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The orientation of the small intestine varies among frames of a cinematic-magnetic resonance imaging (cine-MRI) sequence owing to small intestine peristalsis, which increases the complexity of its contour tracking. There are also leakage problems owing to the presence of low contrast areas in some frames. An improved fast marching method using an anisotropic Gaussian filter and a boundary penalty is presented for the contour tracking of small intestine segments. Experimental results show that the proposed method can track accurate contours of small intestine segments without leakage problems.