Creating a Study Specific Template

My lab is trying to create a study specific template. We are using (ANTs/ at master · ANTsX/ANTs · GitHub)
Eventually, we are planning to skull-strip this template and register it into MNI space,

Essentially, we are using fMRIprep to produce preprocessed T1 images. Then, we are using each of our participant’s preprocessed T1 images to create our study specific template.

I was wondering if it is best to create a study specific template from skull-stripped T1’s? Or, is it sufficient to skull-strip the study specific template after we feed in T1’s (that haven’t been skull-stripped)? I’m unsure if this would make a difference.

I’m very new to working with fMRI data, so I apologize in advance if my questions or explanations are unclear! I’m more than happy to clarify if need be. Thanks to anyone in advance who is willing to help!