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Hi, It is clear how you are calculating the mean using fslmeants, but what are you using for getting "FA from different ROIs"? It is important to know exactly what you comparing in order to know how to interpret it. All the best, Mark On 15 May 2014, at 15:24, Maria Diez Cirarda <[log in to unmask]> wrote: > Dear FSL Experts, > > I´m calculating two TBSS with different samples (neurodegenerative disease and healthy control) and comparing their mean FA and their FA from different ROIs. The logical result is to find FA from neurodegenerative group<Healthy group > The results that I find are: > -FA from ROIs: higher in healthy control group > -mean FA: higher in neurodegenerative disease group > > The TBSS is calculated: > > 1. tbss_1_preproc *.nii.gz > 2. tbss_2_reg –T > 3. tbss_3_postreg –S > 4. Tbss_4_prestats 0.2 > > > The mean FA is calculated with: > fslmeants : “fslmeants -i all_FA_skeletonised.nii.gz -mmean_FA_skeleton.nii.gz -o FAmedia” > > I have checked the brain mask and the DTIFIT from all subjects and the images are ok. > > Something I´m doing wrong, because results are contradictory. Can you help me? > > Is there any other way for calculating the mean FA? > > Thanks in advance, > > > María.