2017-08-21 23:13 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>:

oh, sorry, i thought it was another file. yes, in the .dat file, the
value is the mean from inside the cluster. The input is the file you
passed with --y. from the help:

csdbase.y.ocn.dat - this is a summary of the input (y) over each
cluster. It has a column for each cluster. Each row is a subject. The
value is the average of the input (y) in each cluster. This is a
simple text file.

On 08/21/2017 05:07 PM, Patrícia Klobušiaková wrote:
> I meant this file: cache.th40.pos.sig.y.ocn.dat - it should contain
> the average value of each subject in each cluster. Are we writing
> about the same file?
>
> 2017-08-21 22:07 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto: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>
> > <mailto: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>
> <mailto: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>

> > <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
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