Hello,

I hope you are doing well!

I am trying to use AFNI proc.py to run first-level analyses on data that have been preprocessed using fmriPREP.

I specifically have a question about the regress_stim_times_offset option.

In fmriPREP, slice timing was performed on the BOLD data in the following way:

Slice time correction was performed prior to other signal resampling processes using AFNI 3dTShift. All slices are realigned in time to the middle of each TR.
BOLD runs were slice-time corrected to 0.831s (0.5 of slice acquisition range 0s-1.66s) using 3dTshift from AFNI 20160207 (Cox and Hyde 1997, RRID:SCR_005927).

Because of this, I believe I need to use regress_stim_times_offset when running AFNI proc.py. However, I'm a little unclear on what input to give regress_stim_times_offset. If the BOLD data was shifted towards the middle of the TR, I should be ADDING a timing offset to my timing files correct? I read that TR/2 would be a good offset (1.75/2 = 0.875). But the fmriPREP output stated it used slice-timing correction of 0.831. So should I use that input instead?

Thank you! Please let me know if you need more info!