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We investigated a 2-dimensional (2D) U-Net model to delineate lumbar bone marrow (BM) using a high resolution T1-weighted magnetic resonance imaging.Healthy controls (n = 44, 836 images) and patients with hematologic diseases (n = 56, 1064 images) received MRI of the lumbar spines. Lumbar BM on each image was manually delineated by an experienced radiologist as a ground-truth. The 2D U-Net models were trained using a healthy lumbar BM only, diseased BM only, and using healthy and diseased BM combined, respectively. The models were validated using healthy and diseased subjects, separately. A repeated-measures analysis of variance was performed to compare segmentation accuracies with 2 validation cohorts among U-Net trained with healthy subjects (UNET_HC), U-Net trained with diseased subjects (UNET_HD), U-Net trained with all subjects including both healthy and diseased subjects (UNET_HCHD), and 3-dimensional Grow-Cut algorithm (3DGC).When validated with the healthy subjects, UNET_HC, UNET_HD, UNET_HCHD and 3DGC achieved the mean and standard deviation of the Dice Similarity Coefficient (DSC) of 0.9415 ± 0.07056, 0.9583 ± 0.05146, 0.9602 ± 0.0486 and 0.9139 ± 0.2039, respectively. When validated with the diseased subjects, DSCs of UNET_HC, UNET_HD, UNET_HCHD and 3DGC were 0.8303 ± 0.1073, 0.9502 ± 0.0217, 0.9502 ± 0.0217 and 0.8886 ± 0.2179, respectively. The U-Net models segmented BM better than the semi-automatic 3DGC (P 0.0001), and UNET_HD produced better results than UNET_HC (P 0.0001).We successfully constructed a fully automatic lumbar BM segmentation model for a high-resolution T1-weighted MRI using U-Net, which outperformed most of the previously reported approaches and the existing semi-automatic algorithm.