If you want to do a simple t-test between the two groups then you should be able to use FEAT and do a 'higher-level' analysis testing your CBF maps as the parameter estimates. This would then be the same procedure as a BOLD higher level analysis so you can consult that section of the help pages. Alternatively you can use the non-parametric method in randomise for the same job.
You might like to determine if the CBF images you are getting from your scanner are in absolute or relative units. If the latter then there could be some extra global scaling between individuals that is not purely perfusion differences.

Michael

On 15 Apr 2013, at 10:07, Bhaswati Roy <[log in to unmask]> wrote:

> Dear Sir,
>
> We have obtained CBF maps derived from 3D pseudocontinous ASL imaging from 20 controls and 20 patients. CBF maps are generated from the scanner itself. We want to generate maps showing regions where CBF values are different of patients than control. I am very much confused as to use which FSL tool for generating these maps.
>
> Thanks in advance
>
> Regards
> Bhaswati