area of mathematical and numerical modelling of the brain biomechanics for neurosurgical simulation and brain image registration. These processes can reasonably be described in purely mechanical terms, such as displacements, strains and stresses and therefore can be analysed using established methods of continuum mechanics. We advocate the use of fully non-linear theory of continuum mechanics. We discuss in some detail modelling geometry, boundary conditions, loading and material properties. We consider numerical problems such as the use of hexahedral and mixed hexahedral-tetrahedral meshes as well as meshless spatial discretisation schemes. We advocate the use of Total Lagrangian Formulation of both finite element and meshless methods together with explicit time-stepping procedures. We support our recommendations and conclu...
Progress in biophysics and molecular biology, 2010
Long computation times of non-linear (i.e. accounting for geometric and material non-linearity) b... more Long computation times of non-linear (i.e. accounting for geometric and material non-linearity) biomechanical models have been regarded as one of the key factors preventing application of such models in predicting organ deformation for image-guided surgery. This contribution presents real-time patient-specific computation of the deformation field within the brain for six cases of brain shift induced by craniotomy (i.e. surgical opening of the skull) using specialised non-linear finite element procedures implemented on a graphics processing unit (GPU). In contrast to commercial finite element codes that rely on an updated Lagrangian formulation and implicit integration in time domain for steady state solutions, our procedures utilise the total Lagrangian formulation with explicit time stepping and dynamic relaxation. We used patient-specific finite element meshes consisting of hexahedral and non-locking tetrahedral elements, together with realistic material properties for the brain t...
Medical image analysis, 2009
Real time computation of soft tissue deformation is important for the use of augmented reality de... more Real time computation of soft tissue deformation is important for the use of augmented reality devices and for providing haptic feedback during operation or surgeon training. This requires algorithms that are fast, accurate and can handle material nonlinearities and large deformations. A set of such algorithms is presented in this paper, starting with the finite element formulation and the integration scheme used and addressing common problems such as hourglass control and locking. The computation examples presented prove that by using these algorithms, real time computations become possible without sacrificing the accuracy of the results. For a brain model having more than 7,000 degrees of freedom, we computed the reaction forces due to indentation with frequency of around 1,000 Hz using a standard dual core PC. Similarly, we conducted simulation of brain shift using a model with more than 50,000 degrees of freedom in less than one minute. The speed benefits of our models result fr...
Computational Biomechanics for Medicine, 2011
International Journal for Numerical Methods in Biomedical Engineering, 2012
Motivated by patient-specific computational modelling in the context of image-guided brain surger... more Motivated by patient-specific computational modelling in the context of image-guided brain surgery, we propose a new fuzzy mesh-free modelling framework. The method works directly on an unstructured cloud of points that do not form elements so that mesh generation is not required. Mechanical properties are assigned directly to each integration point based on fuzzy tissue classification membership functions without the need for image segmentation. Geometric integration is performed over an underlying uniform background grid. The verification example shows that, while requiring no hard segmentation and meshing, the proposed model gives, for all practical purposes, equivalent results to a finite element model.
We present selected topics in the area of mathematical and numerical modelling of the brain biome... more We present selected topics in the area of mathematical and numerical modelling of the brain biomechanics for brain image registration. We show how to describe registration in purely mechanical terms, such as displacements, strains and stresses and perform it using established methods of continuum mechanics. We advocate the use of fully non-linear theory of continuum mechanics. We discuss in some
Biological and Medical Physics, Biomedical Engineering, 2011
ABSTRACT During neurosurgery, the brain significantly deforms. Despite the enormous complexity of... more ABSTRACT During neurosurgery, the brain significantly deforms. Despite the enormous complexity of the brain (see Chap. 2) many aspects of its response can be reasonably described in purely mechanical terms, such as displacements, strains and stresses. They can therefore be analyzed using established methods of continuum mechanics. In this chapter, we discuss approaches to biomechanical modeling of the brain from the perspective of two distinct applications: neurosurgical simulation and neuroimage registration in image-guided surgery. These two challenging applications are described below.1
Computational Biomechanics for Medicine, 2012
Computational Biomechanics for Medicine, 2013
Computational Biomechanics for Medicine, 2010
Page 1. Chapter 6 Cortical Surface Motion Estimation for Brain Shift Prediction Grand Roman Jolde... more Page 1. Chapter 6 Cortical Surface Motion Estimation for Brain Shift Prediction Grand Roman Joldes, Adam Wittek, and Karol Miller Abstract In this chapter we present an algorithm for computing the displacement of the exposed surface of the brain during surgery. ...
International Journal for Numerical Methods in Biomedical Engineering, 2010
A method is presented for computing deformation of very soft tissue. The method is motivated by t... more A method is presented for computing deformation of very soft tissue. The method is motivated by the need for simple, automatic model creation for real-time simulation. The method is meshless in the sense that deformation is calculated at nodes that are not part of an element mesh. Node placement is almost arbitrary. Fully geometrically nonlinear Total Lagrangian formulation is used. Geometric integration is performed over a regular background grid that does not conform to the simulation geometry. Explicit time integration is used via the central difference method. As an example the simple but fully nonlinear Neo-Hookean material model is employed. The results are compared with a finite element simulation to verify the usefulness of the method.
Lecture Notes in Computer Science, 2009
Patient-specific biomechanical models implemented using specialized nonlinear (i.e. taking into a... more Patient-specific biomechanical models implemented using specialized nonlinear (i.e. taking into account material and geometric nonlinearities) finite element procedures were applied to predict the deformation field within the brain for five cases of craniotomy-induced brain shift. The procedures utilize the Total Lagrangian formulation with explicit time stepping. The loading was defined by prescribing deformations on the brain surface under the craniotomy. Application of the computed deformation fields to register the preoperative images with the intraoperative ones indicated that the models very accurately predict the intraoperative positions and deformations of the brain anatomical structures for limited information about the brain surface deformations. For each case, it took less than 40 s to compute the deformation field using a standard personal computer, and less than 4 s using a Graphics Processing Unit (GPU). The results suggest that nonlinear biomechanical models can be regarded as one possible method of complementing medical image processing techniques when conducting non-rigid registration within the real-time constraints of neurosurgery.