Patient-specific computational haemodynamics: generation of structured and conformal hexahedral meshes from triangulated surfaces of vascular bifurcations

Measuring the blood flow is still limited by current imaging technologies and is generally overcome using computational fluid dynamics (CFD) which, because of the complex geometry of blood vessels, has widely relied on tetrahedral meshes. Hexahedral meshes offer more accurate results with lower-density meshes and faster computation as compared to tetrahedral meshes, but their use is limited by the far more complex mesh generation. We present a robust methodology for conformal and structured hexahedral mesh generation - applicable to complex arterial geometries as bifurcating vessels - starting from triangulated surfaces. Cutting planes are used to slice the lumen surface and to construct longitudinal Bezier splines. Afterwards, an isoparametric transformation is used to map a parametrically defined quadrilateral surface mesh into the vessel volume, resulting in stacks of sections which can then be used for sweeping. Being robust and open source based, this methodology may improve the current standard in patient-specific mesh generation and enhance the reliability of CFD to patient-specific haemodynamics.     

Patient-specific computational haemodynamics: generation of structured and conformal hexahedral meshes from triangulated surfaces of vascular bifurcations

Measuring the blood flow is still limited by current imaging technologies and is generally overcome using computational fluid dynamics (CFD) which, because of the complex geometry of blood vessels, has widely relied on tetrahedral meshes. Hexahedral meshes offer more accurate results with lower-density meshes and faster computation as compared to tetrahedral meshes, but their use is limited by the far more complex mesh generation. We present a robust methodology for conformal and structured hexahedral mesh generation – applicable to complex arterial geometries as bifurcating vessels – starting from triangulated surfaces. Cutting planes are used to slice the lumen surface and to construct longitudinal Bezier splines. Afterwards, an isoparametric transformation is used to map a parametrically defined quadrilateral surface mesh into the vessel volume, resulting in stacks of sections which can then be used for sweeping. Being robust and open source based, this methodology may improve the current standard in patient-specific mesh generation and enhance the reliability of CFD to patient-specific haemodynamics.     

An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

Advances in imaging methods such as electron microscopy, tomography, and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this work, we outline the steps for a naïve user to approach the Geometry-preserving Adaptive MeshER software version 2, a mesh generation code written in C++ designed to convert structural data sets to realistic geometric meshes while preserving the underlying shapes. We present two example cases: 1) mesh generation at the subcellular scale as informed by electron tomography and 2) meshing a protein with a structure from x-ray crystallography. We further demonstrate that the meshes generated by the Geometry-preserving Adaptive MeshER software are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric meshes from structural biology data.     

RV functional imaging: 3-D echo-derived dynamic geometry and flow field simulations

We describe a novel functional imaging approach for quantitative analysis of right ventricular (RV) blood flow patterns in specific experimental animals (or humans) using real-time, three-dimensional (3-D) echocardiography (RT3D). The method is independent of the digital imaging modality used. It comprises three parts. First, a semiautomated segmentation aided by intraluminal contrast medium locates the RV endocardial surface. Second, a geometric scheme for dynamic RV chamber reconstruction applies a time interpolation procedure to the RT3D data to quantify wall geometry and motion at 400 Hz. A volumetric prism method validated the dynamic geometric reconstruction against simultaneous sonomicrometric canine measurements. Finally, the RV endocardial border motion information is used for mesh generation on a computational fluid dynamics solver to simulate development of the early RV diastolic inflow field. Boundary conditions (tessellated endocardial surface nodal velocities) for the solver are directly derived from the endocardial geometry and motion information. The new functional imaging approach may yield important kinematic information on the distribution of instantaneous velocities in the RV diastolic flow field of specific normal or diseased hearts.     

Image segmentation methods for intracranial aneurysm haemodynamic research

Patient-specific haemodynamic technology is being increasingly utilised in clinical applications. Under normal circumstances, computational haemodynamic simulation is performed using geometric results obtained via medical image segmentation. However, even when employed upon the same set of medical imaging data, both the geometry and volume of intracranial aneurysm models are highly dependent upon varying insufficiently validated vascular segmentation methods. In this study, we compared three segmentation methods to segment the geometry of the aneurysm. These include: the Region Growing Threshold (RGT), Chan-Vese model (CV) and Threshold-Based Level Set (TLS). The results obtained were evaluated via measurement of arterial volume differences (VD), local geometric shapes, and haemodynamic simulation results. In total, 45 patient-specific aneurysm cases with three different anatomy locations were assessed in this study. From this, we discovered that the average VD of all three segmentation methods lay in the vicinity of 9.3% (SD=±4.6%). The computational haemodynamic simulation was performed via the use of the vessel geometries. Analyses produced an average of 23.2% (SD=±8.7%) difference in energy loss (EL) between the varying segmentation methods, with the difference in Wall Shear Stress (WSS) averaging 24.0% (SD=±8.5%) and 126.4% (SD=±124.4%) for the highest and lowest volumes of WSS respectively. The results of the lowest WSS, was seen to be significantly dependent upon the geometry of the aneurysm surface. It is therefore essential, in order to confirm the quality of segmentation processes in the application of patient-specific analyses of cerebrovascular haemodynamics – to validate these individual segmentation methods.     

The use of sparse CT datasets for auto-generating accurate FE models of the femur and pelvis

The finite element (FE) method when coupled with computed tomography (CT) is a powerful tool in orthopaedic biomechanics. However, substantial data is required for patient-specific modelling. Here we present a new method for generating a FE model with a minimum amount of patient data. Our method uses high order cubic Hermite basis functions for mesh generation and least-square fits the mesh to the dataset. We have tested our method on seven patient data sets obtained from CT assisted osteodensitometry of the proximal femur. Using only 12 CT slices we generated smooth and accurate meshes of the proximal femur with a geometric root mean square (RMS) error of less than 1 mm and peak errors less than 8 mm. To model the complex geometry of the pelvis we developed a hybrid method which supplements sparse patient data with data from the visible human data set. We tested this method on three patient data sets, generating FE meshes of the pelvis using only 10 CT slices with an overall RMS error less than 3 mm. Although we have peak errors about 12 mm in these meshes, they occur relatively far from the region of interest (the acetabulum) and will have minimal effects on the performance of the model. Considering that linear meshes usually require about 70-100 pelvic CT slices (in axial mode) to generate FE models, our method has brought a significant data reduction to the automatic mesh generation step. The method, that is fully automated except for a semi-automatic bone/tissue boundary extraction part, will bring the benefits of FE methods to the clinical environment with much reduced radiation risks and data requirement.     

Growing multiblock structures: a semi-automated approach to block placement for multiblock hexahedral meshing

Finite element (FE) analysis is a cornerstone of orthopaedic biomechanics research. Three-dimensional medical imaging provides sufficient resolution for the subject-specific FE models to be generated from these data-sets. FE model development requires discretisation of a three-dimensional domain, which can be the most time-consuming component of a FE study. Hexahedral meshing tools based on the multiblock method currently rely on the manual placement of building blocks for mesh generation. We hypothesise that angular analysis of the geometric centreline for a three-dimensional surface could be used to automatically generate building block structures for the multiblock hexahedral mesh generation. Our algorithm uses a set of user-defined points and parameters to automatically generate a multiblock structure based on a surface's geometric centreline. This significantly reduces the time required for model development. We have applied this algorithm to 47 bones of varying geometries and successfully generated a FE mesh in all cases. This work represents significant advancement in automatically generating multiblock structures for a wide range of geometries.     

ImageParser: a tool for finite element generation from three-dimensional medical images

Background

The finite element method (FEM) is a powerful mathematical tool to simulate and visualize the mechanical deformation of tissues and organs during medical examinations or interventions. It is yet a challenge to build up an FEM mesh directly from a volumetric image partially because the regions (or structures) of interest (ROIs) may be irregular and fuzzy.

Methods

A software package, ImageParser, is developed to generate an FEM mesh from 3-D tomographic medical images. This software uses a semi-automatic method to detect ROIs from the context of image including neighboring tissues and organs, completes segmentation of different tissues, and meshes the organ into elements.

Results

The ImageParser is shown to build up an FEM model for simulating the mechanical responses of the breast based on 3-D CT images. The breast is compressed by two plate paddles under an overall displacement as large as 20% of the initial distance between the paddles. The strain and tangential Young's modulus distributions are specified for the biomechanical analysis of breast tissues.

Conclusion

The ImageParser can successfully exact the geometry of ROIs from a complex medical image and generate the FEM mesh with customer-defined segmentation information.

     

Growing multiblock structures: a semi-automated approach to block placement for multiblock hexahedral meshing

Finite element (FE) analysis is a cornerstone of orthopaedic biomechanics research. Three-dimensional medical imaging provides sufficient resolution for the subject-specific FE models to be generated from these data-sets. FE model development requires discretisation of a three-dimensional domain, which can be the most time-consuming component of a FE study. Hexahedral meshing tools based on the multiblock method currently rely on the manual placement of building blocks for mesh generation. We hypothesise that angular analysis of the geometric centreline for a three-dimensional surface could be used to automatically generate building block structures for the multiblock hexahedral mesh generation. Our algorithm uses a set of user-defined points and parameters to automatically generate a multiblock structure based on a surface's geometric centreline. This significantly reduces the time required for model development. We have applied this algorithm to 47 bones of varying geometries and successfully generated a FE mesh in all cases. This work represents significant advancement in automatically generating multiblock structures for a wide range of geometries.     

Biomechanical analysis of the anterior cervical fusion

This paper presents a biomechanical analysis of the cervical C5–C6 functional spine unit before and after the anterior cervical discectomy and fusion. The aim of this work is to study the influence of the medical procedure and its instrumentation on range of motion and stress distribution. First, a three-dimensional finite element model of the lower cervical spine is obtained from computed tomography images using a pipeline of image processing, geometric modelling and mesh generation software. Then, a finite element study of parameters' influence on motion and a stress analysis at physiological and different post-operative scenarios were made for the basic movements of the cervical spine. It was confirmed that the results were very sensitive to intervertebral disc properties. The insertion of an anterior cervical plate influenced the stress distribution at the vertebral level as well as in the bone graft. Additionally, stress values in the graft decreased when it is used together with a cage.     

Numerical simulation of haemodynamics of the descending aorta in the non-diabetic and diabetic rabbits

Diabetes mellitus (DM) is a predisposing risk factor leading to macrovascular diseases. Changes in haemodynamics of the diabetic aortas remain largely unclear and relevant computational analyses are lacking in the literature. Ten adult rabbits (1.6–2.2 kg) were collected and the type I diabetic rabbit model was induced by injection of alloxan. A total of five control and five diabetic rabbit aortas were considered for subsequent numerical simulation. The CT scanning was performed to reconstruct three-dimensional model of the individual rabbit descending aorta. The flow velocity waveforms were measured by ultrasound machine and were set to be the inlet boundary conditions. The reconstructed aortas were then imported into ANSYS to perform mesh generation and computational analysis. Results showed that the distributions of haemodynamic indicators time-averaged wall shear stress (TAWSS), oscillating shear index (OSI) and transverse wall shear stress (transWSS) in the non-diabetic rabbit aortas were similar to those in the diabetic rabbit aortas. However, the mean values of TAWSS and transWSS in the non-diabetic rabbit aortas were significantly higher than those values in the diabetic rabbit aortas (TAWSS: p = 0.04; transWSS: p = 0.02). The back of right renal artery tended to have high OSI in both the non-diabetic and the diabetic rabbit aortas. Notably, the regions with high OSI tended to have intense disturbed flow and low TAWSS in the most diabetic rabbit aortas. The results suggest that diabetes leads to changes in haemodynamic parameters in the rabbit aortas. In particular, the lower TAWSS and the higher OSI within the diabetic aortas may further contribute to aortic wall remodeling.     

A generic 3-dimensional system to mimic trabecular bone surface adaptation

The paper presents the structure optimizing system based on surface remodelling. The grounds for algorithm formulation are given by the bone remodelling phenomenon leading to optimization of trabecular network in the bone. The assumptions, algorithms and limitations of the own mesh generator Cosmoprojector are described. Unlike other approaches, the system is able to mimic real bone evolution including tissue consolidation and separation. The article presents a closed system consisting of finite element mesh generation, decision criteria for structure adaptation and finite element analysis in parallel environment. It also provides some computation results obtained by using specially designed software.     

A generic 3-dimensional system to mimic trabecular bone surface adaptation

The paper presents the structure optimizing system based on surface remodelling. The grounds for algorithm formulation are given by the bone remodelling phenomenon leading to optimization of trabecular network in the bone. The assumptions, algorithms and limitations of the own mesh generator Cosmoprojector are described. Unlike other approaches, the system is able to mimic real bone evolution including tissue consolidation and separation. The article presents a closed system consisting of finite element mesh generation, decision criteria for structure adaptation and finite element analysis in parallel environment. It also provides some computation results obtained by using specially designed software.     

Biomechanical analysis of the anterior cervical fusion

This paper presents a biomechanical analysis of the cervical C5-C6 functional spine unit before and after the anterior cervical discectomy and fusion. The aim of this work is to study the influence of the medical procedure and its instrumentation on range of motion and stress distribution. First, a three-dimensional finite element model of the lower cervical spine is obtained from computed tomography images using a pipeline of image processing, geometric modelling and mesh generation software. Then, a finite element study of parameters' influence on motion and a stress analysis at physiological and different post-operative scenarios were made for the basic movements of the cervical spine. It was confirmed that the results were very sensitive to intervertebral disc properties. The insertion of an anterior cervical plate influenced the stress distribution at the vertebral level as well as in the bone graft. Additionally, stress values in the graft decreased when it is used together with a cage.     

The effects of different mesh generation methods on computational fluid dynamic analysis and power loss assessment in total cavopulmonary connection

The flow field and energetic efficiency of total cavopulmonary connection (TCPC) models have been studied by both in vitro experiment and computational fluid dynamics (CFD). All the previous CFD studies have employed the structured mesh generation method to create the TCPC simulation model. In this study, a realistic TCPC model with complete anatomical features was numerically simulated using both structured and unstructured mesh generation methods. The flow fields and energy losses were compared in these two meshes. Two different energy loss calculation methods, the control volume and viscous dissipation methods, were investigated. The energy losses were also compared to the in vitro experimental results. The results demonstrated that: (1) the flow fields in the structured model were qualitatively similar to the unstructured model; (2) more vortices were present in the structured model than in the unstructured model; (3) both models had the least energy loss when flow was equally distributed to the left and right pulmonary arteries, while high losses occurred for extreme pulmonary arterial flow splits; (4) the energy loss results calculated using the same method were significantly different for different meshes; and (5) the energy loss results calculated using different methods were significantly different for the same mesh.     

Alterations in regional vascular geometry produced by theoretical stent implantation influence distributions of wall shear stress: analysis of a curved coronary artery using 3D computational fluid dynamics modeling

Background  

The success of stent implantation in the restoration of blood flow through areas of vascular narrowing is limited by restenosis. Several recent studies have suggested that the local geometric environment created by a deployed stent may influence regional blood flow characteristics and alter distributions of wall shear stress (WSS) after implantation, thereby rendering specific areas of the vessel wall more susceptible to neointimal hyperplasia and restenosis. Stents are most frequently implanted in curved vessels such as the coronary arteries, but most computational studies examining blood flow patterns through stented vessels conducted to date use linear, cylindrical geometric models. It appears highly probable that restenosis occurring after stent implantation in curved arteries also occurs as a consequence of changes in fluid dynamics that are established immediately after stent implantation.     

Numerical analysis of dynamic temperature in response to different levels of reactive hyperaemia in a three-dimensional image-based hand model

Vascular reactivity (VR) is considered as an effective index to predict the risk of cardiovascular events. A cost-effective alternative technique used to evaluate VR called digital thermal monitoring (DTM) is based on the response of finger temperature to vessel occlusion and reperfusion. In this work, a simulation has been developed to investigate hand temperature in response to vessel occlusion and perfusion. The simulation consists of image-based mesh generation and finite element analysis of blood flow and heat transfer in tissues. In order to reconstruct a real geometric model of human hand, a computer programme including automatic image processing for sequential MR data and mesh generation based on the transfinite interpolation method is developed. In the finite element analysis part, blood flow perfused in solid tissues is considered as fluid phase through porous media. Heat transfer in tissues is described by Pennes bioheat equation and blood perfusion rate is obtained from Darcy velocities. Capillary pressure, blood perfusion and temperature distribution of hand are obtained. The results reveal that fingertip temperature is strongly dependent on larger arterial pressure. This simulation is of potential to quantify the indices used for evaluating the VR in DTM test if it is integrated with the haemodynamic model of blood circulation in upper limb.     

GALGO: an R package for multivariate variable selection using genetic algorithms

SUMMARY: The development of statistical models linking the molecular state of a cell to its physiology is one of the most important tasks in the analysis of Functional Genomics data. Because of the large number of variables measured a comprehensive evaluation of variable subsets cannot be performed with available computational resources. It follows that an efficient variable selection strategy is required. However, although software packages for performing univariate variable selection are available, a comprehensive software environment to develop and evaluate multivariate statistical models using a multivariate variable selection strategy is still needed. In order to address this issue, we developed GALGO, an R package based on a genetic algorithm variable selection strategy, primarily designed to develop statistical models from large-scale datasets.     

Influence of inlet boundary conditions on the local haemodynamics of intracranial aneurysms

Haemodynamics is believed to play an important role in the initiation, growth and rupture of intracranial aneurysms. In this context, computational haemodynamics has been extensively used in an effort to establish correlations between flow variables and clinical outcome. It is common practice in the application of Dirichlet boundary conditions at domain inlets to specify transient velocities as either a flat (plug) profile or a spatially developed profile based on Womersley's analytical solution. This paper provides comparative haemodynamics measures for three typical cerebral aneurysms.

Three dimentional rotational angiography images of aneurysms at three common locations, viz. basilar artery tip, internal carotid artery and middle cerebral artery were obtained. The computational tools being developed in the European project @neurIST were used to reconstruct the fluid domains and solve the unsteady Navier–Stokes equations, using in turn Womersley and plug-flow inlet velocity profiles. The effects of these assumptions were analysed and compared in terms of relevant haemodynamic variables within the aneurismal sac. For the aneurysm at the basilar tip geometries with different extensions of the afferent vasculature were considered to study the plausibility of a fully-developed axial flow at the inlet boundaries.

The study shows that assumptions made on the velocity profile while specifying inlet boundary conditions have little influence on the local haemodynamics in the aneurysm, provided that a sufficient extension of the afferent vasculature is considered and that geometry is the primary determinant of the flow field within the aneurismal sac. For real geometries the Womersley profile is at best an unnecessary over-complication, and may even be worse than the plug profile in some anatomical locations (e.g. basilar confluence).     

Impedance-based outflow boundary conditions for human carotid haemodynamics

In this study, we develop structured tree outflow boundary conditions for modelling the human carotid haemodynamics. The model geometry was reconstructed through computerised tomography scan. Unsteady-state computational fluid dynamic analyses were performed under different conditions using a commercial software package ADINA R&D, Inc., (Watertown, MA, USA) in order to assess the impact of the boundary conditions on the flow variables. In particular, the results showed that the peripheral vessels massively impact the pressure while the flow is relatively unaffected. As an example of application of these outflow conditions, an unsteady fluid-structure interaction (FSI) simulation was carried out and the dependence of the wall shear stress (WSS) on the arterial wall compliance in the carotid bifurcation was studied. In particular, a comparison between FSI and rigid-wall models was conducted. Results showed that the WSS distributions were substantially affected by the diameter variation of the arterial wall. In particular, even similar WSS distributions were found for both cases, and differences in the computed WSS values were also found.