Hi Yolanda,

No.
It is better to remove the two subjects. Mixing versions is never a good idea 
as results are expected to differ. Same is true for different acquisitions 
(parameters, scanners etc). If anything has to be different it needs to be 
asserted that it is spread equally among your groups.

Best Martin

On Jun  10, 2011, at 7:16 AM, Yolanda Vives <yvi...@pic.es> wrote:

> Dear Freesurfers,
>  
> I have a dataset processed with a classical recon-all of Freesurfer v.4.3.1 
> and there are two MRIs that were not segmented correctly due to the register. 
> After several unsuccessful attempts to improve this step using tkregister2, 
> finally I have successfully processed them with FS v5.0. Would it be correct 
> to perform a QDEC analysis to analyse cortical thickness using all my dataset 
> (mixing MRIs processed with FS 4.3.1 and two of them processed with FS 5.0) ?
>  
> Thank you for your help,
> Yolanda
> 
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