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Thank you for the reply John,

In fact, data of each group come from different scanners and the number
of volumes/scanner is different (but on the all I've got the same number
of subjects in gp A & B).

But it's definitely a good idea to include that in the statistical
design... thank you again

Best,
Cyril

>Custom templates are only recommended for when the contrast in your image
>differs from that of the templates, or if analysing a particularly unusual
>patient population.  Voxel-sizes shouldn't really matter too much.
>
>If you plan to use data from different scanners, then this fact should be
>included in your design matrix.  If you compare one group acquired on one
>scanner, with another group, acquired on another, then this would prevent you
>from getting significant results.  The idea is that the analysis should not
>simply detect scanner or sequence differences.
>