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
<gr...@nmr.mgh.harvard.edu <mailto:gr...@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
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@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.radai...@hu.edu.jo
<mailto:ali.radai...@hu.edu.jo> <mailto:ali.radai...@hu.edu.jo
<mailto:ali.radai...@hu.edu.jo>>
> <mailto:ali.radai...@hu.edu.jo
<mailto:ali.radai...@hu.edu.jo> <mailto:ali.radai...@hu.edu.jo
<mailto:ali.radai...@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
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
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>
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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.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo>
<mailto:ali.radai...@hu.edu.jo <mailto:ali.radai...@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
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo>
/
/webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
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