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We have developed a fully automatic three-dimensional MRI analysis software program for automatic segmentation of knee cartilage using a deep neural network. The purpose of this study was to use this software to clarify the interscan measurement error of the knee cartilage thickness and projected cartilage area ratio at 9 regions and 45 subregions in the knee. Ten healthy volunteers underwent MRI twice in the same day. The software provided cartilage thickness and projected cartilage area ratio (thickness ≥ 1.5 mm) at 9 regions and 45 s