Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

2017-03-02 Thread Xiuyi Wang
Hello Bruce, Thank you so much. I will try later. Xiuyi On 2 March 2017 at 17:11, Douglas N Greve 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 fo

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

2017-03-02 Thread Ruopeng Wang
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 wrote: > > Hi Bruce, > > Sorry for the misunderstanding. > > After showing the message "Did

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

2017-03-02 Thread Douglas N Greve
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

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

2017-03-02 Thread Douglas N Greve
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

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

2017-03-02 Thread Xiuyi Wang
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 rec

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

2017-03-02 Thread Xiuyi Wang
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 wrote: > That is not an error, the program should have run normally a

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

2017-03-02 Thread Douglas N Greve
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

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

2017-03-02 Thread Douglas N Greve
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/G

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

2017-03-02 Thread Xiuyi Wang
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=

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

2017-02-10 Thread Douglas Greve
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