Hi Steve,

I managed to set up a design matrix (12 subjects and two scan for each subject) and ran vertex analysis of FIRST hoping to run a paired test.
But, I see 13 vtk files (the same as the EVs) for each subcortical structures.
I can tell neither if I ran a paired test nor which vtk file I should look at (if I successfully ran a paired vertex analysis).
I have attached the design matrix used.

Thank you,

Buyean Lee

Hi - this should be fine. 
Cheers. 
 
On 4 Sep 2009, at 20:28, Buyean Lee wrote: 
 
> Sorry. The last sentence should have been a question. 
> 
> Or, is it wrong for one to use FIRST for this kind of analysis > (i.e., analysis of scan1 vs. scan2 for the same subjects)? 
> 
> 
> -----Original Message----- 
> From: Buyean Lee <[log in to unmask]> 
> To: [log in to unmask] 
> Sent: Fri, Sep 4, 2009 11:53 am 
> Subject: [FSL] FIRST: paired vertex analysis? 
> 
> Dear Mark and Brian, 
> 
> I thought it would be nice if FSL FIRST can detect longitudinal > changes of subcortical structures. 
> Is there any way to set up such a design matrix for paired analysis > in FIRST? 
> Or, FIRST should not be used for this kind of analysis (i.e., > analysis of scan1 vs. scan2 for the same subjects). 
> 
> Thank you, 
> 
> Buyean 
> p.s., I know that one can use Siena for this purpose. 
> 
> 
> 
 
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Stephen M. Smith, Professor of Biomedical Engineering 
Associate Director, Oxford University FMRIB Centre 
 
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK 
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[log in to unmask] http://www.fmrib.ox.ac.uk/~steve 
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