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We developed an open-sourced program that accounts for the current limitations of B-mode ultrasound and extends the clinical utility of ultrasound for assessing femoral trochlear cartilage thickness. Images were collected on 18 patients with a history of knee surgery. By failing to account for ultrasound acoustics and beam refraction, cartilage thickness was underestimated by 26% and overestimated by 0–4%, respectively (p < 0.001). Comprehensive thickness measurements achieved by measuring the Euclidean distance between every point were significantly different than traditional single-location measurements or by using the area/length (p = 0.004–0.006). Sub-regions were significantly different than all whole regions of interest (p = 0.001–0.012). [ABSTRACT FROM AUTHOR]