Anatomical-functional misalignment happened to some of the images after fMRIprep preprocessing (about 10% of the images; see the attached screenshots for an example). I used fmriprep 1.5.0 and the misalignment happened without errors in the report. However, I tested running registration using FLIRT in a separate FSL on a couple of those images, and the anatomical and functional could be well registered by FSL.
I wonder if anyone else experience this and any recommendations for how to deal with this?
Best,
Jinxiao