Any software package will do the inference on images with different 
characteristics, the question is whether the inference is valid. If you 
use different types of images, you will get different results (all 
software packages). If you try to compare two groups each with image 
types, you will have a confound with your image type and your groups and 
the inference will not be valid. Having said that, if you want to 
analyze some of your subject with T1 and some with T1+T2 and some with 
T1+FLAIR, then can certainly do so.

On 2/13/2020 8:13 AM, Renew Andrade wrote:
>          External Email - Use Caution
> Dear FreeSurfer experts:
> I am dealing with a crossectional retrospective case control  study where I 
> don't have all subjects with the same inaging protocols. I do have T1 for all 
> of them although some have T2 others FLAIR others T2+FLAIR (besides T1 for 
> all of them). My question is regarding VBM can I do inference on images with 
> different characteristics? Or should them all have T1 + T2 or T1 + FLAIR. I 
> guess this is the case that is all subjects should be processed with the same 
> protocols.  This is in Multiple Sclerosis by the way just in case it matters.
> Sincerely,
> Andrade.
> Sent from my iPhone
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