thank you for your reply. There is indeed a parameter that I am not sure about: Mask brain. If I tick Mask brain, the template image for brain masking is T1. Meanwhile my data is not normalized yet, plus when I substitute T1 with coregistered structural, I got an error. But fmap correction is applied in the beginning of the pipeline, so the data are not normalized anyways. Why is there a T1 default template then?

How crucial is it if I don't apply masking? I tried both: visually masked and unmasked images do not differ.

Thank you.

best,

Lara