[Freesurfer] Fwd: Error of fsaverage unknown during mri_glmfit
Hello FreeSurfer Developers, I am attempting to repeat the group analysis with the tutorial data on FreeSurfer website, as described on the FsTutorial/GroupAnalysis ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). But I received an error message when running the mri_glmfit command lines. At first, the command lines that I types: mri_glmfit --y xiuyi_lh_thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx \ —-surf fsaverage lh \—-cortex —glmdir xiuyi_lh.gender_age.glmdir Errors: MRISread(/Users/xiuyi/Documents/tutorial_data/buckner_data/tutorial_subjs/ group_analysis_tutorial/glm/fsaverage/surf/lh. —-cortex): could not open file No such file or directory mri_glmfit: could not read surface /Users/xiuyi/Documents/tutorial_data/ buckner_data/tutorial_subjs/group_analysis_tutorial/glm/fsaverage/surf/lh. —-cortex No such file or directory Then I changed the command lines, replacing "surf fsaverage lh.white" with "surf fsaverage lh". The exact command lines are: mri_glmfit --y xiuyi_lh_thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx \ —-surf fsaverage lh.white \—-cortex —glmdir xiuyi_lh.gender_age.glmdir The error message is: gdfReadHeader: reading gender_age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 57.175 26.6006 Class Means of each Continuous Variable 1 genderFemale 59.1429 2 genderMale 55. INFO: gd2mtx_method is dods *ERROR: Option fsaverage unknown.* I have searched the list and found this type of error has been reported by another person but no reply was found.(https://mail.nmr.mgh. harvard.edu/pipermail//freesurfer/2010-May/014401.html) 1) FreeSurfer Version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Flatform: macOS Sierra version 10:12 Thank you for your reply. Xiuyi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fwd: FreeSurfer group analysis visualize data
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 $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:o verlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d But I received another error message: Did not find any volume geometry information in the surface. I found some researchers also have encountered this problem, but it has not been solved. Could you please tell me the solution of the problem? Thank you for your suggestion. Best. Xiuyi Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data
Hi, I am learning Group Analysis using FreeSurfer 5.3 on Linux system. I followed the detailed instruction on the tutorial website. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis These are the commands that I typed: freeview -f$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 > 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 >> listfreesur...@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. >> >> > ___ 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.
Re: [Freesurfer] 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 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 > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot: > overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig. > mgh:overlay_threshold=4,5 > > -viewport 3d > > > > But I received another error message: > > > > Did not find any volume geometry information in the surface. > > > > So I still can not view the data. > > > > Thanks. > > > > Xiuyi > > > > On 2 March 2017 at 16:01, Douglas N Greve > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > You can use that command, just remove annot_outline=1: > > > > > > On 03/02/2017 07:18 AM, Xiuyi Wang wrote: > > > Hi, > > > > > > I am learning Group Analysis using FreeSurfer 5.3 on Linux system. > > > > > > I followed the detailed instruction on the tutorial website. > > > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > >> > > > > > > These are the commands that I typed: > > > > > > freeview > > > > > -f$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 > > > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@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 m
Re: [Freesurfer] 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 $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:o verlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d But I received another error message: Did not find any volume geometry information in the surface. So I still can not view the data. Thanks. Xiuyi On 2 March 2017 at 16:01, Douglas N Greve wrote: > You can use that command, just remove annot_outline=1: > > > On 03/02/2017 07:18 AM, Xiuyi Wang wrote: > > Hi, > > > > I am learning Group Analysis using FreeSurfer 5.3 on Linux system. > > > > I followed the detailed instruction on the tutorial website. > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > > > These are the commands that I typed: > > > > freeview > > -f$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 > > mailto:gr...@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/mailm
Re: [Freesurfer] 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 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 > <mailto:gr...@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 > > mailto:gr...@nmr.mgh.harvard.edu> > > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > > > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > > <mailto:gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu> > > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@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.
[Freesurfer] mris_convert Segmentation fault.
External Email - Use Caution
Hi,
I am planning to convert an ASCII file to a gifti file using mris_convert.
I am using FreeSurfer 5.3 on Linux 9 stretch.
The ASCII file includes the vertex id , its MNI305 coordinates and p
value. Vertex id is 0-based, from 0 to 20483.
I used fsaverage5 as the template and extracted the coordinates of each
vertex on that surface using the following commands.
SW = SurfStatReadSurf({[template_path
'fsaverage5/surf/lh.white'],[template_path
'fsaverage5/surf/rh.white']});
coordis = SurfStatInd2Coord(vertex_id, SW)
Then I typed
mris_convert file_SW.asc lh_SW.gii # because I learnt that generally
surface files starts with a hemisphere specifier.
or
mris_convert file_SW.asc SW.gii
The error message is ERROR: MRISalloc: nfaces=-36 < 0. I guess one possible
reason is the first coordinate of the first index is negative (-36). So I
generated a new file, replacing all the negative x coordinates with its
absolute value - unthreshold_file_SW_abs.asc and then typed:
mris_convert SW_abs.asc SW_abs.gii
This time the error message is Segmentation fault.
Could you please give me any clue how to solve this problem?
I also tried this command and it works well, suggesting I can use
mris_convert smoothly.
mris_convert -v lh.white lh.white.neighbors.asc #
Many thanks in advance,
Xiuyi Wang
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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.
