QDEC transform your data into a common spherical space. So this file y.mgh is already in a common space.
Running that script into your y.mgh (from QDEC directory) will retrieve the values of the surface stat in fsaverage space.
mri_convert --frame $i y.mgh ../../fsaverage/surf/lh.$i.mgh
This line break apart the volume of each subject.
mris_convert -c $i.mgh ../../fsaverage/surf/lh.inflated
lh.$i.asc This one convert all values to fsaverage space.
Is that what you want?
2008/10/9 Mishkin Derakhshan mishkind@gmail.com
Hi Pedro, Thanks a lot for the help. Reading through all the FreeSurfer mail archives you are almost as helpful as Nick!
Anyway, I just posted a msg to the list describing what it is i want to do which is transform my own custom surface stats, into fsaverage space.
You can read my post for more details, but if you have any input (or scripts) on how to do this, it would be greatly appreciated.
thanks, mishkin
On Thu, Oct 2, 2008 at 9:08 PM, Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br wrote:
Sure.
y.mgh is the volume created by QDEC when you start a stat design. You'll find it usually in $SUBJECTS_DIR/qdec
The other command is to export al values in asc format:
x,y,z - value
where value is what you studied in QDEC, for instance, thickness.
If you need any other help, contact me. Maybe if you describe what you are trying to do I could have a script ready.
Cheers,
PPJ
On 10/2/08, Mishkin Derakhshan mishkind@gmail.com wrote:
Hi Pedro, I wrote to the FreeSurfer list a while ago about a problem I was having
(see
emails below). You told me to try your qdec-coord script from the wiki:
# Script created December 2007 by Pedro Paulo Oliveira Jr. # Use with Freesurfer 4.x
cd #your directory where qdec data are stored.
set numsubject = 17 #your value
for i in `seq 1 $numsubject` do mri_convert --frame $i y.mgh ../../fsaverage/surf/lh.$i.mgh mris_convert -c $i.mgh ../../fsaverage/surf/lh.inflated
lh.$i.asc
done
I have a few questions as I am new to the whole qdec group analysis
thing.
Could you explain to me briefly what your two commads are doing, or at
the
least answer these two questions:
- What is y.mgh in your first command? how is it created?
- In the second command, should $i.mgh really be
"../../fsaverage/surf/lh.$i.mgh" ie. the output from the first command?
thanks, mishkin
On Thu, May 1, 2008 at 6:45 PM, Pedro Paulo de Magalhães Oliveira Junior
<
ppj@netfilter.com.br> wrote:
I think this page can give you an insight:
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions_2fScripts_2fppaul...
2008/5/1 Mishkin Derakhshan mishkind@gmail.com:
Hi,
I know that at some point in the pipeline, the surfaces are
registered
to a common sphere, and thus I'm hopping there is a one-to-one vertex correspondance between subjects.
My question is, let's say I look at vertex X, on subject1, how do I find out the corresponding vertex location on subjectN.
thanks, mishkin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Pedro Paulo de Magalhães Oliveira Junior