(continued from last post) As I was looking at QC_anatSS.151204.jpg, I noticed a skull-stripping issue - it seems that small bits of the cortex were being left-out/cut-off (emphasized using yellow circles). The skullstrip problem also seems to affect the anatomy-EPI alignment (screenshot showing anatomy -EPI alignment through @ss_review_driver)? I have searched some online resources, and learned that using “push_to_edge” with 3dSkullStrip is a potential solution. However, I am not sure how to incorporate this solution into the @SSWarper step, or my afni.proc.py script ... Or is there any other option that I can specify in my afni.proc.py script to make the skullstrip less aggressive on this participant? Or if there is more than a skullstrip problem?
I apologize for asking many basic questions... this is my first time learning how to independently analyze and troubleshoot the data, and really want to understand the problems and learning how to deal with them the right way. Thank you so much again for your patience!