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Magnetic resonance imaging is considered the gold standard technique for quantifying thigh muscle and fat cross-sectional area. We have developed a semi-automated technique to segment seven thigh compart-ments in persons with spinal cord injury. Thigh magnetic resonance images from 18 men (18–50 years old) with traumatic motor-complete spinal cord injury were analyzed in a blinded fashion using the threshold technique. The cross-sectional area values acquired by thresholding were compared to the manual tracing technique. The percentage errors for thigh circumference were (threshold: 170.71 ± 38.67; manual: 169.45 ± 38.27 cm2) 0.74％, subcutaneous adipose tissue (threshold: 65.99±30.79; manual: 62.68 ± 30.22) 5.2％, whole muscle (threshold: 98.18 ± 20.19; manual: 98.20 ± 20.08 cm2) 0.13％, femoral bone (threshold: 6.53 ± 1.09;manual: 6.53 ± 1.09 cm2) 0.64％, bone marrow fat (threshold: 3.12 ± 1.12; manual: 3.1 ± 1.11 cm2) 0.36％, knee extensor (threshold: 43.98 ± 7.66; manual: 44.61 ± 7.81 cm2) 1.78％ and ％ intramuscular fat (threshold:10.45 ± 4.29; manual: 10.92 ± 8.35％) 0.47％. Collectively, these results suggest that the threshold technique provided a robust accuracy in measuring the seven main thigh compartments, while greatly reducing the analysis time.