Hi Paul and Daniel,
Thank you so much for helping me understand the options, meaning, and consequences of deoblique, and what is the reason that caused my trouble with the participant’s data! It is SO helpful!

The data I am currently analyzing do have both oblique anatomical and EPI data with the same oblique angles for each participant (except for the one that I am having trouble with [mentioned in the initial post]). Following your suggestion, I ran the following codes on each participant’s anatomical data:
3dcopy $anat+orig $anat.deoblique
3drefit -oblique_recenter $anat.deoblique+orig
3drefit -deoblique $anat.deoblique+orig

I then put the $anat.deoblique+orig data and original EPI data (did not deoblique) through my afni.proc.py script. The script ran smoothly, and I opened @ss_review_driver and the html file to check the quality of pre-processing (e.g., the alignment of anatomy and EPI). I have attached two screenshots of what it looks like in the GUI and on the html page.

Paul, I know you mentioned that obliquity is annoying because it causes a visualization problem and would make datasets appear to be in different locations (my deobliqued anatomy and original oblique EPI). However, I also want to make sure that I am analyzing my data correctly. Is this what you would expect to see through @ss_review_driver and html output file? If yes, is there a way for me to accurately check the quality of my pre-processing (e.g., alignment)? Because currently the datasets do appear in different places visually which made it harder for quality check. If not, is there something that I did wrong?

Thank you so much!