Segmentation of the Aorta and Pulmonary Arteries Based on 4D Flow MRI in the Pediatric Setting Using Fully Automated Multi-Site, Multi-Vendor, and Multi-Label Dense U-Net

Impact of training data composition on the generalizability of convolutional neural network aortic cross-section segmentation in four-dimensional magnetic resonance flow imaging

BACKGROUND

Four-dimensional cardiovascular magnetic resonance flow imaging (4D flow CMR) plays an important role in assessing cardiovascular diseases. However, the manual or semi-automatic segmentation of aortic vessel boundaries in 4D flow data introduces variability and limits the reproducibility of aortic hemodynamics visualization and quantitative flow-related parameter computation. This paper explores the potential of deep learning to improve 4D flow CMR segmentation by developing models for automatic segmentation and analyzes the impact of the training data on the generalization of the model across different sites, scanner vendors, sequences, and pathologies.

METHODS

The study population consists of 260 4D flow CMR datasets, including subjects without known aortic pathology, healthy volunteers, and patients with bicuspid aortic valve (BAV) examined at different hospitals. The dataset was split to train segmentation models on subsets with different representations of characteristics, such as pathology, gender, age, scanner model, vendor, and field strength. An enhanced three-dimensional U-net convolutional neural network (CNN) architecture with residual units was trained for time-resolved two-dimensional aortic cross-sectional segmentation. Model performance was evaluated using Dice score, Hausdorff distance, and average symmetric surface distance on test data, datasets with characteristics not represented in the training set (model-specific), and an overall evaluation set. Standard diagnostic flow parameters were computed and compared with manual segmentation results using Bland-Altman analysis and interclass correlation.

RESULTS

The representation of technical factors, such as scanner vendor and field strength, in the training dataset had the strongest influence on the overall segmentation performance. Age had a greater impact than gender. Models solely trained on BAV patients' datasets performed well on datasets of healthy subjects but not vice versa.

CONCLUSION

This study highlights the importance of considering a heterogeneous dataset for the training of widely applicable automatic CNN segmentations in 4D flow CMR, with a particular focus on the inclusion of different pathologies and technical aspects of data acquisition.

Machine Learning-Based Segmentation of the Thoracic Aorta with Congenital Valve Disease Using MRI

Subjects with bicuspid aortic valves (BAV) are at risk of developing valve dysfunction and need regular clinical imaging surveillance. Management of BAV involves manual and time-consuming segmentation of the aorta for assessing left ventricular function, jet velocity, gradient, shear stress, and valve area with aortic valve stenosis. This paper aims to employ machine learning-based (ML) segmentation as a potential for improved BAV assessment and reducing manual bias. The focus is on quantifying the relationship between valve morphology and vortical structures, and analyzing how valve morphology influences the aorta's susceptibility to shear stress that may lead to valve incompetence. The ML-based segmentation that is employed is trained on whole-body Computed Tomography (CT). Magnetic Resonance Imaging (MRI) is acquired from six subjects, three with tricuspid aortic valves (TAV) and three functionally BAV, with right-left leaflet fusion. These are used for segmentation of the cardiovascular system and delineation of four-dimensional phase-contrast magnetic resonance imaging (4D-PCMRI) for quantification of vortical structures and wall shear stress. The ML-based segmentation model exhibits a high Dice score (0.86) for the heart organ, indicating a robust segmentation. However, the Dice score for the thoracic aorta is comparatively poor (0.72). It is found that wall shear stress is predominantly symmetric in TAVs. BAVs exhibit highly asymmetric wall shear stress, with the region opposite the fused coronary leaflets experiencing elevated tangential wall shear stress. This is due to the higher tangential velocity explained by helical flow, proximally of the sinutubal junction of the ascending aorta. ML-based segmentation not only reduces the runtime of assessing the hemodynamic effectiveness, but also identifies the significance of the tangential wall shear stress in addition to the axial wall shear stress that may lead to the progression of valve incompetence in BAVs, which could guide potential adjustments in surgical interventions.

Segmentation of the aorta in systolic phase from 4D flow MRI: multi-atlas vs. deep learning

OBJECTIVE

In the management of the aortic aneurysm, 4D flow magnetic resonance Imaging provides valuable information for the computation of new biomarkers using computational fluid dynamics (CFD). However, accurate segmentation of the aorta is required. Thus, our objective is to evaluate the performance of two automatic segmentation methods on the calculation of aortic wall pressure.

METHODS

Automatic segmentation of the aorta was performed with methods based on deep learning and multi-atlas using the systolic phase in the 4D flow MRI magnitude image of 36 patients. Using mesh morphing, isotopological meshes were generated, and CFD was performed to calculate the aortic wall pressure. Node-to-node comparisons of the pressure results were made to identify the most robust automatic method respect to the pressures obtained with a manually segmented model.

RESULTS

Deep learning approach presented the best segmentation performance with a mean Dice similarity coefficient and a mean Hausdorff distance (HD) equal to 0.92+/- 0.02 and 21.02+/- 24.20 mm, respectively. At the global level HD is affected by the performance in the abdominal aorta. Locally, this distance decreases to 9.41+/- 3.45 and 5.82+/- 6.23 for the ascending and descending thoracic aorta, respectively. Moreover, with respect to the pressures from the manual segmentations, the differences in the pressures computed from deep learning were lower than those computed from multi-atlas method.

CONCLUSION

To reduce biases in the calculation of aortic wall pressure, accurate segmentation is needed, particularly in regions with high blood flow velocities. Thus, the deep learning segmen-tation method should be preferred.

Reconstruction and Validation of Arterial Geometries for Computational Fluid Dynamics Using Multiple Temporal Frames of 4D Flow-MRI Magnitude Images

PURPOSE

Segmentation and reconstruction of arterial blood vessels is a fundamental step in the translation of computational fluid dynamics (CFD) to the clinical practice. Four-dimensional flow magnetic resonance imaging (4D Flow-MRI) can provide detailed information of blood flow but processing this information to elucidate the underlying anatomical structures is challenging. In this study, we present a novel approach to create high-contrast anatomical images from retrospective 4D Flow-MRI data.

METHODS

For healthy and clinical cases, the 3D instantaneous velocities at multiple cardiac time steps were superimposed directly onto the 4D Flow-MRI magnitude images and combined into a single composite frame. This new Composite Phase-Contrast Magnetic Resonance Angiogram (CPC-MRA) resulted in enhanced and uniform contrast within the lumen. These images were subsequently segmented and reconstructed to generate 3D arterial models for CFD. Using the time-dependent, 3D incompressible Reynolds-averaged Navier-Stokes equations, the transient aortic haemodynamics was computed within a rigid wall model of patient geometries.

RESULTS

Validation of these models against the gold standard CT-based approach showed no statistically significant inter-modality difference regarding vessel radius or curvature (p > 0.05), and a similar Dice Similarity Coefficient and Hausdorff Distance. CFD-derived near-wall hemodynamics indicated a significant inter-modality difference (p > 0.05), though these absolute errors were small. When compared to the in vivo data, CFD-derived velocities were qualitatively similar.

CONCLUSION

This proof-of-concept study demonstrated that functional 4D Flow-MRI information can be utilized to retrospectively generate anatomical information for CFD models in the absence of standard imaging datasets and intravenous contrast.

4D Flow cardiovascular magnetic resonance consensus statement: 2023 update

Hemodynamic assessment is an integral part of the diagnosis and management of cardiovascular disease. Four-dimensional cardiovascular magnetic resonance flow imaging (4D Flow CMR) allows comprehensive and accurate assessment of flow in a single acquisition. This consensus paper is an update from the 2015 '4D Flow CMR Consensus Statement'. We elaborate on 4D Flow CMR sequence options and imaging considerations. The document aims to assist centers starting out with 4D Flow CMR of the heart and great vessels with advice on acquisition parameters, post-processing workflows and integration into clinical practice. Furthermore, we define minimum quality assurance and validation standards for clinical centers. We also address the challenges faced in quality assurance and validation in the research setting. We also include a checklist for recommended publication standards, specifically for 4D Flow CMR. Finally, we discuss the current limitations and the future of 4D Flow CMR. This updated consensus paper will further facilitate widespread adoption of 4D Flow CMR in the clinical workflow across the globe and aid consistently high-quality publication standards.

Segmentation of 4D Flow MRI: Comparison between 3D Deep Learning and Velocity-Based Level Sets

A thoracic aortic aneurysm is an abnormal dilatation of the aorta that can progress and lead to rupture. The decision to conduct surgery is made by considering the maximum diameter, but it is now well known that this metric alone is not completely reliable. The advent of 4D flow magnetic resonance imaging has allowed for the calculation of new biomarkers for the study of aortic diseases, such as wall shear stress. However, the calculation of these biomarkers requires the precise segmentation of the aorta during all phases of the cardiac cycle. The objective of this work was to compare two different methods for automatically segmenting the thoracic aorta in the systolic phase using 4D flow MRI. The first method is based on a level set framework and uses the velocity field in addition to 3D phase contrast magnetic resonance imaging. The second method is a U-Net-like approach that is only applied to magnitude images from 4D flow MRI. The used dataset was composed of 36 exams from different patients, with ground truth data for the systolic phase of the cardiac cycle. The comparison was performed based on selected metrics, such as the Dice similarity coefficient (DSC) and Hausdorf distance (HD), for the whole aorta and also three aortic regions. Wall shear stress was also assessed and the maximum wall shear stress values were used for comparison. The U-Net-based approach provided statistically better results for the 3D segmentation of the aorta, with a DSC of 0.92 ± 0.02 vs. 0.86 ± 0.5 and an HD of 21.49 ± 24.8 mm vs. 35.79 ± 31.33 mm for the whole aorta. The absolute difference between the wall shear stress and ground truth slightly favored the level set method, but not significantly (0.754 ± 1.07 Pa vs. 0.737 ± 0.79 Pa). The results showed that the deep learning-based method should be considered for the segmentation of all time steps in order to evaluate biomarkers based on 4D flow MRI.

4D segmentation of the thoracic aorta from 4D flow MRI using deep learning

BACKGROUND

4D flow MRI allows the analysis of hemodynamic changes in the aorta caused by pathologies such as thoracic aortic aneurysms (TAA). For personalized management of TAA, new biomarkers are required to analyze the effect of fluid structure iteration which can be obtained from 4D flow MRI. However, the generation of these biomarkers requires prior 4D segmentation of the aorta.

OBJECTIVE

To develop an automatic deep learning model to segment the aorta in 4D from 4D flow MRI.

METHODS

Segmentation is addressed with a U-Net based segmentation model that treats each 4D flow MRI frame as an independent sample. Performance is measured with respect to Dice score (DS) and Hausdorff distance (HD). In addition, the maximum and minimum surface areas at the level of the ascending aorta are measured and compared with those obtained from cine-MRI.

RESULTS

The segmentation performance was 0.90 ± 0.02 for the DS and the mean HD was 9.58 ± 4.36 mm. A correlation coefficient of r = 0.85 was obtained for the maximum surface and r = 0.86 for the minimum surface between the 4D flow MRI and cine-MRI.

CONCLUSION

The proposed automatic approach of 4D aortic segmentation from 4D flow MRI seems to be accurate enough to contribute to the wider use of this imaging technique in the analysis of pathologies such as TAA.

The role of 4-dimensional flow in the assessment of bicuspid aortic valve and its valvulo-aortopathies

Bicuspid aortic valve is the most common congenital cardiac malformation and the leading cause of aortopathy and aortic stenosis in younger patients. Aortic wall remodelling secondary to altered haemodynamic flow patterns, changes in peak velocity, and wall shear stress may be implicated in the development of aortopathy in the presence of bicuspid aortic valve and dysfunction. Assessment of these parameters as potential predictors of disease severity and progression is thus desirable. The anatomic and functional information acquired from 4D flow MRI can allow simultaneous visualisation and quantification of the pathological geometric and haemodynamic changes of the aorta. We review the current clinical utility of haemodynamic quantities including velocity, wall sheer stress and energy losses, as well as visual descriptors such as vorticity and helicity, and flow direction in assessing the aortic valve and associated aortopathies.