Excluding subjects in FBA post-template creation


I have a small question regarding possible biases in population templates used for fixel-based analysis.

I have created a population template for FBA using all my subjects (2 groups, patients and controls). Now I am trying to test different sub-groups within my subjects, and I was wondering if I would have to create a separate population template for each sub-group test separately or would simply excluding the unneeded subjects at the statistical analysis step be enough? I’m sure that doing so would introduce a bias of some kind, but I was wondering if that bias would be negligible or not. Thanks!