Hi Bruce,
so I tried fmri/galadriel/_personal/riha_klobusiakova$ mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness s0110B rh but I get the same error - label point 178 has vertex number = 154391, but surface only has 140611 vertices
My labels were created by mri_surfcluster --in $SUBJECTS_DIR/glm/rh.Apgem1_FSGD_HCvsPD-MCIreal.glmdir/Apgem1_FSGD_HCvsPD-MCIreal/sig.mgh --subject fsaverage --hemi rh --thmin 4 --thmax 5 --thsign pos --sign pos --sum $SUBJECTS_DIR/glm/analyza/HCvsPD-MCIunc_rh --o /$SUBJECTS_DIR/glm/analyza/clvals --ocn /$SUBJECTS_DIR/glm/analyza/clnums --olab /$SUBJECTS_DIR/glm/analyza/cllabel
Am I missing something here? Should I create labels for every subject? I thought sig.mgh belongs to fsaverage, that's why I wanted to use rh. thickness.fwhm10.fsaverage.mgh. I wanted to create something similar to y.ocn.dat which I get after multiple comparisons correction (but for clusters significant at lower threshold).
Thanks,
Patricia
2017-08-18 2:58 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Patricia
try using the subject's rh.thickness instead (it is in subject space, as I think is your label)
cheers Bruce
On Thu, 17 Aug 2017, Patrícia Klobušiaková wrote:
Dear Freesurfer experts,
I have labels representing clusters that I created using mri_surfcluster on sig.mgh file using a specific threshold. Now I want to use these labels to extract average thickness values for every subject. I tried to use mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh s0110B rh to calculate it for one subject, but it doesn't work - I get error because the number of vertices in subject's file rh.thickness.fwhm10.fsaverage. mgh doesn't match surface. I should use fsaverage as a subject, right? So I tried mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh fsaverage rh but then I get error, that it cannot read fsaverage/mri/wm.mgz file. The wm.mgz file isn't in fsaverage folder.
How can I calculate this?
Thanks for your help!
Patricia
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