The result of imaging segmentation becomes different with the parameters involved in the segmentation algorithms; therefore, the parameters for the optimal segmentation have been found through a try and error.In this paper, we propose the method to find the best values of parameters involved in the area-based active contour method using three-way ANOVA. The segmentation result applied by three-way ANOVA is compared with the optimal segmentation which is drawn by user. We use the global consistency rate for comparing two segmentations. Finally, we estimate the main effects and interactions between each parameter using three-way ANOVA, and then calculate the point and interval estimate to find the best values of three parameters. The proposed method will be a great help to find the optimal parameters before working the motion segmentation using piecewise constant model.