2017-08-21 22:07 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>:

The numbers in that file are just indices indicating the cluster number
(eg, 1=cluster1, 2=cluster2, etc). They are the output of the multiple
comparisons correction, so they are gennerated from all the input

On 08/18/2017 03:28 PM, Patrícia Klobušiaková wrote:
> OK, this works now, when I map the label on subject and use
> rh.thickness as an input. Don't you know why it didn't work before,
> when I had label from fsaverage and was trying to use
> rh.thickness.fwhm10.fsaverage.mgh? Aren't they both in fsaverage space?
>
> And can I ask you one more question - how exactly are numbers
> iny.ocn.dat calculated (which files are used as a input)?
>
>
>
> 2017-08-18 21:14 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>:
>
> 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 <mailto: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

> <mailto: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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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