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hi, Reich, In my study, it works well ( bet t1.nii.gz bt1.nii.gz -B -n -m). bt1_mask.nii.gz is just one of the output for T2, perhaps you can try it on the mean of 4D to get a brain mask and then apply to 4D anyway, if you have got image betted and want further mask, maybe you can use - fslmaths mean4D.nii.gz -bin mask.nii.gz - fslmaths mask -dilF mask may it help! 2009/2/19 Daniel Reich <[log in to unmask]> > I'm running BET with the -B option to remove the residual neck and orbit > voxels. (It works well on my DE-TSE T2-weighted images.) I also want to > save > a binary brain mask, but the mask generated with the -m option is not > updated after the -B portion of the routine is run, so it includes the neck > and orbit voxels I want to remove. > > Thanks in advance. > -- Chun Meng NeuroImage Computing group, State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China