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Hi, You didn't specify a mask, so the mean is across the whole image, and include background voxels that contain just zeros (the vast majority), hence the very small values you found. Use the option -m to supply a mask. All the best, Anderson On 10/01/2014 07:15, Hsekar B wrote: > Hi FSL experts, > I performed TBSS analysis between 2 groups (S000X & P000X) as mentioned in the manual > i did get significant results between the 2 groups. > to measure the mean FA values (of white matter ) of all the subjects. i performed the fslmeants > "fslmeants -i all_FA_skeletonised.nii.gz -o results_DTI.xls" kindly find the excel sheet attached to this mail > but i observe weird values of FA, compared to the FA values described in the article "Diffusion Tensor Imaging of the Brain. Andrew L. Alexander, Jee Eun Lee, Mariana Lazar, and Aaron S. Neurotherapeutics. 2007 July; 4(3): 316–329" > i have rechecked the registration. all looks fine. > can anyone suggest me what could have possibly gone wrong. > > thank you in advance > > regards > HB > >