Deep convolutional neural networks with multiplane consensus labeling for lung function quantification using UTE proton MRI

Abstract

Background: Ultrashort echo time (UTE) proton MRI has gained popularity for assessing lung structure and function in pulmonary imaging; however, the development of rapid biomarker extraction and regional quantification has lagged behind due to labor-intensive lung segmentation. Purpose: To evaluate a deep learning (DL) approach for automated lung segmentation to extract image-based biomarkers from functional lung imaging using 3D radial UTE oxygen-enhanced (OE) MRI. Study Type: Retrospective study aimed to evaluate a technical development. Population: Forty-five human subjects, including 16 healthy volunteers, 5 asthma, and 24 patients with cystic fibrosis. Field Strength/Sequence: 1.5T MRI, 3D radial UTE (TE = 0.08 msec) sequence. Assessment: Two 3D radial UTE volumes were acquired sequentially under normoxic (21% O2) and hyperoxic (100% O2) conditions. Automated segmentation of the lungs using 2D convolutional encoder-decoder based DL method, and the subsequent functional quantification via adaptive K-means were compared with the results obtained from the reference method, supervised region growing. Statistical Tests: Relative to the reference method, the performance of DL on volumetric quantification was assessed using Dice coefficient with 95% confidence interval (CI) for accuracy, two-sided Wilcoxon signed-rank test for computation time, and Bland–Altman analysis on the functional measure derived from the OE images. Results: The DL method produced strong agreement with supervised region growing for the right (Dice: 0.97; 95% CI = [0.96, 0.97]; P < 0.001) and left lungs (Dice: 0.96; 95% CI = [0.96, 0.97]; P < 0.001). The DL method averaged 46 seconds to generate the automatic segmentations in contrast to 1.93 hours using the reference method (P < 0.001). Bland–Altman analysis showed nonsignificant intermethod differences of volumetric (P ≥ 0.12) and functional measurements (P ≥ 0.34) in the left and right lungs. Data Conclusion: DL provides rapid, automated, and robust lung segmentation for quantification of regional lung function using UTE proton MRI. Level of Evidence: 2. Technical Efficacy: Stage 1. J. Magn. Reson. Imaging 2019;50:1169–1181.