Hi Douglas, I would go to the annotation drop down menu in freeview, select l/rh.aparc.a2009s.annot and then it would freeze. I can't seem to reproduce that problem today, but for every subject that I load an annotation for now, the rh annotation loads properly, but the lh annotation loads onto the right hemisphere and is tye-died in appearance.
Thanks, Laura On Tue, Dec 17, 2013 at 11:57 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > > So when you say you cannot load it, what do you mean? > doug > > > > > On 12/17/2013 02:55 PM, Laura Taylor wrote: > >> Hi Douglas, >> >> I checked the status of each subject once recon-all was completed (by >> looking in the terminal window before I closed it). Each of my roughly 90 >> subects had the message "/recon-all -s/ subjectID /finished without error/ >> at date and time". >> >> >> When I look at the recon-all.log file the same message is there at the >> end. Is there somewhere else where i should look for an error message?? >> >> Thank you, >> Laura >> >> >> On Tue, Dec 17, 2013 at 10:44 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> >> For the subject that you were not able to load the annot, did you >> check the recon-all log file? Did recon-all complete properly? >> doug >> >> >> On 12/17/2013 01:35 PM, Laura Taylor wrote: >> >> Hi again, Douglas and freesurfer experts. >> >> Unfortunately my problem cannot be explained by having made >> manual edits and then not finishing recon-all. When I load >> subjects that I did not manually edit, I am either unable to >> load an annotation file (specifically r/lh.aparc.a2009s.annot) >> at all, or I can load it but have problems with the output. >> When I am able to load an image I get a the same tye-died >> appearing surface for one hemisphere (and it is projected onto >> the opposite hemisphere that the label is for) or I get a >> proper surface when I load the label for the other hemisphere >> (and it appears on the correct hemisphere). >> >> Can you help at all with this? >> >> Thank you, >> >> Laura >> >> >> On Tue, Dec 10, 2013 at 11:45 AM, Laura Taylor >> <taylor.cnos....@gmail.com <mailto:taylor.cnos....@gmail.com> >> <mailto:taylor.cnos....@gmail.com >> >> <mailto:taylor.cnos....@gmail.com>>> wrote: >> >> Hi, yes thank you both. That is exactly what the problem was. >> >> Laura >> >> >> On Tue, Dec 10, 2013 at 11:12 AM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> >> Yep, looks like your annot is out of sync with the >> surfaces >> >> On 12/10/2013 01:51 PM, Chris Watson wrote: >> > I've seen this happen after making manual edits and >> then not >> finishing >> > a re-run of recon-all. >> > Chris >> > >> > On 12/10/2013 02:00 PM, Laura Taylor wrote: >> >> Hi, >> >> >> >> I'm trying to load lh.aparc.a2009s.annot onto the >> lh pial >> surface of >> >> a subject. When I use the freeview gui and select >> >> lh.aparc.a2009s.annot under the annotations menu a >> strange >> >> multicolored surface is loaded. It looks like >> something >> that has >> >> been tie-dyed and not like the examples of parcellation >> that are >> >> shown on some of the freesurfer pages. >> >> >> >> I have attached a screenshot of the output that I get. >> >> >> >> Any help would be appreciated. >> >> >> >> Thank you, >> >> >> >> Laura >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> >> <mailto: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 >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> >> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 >> >> <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard. >> edu/facility/filedrop/index.html> >> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> >> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> > -- > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >
_______________________________________________ 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.
