Dataset Information

Fully-automated global and segmental strain analysis of DENSE cardiovascular magnetic resonance using deep learning for segmentation and phase unwrapping.

ABSTRACT:

Background

Cardiovascular magnetic resonance (CMR) cine displacement encoding with stimulated echoes (DENSE) measures heart motion by encoding myocardial displacement into the signal phase, facilitating high accuracy and reproducibility of global and segmental myocardial strain and providing benefits in clinical performance. While conventional methods for strain analysis of DENSE images are faster than those for myocardial tagging, they still require manual user assistance. The present study developed and evaluated deep learning methods for fully-automatic DENSE strain analysis.

Methods

Convolutional neural networks (CNNs) were developed and trained to (a) identify the left-ventricular (LV) epicardial and endocardial borders, (b) identify the anterior right-ventricular (RV)-LV insertion point, and (c) perform phase unwrapping. Subsequent conventional automatic steps were employed to compute strain. The networks were trained using 12,415 short-axis DENSE images from 45 healthy subjects and 19 heart disease patients and were tested using 10,510 images from 25 healthy subjects and 19 patients. Each individual CNN was evaluated, and the end-to-end fully-automatic deep learning pipeline was compared to conventional user-assisted DENSE analysis using linear correlation and Bland Altman analysis of circumferential strain.

Results

LV myocardial segmentation U-Nets achieved a DICE similarity coefficient of 0.87?±?0.04, a Hausdorff distance of 2.7?±?1.0 pixels, and a mean surface distance of 0.41?±?0.29 pixels in comparison with manual LV myocardial segmentation by an expert. The anterior RV-LV insertion point was detected within 1.38?±?0.9 pixels compared to manually annotated data. The phase-unwrapping U-Net had similar or lower mean squared error vs. ground-truth data compared to the conventional path-following method for images with typical signal-to-noise ratio (SNR) or low SNR (p?ConclusionsDeep learning enables fully-automatic global and segmental circumferential strain analysis of DENSE CMR providing excellent agreement with conventional user-assisted methods. Deep learning-based automatic strain analysis may facilitate greater clinical use of DENSE for the quantification of global and segmental strain in patients with cardiac disease.

SUBMITTER: Ghadimi S

PROVIDER: S-EPMC7949250 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Publications

Fully-automated global and segmental strain analysis of DENSE cardiovascular magnetic resonance using deep learning for segmentation and phase unwrapping.

Ghadimi Sona S Auger Daniel A DA Feng Xue X Sun Changyu C Meyer Craig H CH Bilchick Kenneth C KC Cao Jie Jane JJ Scott Andrew D AD Oshinski John N JN Ennis Daniel B DB Epstein Frederick H FH

Journal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance 20210311 1

<h4>Background</h4>Cardiovascular magnetic resonance (CMR) cine displacement encoding with stimulated echoes (DENSE) measures heart motion by encoding myocardial displacement into the signal phase, facilitating high accuracy and reproducibility of global and segmental myocardial strain and providing benefits in clinical performance. While conventional methods for strain analysis of DENSE images are faster than those for myocardial tagging, they still require manual user assistance. The present s ...[more]

PMID: 33691739

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Project description:IntroductionAs the life expectancy of children with congenital heart disease (CHD) is rapidly increasing and the adult population with CHD is growing, there is an unmet need to improve clinical workflow and efficiency of analysis. Cardiovascular magnetic resonance (CMR) is a noninvasive imaging modality for monitoring patients with CHD. CMR exam is based on multiple breath-hold 2-dimensional (2D) cine acquisitions that should be precisely prescribed and is expert and institution dependent. Moreover, 2D cine images have relatively thick slices, which does not allow for isotropic delineation of ventricular structures. Thus, development of an isotropic 3D cine acquisition and automatic segmentation method is worthwhile to make CMR workflow straightforward and efficient, as the present work aims to establish.MethodsNinety-nine patients with many types of CHD were imaged using a non-angulated 3D cine CMR sequence covering the whole-heart and great vessels. Automatic supervised and semi-supervised deep-learning-based methods were developed for whole-heart segmentation of 3D cine images to separately delineate the cardiac structures, including both atria, both ventricles, aorta, pulmonary arteries, and superior and inferior vena cavae. The segmentation results derived from the two methods were compared with the manual segmentation in terms of Dice score, a degree of overlap agreement, and atrial and ventricular volume measurements.ResultsThe semi-supervised method resulted in a better overlap agreement with the manual segmentation than the supervised method for all 8 structures (Dice score 83.23 ± 16.76% vs. 77.98 ± 19.64%; P-value ≤0.001). The mean difference error in atrial and ventricular volumetric measurements between manual segmentation and semi-supervised method was lower (bias ≤ 5.2 ml) than the supervised method (bias ≤ 10.1 ml).DiscussionThe proposed semi-supervised method is capable of cardiac segmentation and chamber volume quantification in a CHD population with wide anatomical variability. It accurately delineates the heart chambers and great vessels and can be used to accurately calculate ventricular and atrial volumes throughout the cardiac cycle. Such a segmentation method can reduce inter- and intra- observer variability and make CMR exams more standardized and efficient.

Project description:BACKGROUND:Phase contrast (PC) cardiovascular magnetic resonance (CMR) is widely employed for flow quantification, but analysis typically requires time consuming manual segmentation which can require human correction. Advances in machine learning have markedly improved automated processing, but have yet to be applied to PC-CMR. This study tested a novel machine learning model for fully automated analysis of PC-CMR aortic flow. METHODS:A machine learning model was designed to track aortic valve borders based on neural network approaches. The model was trained in a derivation cohort encompassing 150 patients who underwent clinical PC-CMR then compared to manual and commercially-available automated segmentation in a prospective validation cohort. Further validation testing was performed in an external cohort acquired from a different site/CMR vendor. RESULTS:Among 190 coronary artery disease patients prospectively undergoing CMR on commercial scanners (84% 1.5T, 16% 3T), machine learning segmentation was uniformly successful, requiring no human intervention: Segmentation time was <?0.01?min/case (1.2?min for entire dataset); manual segmentation required 3.96?±?0.36?min/case (12.5?h for entire dataset). Correlations between machine learning and manual segmentation-derived flow approached unity (r?=?0.99, p?<?0.001). Machine learning yielded smaller absolute differences with manual segmentation than did commercial automation (1.85?±?1.80 vs. 3.33?±?3.18?mL, p?<?0.01): Nearly all (98%) of cases differed by ?5?mL between machine learning and manual methods. Among patients without advanced mitral regurgitation, machine learning correlated well (r?=?0.63, p?<?0.001) and yielded small differences with cine-CMR stroke volume (? 1.3?±?17.7?mL, p?=?0.36). Among advanced mitral regurgitation patients, machine learning yielded lower stroke volume than did volumetric cine-CMR (? 12.6?±?20.9?mL, p?=?0.005), further supporting validity of this method. Among the external validation cohort (n?=?80) acquired using a different CMR vendor, the algorithm yielded equivalently small differences (? 1.39?±?1.77?mL, p?=?0.4) and high correlations (r?=?0.99, p?<?0.001) with manual segmentation, including similar results in 20 patients with bicuspid or stenotic aortic valve pathology (? 1.71?±?2.25?mL, p?=?0.25). CONCLUSION:Fully automated machine learning PC-CMR segmentation performs robustly for aortic flow quantification - yielding rapid segmentation, small differences with manual segmentation, and identification of differential forward/left ventricular volumetric stroke volume in context of concomitant mitral regurgitation. Findings support use of machine learning for analysis of large scale CMR datasets.

Project description:Cardiovascular resonance (CMR) imaging is a standard imaging modality for assessing cardiovascular diseases (CVDs), the leading cause of death globally. CMR enables accurate quantification of the cardiac chamber volume, ejection fraction and myocardial mass, providing information for diagnosis and monitoring of CVDs. However, for years, clinicians have been relying on manual approaches for CMR image analysis, which is time consuming and prone to subjective errors. It is a major clinical challenge to automatically derive quantitative and clinically relevant information from CMR images.Deep neural networks have shown a great potential in image pattern recognition and segmentation for a variety of tasks. Here we demonstrate an automated analysis method for CMR images, which is based on a fully convolutional network (FCN). The network is trained and evaluated on a large-scale dataset from the UK Biobank, consisting of 4,875 subjects with 93,500 pixelwise annotated images. The performance of the method has been evaluated using a number of technical metrics, including the Dice metric, mean contour distance and Hausdorff distance, as well as clinically relevant measures, including left ventricle (LV) end-diastolic volume (LVEDV) and end-systolic volume (LVESV), LV mass (LVM); right ventricle (RV) end-diastolic volume (RVEDV) and end-systolic volume (RVESV).By combining FCN with a large-scale annotated dataset, the proposed automated method achieves a high performance in segmenting the LV and RV on short-axis CMR images and the left atrium (LA) and right atrium (RA) on long-axis CMR images. On a short-axis image test set of 600 subjects, it achieves an average Dice metric of 0.94 for the LV cavity, 0.88 for the LV myocardium and 0.90 for the RV cavity. The mean absolute difference between automated measurement and manual measurement is 6.1 mL for LVEDV, 5.3 mL for LVESV, 6.9 gram for LVM, 8.5 mL for RVEDV and 7.2 mL for RVESV. On long-axis image test sets, the average Dice metric is 0.93 for the LA cavity (2-chamber view), 0.95 for the LA cavity (4-chamber view) and 0.96 for the RA cavity (4-chamber view). The performance is comparable to human inter-observer variability.We show that an automated method achieves a performance on par with human experts in analysing CMR images and deriving clinically relevant measures.

Project description:BackgroundCine Displacement Encoding with Stimulated Echoes (DENSE) facilitates the quantification of myocardial deformation, by encoding tissue displacements in the cardiovascular magnetic resonance (CMR) image phase, from which myocardial strain can be estimated with high accuracy and reproducibility. Current methods for analyzing DENSE images still heavily rely on user input, making this process time-consuming and subject to inter-observer variability. The present study sought to develop a spatio-temporal deep learning model for segmentation of the left-ventricular (LV) myocardium, as spatial networks often fail due to contrast-related properties of DENSE images.Methods2D + time nnU-Net-based models have been trained to segment the LV myocardium from DENSE magnitude data in short- and long-axis images. A dataset of 360 short-axis and 124 long-axis slices was used to train the networks, from a combination of healthy subjects and patients with various conditions (hypertrophic and dilated cardiomyopathy, myocardial infarction, myocarditis). Segmentation performance was evaluated using ground-truth manual labels, and a strain analysis using conventional methods was performed to assess strain agreement with manual segmentation. Additional validation was performed using an externally acquired dataset to compare the inter- and intra-scanner reproducibility with respect to conventional methods.ResultsSpatio-temporal models gave consistent segmentation performance throughout the cine sequence, while 2D architectures often failed to segment end-diastolic frames due to the limited blood-to-myocardium contrast. Our models achieved a DICE score of 0.83 ± 0.05 and a Hausdorff distance of 4.0 ± 1.1 mm for short-axis segmentation, and 0.82 ± 0.03 and 7.9 ± 3.9 mm respectively for long-axis segmentations. Strain measurements obtained from automatically estimated myocardial contours showed good to excellent agreement with manual pipelines, and remained within the limits of inter-user variability estimated in previous studies.ConclusionSpatio-temporal deep learning shows increased robustness for the segmentation of cine DENSE images. It provides excellent agreement with manual segmentation for strain extraction. Deep learning will facilitate the analysis of DENSE data, bringing it one step closer to clinical routine.

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Dataset Information

Fully-automated global and segmental strain analysis of DENSE cardiovascular magnetic resonance using deep learning for segmentation and phase unwrapping.

Background

Methods

Results

Publications

Fully-automated global and segmental strain analysis of DENSE cardiovascular magnetic resonance using deep learning for segmentation and phase unwrapping.

Similar Datasets

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