Re: [Freesurfer] extract average thickness using label for every subject

OK, thank you. I appreciate your help.

Patricia

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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