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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.