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:
>> 1. What is y.mgh in your first command? how is it created?
>> 2. 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_2fppaulo_2fqdec_2dcoord
>>>
>>>
>>> 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
>>> >
>>>
>>
>
> --
> Sent from my mobile device
>
> -----------------------------------------------------------
> Pedro Paulo de M. Oliveira Junior
> Diretor de Operações
> Netfilter & SpeedComm Telecom
>