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I am getting strange results using bet on a NIFTI file -- it seems to use a wrong interpretation of the orientation. For testing, I ran "bet file.nii.gz file-bet.nii.gz -g 1": I get an outline that cuts into the brain on the right, but leaves the left untouched (expected result is a large brain outline at the bottom, small at the top). FSLView loads the input file correctly (i.e. S, I, A, P, R and L labels are as expected). I tried working around the issue by running betpremask on file.nii, but although it generates a reasonably-looking premasked image, the same orientation problem occurs when I use bet on it. How can I get bet to read this type of file properly? Thanks Rolf -- Rolf A Heckemann, PhD Research Associate Division of Neuroscience and Mental Health MRC Clinical Sciences Centre Imperial College London Hammersmith Hospital Campus Du Cane Road London W12 0HS United Kingdom