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 <fis...@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. > >
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