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Hi, Your fslstats command is fine. So it is hard to know what is happening here. Can you upload the images to our site? All the best, Mark On 18 Dec 2007, at 19:57, James Andrews wrote: > Hi, > > I am using fslstats to calculate summary statistics for DTI data. > I have > run TBSS, converted the significant voxels back into native space, > and now > would like to calculate statistics like mean FA for the masked region. > However, the intensities that fslstats calculates when I run the > following > command line are not the same as when I click on the voxels in the > fslview GUI!? > > fslstats <my input in native space> -k <my mask in native space> -R > > Am I doing something wrong with fslstats? > > Many thanks, > James >