With the advent of diffusion tensor imaging,the number of brain studies with DTI is growing steadily.Accordingly,the relevant software are also emerging.Notably,the fiber tracking algorithm in FSL is probabilistic diffusion tractography.It is suitable for the study on regions of fiber crossing and gray matter.Here,we mainly introduce the two sub-tools (tract-based spatial statistics,TBSS and FMRIB’s diffusion toolbox,FDT) and their application in DTI brain image analysis classified by the different data analysis methods,mainly involving depression,schizophrenia and cognitive function and so on.In this paper,we briefly explain the basic principle of DTI at first.Next,according the different data analysis methods,we introduce the application of TBSS and FDT.In TBSS,there are two parts:the whole brain and region of interest (ROI). In FDT,there are three parts:the whole brain,ROI and the classification of connectivity.Finally,we summarize the limitation and the development of FSL currently.