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Hi Zhiliang, The fdt_paths file gives you the visitation map from the probabilistic tractography, i.e. how many streamlines reach each given voxel. To use it as a mask, you have to choose a threshold for fdt_paths and use and compute the mean FA for the given tract. Example: fslmaths tracto/fdt_paths -thr 400 -bin -mul DTI/dti_FA FA_tracto fslstats FA_tracto.nii.gz -M Gives you the mean FA for the tract in fdt_paths with a threshold of 400 streamlines. Cheers, Manu