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
