it really depends on what the differences are. The best thing to do would 
be to scan some controls with both sequences and see what the differences 
are, although that won't rule out some disease-specific differences that 
you only see in the patients

On Thu, 28 Mar 2013, _andre...@sapo.pt wrote:

> Hello list,
>
> I have a group of subjects (4 patients  and 8 controls) in which one
> MPRAGE sequence was used and another group of subjects (2 patients and
> 2 controls) where a diffent MPRAGE was used. Both groups were acquired
> in the same scanner. For each subject I have two anatomical sequences
> and I'm working with the average dataset. My question is can I put
> both groups together for comparision?
>
> I've thought about this and I can't really be sure... I was thinking
> that since for group 2 the number of acquisitions is balanced maybe
> the overall impact of different sequences won't be significative...
> Patients and subjects are age-matched in both groups.
>
> Please, any advice will be greatly appreciated!
>
> Thank you!
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>
>
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