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Hi, I'm in the process of uploading. Her are the subjects that had the orientation issue: FSL #/Subid 25/HCC_1213 50/LCC_1118 51/LCC_1121 66/LCC_1191 84/SZ_1107 85/SZ_1111 89/SZ_1187 100/SZ_1254 112/SZ_1310 On Tue, Jul 5, 2016 at 9:54 AM, Matthew Webster < [log in to unmask]> wrote: > Hello, > This sounds quite odd, I think we need to have a look at all the files > - can you tar and upload the whole directory to the oxfile link ( > https://oxfile.ox.ac.uk/oxfile/work/extBox?id=700839B35190E48BF )? > > Kind Regards > Matthew > > On 5 Jul 2016, at 14:15, Amanda Rodrigue <[log in to unmask] > <[log in to unmask]>> wrote: > > 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 > > > -- Amanda Rodrigue Doctoral Candidate Franklin Foundation Neuroimaging Fellow Psychology: Brain and Behavior Sciences University of Georgia