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Dear Walid, The MD values you are reporting are in the normal range of MD in white matter (in mm^2.s^-1). You can scale them up if you prefer with fslmaths: fslmaths all_md_skeletonized -mul 1000 all_MD_skeletonized_scaled Cheers, Manu On 3 Feb 2017, at 08:49, Walid Yassin <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Matt, Thanks for letting me know that it’s the same as fslmaths! I just tried however the solution didn’t work! Anyone knows where i should trace the low MD values in my all_MD_skeletonized file? Thank you, Walid On Feb 3, 2017, at 5:37 PM, Matt Glasser <[log in to unmask]<mailto:[log in to unmask]>> wrote: Replace avw with fsl in the commands. Peace, Matt. From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Walid Yassin <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Friday, February 3, 2017 at 2:27 AM To: <[log in to unmask]<mailto:[log in to unmask]>> Subject: [FSL] Low MD values Dear FSLers, I ran the tbss_non_FA script on my data, and got the results with no error! Later i extracted the MD values and found them to be very low, somthing like 0.000774498559 So i checked my files and it appears that my all_MD_skeletonised has low values example 0.00064... I saw a previous post that got recommended avwutils, but i dont even have that command! "command not found" Any help to solve this problem? If avwmaths can solve it, how can i add this command? Please note that the FA processs went smoothly! Thank you in advance, Walid