HI Bruce, thanks so much for the reply. All of the surfaces we have needed to view to fix the Talairach (was OK), white matter, etc., have been there. It's only when I tried to look at the inflated brain during the WhiteMatterEdits step that something seemed to be missing. I will look at tkmedit and tkregister2 documentation to see if there are different ways to look for the inflated brain, but if anybody has suggestions on why I'm seeing only a tiny fraction it would be great. It sort of seems like a thresholding issue, but I have no idea why on little 2 square inch or so section of cortex is there and the rest is not, or I can't see it. The edges of what I see are very sharp and defined.
Jim On Sat, Apr 23, 2011 at 9:16 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Jim > Have you been able to view other surfaces in tksurfer? The situation you > describe sounds normal except for the display issue (e.g. The thalamus > should be interior to the white surface) > Cheers > Bruce > > > > On Apr 22, 2011, at 12:28 PM, jim kroger <jkk...@gmail.com> wrote: > > Hello, I am following the sequence in the "FreeSurfer Troubleshooting > Reconstruction Work Flow" instructions, and am at step 8, > FsTutorial/WhiteMatterEdits. It looks like the thalamus and corpus callosum > are included as white matter, and the pial surface surrounds some > subcortical structures. Assuming this is not correct, I decided to look at > the inflated surface as suggested in the referenced page " Making Edits to > the White Matter." Unfortunately when I issue: > > tksurfer wm1_edits_before rh inflated > > I only see what looks like a very small fraction of an egg shell for the > rh, and nothing for lh. Can I check somehow to see why I have almost no > inflated brain? > > Thanks, > Jim > > > -- > Cell: 575-571-8274 > Email: <jkk...@gmail.com>jkk...@gmail.com > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > 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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