Hello! I would like to make sure I am understanding the default settings of 3dTshift correctly. I’m working with data that I have run through fmriprep so that tzero is not set to 0 as in afni_proc.py. Based on some other posts on this board, I believed I needed to subtract ~1/2 TR from my onset times to make the model in 3dDeconvolve reflect the slice time corrected data. It was my understanding that 3dTshift temporally aligns the data to the average of the slice times, which in my case is ~970 ms.
I just discovered this blog post that instead says that AFNi users should add ~1/2 TR to onset times if preprocessing is done with fmriprep: https://reproducibility.stanford.edu/slice-timing-correction-in-fmriprep-and-linear-modeling/
If I have a TR of 2 seconds and my original volumes are 0, 2, 4, 6, . . . seconds, after 3dTshift, they become approximately 1, 3, 5, 7 . . . right? In that case, shouldn’t an event that happened at 6 seconds after the start of my run actually be coded as 5 seconds in the model to account for the first volume moving forward by ~1 second? It seems to me that adding ~1/2 TR would instead move the starting point of the run backward in time, but I might be misunderstanding something fundamental here.
As always, thanks for the advice!