Cardiac Magnetic Resonance Imaging in the German National Cohort: Automated Segmentation of Short-Axis Cine Images and Post-Processing Quality Control

PurposeTo develop a segmentation and quality control pipeline for short-axis cardiac magnetic resonance (CMR) cine images from the prospective, multi-center German National Cohort (NAKO). Materials and MethodsA deep learning model for semantic segmentation, based on the nnU-Net architecture, was applied to full-cycle short-axis cine images from 29,908 baseline participants. The primary objective was to determine data on structure and function for both ventricles (LV, RV), including end diastolic volumes (EDV), end systolic volumes (ESV), and LV myocardial mass. Quality control measures included a visual assessment of outliers in morphofunctional parameters, inter- and intra-ventricular phase differences, and LV time-volume curves (TVC). These were adjudicated using a five-point rating scale, ranging from five (excellent) to one (non-diagnostic), with ratings of three or lower subject to exclusion. The predictive value of outlier criteria for inclusion and exclusion was analyzed using receiver operating characteristics. ResultsThe segmentation model generated complete data for 29,609 participants (incomplete in 1.0%) and 5,082 cases (17.0 %) were visually assessed. Quality assurance yielded a sample of 26,899 participants with excellent or good quality (89.9%; exclusion of 1,875 participants due to image quality issues and 835 cases due to segmentation quality issues). TVC was the strongest single discriminator between included and excluded participants (AUC: 0.684). Of the two-category combinations, the pairing of TVC and phases provided the greatest improvement over TVC alone (AUC difference: 0.044; p<0.001). The best performance was observed when all three categories were combined (AUC: 0.748). Extending the quality-controlled sample to include acceptable quality ratings, a total of 28,413 (95.0%) participants were available. ConclusionThe implemented pipeline facilitated the automated segmentation of an extensive CMR dataset, integrating quality control measures. This methodology ensures that ensuing quantitative analyses are conducted with a diminished risk of bias.