that will generate a parcellation on the individual subject surface of Thomas Yeo's 17-network clustering. It won't do anything with the thickness though. What are you trying to do?
On Tue, 29 Sep 2015, Ali Radaideh wrote:
mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh
--sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot
--tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot
scz10 is my subject name
On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve <greve@nmr.mgh.harvard.edu>
wrote:
what is your surf2surf command?
On 9/28/15 5:11 PM, Ali Radaideh wrote:
Dear Douglas,
Thanks for your email. I meant to say that after running the
recon-all, i ran the sur2surf command to get the cortical
parcellation using Thomas Yeo Atlas.
I thought that the extracted cortical thickness after running
the surf2surf command will be different from the one extracted
before running the command. But, Bruce kindly replied to my
email saying that it is the same if it is calculated on
vertex-wise basis.
Thanks,
Ali
On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu> wrote:
I can't understand what you are asking. Can you
elaborate?
On 09/28/2015 01:51 PM, Ali Radaideh wrote:
> Thanks alot Douglas,
>
> Yes it is there but after checking it many time I
found it corrupted
> for some subjects due to copying them many times
between machines.
>
> But May I ask you some thing related. I have just
posted a question
> regarding getting the cortical thickness after
running the surf2surf
> command (17 networks cortical parcellation). Now I
found the stats
> file not updated after running this command only
the annotation files
> in label folder.
[rh.Yeo2011_17Networks_N1000.annot]. We thought that
> using Yeo Atlas will give slightly different
cortical thickness, are
> we correct?
>
> Thanks,
> Ali
>
> On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> does that file exist?
>
> On 09/28/2015 01:05 PM, Ali Radaideh wrote:
> > Dear FreeSurfer experts,
> > After finishing the recon-all, I am trying
to extract the cortical
> > thickness for each subject and group them
into one table but
> > unfortunately i keep getting the following
error:
> >
> > rh.aparc.DKTatlas40.stats is not found or is
too small to be a
> valid
> > statsfile
> > Use --skip flag to automatically skip bad
stats files
> >
> > i tried to change the stats file (e.g I used
aparc.a2009s) but I got
> > the same error.
> >
> > I tried each brain alone and also got the
same error.
> >
> > Any ideas please
> > Thanks,
> > Ali
> >
> > --
> > /Ali M. Al-Radaideh. PhD
> > Head of Department of Medical Imaging
> > Vice Dean of the Faculty of Allied Health
Sciences
> > The Hashemite University,
> > Zarqa, Jordan
> > W.phone +962 5 3903333 ext.5422, 5355, 5364
> > Email: ali.radaideh@hu.edu.jo
<mailto:ali.radaideh@hu.edu.jo>
> <mailto:ali.radaideh@hu.edu.jo
<mailto:ali.radaideh@hu.edu.jo>>
> > /
> > /webpage:
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
> >
> >
> >
> >
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
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<mailto:greve@nmr.mgh.harvard.edu>
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> /Ali M. Al-Radaideh. PhD
> Head of Department of Medical Imaging
> Vice Dean of the Faculty of Allied Health Sciences
> The Hashemite University,
> Zarqa, Jordan
> W.phone +962 5 3903333 ext.5422, 5355, 5364
> Email: ali.radaideh@hu.edu.jo
<mailto:ali.radaideh@hu.edu.jo>
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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--
Ali M. Al-Radaideh. PhD
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radaideh@hu.edu.jo
webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
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The information in this e-mail is intended only for the person to whom
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contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
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but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
--
Ali M. Al-Radaideh. PhD
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radaideh@hu.edu.jo
webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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