after having run fmriprep (20.2.3) I noted a problem in the alignment between the anat and func images for the last 5 participants of my sample (no problems with the other participants). Both the raw anatomical and functional scans look perfectly ok, spikes also look not problematic. I attach here a screenshot of one output, as an example.
I tried to re-run fmriprep on the same participant but I got the same issue. I re-run the pipelines also for an old participant (to check whether maybe there was an internal bug in the program) but I got good results. Do you have any suggestion about how to proceed/what else I could check?
yes, I tried to re-run fmriprep with both 20.2.7 and 21.0.1 versions but I got the same issues.
I saw that BBR refinement using FSL flirt every time got rejected and I finally noted that my functional images are not in the correct orientation. I tried to reorient them (rotate) so that they look like other functional images from the remaining sample, but the problem is still there. I am not sure what to do to solve the issue.
apparently, it was a problem linked to the orientation of my images: they were rotated in the opposite direction (180°). Running again fmriprep was this time succesful, also for the rest of the other participants.
