I had to re-process some task-fMRI with a newer version of fMRIPrep (v20.2.0) and ran into some issues. The registration to standard space in the report looks fine. However, when I try to overlay the bold image on the MNI template in any other software (FSLeyes, mricron, nilearn), the registration looks completely off.
The background image is the ICBM152 2009c non-linear asymmetric template. The overlay is the brain mask generated by fMRIPrep, i.e. sub-…/func/sub-…_task-…_space-MNI152NLin2009cAsym_desc-brain_mask
I find this quite puzzling because I processed the same BIDS dataset with fMRIPrep v.1.2.1 and did not have any issues.
Any pointers for what I could try to fix this are massively appreciated!