A novel method of semi-automatic tongue contour extraction in rtMRI sequences is proposed. The initial boundary image is obtained with combined multi-directional Sobel operators in registered region; then a boundary intensity map is constructed to find the most probable tongue contour points by searching for the optimal route with Viterbi algorithm; finally the tongue contour is obtained using B-Spline approximation. Experiments show that the proposed method is of higher accuracy in tongue contour extraction, especially when some parts of tongue touch other organs. The proposed method could be extended to extract contours of other organs such as joints and backbones in MRI, Ultrasonic or X-ray images.