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 the surface registration is starting with the surface misoriented like it is in tkmedit. 

John


---
John Plass
Ph.D. Candidate
Visual Perception, Neuroscience, and Cognition Lab
Northwestern University

On Tue, Mar 1, 2016 at 7:38 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
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 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 axes
swapped. E.g., from the coronal view in tkmedit, I see a coronal slice of
the volume, but the outline of an axial slice of the surface, with the
anterior part pointing down.

John




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