Hey Bruce, I've uploaded the data via ftp to: transfer/incoming/EK_umn_052710.tar.gz
Please let me know if I can supply any further information. Thanks for taking a look! -Elias On Thu, 2010-05-27 at 10:58 -0400, Bruce Fischl wrote: > no idea. Can you tar and gzip the subject and put it on our filedrop? > > thanks > Bruce > On > Thu, 27 May 2010, Elias Kersten wrote: > > > 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
