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 >>> >>> >>> >>> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
