Hi Marcos, we're not really set up to do this kind of thing. The 
subcortical structures in fsaverage are not appropriate for 
surface-based analysis. We do not generate surface for subcortical 
structures from individuals. I think FSL might do this kind of thing.
doug




On 08/07/2013 04:03 PM, Marcos Martins da Silva wrote:
> Hi, FreeSurfers.
> Is it possible to use FreeSurfer's group analysis tools to investigate 
> surface deformation instead of thickness? I guess it would be 
> interesting for subcortical structures like putamen, amygdala or 
> hippocampus. Let's say you get the putamen data from 15 subjects and 
> compare it to putamen data from fsaverage, After correct registration, 
> I guess we can detect regions of contraction and expansion leading to 
> changes in the putamen contour. I imagined it could be done if we 
> calculate the signed Euclidean distances between the corresponding 
> points of for each subject's putamen and fsaverage, with positive and 
> negative values indicating, for example, the presence of an outward or 
> inward surface deformation. After all calculation I guess we can get a 
> similar result to the pictures we can see at 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis 
> <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis%A0> 
> but showing only a putamen and the colors meaning surface deformation 
> instead of thickness. This way, you can notice morphological 
> differences among subjects even if they have the same volume.
> Thanks in advance,
> Marcos
>
>
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