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Hi Saad, Thanks a lot. That clears things up. And I tried to use the option 2 but some problem pops up. 1) I have one seed mask and another roi. When I used the roi as waypoint mask, the path and the intensity hugely differs from those using the same roi as target mask. In the waypoint mask case, the intensity is from 0 to hundreds but in the target mask case, the intensity is from 0 to tens of thousands. Why the results shrink largely when I use the roi as waypoint mask? 2) And I wanna normalize the paths and I found it came out the same images while using these two different commands: fslmaths fdt_paths -div `cat waytotal` -thrP 99 -bin fdt_paths_norm_thresh fslmaths fdt_paths -thrP 99 -bin fdt_paths_norm_thresh If the images are the same, what is the point to do the normalization? 3) I used the individual tracking result as mask to get the mean FA. But I found out that 2 out of 47 subjects' FA values within their own path are lower than 0.2. Is there anything I did wrong? Best regards, Lijun