Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

Hi Bruce, When I run the last stage of the ex-vivo processing (recon-all -cortribbon -sphere -surfreg -cortparc -parcstats -subjid $SUBID -noaseg), the parcellation labels come out in the wrong place. I haven't been able to figure out why this is happening, so I was wondering if its possible that

Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

Hi John this is pretty puzzling. Is it causing any problems? tkmedit has been deprecated and it may just not be properly reading some header information or other. If nothing else is affected you can probably ignore it cheers Bruce On Mon, 29 Feb 2016, John Plass wrote: > Hi Bruce, > Thanks

Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

Hi Bruce, Thanks for your help. In freeview, the surface outline overlays on the volume correctly, and both the volume and the surface are oriented correctly in terms of R-L, A-P, and S-I axes. In tkmedit, the volume is oriented correctly, but the surface appears to be oriented with some of the

Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

Hi John when you say that they are oriented correctly in freeview, does that mean that they just overlay properly on the volume? Or that e.g. what freeview thinks is anterior is actually anterior, etc...? cheers Bruce On Mon, 29 Feb 2016, John Plass wrote: Hello Freesurfer Experts, I

[Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

Hello Freesurfer Experts, I wrote in recently about my parcellation troubles with an ex-vivo scan ( link ). Digging further, I've found that the surfaces I've produced following the Ex-Vivo recon instructions