We propose a method to quantify superior-inferior (SI) motion of a rigid target using the 3D contour from free-breathing CT (FBCT). The technique utilizes similarity between 2D contours (Jaccard Index) and a population based density function for probability of motion amplitude, and is applicable both when the static target shape is and is not known beforehand. Simulations and phantom measurements showed that motion reconstruction is often feasible, with decreasing accuracy as discrepancy is introduced between assumed and actual static shape. When no static shape is used the analysis is most robust for slow scanning speeds relative to the motion period.