2 Mar
2017
2 Mar
'17
7:18 a.m.
Hi,
I am learning Group Analysis using FreeSurfer 5.3 on Linux system.
I followed the detailed instruction on the tutorial website.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
These are the commands that I typed:
freeview -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot :annot_outline=1: overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_thres hold=4,5 -viewport 3d
But I got an error message "Unrecognized sub-option flag ‘annot_outline’ " when running this command to visualize uncorrected significance map with freeview.
Douglas Greve told me it's because the outline only works on 6.0.
I am wondering what commands should I use to visualize the uncorrected significance map with freeview 5.3.
Thank you for your help.
On 10 February 2017 at 17:47, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
The outline only works on 6.0
On 2/10/17 11:57 AM, Xiuyi Wang wrote:
Hi,
I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system.
I followed the detailed instruction on the tutorial website.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
But I got an error message when running this command to visualize uncorrected significance map with freeview.
This is the command I typed:
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:a nnot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness -age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d
I received this error message:
Unrecognized sub-option flag ‘annot_outline’
I browsed the internet and found that “That option is only available in the development version of freeview. You can try removing :annot_ouline=1 from the command-line and turn it on manually from the GUI.”
So I deleted “:annot_outline=1” and the command line is :
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:o verlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d
But I received another error message:
Did not find any volume geometry information in the surface.
I found some researchers also have encountered this problem, but it has not been solved.
Could you please tell me the solution of the problem?
Thank you for your suggestion.
Best.
Xiuyi Wang
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
2 Mar
2 Mar
11:01 a.m.
New subject: Fwd: FreeSurfer group analysis visualize data
You can use that command, just remove annot_outline=1:
On 03/02/2017 07:18 AM, Xiuyi Wang wrote:
Hi,
I am learning Group Analysis using FreeSurfer 5.3 on Linux system.
I followed the detailed instruction on the tutorial website.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
These are the commands that I typed:
freeview -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1: overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg http://sig.mg/h:overlay_thres hold=4,5 -viewport 3d
But I got an error message "Unrecognized sub-option flag ‘annot_outline’ " when running this command to visualize uncorrected significance map with freeview.
Douglas Greve told me it's because the outline only works on 6.0.
I am wondering what commands should I use to visualize the uncorrected significance map with freeview 5.3.
Thank you for your help.
On 10 February 2017 at 17:47, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: The outline only works on 6.0 On 2/10/17 11:57 AM, Xiuyi Wang wrote:Hi, I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system. I followed the detailed instruction on the tutorial website. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> But I got an error message when running this command to visualize uncorrected significance map with freeview. This is the command I typed: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d I received this error message: Unrecognized sub-option flag ‘annot_outline’ I browsed the internet and found that “That option is only available in the development version of freeview. You can try removing :annot_ouline=1 from the command-line and turn it on manually from the GUI.” So I deleted “:annot_outline=1” and the command line is : freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d But I received another error message: Did not find any volume geometry information in the surface. I found some researchers also have encountered this problem, but it has not been solved. Could you please tell me the solution of the problem? Thank you for your suggestion. Best. Xiuyi Wang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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/
11:23 a.m.
New subject: Fwd: FreeSurfer group analysis visualize data
Hello Bruce,
Thank you for your reply.
I have tried to delete “:annot_outline=1: before and the command lines are:
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:o verlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d
But I received another error message: Did not find any volume geometry information in the surface.
So I still can not view the data.
Thanks.
Xiuyi
On 2 March 2017 at 16:01, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You can use that command, just remove annot_outline=1:
On 03/02/2017 07:18 AM, Xiuyi Wang wrote:
Hi,
I am learning Group Analysis using FreeSurfer 5.3 on Linux system.
I followed the detailed instruction on the tutorial website.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
These are the commands that I typed:
freeview -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.
annot:annot_outline=1:
overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg http://sig.mg/h:overlay_thres hold=4,5 -viewport 3d
But I got an error message "Unrecognized sub-option flag ‘annot_outline’ " when running this command to visualize uncorrected significance map with freeview.
Douglas Greve told me it's because the outline only works on 6.0.
I am wondering what commands should I use to visualize the uncorrected significance map with freeview 5.3.
Thank you for your help.
On 10 February 2017 at 17:47, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>wrote:
The outline only works on 6.0 On 2/10/17 11:57 AM, Xiuyi Wang wrote:Hi, I am learning GroupAnalysis using FreeSurfer 5.3 on Linuxsystem.
I followed the detailed instruction on the tutorial website. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>
But I got an error message when running this command to visualize uncorrected significance map with freeview. This is the command I typed: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg- thickness-age-Cor/sig.mgh:overlay_threshold=4,5
-viewport 3d I received this error message: Unrecognized sub-option flag ‘annot_outline’ I browsed the internet and found that “That option is only available in the development version of freeview. You can try removing :annot_ouline=1 from the command-line and turn it on manually from the GUI.” So I deleted “:annot_outline=1” and the command line is : freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig. mgh:overlay_threshold=4,5
-viewport 3d But I received another error message: Did not find any volume geometry information in the surface. I found some researchers also have encountered this problem, but it has not been solved. Could you please tell me the solution of the problem? Thank you for your suggestion. Best. Xiuyi Wang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
11:26 a.m.
New subject: Fwd: FreeSurfer group analysis visualize data
That is not an error, the program should have run normally after that. This has been fixed in v6.
On 03/02/2017 11:23 AM, Xiuyi Wang wrote:
Hello Bruce,
Thank you for your reply.
I have tried to delete “:annot_outline=1: before andthe command lines are:
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d
But I received another error message:
Did not find any volume geometry information in the surface.
So I still can not view the data.
Thanks.
Xiuyi
On 2 March 2017 at 16:01, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You can use that command, just remove annot_outline=1: On 03/02/2017 07:18 AM, Xiuyi Wang wrote: > Hi, > > I am learning Group Analysis using FreeSurfer 5.3 on Linux system. > > I followed the detailed instruction on the tutorial website. > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > > These are the commands that I typed: > > freeview > -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1: > overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg <http://sig.mg> > <http://sig.mg/>h:overlay_thres > hold=4,5 -viewport 3d > > But I got an error message "Unrecognized sub-option flag > ‘annot_outline’ " when running this command to visualize uncorrected > significance map with freeview. > > Douglas Greve told me it's because the outline only works on 6.0. > > I am wondering what commands should I use to visualize the uncorrected > significance map with freeview 5.3. > > Thank you for your help. > > > On 10 February 2017 at 17:47, Douglas 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: > > The outline only works on 6.0 > > > On 2/10/17 11:57 AM, Xiuyi Wang wrote: >> >> Hi, >> >> >> I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system. >> >> >> I followed the detailed instruction on the tutorial website. >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> >> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> >> >> >> But I got an error message when running this command to >> visualize uncorrected significance map with freeview. >> >> >> This is the command I typed: >> >> freeview -f >> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 >> -viewport 3d >> >> I received this error message: >> >> Unrecognized sub-option flag ‘annot_outline’ >> >> >> I browsed the internet and found that “That option is only >> available in the development version of freeview. You can try >> removing :annot_ouline=1 from the command-line and turn it on >> manually from the GUI.” >> >> >> So I deleted “:annot_outline=1” and the command line is : >> >> freeview -f >> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 >> -viewport 3d >> >> But I received another error message: >> >> Did not find any volume geometry information in the surface. >> >> >> I found some researchers also have encountered this problem, >> but it has not been solved. >> >> >> Could you please tell me the solution of the problem? >> >> Thank you for your suggestion. >> >> >> Best. >> >> Xiuyi Wang >> >> >> >> >> _______________________________________________ >> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > _______________________________________________ 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <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 <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/ <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 <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
--
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/
11:29 a.m.
New subject: Fwd: FreeSurfer group analysis visualize data
Hello Bruce,
The program stops after displaying this message.
So I guess your solution is to use FreeSurfer 6 and I am not able to view the data using FreeSurfer 5.3.
Thanks.
Xiuyi
On 2 March 2017 at 16:26, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
That is not an error, the program should have run normally after that. This has been fixed in v6.
On 03/02/2017 11:23 AM, Xiuyi Wang wrote:
Hello Bruce,
Thank you for your reply.
I have tried to delete “:annot_outline=1: before andthe command lines
are:
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:
overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig. mgh:overlay_threshold=4,5
-viewport 3d
But I received another error message:
Did not find any volume geometry information in the surface.
So I still can not view the data.
Thanks.
Xiuyi
On 2 March 2017 at 16:01, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You can use that command, just remove annot_outline=1: On 03/02/2017 07:18 AM, Xiuyi Wang wrote: > Hi, > > I am learning Group Analysis using FreeSurfer 5.3 on Linux system. > > I followed the detailed instruction on the tutorial website. > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > These are the commands that I typed: > > freeview > -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:
> overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg <http://sig.mg> > <http://sig.mg/>h:overlay_thres > hold=4,5 -viewport 3d > > But I got an error message "Unrecognized sub-option flag > ‘annot_outline’ " when running this command to visualizeuncorrected
> significance map with freeview. > > Douglas Greve told me it's because the outline only works on 6.0. > > I am wondering what commands should I use to visualize the uncorrected > significance map with freeview 5.3. > > Thank you for your help. > > > On 10 February 2017 at 17:47, Douglas 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: > > The outline only works on 6.0 > > > On 2/10/17 11:57 AM, Xiuyi Wang wrote: >> >> Hi, >> >> >> I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system. >> >> >> I followed the detailed instruction on the tutorial website. >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> >> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> >> >> But I got an error message when running this command to >> visualize uncorrected significance map with freeview. >> >> >> This is the command I typed: >> >> freeview -f >> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg- thickness-age-Cor/sig.mgh:overlay_threshold=4,5
>> -viewport 3d >> >> I received this error message: >> >> Unrecognized sub-option flag ‘annot_outline’ >> >> >> I browsed the internet and found that “That option is only >> available in the development version of freeview. You can try >> removing :annot_ouline=1 from the command-line and turn it on >> manually from the GUI.” >> >> >> So I deleted “:annot_outline=1” and the command line is : >> >> freeview -f >> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig. mgh:overlay_threshold=4,5
>> -viewport 3d >> >> But I received another error message: >> >> Did not find any volume geometry information in the surface. >> >> >> I found some researchers also have encountered this problem, >> but it has not been solved. >> >> >> Could you please tell me the solution of the problem? >> >> Thank you for your suggestion. >> >> >> Best. >> >> Xiuyi Wang >> >> >> >> >> _______________________________________________ >> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > _______________________________________________ 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<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 wassent
> to you in error and the e-mail contains patientinformation,
> please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <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 <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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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11:31 a.m.
New subject: Fwd: FreeSurfer group analysis visualize data
when you say it stops, you mean it crashes and returns control to the command line? Or that the GUI stays up but is unresponsive?
On 03/02/2017 11:29 AM, Xiuyi Wang wrote:
Hello Bruce,
The program stops after displaying this message.
So I guess your solution is to use FreeSurfer 6 and I am not able to view the data using FreeSurfer 5.3.
Thanks.
Xiuyi
On 2 March 2017 at 16:26, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That is not an error, the program should have run normally after that. This has been fixed in v6. On 03/02/2017 11:23 AM, Xiuyi Wang wrote: > Hello Bruce, > > Thank you for your reply. > > I have tried to delete “:annot_outline=1: before andthe command lines are: > > freeview -f > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 > -viewport 3d > > But I received another error message: > > Did not find any volume geometry information in the surface. > > So I still can not view the data. > > Thanks. > > Xiuyi > > On 2 March 2017 at 16:01, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > You can use that command, just remove annot_outline=1: > > > On 03/02/2017 07:18 AM, Xiuyi Wang wrote: > > Hi, > > > > I am learning Group Analysis using FreeSurfer 5.3 on Linux system. > > > > I followed the detailed instruction on the tutorial website. > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>> > > > > These are the commands that I typed: > > > > freeview > > > -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1: > > overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg <http://sig.mg> > <http://sig.mg> > > <http://sig.mg/>h:overlay_thres > > hold=4,5 -viewport 3d > > > > But I got an error message "Unrecognized sub-option flag > > ‘annot_outline’ " when running this command to visualize uncorrected > > significance map with freeview. > > > > Douglas Greve told me it's because the outline only works on 6.0. > > > > I am wondering what commands should I use to visualize the > uncorrected > > significance map with freeview 5.3. > > > > Thank you for your help. > > > > > > On 10 February 2017 at 17:47, Douglas 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: > > > > The outline only works on 6.0 > > > > > > On 2/10/17 11:57 AM, Xiuyi Wang wrote: > >> > >> Hi, > >> > >> > >> I am learning GroupAnalysis using FreeSurfer 5.3 on > Linux system. > >> > >> > >> I followed the detailed instruction on the tutorial > website. > >> > >> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > >> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>> > >> > >> > >> But I got an error message when running this command to > >> visualize uncorrected significance map with freeview. > >> > >> > >> This is the command I typed: > >> > >> freeview -f > >> > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 > >> -viewport 3d > >> > >> I received this error message: > >> > >> Unrecognized sub-option flag ‘annot_outline’ > >> > >> > >> I browsed the internet and found that “That option is only > >> available in the development version of freeview. You > can try > >> removing :annot_ouline=1 from the command-line and turn > it on > >> manually from the GUI.” > >> > >> > >> So I deleted “:annot_outline=1” and the command line is : > >> > >> freeview -f > >> > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 > >> -viewport 3d > >> > >> But I received another error message: > >> > >> Did not find any volume geometry information in the > surface. > >> > >> > >> I found some researchers also have encountered this > problem, > >> but it has not been solved. > >> > >> > >> Could you please tell me the solution of the problem? > >> > >> Thank you for your suggestion. > >> > >> > >> Best. > >> > >> Xiuyi Wang > >> > >> > >> > >> > >> _______________________________________________ > >> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > _______________________________________________ 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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/ <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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--
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/
11:50 a.m.
New subject: Fwd: FreeSurfer group analysis visualize data
Hi Bruce,
Sorry for the misunderstanding.
After showing the message "Did not find any volume geometry information in the surface", the FreeView shows this image. It is not the same as the tutorial website.
Is there anything I can do to view the data?
Thank you.
Xiuyi
On 2 March 2017 at 16:31, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
when you say it stops, you mean it crashes and returns control to the command line? Or that the GUI stays up but is unresponsive?
On 03/02/2017 11:29 AM, Xiuyi Wang wrote:
Hello Bruce,
The program stops after displaying this message.
So I guess your solution is to use FreeSurfer 6 and I am not able to view the data using FreeSurfer 5.3.
Thanks.
Xiuyi
On 2 March 2017 at 16:26, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That is not an error, the program should have run normally afterthat.
This has been fixed in v6. On 03/02/2017 11:23 AM, Xiuyi Wang wrote: > Hello Bruce, > > Thank you for your reply. > > I have tried to delete “:annot_outline=1: before andthe command lines are: > > freeview -f > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig. mgh:overlay_threshold=4,5
> -viewport 3d > > But I received another error message: > > Did not find any volume geometry information in the surface. > > So I still can not view the data. > > Thanks. > > Xiuyi > > On 2 March 2017 at 16:01, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > You can use that command, just remove annot_outline=1: > > > On 03/02/2017 07:18 AM, Xiuyi Wang wrote: > > Hi, > > > > I am learning Group Analysis using FreeSurfer 5.3 on Linux system. > > > > I followed the detailed instruction on the tutorial website. > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > > These are the commands that I typed: > > > > freeview > > > -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:
> > overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg <http://sig.mg> > <http://sig.mg> > > <http://sig.mg/>h:overlay_thres > > hold=4,5 -viewport 3d > > > > But I got an error message "Unrecognized sub-option flag > > ‘annot_outline’ " when running this command to visualize uncorrected > > significance map with freeview. > > > > Douglas Greve told me it's because the outline only works on 6.0. > > > > I am wondering what commands should I use to visualize the > uncorrected > > significance map with freeview 5.3. > > > > Thank you for your help. > > > > > > On 10 February 2017 at 17:47, Douglas 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: > > > > The outline only works on 6.0 > > > > > > On 2/10/17 11:57 AM, Xiuyi Wang wrote: > >> > >> Hi, > >> > >> > >> I am learning GroupAnalysis using FreeSurfer 5.3 on > Linux system. > >> > >> > >> I followed the detailed instruction on the tutorial > website. > >> > >> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> >> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> >> > >> > >> But I got an error message when running this command to > >> visualize uncorrected significance map withfreeview.
> >> > >> > >> This is the command I typed: > >> > >> freeview -f > >> > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg- thickness-age-Cor/sig.mgh:overlay_threshold=4,5
> >> -viewport 3d > >> > >> I received this error message: > >> > >> Unrecognized sub-option flag ‘annot_outline’ > >> > >> > >> I browsed the internet and found that “That option is only > >> available in the development version of freeview.You
> can try > >> removing :annot_ouline=1 from the command-line and turn > it on > >> manually from the GUI.” > >> > >> > >> So I deleted “:annot_outline=1” and the command line is : > >> > >> freeview -f > >> > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig. mgh:overlay_threshold=4,5
> >> -viewport 3d > >> > >> But I received another error message: > >> > >> Did not find any volume geometry information in the > surface. > >> > >> > >> I found some researchers also have encountered this > problem, > >> but it has not been solved. > >> > >> > >> Could you please tell me the solution of theproblem?
> >> > >> Thank you for your suggestion. > >> > >> > >> Best. > >> > >> Xiuyi Wang > >> > >> > >> > >> > >> _______________________________________________ > >> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > _______________________________________________ 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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<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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- 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/
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12:11 p.m.
New subject: Fwd: FreeSurfer group analysis visualize data
Click the button that says to show the annotation in outline (since you could not load it in outline mode
On 03/02/2017 11:50 AM, Xiuyi Wang wrote:
Hi Bruce,
Sorry for the misunderstanding.
After showing the message "Did not find any volume geometry information in the surface", the FreeView shows this image. It is not the same as the tutorial website.
Is there anything I can do to view the data?
Thank you.
Xiuyi
On 2 March 2017 at 16:31, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
when you say it stops, you mean it crashes and returns control to the command line? Or that the GUI stays up but is unresponsive? On 03/02/2017 11:29 AM, Xiuyi Wang wrote: > Hello Bruce, > > The program stops after displaying this message. > > So I guess your solution is to use FreeSurfer 6 and I am not able to > view the data using FreeSurfer 5.3. > > Thanks. > > Xiuyi > > On 2 March 2017 at 16:26, 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: > > That is not an error, the program should have run normally after that. > This has been fixed in v6. > > > On 03/02/2017 11:23 AM, Xiuyi Wang wrote: > > Hello Bruce, > > > > Thank you for your reply. > > > > I have tried to delete “:annot_outline=1: before andthe command > lines are: > > > > freeview -f > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 > > -viewport 3d > > > > But I received another error message: > > > > Did not find any volume geometry information in the surface. > > > > So I still can not view the data. > > > > Thanks. > > > > Xiuyi > > > > On 2 March 2017 at 16:01, 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: > > > > You can use that command, just remove annot_outline=1: > > > > > > On 03/02/2017 07:18 AM, Xiuyi Wang wrote: > > > Hi, > > > > > > I am learning Group Analysis using FreeSurfer 5.3 on Linux > system. > > > > > > I followed the detailed instruction on the tutorial website. > > > > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>> > > > > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>>> > > > > > > These are the commands that I typed: > > > > > > freeview > > > > > > -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1: > > > > overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg <http://sig.mg> > <http://sig.mg> > > <http://sig.mg> > > > <http://sig.mg/>h:overlay_thres > > > hold=4,5 -viewport 3d > > > > > > But I got an error message "Unrecognized sub-option flag > > > ‘annot_outline’ " when running this command to visualize > uncorrected > > > significance map with freeview. > > > > > > Douglas Greve told me it's because the outline only works > on 6.0. > > > > > > I am wondering what commands should I use to visualize the > > uncorrected > > > significance map with freeview 5.3. > > > > > > Thank you for your help. > > > > > > > > > On 10 February 2017 at 17:47, Douglas 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: > > > > > > The outline only works on 6.0 > > > > > > > > > On 2/10/17 11:57 AM, Xiuyi Wang wrote: > > >> > > >> Hi, > > >> > > >> > > >> I am learning GroupAnalysis using FreeSurfer 5.3 on > > Linux system. > > >> > > >> > > >> I followed the detailed instruction on the tutorial > > website. > > >> > > >> > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>> > > >> > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>>> > > >> > > >> > > >> But I got an error message when running this > command to > > >> visualize uncorrected significance map with freeview. > > >> > > >> > > >> This is the command I typed: > > >> > > >> freeview -f > > >> > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 > > >> -viewport 3d > > >> > > >> I received this error message: > > >> > > >> Unrecognized sub-option flag ‘annot_outline’ > > >> > > >> > > >> I browsed the internet and found that “That > option is only > > >> available in the development version of freeview. You > > can try > > >> removing :annot_ouline=1 from the command-line > and turn > > it on > > >> manually from the GUI.” > > >> > > >> > > >> So I deleted “:annot_outline=1” and the command > line is : > > >> > > >> freeview -f > > >> > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 > > >> -viewport 3d > > >> > > >> But I received another error message: > > >> > > >> Did not find any volume geometry information in the > > surface. > > >> > > >> > > >> I found some researchers also have encountered this > > problem, > > >> but it has not been solved. > > >> > > >> > > >> Could you please tell me the solution of the problem? > > >> > > >> Thank you for your suggestion. > > >> > > >> > > >> Best. > > >> > > >> Xiuyi Wang > > >> > > >> > > >> > > >> > > >> _______________________________________________ > > >> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. 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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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12:14 p.m.
New subject: Fwd: FreeSurfer group analysis visualize data
Hello Bruce,
Thank you so much.
I will try later.
Xiuyi
On 2 March 2017 at 17:11, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Click the button that says to show the annotation in outline (since you could not load it in outline mode
On 03/02/2017 11:50 AM, Xiuyi Wang wrote:
Hi Bruce,
Sorry for the misunderstanding.
After showing the message "Did not find any volume geometry information in the surface", the FreeView shows this image. It is not the same as the tutorial website.
Is there anything I can do to view the data?
Thank you.
Xiuyi
On 2 March 2017 at 16:31, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
when you say it stops, you mean it crashes and returns control to the command line? Or that the GUI stays up but is unresponsive? On 03/02/2017 11:29 AM, Xiuyi Wang wrote: > Hello Bruce, > > The program stops after displaying this message. > > So I guess your solution is to use FreeSurfer 6 and I am not ableto
> view the data using FreeSurfer 5.3. > > Thanks. > > Xiuyi > > On 2 March 2017 at 16:26, 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:
> > That is not an error, the program should have run normally after that. > This has been fixed in v6. > > > On 03/02/2017 11:23 AM, Xiuyi Wang wrote: > > Hello Bruce, > > > > Thank you for your reply. > > > > I have tried to delete “:annot_outline=1: before andthe command > lines are: > > > > freeview -f > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig. mgh:overlay_threshold=4,5
> > -viewport 3d > > > > But I received another error message: > > > > Did not find any volume geometry information in the surface. > > > > So I still can not view the data. > > > > Thanks. > > > > Xiuyi > > > > On 2 March 2017 at 16:01, 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: > > > > You can use that command, just remove annot_outline=1: > > > > > > On 03/02/2017 07:18 AM, Xiuyi Wang wrote: > > > Hi, > > > > > > I am learning Group Analysis using FreeSurfer 5.3 on Linux > system. > > > > > > I followed the detailed instruction on the tutorial website. > > > > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > > > > These are the commands that I typed: > > > > > > freeview > > > > > > -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:
> > > > overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg <http://sig.mg> > <http://sig.mg> > > <http://sig.mg> > > > <http://sig.mg/>h:overlay_thres > > > hold=4,5 -viewport 3d > > > > > > But I got an error message "Unrecognized sub-optionflag
> > > ‘annot_outline’ " when running this command tovisualize
> uncorrected > > > significance map with freeview. > > > > > > Douglas Greve told me it's because the outline only works > on 6.0. > > > > > > I am wondering what commands should I use to visualize the > > uncorrected > > > significance map with freeview 5.3. > > > > > > Thank you for your help. > > > > > > > > > On 10 February 2017 at 17:47, Douglas 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: > > > > > > The outline only works on 6.0 > > > > > > > > > On 2/10/17 11:57 AM, Xiuyi Wang wrote: > > >> > > >> Hi, > > >> > > >> > > >> I am learning GroupAnalysis using FreeSurfer 5.3 on > > Linux system. > > >> > > >> > > >> I followed the detailed instruction on the tutorial > > website. > > >> > > >> > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > >> > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > >> > > >> > > >> But I got an error message when running this > command to > > >> visualize uncorrected significance map with freeview. > > >> > > >> > > >> This is the command I typed: > > >> > > >> freeview -f > > >> > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg- thickness-age-Cor/sig.mgh:overlay_threshold=4,5
> > >> -viewport 3d > > >> > > >> I received this error message: > > >> > > >> Unrecognized sub-option flag ‘annot_outline’ > > >> > > >> > > >> I browsed the internet and found that “That > option is only > > >> available in the development version of freeview. You > > can try > > >> removing :annot_ouline=1 from the command-line > and turn > > it on > > >> manually from the GUI.” > > >> > > >> > > >> So I deleted “:annot_outline=1” and thecommand
> line is : > > >> > > >> freeview -f > > >> > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig. mgh:overlay_threshold=4,5
> > >> -viewport 3d > > >> > > >> But I received another error message: > > >> > > >> Did not find any volume geometry information in the > > surface. > > >> > > >> > > >> I found some researchers also have encountered this > > problem, > > >> but it has not been solved. > > >> > > >> > > >> Could you please tell me the solution of the problem? > > >> > > >> Thank you for your suggestion. > > >> > > >> > > >> Best. > > >> > > >> Xiuyi Wang > > >> > > >> > > >> > > >> > > >> _______________________________________________ > > >> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. 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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>> > > <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 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <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 <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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > > > > > _______________________________________________ > > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 Fax: 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 <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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- 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/
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12:12 p.m.
New subject: Fwd: FreeSurfer group analysis visualize data
That was just a informational message and it can be ignored. Try check “Show Outline only” on the GUI, since it should be invoked from the command-line in V6.
On Mar 2, 2017, at 11:50 AM, Xiuyi Wang xw1365@york.ac.uk wrote:
Hi Bruce,
Sorry for the misunderstanding.
After showing the message "Did not find any volume geometry information in the surface", the FreeView shows this image. It is not the same as the tutorial website.
<group_analysis.png> Is there anything I can do to view the data?
Thank you.
Xiuyi
On 2 March 2017 at 16:31, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote: when you say it stops, you mean it crashes and returns control to the command line? Or that the GUI stays up but is unresponsive?
On 03/02/2017 11:29 AM, Xiuyi Wang wrote:
Hello Bruce,
The program stops after displaying this message.
So I guess your solution is to use FreeSurfer 6 and I am not able to view the data using FreeSurfer 5.3.
Thanks.
Xiuyi
On 2 March 2017 at 16:26, 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:
That is not an error, the program should have run normally after that. This has been fixed in v6. On 03/02/2017 11:23 AM, Xiuyi Wang wrote: > Hello Bruce, > > Thank you for your reply. > > I have tried to delete “:annot_outline=1: before andthe command lines are: > > freeview -f > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 > -viewport 3d > > But I received another error message: > > Did not find any volume geometry information in the surface. > > So I still can not view the data. > > Thanks. > > Xiuyi > > On 2 March 2017 at 16:01, 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: > > You can use that command, just remove annot_outline=1: > > > On 03/02/2017 07:18 AM, Xiuyi Wang wrote: > > Hi, > > > > I am learning Group Analysis using FreeSurfer 5.3 on Linux system. > > > > I followed the detailed instruction on the tutorial website. > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>> > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>>> > > > > These are the commands that I typed: > > > > freeview > > > -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1: > > overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg <http://sig.mg/> <http://sig.mg <http://sig.mg/>> > <http://sig.mg <http://sig.mg/>> > > <http://sig.mg/ <http://sig.mg/>>h:overlay_thres > > hold=4,5 -viewport 3d > > > > But I got an error message "Unrecognized sub-option flag > > ‘annot_outline’ " when running this command to visualize uncorrected > > significance map with freeview. > > > > Douglas Greve told me it's because the outline only works on 6.0. > > > > I am wondering what commands should I use to visualize the > uncorrected > > significance map with freeview 5.3. > > > > Thank you for your help. > > > > > > On 10 February 2017 at 17:47, Douglas 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: > > > > The outline only works on 6.0 > > > > > > On 2/10/17 11:57 AM, Xiuyi Wang wrote: > >> > >> Hi, > >> > >> > >> I am learning GroupAnalysis using FreeSurfer 5.3 on > Linux system. > >> > >> > >> I followed the detailed instruction on the tutorial > website. > >> > >> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>> > >> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>>> > >> > >> > >> But I got an error message when running this command to > >> visualize uncorrected significance map with freeview. > >> > >> > >> This is the command I typed: > >> > >> freeview -f > >> > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 > >> -viewport 3d > >> > >> I received this error message: > >> > >> Unrecognized sub-option flag ‘annot_outline’ > >> > >> > >> I browsed the internet and found that “That option is only > >> available in the development version of freeview. You > can try > >> removing :annot_ouline=1 from the command-line and turn > it on > >> manually from the GUI.” > >> > >> > >> So I deleted “:annot_outline=1” and the command line is : > >> > >> freeview -f > >> > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 > >> -viewport 3d > >> > >> But I received another error message: > >> > >> Did not find any volume geometry information in the > surface. > >> > >> > >> I found some researchers also have encountered this > problem, > >> but it has not been solved. > >> > >> > >> Could you please tell me the solution of the problem? > >> > >> Thank you for your suggestion. > >> > >> > >> Best. > >> > >> Xiuyi Wang > >> > >> > >> > >> > >> _______________________________________________ > >> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > _______________________________________________ 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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>> > <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 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <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 <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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Fax: 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 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/ 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 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
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freesurfer@nmr.mgh.harvard.edu
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participants (3)
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Douglas N Greve -
Ruopeng Wang -
Xiuyi Wang