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核心技术专利:CN118964589B侵权必究
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Developing a nearly automated open-source pipeline for conducting computational fluid dynamics simulations in anterior brain vasculature: a feasibility study.

作者信息

Rezaeitaleshmahalleh Mostafa, Mu Nan, Lyu Zonghan, Gemmete Joseph, Pandey Aditya, Jiang Jingfeng

机构信息

Department of Biomedical Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, USA.

Center for Biocomputing and Digital Health, Institute of Computing and Cybernetics and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, USA.

出版信息

Sci Rep. 2024 Dec 4;14(1):30181. doi: 10.1038/s41598-024-80891-4.


DOI:10.1038/s41598-024-80891-4
PMID:39632927
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11618461/
Abstract

Intracranial aneurysms (IA) pose significant health risks and are often challenging to manage. Computational fluid dynamics (CFD) simulation has emerged as a powerful tool for understanding lesion-specific hemodynamics in and around IAs, aiding in the clinical management of patients with an IA. However, the current workflow of CFD simulations is time-consuming, complex, and labor-intensive and, thus, does not fit the clinical environment. To address these challenges, we have developed a semi-automated pipeline integrating multiple open-source software packages to streamline the CFD simulation process. Specifically, the study utilized medical angiography data from 18 patients. An in-house open-source DL image segmentation model (ARU-Net) was employed to generate 3D computer models of the anterior circulation. The segmented intracranial vasculature models, including IAs, were further refined using the Vascular Modeling Toolkit (VMTK), an open-source Python package. This step involved smoothing the surface of the models and extending the inlet and outlet regions to ensure a realistic representation of the vascular geometry. The refined vascular models were then converted into computational meshes using an open-source mesh generator known as TetGen. This process was nearly automated and required minimal user interaction(s). Blood flow simulations of the cerebral vascular models were performed using established SimVascular solvers (an open-source finite element platform for vascular applications) through an application programming interface (API). The CFD simulation process was also conducted using the manual workflow for comparative purposes. The initial assessment compared the geometries derived from manual and DL-based segmentation. The DL-based segmentation demonstrated reliable performance, closely aligning with manually segmented results, evidenced by excellent Pearson correlation coefficient (PCC) values and low relative difference (RD) values ranging from 3% to 10% between the computed geometrical variables derived from both methods. The statistical analysis of the computed hemodynamic variables, including velocity informatics and WSS-related variables, indicated good to excellent reliability for most parameters (e.g., ICC of 0.85-0.95). Given the data investigated, the proposed automated workflow streamlines the process of conducting CFD simulations. It generates results consistent with the current standard manual CFD protocol while minimizing dependence on user input.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/7ff704992d39/41598_2024_80891_Fig12_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/a91196ff19f5/41598_2024_80891_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/5ddfcc423b28/41598_2024_80891_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/accffd8e3989/41598_2024_80891_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/652b4eed7704/41598_2024_80891_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/6b319f5f3e09/41598_2024_80891_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/e7841e382d2a/41598_2024_80891_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/3b9b2bfaee10/41598_2024_80891_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/60fcd732cfb7/41598_2024_80891_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/a1c5ef83e877/41598_2024_80891_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/2425dab8b9a3/41598_2024_80891_Fig10_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/77e43cd94077/41598_2024_80891_Fig11_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/7ff704992d39/41598_2024_80891_Fig12_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/a91196ff19f5/41598_2024_80891_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/5ddfcc423b28/41598_2024_80891_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/accffd8e3989/41598_2024_80891_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/652b4eed7704/41598_2024_80891_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/6b319f5f3e09/41598_2024_80891_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/e7841e382d2a/41598_2024_80891_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/3b9b2bfaee10/41598_2024_80891_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/60fcd732cfb7/41598_2024_80891_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/a1c5ef83e877/41598_2024_80891_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/2425dab8b9a3/41598_2024_80891_Fig10_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/77e43cd94077/41598_2024_80891_Fig11_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e72e/11618461/7ff704992d39/41598_2024_80891_Fig12_HTML.jpg

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[4]
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引用本文的文献

[1]
The Robust Vessel Segmentation and Centerline Extraction: One-Stage Deep Learning Approach.

J Imaging. 2025-6-26

本文引用的文献

[1]
USING CONVOLUTIONAL NEURAL NETWORK-BASED SEGMENTATION FOR IMAGE-BASED COMPUTATIONAL FLUID DYNAMICS SIMULATIONS OF BRAIN ANEURYSMS: INITIAL EXPERIENCE IN AUTOMATED MODEL CREATION.

J Mech Med Biol. 2023-5

[2]
Exploring a frequency-domain attention-guided cascade U-Net: Towards spatially tunable segmentation of vasculature.

Comput Biol Med. 2023-12

[3]
Deep-learning-based image segmentation for image-based computational hemodynamic analysis of abdominal aortic aneurysms: a comparison study.

Biomed Phys Eng Express. 2023-9-12

[4]
Characterization of small abdominal aortic aneurysms' growth status using spatial pattern analysis of aneurismal hemodynamics.

Sci Rep. 2023-8-24

[5]
Physics-informed neural networks (PINNs) for 4D hemodynamics prediction: An investigation of optimal framework based on vascular morphology.

Comput Biol Med. 2023-9

[6]
AGMN: Association Graph-based Graph Matching Network for Coronary Artery Semantic Labeling on Invasive Coronary Angiograms.

Pattern Recognit. 2023-11

[7]
Augmenting Prediction of Intracranial Aneurysms' Risk Status Using Velocity-Informatics: Initial Experience.

J Cardiovasc Transl Res. 2023-10

[8]
An attention residual u-net with differential preprocessing and geometric postprocessing: Learning how to segment vasculature including intracranial aneurysms.

Med Image Anal. 2023-2

[9]
Transient wall shear stress estimation in coronary bifurcations using convolutional neural networks.

Comput Methods Programs Biomed. 2022-10

[10]
WSSNet: Aortic Wall Shear Stress Estimation Using Deep Learning on 4D Flow MRI.

Front Cardiovasc Med. 2022-1-24

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