Hi Paul and Daniel,

So sorry that it took me a while to respond! I have been getting support from our IT department to get the most updated AFNI working on our server. The @djunct_overlay_check command did not exist in the older version of AFNI folder, but it’s now finally working with the update! I ran this command on some of my participants, I have attached sample outputs from 2 of them (151204 & 151422_overlap_check.PNG). I also put the check_olap.jpg and check_olap_DEOB.jpg side by side (is check_olap_DEOB.jpg showing how anatomy and EPI overlap after both of them are deobliqued?)

I also tried the two options that Daniel provided: 1) skip the @Align_Centers step and the previous 3dWarp steps used, and just run @SSwarper and afni_proc.py command. The skullstrip somehow failed during the pre-processing; 2) I still de-obliqued the anatomy, but left the EPI data oblique, and then added “-giant_move” to the -aligh_opts_aea line. This method worked, and I think it solved the alignment issue that I was seeing through @ss_review_driver?! (151422_review_driver.PNG)

Thank you both so much for helping me patiently with this issue! I do have two more trouble-shooting questions regarding this first participant (151204) related to skull-strip and anatomy-EPI alignment issues if that’s okay! (Sorry I have to explain the problems in another post as this post only allows for two attachments).