if you want to apply it to an individual you could map the label from fsaverage to that subject using mri_label2label

On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote:

Yes, it was. I just don't know, how to apply that on individual subjects.
Thanks!

2017-08-18 21:06 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
      I'll defer to Doug on this, but it looks like your label was
      created on fsaverage
      On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote:

            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_HCvs
            PD-M
            CIreal/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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