fMRIprep partial field of view EPI preprocessing

I am analyzing partial field of view (FOV) resting state images.
I used fMRIprep for preprocessing, however there seems to be a co-registration issue with the anatomical image. I have also collected whole brain EPI. I am wondering if there is a way that I can improve my partial FOV functional image registration to T1. Is there a way that I can also use my whole brain EPI to help with an improved registration?

Any help would be greatly appreciated.

Kind regards,