Title: Direct medical image to simulation using auto-segmentation and point cloud-based CFD
Cardiovascular disease (CVD) remains one of the leading causes of mortality worldwide. Computational medicine and digital twins hold promise in mitigating the impact and prevalence of CVD. Recent advances in image-based computational methods have enabled the quantification of functional and biologically important metrics that would otherwise be difficult to obtain from the standard of care. However, significant challenges remain due to the manual/semi-automated nature of the processes and the domain expertise required to perform them. This paper addresses these challenges by proposing a novel framework that builds on our recently developed direct point cloud-to-CFD approach using immersogeometric analysis. The proposed method leverages advanced auto-segmentation techniques to extract medically relevant geometries as point clouds, which are then directly used for CFD simulations. The framework is validated using benchmark flow problems with analytical and computational solutions and is subsequently applied to patient-specific images to demonstrate its capabilities. The results highlight the method's ability to facilitate rapid CFD simulations directly on point clouds derived from patient scans, underscoring its potential to accelerate the image-to-simulation pipeline and enable the tractability of cardiovascular digital twins.  more » « less
Award ID(s):
2047127 2436623 2436624
PAR ID:
10590097
Author(s) / Creator(s):
; ; ; ; ;
Publisher / Repository:
AIMS
Date Published:
Journal Name:
Advances in Computational Science and Engineering
Volume:
3
ISSN:
2837-1739
Page Range / eLocation ID:
95-124
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Digital twins represent a key technology for precision health. Medical digital twins consist of computational models that represent the health state of individual patients over time, enabling optimal therapeutics and forecasting patient prognosis. Many health conditions involve the immune system, so it is crucial to include its key features when designing medical digital twins. The immune response is complex and varies across diseases and patients, and its modelling requires the collective expertise of the clinical, immunology, and computational modelling communities. This review outlines the initial progress on immune digital twins and the various initiatives to facilitate communication between interdisciplinary communities. We also outline the crucial aspects of an immune digital twin design and the prerequisites for its implementation in the clinic. We propose some initial use cases that could serve as “proof of concept” regarding the utility of immune digital technology, focusing on diseases with a very different immune response across spatial and temporal scales (minutes, days, months, years). Lastly, we discuss the use of digital twins in drug discovery and point out emerging challenges that the scientific community needs to collectively overcome to make immune digital twins a reality. 
    more » « less
  2. Point cloud representations of three-dimensional objects have remained indispensable across a diverse array of applications, given their ability to represent complex real-world geometry with just a set of points. The high fidelity and versatility of point clouds have been utilized in directly performing numerical analysis for engineering applications, bypassing the labor-intensive and time-consuming tasks of creating analysis-suitable CAD models. However, point clouds exhibit various levels of quality, often containing defects such as holes, noise, and sparse regions, leading to sub-optimal geometry representation that can impact the stability and accuracy of any analysis study. This paper aims to overcome such challenges by proposing a novel method that expands upon our recently developed direct point cloud-to-CFD approach based on immersogeometric analysis. The proposed method features a mesh-driven resampling technique to fill any unintended gaps and regularize the point cloud, making it suitable for CFD analysis. Additionally, ghost penalty stabilization is employed for incompressible flow to improve the conditioning and stability compromised by the small cut elements in immersed methods. The developed method is validated against standard benchmark geometries and real-world point clouds obtained in-house with photogrammetry. Results demonstrate the proposed framework’s robustness in facilitating CFD simulations directly on point clouds of varying quality, underscoring its potential for practical applications in analyzing real-world structures. 
    more » « less
  3. Abstract Computational fluid dynamics (CFD) modeling of left ventricle (LV) flow combined with patient medical imaging data has shown great potential in obtaining patient-specific hemodynamics information for functional assessment of the heart. A typical model construction pipeline usually starts with segmentation of the LV by manual delineation followed by mesh generation and registration techniques using separate software tools. However, such approaches usually require significant time and human efforts in the model generation process, limiting large-scale analysis. In this study, we propose an approach toward fully automating the model generation process for CFD simulation of LV flow to significantly reduce LV CFD model generation time. Our modeling framework leverages a novel combination of techniques including deep-learning based segmentation, geometry processing, and image registration to reliably reconstruct CFD-suitable LV models with little-to-no user intervention.1 We utilized an ensemble of two-dimensional (2D) convolutional neural networks (CNNs) for automatic segmentation of cardiac structures from three-dimensional (3D) patient images and our segmentation approach outperformed recent state-of-the-art segmentation techniques when evaluated on benchmark data containing both magnetic resonance (MR) and computed tomography(CT) cardiac scans. We demonstrate that through a combination of segmentation and geometry processing, we were able to robustly create CFD-suitable LV meshes from segmentations for 78 out of 80 test cases. Although the focus on this study is on image-to-mesh generation, we demonstrate the feasibility of this framework in supporting LV hemodynamics modeling by performing CFD simulations from two representative time-resolved patient-specific image datasets. 
    more » « less
  4. We are rapidly approaching a future in which cancer patient digital twins will reach their potential to predict cancer prevention, diagnosis, and treatment in individual patients. This will be realized based on advances in high performance computing, computational modeling, and an expanding repertoire of observational data across multiple scales and modalities. In 2020, the US National Cancer Institute, and the US Department of Energy, through a trans-disciplinary research community at the intersection of advanced computing and cancer research, initiated team science collaborative projects to explore the development and implementation of predictive Cancer Patient Digital Twins. Several diverse pilot projects were launched to provide key insights into important features of this emerging landscape and to determine the requirements for the development and adoption of cancer patient digital twins. Projects included exploring approaches to using a large cohort of digital twins to perform deep phenotyping and plan treatments at the individual level, prototyping self-learning digital twin platforms, using adaptive digital twin approaches to monitor treatment response and resistance, developing methods to integrate and fuse data and observations across multiple scales, and personalizing treatment based on cancer type. Collectively these efforts have yielded increased insights into the opportunities and challenges facing cancer patient digital twin approaches and helped define a path forward. Given the rapidly growing interest in patient digital twins, this manuscript provides a valuable early progress report of several CPDT pilot projects commenced in common, their overall aims, early progress, lessons learned and future directions that will increasingly involve the broader research community. 
    more » « less
  5. Patient-specific cardiovascular simulations are an integral part of cardiovascular research and are increasingly finding use in clinical practice. A primary factor hindering large cohort studies and clinical utilization of cardiovascular simulations is the time-consuming process of constructing simulation-suitable computer models from medical image data. Methods have been proposed to automate the model construction process, but are tailored to either vascular or cardiac models. We herein propose a framework, MeshGrow, that is capable of combining automated modeling of cardiac and extended vascular territories. Namely, we demonstrate that this method can be used to reconstruct the main cardiac chambers along with the aorta and its main sub-branches, and returns a simulation-suitable mesh with a defined aortic valve surface and other surfaces needed for boundary condition specification. MeshGrow combines two different machine learning based techniques to address the specific challenges involved with cardiac and vascular model construction. This results in a two-stage approach; (a) meshing the cardiac structures and (b) growing the vasculature out from it. We present results of our method on five CT test datasets and compare predictions against state-of-the-art benchmark methods, as well as ground truth manually constructed models. Results show that MeshGrow achieves higher metric scores than benchmark methods on the test data. Additionally, we showcase the applicability of the method by running three-dimensional computational fluid dynamics simulations with two of the test cases. With this work, we demonstrate a method that can automate the construction of combined cardiac and vascular models for patient-specific cardiovascular hemodynamic simulation. 
    more » « less