Hi @KFDK , my name is Eilidh and I’m one of the developers of fMRIPrep-rodents.
First: I should include the disclaimer that fMRIPrep-rodents is still very much in its infancy, and although I really welcome your enthusiasm to use it, we are not quite in a place where we can encourage its use unless users really want to get involved with debugging, etc because we are not as established as its sister project just yet.
Importantly, an example of known problems in the workflow includes the fact that we have not yet integrated susceptibility distortion correction into fMRIPrep-rodents so epi-to-anatomical transformations are less than ideal, so please look carefully at your reports to make sure that the data processing is of a suitable quality before proceeding to any analysis.
One of the issues here is that fmriprep is expected a T1w image with a T1w contrast, and giving it a T2w contrast must be messing up all the part that normalize the subject anatomy image to the template image.
This is not true for fMRIPrep-rodents; although I plan to address the previously mentioned problem shortly so that we can have compatibility for both T2w and T1w images, T2w anatomicals are conventional with small animal imaging, so fMRIPrep-rodents currently expects a T2w image as part of the pipeline (at least for now).
Having said that, the problem you have experienced has been correctly identified as being rooted in the differing orientation of your image with respect to the template for brain extraction. This step is currently handled by a second tool called NiRodents so this is actually not a problem with fMRIPrep-rodents per se. I’ve talked about some of these issues previously here
Until we work other urgent issues out, we require all images to be RAS+ oriented but I understand that conventions for this are all over the place in the rodent imaging community and so heavily relies on the data conversion to Nifti. Is it possible for you to share your image header? How did you convert your data to nii?