Hi Ruopeng and freesurfer folks,
I am still having trouble loading annotations in freeview, similar to what I mentioned before. When I load 'rh.aparc.a2009s.annot' in freeview, the annotation loads onto the LEFT hemisphere and is tye-died in appearance. In contrast, 'lh.aparc.a2009s.annot' loads correctly onto the left hemisphere and looks normal.
I have had this problem with many of my subjects. Can you help with this??
Thank you,
Laura
---------- Forwarded message ----------
Date: Thu, Jan 2, 2014 at 9:53 AM Subject: Fwd: [Freesurfer] Problems dipslaying annotations in freeview To: rpwang@nmr.mgh.harvard.edu
Hi Ruopeng,
I am forwarding the messages I sent to the freesurfer mailing list and that Doug suggested I ask you.
Basically when I try and load an annotation in freeview, the rh loads properly (looks normal and is on the correct hemisphere), but the lh loads onto the rh and is tye-died in appearance.
Can you help with this?
Thanks,
Laura
---------- Forwarded message ---------- From: Douglas N Greve greve@nmr.mgh.harvard.edu Date: Wed, Dec 18, 2013 at 2:14 PM Subject: Re: [Freesurfer] Problems dipslaying annotations in freeview
Cc: freesurfer@nmr.mgh.harvard.edu
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 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 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 Taylorwrote:
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/
Did you select the right hemisphere when you load rh.annot? Whatever you do from the control panel on the left, it is applied to the selected layer, which is the one highlighted in the layer list.
Ruopeng
On 02/12/2014 01:16 PM, Laura Taylor wrote:
Hi Ruopeng and freesurfer folks,
I am still having trouble loading annotations in freeview, similar to what I mentioned before. When I load 'rh.aparc.a2009s.annot' in freeview, the annotation loads onto the LEFT hemisphere and is tye-died in appearance. In contrast, 'lh.aparc.a2009s.annot' loads correctly onto the left hemisphere and looks normal.
I have had this problem with many of my subjects. Can you help with this??
Thank you,
Laura
---------- Forwarded message ----------
Date: Thu, Jan 2, 2014 at 9:53 AM Subject: Fwd: [Freesurfer] Problems dipslaying annotations in freeview To: rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu
Hi Ruopeng,
I am forwarding the messages I sent to the freesurfer mailing list and that Doug suggested I ask you.
Basically when I try and load an annotation in freeview, the rh loads properly (looks normal and is on the correct hemisphere), but the lh loads onto the rh and is tye-died in appearance.
Can you help with this?
Thanks,
Laura
---------- Forwarded message ---------- From: *Douglas N Greve* <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Date: Wed, Dec 18, 2013 at 2:14 PM Subject: Re: [Freesurfer] Problems dipslaying annotations in freeview
Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
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 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> <mailto: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>> <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: 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 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 >>>> 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>>> <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 <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>>> <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 <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>>> <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 <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>>> <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 <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>>> <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 <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>>> <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 <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> <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> <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>>> <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 <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/ -- 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/
Excellent! That is the answer. Thank you very much.
Laura
On Wed, Feb 12, 2014 at 10:20 AM, Ruopeng Wang rpwang@nmr.mgh.harvard.eduwrote:
Did you select the right hemisphere when you load rh.annot? Whatever you do from the control panel on the left, it is applied to the selected layer, which is the one highlighted in the layer list.
Ruopeng
On 02/12/2014 01:16 PM, Laura Taylor wrote:
Hi Ruopeng and freesurfer folks,
I am still having trouble loading annotations in freeview, similar to what I mentioned before. When I load 'rh.aparc.a2009s.annot' in freeview, the annotation loads onto the LEFT hemisphere and is tye-died in appearance. In contrast, 'lh.aparc.a2009s.annot' loads correctly onto the left hemisphere and looks normal.
I have had this problem with many of my subjects. Can you help with this??
Thank you,
Laura
---------- Forwarded message ----------
Date: Thu, Jan 2, 2014 at 9:53 AM Subject: Fwd: [Freesurfer] Problems dipslaying annotations in freeview To: rpwang@nmr.mgh.harvard.edu
Hi Ruopeng,
I am forwarding the messages I sent to the freesurfer mailing list and that Doug suggested I ask you.
Basically when I try and load an annotation in freeview, the rh loads properly (looks normal and is on the correct hemisphere), but the lh loads onto the rh and is tye-died in appearance.
Can you help with this?
Thanks,
Laura
---------- Forwarded message ---------- From: Douglas N Greve greve@nmr.mgh.harvard.edu Date: Wed, Dec 18, 2013 at 2:14 PM Subject: Re: [Freesurfer] Problems dipslaying annotations in freeview
Cc: freesurfer@nmr.mgh.harvard.edu
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 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 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 Taylorwrote:
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%3E 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%3E < http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html%3E
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/-- 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@nmr.mgh.harvard.edu
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Laura Taylor -
Ruopeng Wang