I just recently found that afni, FSLeyes, Freeview and Mango interpret NIFTI files differently. I performed an epi-anat alignment using AFNI and the alignment looks good in AFNI viewer. But if I visualized the aligned NIFTI files in FSLeys, Freeview or Mango, I can clearly see the mismatch. I know that AFNI uses a LPS+ space and other software use a RAS+ space. But clearly they do not just differ in flipping the coordinates.
My question is, how to somehow modify the header information such that the two files aligned in AFNI viewer can also show up being properly aligned in like FSLeyes or Freeview?