Abstract: The present disclosure provides an operating method of an automatic analysis system on magnetic resonance imaging (MRI), which includes steps as follows. Images are received from of the subject's brain from the MRI machine. Contrast-enhanced T1-weighted images and T2-weighted images are obtained from the images, and the pre-processing is performed on the images. The ratio of T2-weighted images to contrast-enhanced T1-weighted images is calculated to generate contrast-enhanced images. The unsupervised clustering is performed on the region of interest in the contrast-enhanced image to separate a cystic part and a non-cystic part so as to calculate the feature parameters. After radiosurgery is performed on the brain tumor corresponding to the region of interest, the volume change of the tumor is analyzed. The linear regression analysis of the feature parameters and the volume change of the tumor is performed for prognostic evaluation.