I tried the recommended syntax below for looking at the surfaces and they look fine in all three views (coronal, horizontal and sagittal). And the surfaces seem consistent with other subjects I've processed.
Thanks, Elias On Tue, 2010-05-25 at 14:40 -0400, Douglas N Greve wrote: > And all the surfaces look ok? Try looking at them with > > tkmedit subjectname orig.mgz -seg aseg.mgz -surfs > > > > Elias Kersten wrote: > > The subcortical structures, brainstem, thalamus, cerebellum appear to be > > labeled correctly, but the rest of the brain and background are labeled > > as Left-Cerebral-White-Matter. > > > > > > On Tue, 2010-05-25 at 11:51 -0400, Douglas N Greve wrote: > > > >> How does the aparc+aseg.mgz look? > >> > >> Bruce Fischl wrote: > >> > >>> Not sure then. Krish: can you take a look? > >>> > >>> On Tue, 25 May 2010, Elias Kersten wrote: > >>> > >>> > >>> > >>>> I loaded in lh.white and rh.white and the white and pial surfaces look > >>>> fine, as does the aseg.mgz. > >>>> > >>>> Thanks, > >>>> Elias > >>>> > >>>> On Tue, 2010-05-25 at 09:08 -0400, Bruce Fischl wrote: > >>>> > >>>> > >>>>> Hi Elias, > >>>>> > >>>>> have you looked at the surfaces? Are they correct? > >>>>> > >>>>> Bruce > >>>>> On Mon, 24 May 2010, > >>>>> Elias Kersten wrote: > >>>>> > >>>>> > >>>>> > >>>>>> Hi, > >>>>>> > >>>>>> I am trying to run a subject through the entire recon-all pipeline. > >>>>>> However, I noticed the second to last step, "-wmparc", was taking a > >>>>>> very > >>>>>> long time (days). > >>>>>> > >>>>>> Looking over the data, the aparc+aseg.mgz file is almost all labeled as > >>>>>> "Left-Cerebral-White-Matter", including the background. Also, the > >>>>>> lh.ribbon.mgz file appears like a series of speckles, while the > >>>>>> rh.ribbon.mgz file looks normal. > >>>>>> > >>>>>> I'm not sure where this problem is originating from or what my next > >>>>>> steps should be. Any suggestions? > >>>>>> > >>>>>> Thanks, > >>>>>> Elias > >>>>>> > >>>>>> > >>>>>> _______________________________________________ > >>>>>> 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. > >>>>> > >>>>> > >>>>> > >>>> > >>>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >>> > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer