One additional note: I had previously processed this subject through FreeSurfer version 4.0.2 without any problems. For some reason this problem only occurred upon reprocessing with version 4.5.0. I batch processed this subject with about 50 others, and the other subjects look fine.
Any other suggestions? Thanks, Elias On Tue, 2010-05-25 at 14:25 -0500, Elias Kersten wrote: > 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
