Deep learning based automated left ventricle segmentation and flow quantification in 4D flow cardiac MRI

BACKGROUND: 4D flow MRI enables assessment of cardiac function and intra-cardiac blood flow dynamics from a single acquisition. However, due to the poor contrast between the chambers and surrounding tissue, quantitative analysis relies on the segmentation derived from a registered cine MRI acquisition. This requires an additional acquisition and is prone to imperfect spatial and temporal inter-scan alignment. Therefore, in this work we developed and evaluated deep learning-based methods to segment the left ventricle (LV) from 4D flow MRI directly. METHODS: We compared five deep learning-based approaches with different network structures, data pre-processing and feature fusion methods. For the data pre-processing, the 4D flow MRI data was reformatted into a stack of short-axis view slices. Two feature fusion approaches were proposed to integrate the features from magnitude and velocity images. The networks were trained and evaluated on an in-house dataset of 101 subjects with 67,567 2D images and 3030 3D volumes. The performance was evaluated using various metrics including Dice, average surface distance (ASD), end-diastolic volume (EDV), end-systolic volume (ESV), LV ejection fraction (LVEF), LV blood flow kinetic energy (KE) and LV flow components. The Monte Carlo dropout method was used to assess the confidence and to describe the uncertainty area in the segmentation results. RESULTS: Among the five models, the model combining 2D U-Net with late fusion method operating on short-axis reformatted 4D flow volumes achieved the best results with Dice of 84.52% and ASD of 3.14 mm. The best averaged absolute and relative error between manual and automated segmentation for EDV, ESV, LVEF and KE was 19.93 ml (10.39%), 17.38 ml (22.22%), 7.37% (13.93%) and 0.07 mJ (5.61%), respectively. Flow component results derived from automated segmentation showed high correlation and small average error compared to results derived from manual segmentation. CONCLUSIONS: Deep learning-based methods can achieve accurate automated LV segmentation and subsequent quantification of volumetric and hemodynamic LV parameters from 4D flow MRI without requiring an additional cine MRI acquisition.