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Accuracy of automated segmentation methods is of great importance in brain image analysis. In this paper, a comparison evaluation of three common software packages in brain image segmentation is presented. Performance analysis of segmentation methods integrated with the latest versions of SPM, FSL and BrainSuite is considered. In this comparison study, quantitative and qualitative assessment of segmentation algorithms is performed for both simulated and real data. Results obtained in this paper can be utilized to assist the users for selecting the appropriate software for the application of brain tissue segmentation.