Objective We have developed a fully automatic three-dimensional MRI analysis software that measures the projected cartilage area ratio (PCAR) to allow for the quantification of the cartilage in the knee. Our objectives for this cross-sectional study were to verify our software’s accuracy and to quantify cartilage and meniscus extrusion. We also examined which cartilage quantification was most affected by age and analyzed the relationship between PCAR and meniscus extrusion. Methods 108 subjects were selected for training, and Dice similarity coefficients were determined from 5 other subjects. This study included 561 subjects between 30–70 years of age. From their knee MRI data, we quantified cartilage thickness, cartilage volume, and PCAR (0.0–1.5 mm) in four regions, including the medial tibial (MT) cartilage. Furthermore, each region was divided into nine subregions. The medial central (mc) subregion was also analyzed. As a quantification for meniscus extrusion, the medial meniscus coverage ratio (MMCR) was also investigated. Results Dice similarity coefficients were 0.911 and 0.892 for the femoral and tibial cartilage and 0.916 and 0.891 for the medial and lateral meniscus. Among 48 cartilage quantifications, the highest absolute value of the correlation coefficient with age was mcMT PCAR 1.0 mm in females and mcMT cartilage thickness in males. In females, mcMT PCAR 1.0 mm was correlated with MMCR, although MMCR was not correlated with age. In males, mcMT PCAR 0.0 mm was correlated with MMCR. Conclusions Our software showed high segmentation accuracy and provided numerous quantifications of cartilage related to age and meniscus extrusion.