Hello Rick,
I am sorry to come back to this post so late. Somehow, I was not notified by any email alert about your reply.
360 TRs are from four separate runs. The stimulus lasted about 60 seconds in each run. In this case, what is polort for 3dDetrend and for 3dDeconvolve? The new script for PPI looked so different from mine which was created by the suggestions in this website (https://afni.nimh.nih.gov/sscc/gangc/PPI.html). If I want to stick to own script, were there any critical steps from the new script should be included in my script? Thank you very much.
Best,
Veda