Deep learning based automated left atrial segmentation and flow quantification of real time phase contrast MRI in patients with atrial fibrillation

Abstract

Real time 2D phase contrast (RTPC) MRI is useful for flow quantification in atrial fibrillation (AF) patients, but data analysis requires time-consuming anatomical contouring for many cardiac time frames. Our goal was to develop a convolutional neural network (CNN) for fully automated left atrial (LA) flow quantification. Forty-four AF patients underwent cardiac MRI including LA RTPC, collecting a median of 358 timeframes per scan. 15,307 semi-manual derived RTPC LA contours comprised ground truth for CNN training, validation, and testing. CNN vs. human performance was assessed using Dice scores (DSC), Hausdorff distance (HD), and flow measures (stasis, velocities, flow). LA contour DSC across all patients were similar to human inter-observer DSC (0.90 vs. 0.93) and a median 4.6 mm [3.5–5.9 mm] HD. There was no impact of heart rate variability on contouring quality (low vs. high variability DSC: 0.92 ± 0.05 vs. 0.91 ± 0.03, p = 0.95). CNN based LA flow quantification showed good to excellent agreement with semi-manual analysis (r > 0.90) and small bias in Bland-Altman analysis for mean velocity (-0.10 cm/s), stasis (1%), and net flow (-2.4 ml/s). This study demonstrated the feasibility of CNN based LA flow analysis with good agreements in LA contours and flow measures and resilience to heartbeat variability in AF.