Hi @KFDK - is this a rat image or a mouse image? fMRIPrep-rodents has only been tested on rats, although using images derived from mice is in our roadmap.
In particular, this is because our brain extraction in NiRodents works well for rats but is relatively untested in mice. Early tests show that despite similarities in overall anatomy, it seems that the size difference between rats and mice is too large for the registration algorithm to overcome, so using a rat template with a mouse image has not been successful. We have a mouse template available in templateflow, but it is possible that there are more optimisations required for it to work for mice out of the box.
These are definitely things we want to fix and we’d hope to do it sooner with more contributors.