High precision implicit modeling for patient-specific coronary arteries

High precision geometric reconstruction of patient-specific coronary arteries plays a crucial role in visual diagnosis, treatment decision-making, and the evaluation of the therapeutic effect of interventions in coronary artery diseases. It is also a fundamental task and a basic requirement in the numerical simulation of coronary blood flow dynamics. In this paper, a new implicit modeling technique for the geometric reconstruction of patient-specific coronary arteries has been developed. In the proposed method, the coronary arteries geometry is reconstructed segment by segment using radial basis functions with ellipsoid constraint from the point cloud obtained with a volumetric vascular image segmentation method, and the individually reconstructed coronary branches are then combined using a shape-preserving implicit blending operation to form a complete coronary artery surface. The experiment results and validations indicate that the reconstructed vascular shapes are of high smoothness and faithfulness

Numerical study of the unsteady flow in simplified and realistic iliac bifurcation models

Cardiovascular diseases are a major cause of death and disability worldwide and they are commonly associated with the occurrence of atherosclerotic plaque deposition in the vessel walls, a process denoted as atherosclerosis. This is a chronic and progressive inflammatory disease of large-/medium-sized blood vessels that affects blood flow profiles, with the abdominal aorta and its branches being one of the locations prone to the development of this pathology, due to their curvatures and bifurcations. In this regard, the effect of flow patterns was studied and compared for both a simplified three-dimensional model of aorta bifurcation on the iliac arteries and a realistic model of iliac bifurcation, which was constructed from a computational tomography medical image. The flow patterns were analyzed in terms of velocity and wall shear stress distribution, but a special focus was given to the size and location of the recirculation zone. The simulations were performed using the Computational Fluid Dynamics software, FLUENT, taking into account the cardiac cycle profile at the infrarenal aorta. The shear stress and the velocity distribution observed for both models indicated that higher shear stress occurred along the flow divider wall (inner wall) and low shear stress occurred along the outer walls. In addition, the results demonstrated that the wall shear stress profiles were deeply affected by the transient profile of the cardiac cycle, with the deceleration phase being the most critical phase to the occurrence of backflow.This work was supported by FCT—Fundação para a Ciência e Tecnologia through the R&D Units Project Scope: UIDB/00319/2020, UIDB/04077/2020, and NORTE-01-0145-FEDER-030171, funded by COMPETE2020, NORTE 2020, PORTUGAL 2020, and FEDER

Numerical and experimental haemodynamic studies of stenotic coronary arteries

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Biomateriais, Reabilitação e Biomecânica)Cardiovascular diseases remain the most frequent cause of mortality worldwide and constitute a major healthcare challenge. Among them, coronary artery disease causes nearly half of the deaths and, thus it is of great interest to better understand its development and effects. This disease is characterized by the narrowing (stenosis) of coronary arteries due to plaque deposition at the arterial wall, a pathological process known as atherosclerosis. This dissertation aimed to study the hemodynamics in stenotic coronary arteries, in order to get a deeper understanding of the effects of this pathology on the blood flow behavior. For this purpose, both numerical and experimental studies were conducted using idealized models. The numerical research was carried out using Ansys® software by means of computational fluid dynamics which applies the finite volume method. The experimental approach was performed using a high-speed video microscopy system, to visualize and investigate the blood flow in the in vitro stenotic biomodels. Initially, the influence of roughness in flow visualizations was studied, and the best biomodel was the one printed with the lowest resolution having been, therefore, the selected to perform the hemodynamic studies. To compare those results with numerical data, the flow was set to be laminar and stationary and the fluid was considered Newtonian. In general, the numerical and experimental results were in good agreement, not only in the prediction of the flow behavior with the appearance of recirculation zones in the post-stenotic section, but also in the velocity profiles. In a posterior phase, a pulsatile inlet condition was applied to compare the use of laminar and turbulent assumptions, using the SST k- model. The results obtained allowed to conclude that the second one is more appropriate to simulate the blood flow. Subsequently, the main differences in hemodynamics were examined considering blood as a Newtonian and non-Newtonian fluid (Carreau model). For these models, the differences were very slight in terms of velocity fields, but more significant for the wall shear stress measurements, with the Newtonian model predicting lower values. The remaining simulations were performed using the Carreau model and a transient inlet flow, having observed an increase in the velocities and wall shear stress values with the degree of stenosis, which is associated with a greater risk of thrombosis.As doenças cardiovasculares continuam a ser a causa mais frequente de mortalidade em todo o mundo e constituem um grande desafio para a saúde. Entre elas, a doença arterial coronariana causa quase metade das mortes e, portanto, é de enorme interesse entender melhor o seu desenvolvimento e efeitos. Esta doença é caracterizada pelo estreitamento (estenose) das artérias coronárias devido à deposição de placas na parede arterial, um processo patológico conhecido como aterosclerose. Esta dissertação teve como objetivo estudar a hemodinâmica nas artérias coronárias estenóticas, a fim de obter uma compreensão mais profunda dos efeitos desta patologia no comportamento do fluxo sanguíneo. Para tal, foram realizados estudos numéricos e experimentais, utilizando modelos idealizados. A investigação numérica foi realizada no software Ansys®, através da dinâmica computacional dos fluidos, que aplica o método dos volumes finitos. A abordagem experimental foi realizada utilizando um sistema de microscopia de vídeo de alta velocidade, para visualizar e investigar o fluxo sanguíneo nos biomodelos estenóticos in vitro. Inicialmente, estudou-se a influência da rugosidade nas visualizações do escoamento, e o melhor biomodelo foi o impresso com menor resolução tendo sido, portanto, o selecionado para a realização dos estudos hemodinâmicos. Para comparar esses resultados com dados numéricos, o escoamento foi definido como laminar e estacionário e o fluído foi considerado Newtoniano. Em geral, os resultados numéricos e experimentais foram concordantes, não só na previsão do comportamento do fluxo com aparecimento de zonas de recirculação na zona pós-estenótica, mas também nos perfis de velocidade. Numa fase posterior, foi aplicada uma condição de entrada pulsátil para comparar o uso de simulações de natureza laminar e turbulenta, usando o modelo SST k-. Os resultados obtidos permitiram concluir que a segunda é mais apropriado para simular o fluxo sanguíneo. Posteriormente, foram examinadas as principais diferenças hemodinâmicas, considerando o sangue como fluído Newtoniano e não-Newtoniano (modelo de Carreau). Para estes modelos, as diferenças foram muito pequenas nos perfis de velocidade, mas mais significativas nas tensões de corte na parede medidas, com o modelo Newtoniano a prever valores mais baixos. As restantes simulações foram realizadas usando o modelo de Carreau e um escoamento de entrada transiente, tendo-se observado um aumento dos valores das velocidades e da tensão de corte na parede com o grau de estenose, o que está associado a um maior risco de trombose

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Higher-order block-structured hex meshing of tubular structures

Numerical simulations of the cardiovascular system are growing in popularity due to the increasing availability of computational power, and their proven contribution to the understanding of pathodynamics and validation of medical devices with in-silico trials as a potential future breakthrough. Such simulations are performed on volumetric meshes reconstructed from patient-specific imaging data. These meshes are most often unstructured, and result in a brutally large amount of elements, significantly increasing the computational complexity of the simulations, whilst potentially adversely affecting their accuracy. To reduce such complexity, we introduce a new approach for fully automatic generation of higher-order, structured hexahedral meshes of tubular structures, with a focus on healthy blood vessels. The structures are modeled as skeleton-based convolution surfaces. From the same skeleton, the topology is captured by a block-structure, and the geometry by a higher-order surface mesh. Grading may be induced to obtain tailored refinement, thus resolving, e.g., boundary layers. The volumetric meshing is then performed via transfinite mappings. The resulting meshes are of arbitrary order, their elements are of good quality, while the spatial resolution may be as coarse as needed, greatly reducing computing time. Their suitability for practical applications is showcased by a simulation of physiological blood flow modelled by a generalised Newtonian fluid in the human aorta

Simulated hemodynamics in human carotid bifurcation based on Doppler ultrasound data

Background: Atherosclerotic lesions commonly develop at arterial branch sites. Noninvasive carotid artery ultrasound is a well-established and effective method which allows real-time images and measurements of flow velocities. We aimed to develop a methodology for patient-specific computational 3D reconstruction and blood flow simulation based on ultrasound image data.Material and Methods: Subject-specific studies based on the acquisition of a set of longitudinal and sequential cross-sectional ultrasound images and Doppler velocity measurements at common carotid artery (CCA) bifurcation were performed at a university hospital. A developed simulation code of blood flow by the finite element method (FEM) that includes an adequate structured meshing of the common carotid artery bifurcation was used to investigate local flow biomechanics.Results: Hemodynamic simulations of CCA bifurcations for six individuals were analysed. Comparing pairs (Doppler, FEM) of velocity values, Lin's concordance correlation coefficient analysis demonstrated an almost perfect strength of agreement (c = 0.9911), in patients with different degrees of internal carotid artery (ICA) stenosis. Numerical simulations were able to capture areas of low wall shear stress correlated with stagnation zones.Conclusions: Simulated hemodynamic parameters can reproduce the disturbed flow conditions at the bifurcation of CCA and proximal ICA, which play an important role in the development of local atherosclerotic plaques. This novel technology might help to understand the relationship between hemodynamic environment and carotid wall lesions, and have a future impact in carotid stenosis diagnosis and management

Computational modeling of low-density lipoprotein accumulation at the carotid artery bifurcation after stenting

Restenosis typically occurs in regions of low and oscillating wall shear stress, which also favor the accumulation of atherogenic macromolecules such as low-density lipoprotein (LDL). This study aims to evaluate LDL transport and accumulation at the carotid artery bifurcation following carotid artery stenting (CAS) by means of computational simulation. The computational model consists of coupled blood flow and LDL transport, with the latter being modeled as a dilute substance dissolved in the blood and transported by the flow through a convection-diffusion transport equation. The endothelial layer was assumed to be permeable to LDL, and the hydraulic conductivity of LDL was shear-dependent. Anatomically realistic geometric models of the carotid bifurcation were built based on pre- and post-stent computed tomography (CT) scans. The influence of stent design was investigated by virtually deploying two different types of stents (open- and closed-cell stents) into the same carotid bifurcation model. Predicted LDL concentrations were compared between the post-stent carotid models and the relatively normal contralateral model reconstructed from patient-specific CT images. Our results show elevated LDL concentration in the distal section of the stent in all post-stent models, where LDL concentration is 20 times higher than that in the contralateral carotid. Compared with the open-cell stents, the closed-cell stents have larger areas exposed to high LDL concentration, suggesting an increased risk of stent restenosis. This computational approach is readily applicable to multiple patient studies and, once fully validated against follow-up data, it can help elucidate the role of stent strut design in the development of in-stent restenosis after CAS

Modelling the human cardiac fluid mechanics. 3rd ed

The third edition of this article on the modelling and simulation of the flow in human hearts supplements earlier editions. It discusses the flow-structure coupled heart model KAHMO FSI (Karlsruhe Heart Model) and examines patient-specific clinical application of the heart model for cardiac surgery. The KAHMO heart model can be used to predict flow losses and flow structures due to pathalogical ventricle defects. These are considered before and after surgery

Developing DNS Tools to Study Channel Flow Over Realistic Plaque Morphology

In a normal coronary artery, the flow is laminar and the velocity is parabolic in nature. Over time, plaques deposit along the artery wall, narrowing the artery and creating an obstruction, a stenosis. As the stenosis grows, the characteristics of the flow change and transition occurs, resulting in turbulent flow distal to the stenosis. To date, direct numerical simulation (DNS) of turbulent flow has been performed in a number of studies to understand how stenosis modifies flow dynamics. However, the effect of the actual shape and size of the obstruction has been disregarded in these DNS studies. An ideal approach is to obtain geometrical information of the stenotic channel using medical imaging methods such as IVUS (Intravascular Ultrasound) and couple them with numerical solvers that simulate the flow in the stenotic channel. The purpose of the present thesis is to demonstrate the feasibility of coupling the IVUS geometry with DNS solver. This preliminary research will provide the necessary tools to achieve the long term goal of developing a framework for the morphological features of the stenosis on the flow modifications in a diseased coronary artery. In the present study, the geometrical information of the stenotic plaque has been provided by the medical imaging team at the Cleveland Clinic Foundation for 42 patients who underwent IVUS. The integration of the geometrical information of the stenotic plaque with the DNS was performed in 3 stages 1) fuzzy logic scheme was used to group the 42 patients into categories, 2) meshing algorithm was generated to interface with the DNS solver, and 3) the existing DNS for channel flow was modified to account for inhomogeneity in the streamwise direction. A plaque classification system was developed using statistical k-means clustering with fuzzy logic. Four distinct morphological categories were found in plaque measurements obtained from the 42 patients. Patients were then assigned a degree of membership to each category based on a fuzzy evaluation system. Flow simulations showed distinct turbulent flow characteristics when comparing the four categories, and similar characteristics within each category. An existing DNS solver that used the fourth-order velocity second-order vorticity formulation of the Navier-Stokes equations was modified to account for inhomogeneity in the streamwise direction. A multigrid method was implemented, using Green\u27s method to compute unknown boundary conditions at the walls in using an influence matrix approach. The inflow is the free stream laminar flow condition; the outflow is computed explicitly with a buffer domain and by parabolizing the Navier Stokes equation. The transitional flow solver was tested using blowing and suction disturbances at the wall to generate the Tollmien-Schlichting waves predicted by linear stability theory. The toolset developed as a part of this thesis demonstrates the feasibility of integrating realistic geometry with DNS. This tool can be used for patient-specific simulation of stenotic flow in coronary and carotid arteries. Additionally, within the field of fluid dynamics, this framework will contribute to the understanding of transition and turbulence in stenotic flows

Modelling the Human Cardiac Fluid Mechanics. 4th ed

With the Karlsruhe Heart Model (KaHMo) we aim to share our vision of integrated computational simulation across multiple disciplines of cardiovascular research, and emphasis yet again the importance of Modelling the Human Cardiac Fluid Mechanics within the framework of the international STICH study. The focus of this work is on integrated cardiovascular fluid mechanics, and the potential benefits to future cardiovascular research and the wider bio-medical community