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Hello, The registered outputs created during VBM may change orientation, this is fine providing the registration is correct. For one of the problematic subjects, can you check if the first-pass registration has worked - e.g. compare <blah>_GM_to_T_init to template_GM_init in FSLview and let me know if the two are registered? Kind Regards Matthew > On 29 Jun 2016, at 14:30, Amanda Rodrigue <[log in to unmask]> wrote: > > Hello, > I am following the instructions for FSL's VBM analysis and having some difficulties with the fslvbm_2_template step. The script runs fine but when I look at the results (the template_4D_GM.nii.gz in fsl view there are about 8 or 9 subjects that are misoriented. I have looked at them all in fsl view and the labels are correct and all are in the same orientation as those subs that are correctly oriented as reported by fslorient. The brain image is in the correct orientation in all the files produced by the template script until the Sub#_anat_struc_GM_to_T_init.gz. Consequently this is when the orientation switches from neurological to radiological. I have also tried fslorient2standard on these subjects, as suggested by some comments on the message board but it does not seem to make a difference. Any input would be appreciated. > Amanda