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 > From: 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 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.
