> Thank you, Jesper! I have another question regarding the orientation of the images. The output _fieldcoef file is in LPI orientation, and my EPI images to correct are in RAI. Do the fieldcoef and epi images need to be in the same orientation when input to applytopup? I have been re-orienting the epi images to LPI which can be space intensive with 8 epi files. Is it possible for me to reorient the fieldcoef file to RAI instead?
I _think_ it will work fine as long as the input to topup is in the same orientation as the input to applytopup. It would be easy for you to check by comparing the final outputs when you and and when you don’t do the re-orientation.
> Thanks for the help,