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Hello, To get a mask where only voxel with +50% of subjects have FA>0, you can replace line 183 in tbss_3_postreg script by: fslmaths all_FA -max 0 -bin -Tmean -thr 0.5 -bin mean_FA_mask Cheers, Manu > On 20 Feb 2017, at 13:58, SUBSCRIBE FSL Anonymous <[log in to unmask]> wrote: > > Can someone give me a clue as to how to apply masking of voxels to FA images that replaces what is done in tbss_3_postreg? I would like to follow what is done in this paper (http://www.sciencedirect.com/science/article/pii/S1053811914001736) in the methods under section Difference 5, where voxels are included if they are nonzero in at least 50% of the participants.