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
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 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.
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 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
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 <greve@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 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
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 greve@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
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.lab@gmail.comwrote:
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 < greve@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 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
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 greve@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
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.lab@gmail.com mailto:taylor.cnos.lab@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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> >> 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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 <greve@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.lab@gmail.commailto: taylor.cnos.lab@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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> >> 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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@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/ _______________________________________________ Freesurfer mailing list 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 greve@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/
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 <greve@nmr.mgh.harvard.edu mailto:greve@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.lab@gmail.com <mailto:taylor.cnos.lab@gmail.com> <mailto:taylor.cnos.lab@gmail.com <mailto:taylor.cnos.lab@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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/
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 <greve@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 < greve@nmr.mgh.harvard.edu mailto:greve@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.lab@gmail.com <mailto:taylor.cnos.lab@gmail.com> <mailto:taylor.cnos.lab@gmail.com <mailto:taylor.cnos.lab@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@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/
oh, if the lh annot is being loaded onto the rh surface, then that will definitely create the tye-died appearance. Maybe Ruopeng can weigh in on the freeview issue.
doug
On 12/18/2013 04:53 PM, Laura Taylor wrote:
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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.lab@gmail.com <mailto:taylor.cnos.lab@gmail.com> <mailto:taylor.cnos.lab@gmail.com <mailto:taylor.cnos.lab@gmail.com>> <mailto:taylor.cnos.lab@gmail.com <mailto:taylor.cnos.lab@gmail.com> <mailto:taylor.cnos.lab@gmail.com <mailto:taylor.cnos.lab@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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>> <mailto: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>> <mailto: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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel: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>> <tel: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> <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> <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>> <mailto: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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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/ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@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/
freesurfer@nmr.mgh.harvard.edu
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Chris Watson -
Douglas N Greve -
Laura Taylor