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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