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Motion estimation is an important task in the video encoding process. This plays an important role for high definition television (HDTV) and internet broadcasting as well as in medical imaging system like dynamic MRI. Accurate estimation of the predicted frame is required in dynamic MRI. The block search method is very easy to implement, but it estimates very poorly if complex motion is present in the frame sequences. In this paper, we present a new affine based motion estimation method which can be used for medical video processing. The proposed method provides sufficient parallelism in the implementation while giving good result in terms of motion estimation.