FatSegNet: A fully automated deep learning pipeline for adipose tissue segmentation on abdominal dixon MRI

Purpose Introduce and validate a novel, fast, and fully automated deep learning pipeline (FatSegNet) to accurately identify, segment, and quantify visceral and subcutaneous adipose tissue (VAT and SAT) within a consistent, anatomically defined abdominal region on Dixon MRI scans. Methods FatSegNet is composed of three stages: (a) Consistent localization of the abdominal region using two 2D‐Competitive Dense Fully Convolutional Networks (CDFNet), (b) Segmentation of adipose tissue on three views by independent CDFNets, and (c) View aggregation. FatSegNet is validated by: (1) comparison of segmentation accuracy (sixfold cross‐validation), (2) test–retest reliability, (3) generalizability to randomly selected manually re‐edited cases, and (4) replication of age and sex effects in the Rhineland Study—a large prospective population cohort. Results The CDFNet demonstrates increased accuracy and robustness compared to traditional deep learning networks. FatSegNet Dice score outperforms manual raters on VAT (0.850 vs. 0.788) and produces comparable results on SAT (0.975 vs. 0.982). The pipeline has excellent agreement for both test–retest (ICC VAT 0.998 and SAT 0.996) and manual re‐editing (ICC VAT 0.999 and SAT 0.999). Conclusions FatSegNet generalizes well to different body shapes, sensitively replicates known VAT and SAT volume effects in a large cohort study and permits localized analysis of fat compartments. Furthermore, it can reliably analyze a 3D Dixon MRI in ∼1 minute, providing an efficient and validated pipeline for abdominal adipose tissue analysis in the Rhineland Study.