Was the path of the overlay file correct? It looks like it can’t find the file. Try providing the full path of the overlay file in the freeview command.
Best, Ruopeng > On Sep 28, 2015, at 6:46 PM, Dusan Hirjak <dusanhir...@hotmail.com> wrote: > > Many thanks!!!, yes, freeview has opened, but I am still not seeing any > results, just the "lh.inflated" > > It says: "Failed to load surface overlay" > > and than I got the following message: > > bash-3.2$ freeview -f > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh:overlay_threshold=4,5 > -viewport 3d > 2015-09-29 00:41:53.887 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.889 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.905 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.906 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.921 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.922 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable > Did not find any volume geometry information in the surface > ø;C 8Íÿ¿ø;C È+Àá > > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, > -1): could not open file > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, > -1): could not open file > could not read overlay data from > /users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, > -1): could not open file > 2015-09-29 00:42:02.445 Freeview[22049:303] modalSession has been exited > prematurely - check for a reentrant call to endModalSession: > > I dont understand the problem. Do you have any ideas??? > > Thank you! > > Dusan > > > > > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > From: gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Date: Mon, 28 Sep 2015 18:33:50 -0400 > > Subject: Re: [Freesurfer] 3_group_comparison > > > > I think it needs a -f before the surface > > > > On 09/28/2015 06:27 PM, Dusan Hirjak wrote: > > > Many thanks, yes, it did work well. > > > > > > But, than I ran "freeview > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 > > > > > > -viewport 3d" > > > > > > and got the following message: > > > > > > bash-3.2$ freeview > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 > > > > > > -viewport 3d > > > > > > 2015-09-29 00:23:47.366 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.367 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.385 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.386 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.399 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.400 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.420 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.421 Freeview[22019:303] invalid drawable > > > > > > Unrecognized sub-option flag 'annot=aparc.annot'. > > > > > > > > > Freeview has opened, but it showed no results at all:-( > > > > > > > > > What should I do? I read that one has to upgrade the newest > > > freeview-version? Is it possible to get the newest version without > > > installing freesurfer again? > > > > > > Many thanks! > > > > > > Dusan > > > > > > > > > ------------------------------------------------------------------------ > > > Date: Mon, 28 Sep 2015 11:35:50 -0400 > > > From: gr...@nmr.mgh.harvard.edu > > > To: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] 3_group_comparison > > > > > > Did you include the back slashes in your command? If so, remove them > > > and retry. > > > > > > On 9/25/15 7:11 PM, Dusan Hirjak wrote: > > > > > > Dear Freesurfer experts, > > > > > > I am trying to compare 3 groups (aut, sch, ges) according to > > > thickness, area and LGI at once (omnibus test). > > > > > > I did run the following command: > > > > > > mris_preproc --fsgd NSS_3_GR.fsgd \ --cache-in > > > thickness.fwhm15.fsaverage \ --target fsaverage --hemi lh \ --out > > > lh.NSS_3_GR.thickness.15.mgh > > > > > > > > > This step did work properly:-) > > > > > > > > > > > > Now, Im trying to run the following command, but it does not work: > > > > > > > > > mri_glmfit \ --y lh.NSS_3_GR.thickness.15.mgh \ --fsgd > > > NSS_3_GR.fsgd dods\ --C contrasts.mtx \ --surf fsaverage lh \ > > > --cortex \ --glmdir NSS_3_GR.glmdir > > > > > > > > > I got this message: "ERROR: Option--y unknown" > > > > > > > > > What am I doing wrong? > > > > > > > > > Thank you for your help! > > > > > > > > > > > > Best regards > > > > > > > > > Dusan > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > 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 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 > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@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 > _______________________________________________ > 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 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.
