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Hi, I think that's because you didn't set the threshold "0 1" probably. why don't you just use fslview for visualization, it would be much easier : ) On Wed, Jul 26, 2017 at 1:02 PM, Ana Fouto <[log in to unmask]> wrote: > Dear experts, > > I would like to overlay some of my results images like this: > > > > Overlay the MNI image with the template FA-skeleton and my tstat result > with different colors. I tried this code: > > overlay 1 1 /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -a > /usr/share/fsl/5.0/data/standard/FMRIB58_FA-skeleton_1mm.nii.gz 0 1 > overlay > > But all I got was the MNI image all red. Can you please help me > understanding how I should perform these commands so I can reach the > desired result? > > Thanks in advanced for your attention. > > Best regards, > Ana Fouto >