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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.
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An nnU-Net Model to Enhance Segmentation of Cardiac Cine DENSE-MRI Using Phase Information
This study explores the application of deep learning to the segmentation of DENSE cardiovascular magnetic resonance (CMR) images, which is an important step in the analysis of cardiac deformation and may help in the diagnosis of heart conditions. A self-adapting method based on the nnU-Net framework is introduced to enhance the accuracy of DENSE-MR image segmentation, with a particular focus on the left ventricle myocardium (LVM) and left ventricle cavity (LVC), by leveraging the phase information in the cine DENSE-MR images. Two models are built and compared: 1) ModelM, which uses only the magnitude of the DENSE-MR images; and 2) ModelMP, which incorporates magnitude and phase images. DENSE-MR images from 10 human volunteers processed using the DENSE-Analysis MATLAB toolbox were included in this study. The two models were trained using a 2D UNet-based architecture with a loss function combining the Dice similarity coefficient (DSC) and cross-entropy. The findings show the effectiveness of leveraging the phase information with ModelMP resulting in a higher DSC and improved image segmentation, especially in challenging cases, e.g., at early systole and with basal and apical slices.
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- Award ID(s):
- 2205043
- PAR ID:
- 10537732
- Publisher / Repository:
- IEEE
- Date Published:
- ISBN:
- 979-8-3503-8373-7
- Page Range / eLocation ID:
- 670 to 673
- Subject(s) / Keyword(s):
- Image segmentation nnU-Net Magnetic resonance imaging DENSE MRI Phase and magnitude data.
- Format(s):
- Medium: X
- Location:
- Orlando, FL, USA
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1109/ICHI61247.2024.00106
