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Hi Matthew any thoughts on what might be wrong? On Wed, Jun 29, 2016 at 4:56 PM, Amanda Rodrigue <[log in to unmask]> wrote: > So the <blah>_GM_to_T_init is not oriented correctly when overlaid on the template_GM_init > but the <blah>_GM_to_T is correctly oriented when overlaid on > template_GM_init. > > On Wed, Jun 29, 2016 at 10:44 AM, Matthew Webster < > [log in to unmask]> wrote: > >> 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 >> > > > > -- > Amanda Rodrigue > Doctoral Candidate > Franklin Foundation Neuroimaging Fellow > Psychology: Brain and Behavior Sciences > University of Georgia > -- Amanda Rodrigue Doctoral Candidate Franklin Foundation Neuroimaging Fellow Psychology: Brain and Behavior Sciences University of Georgia