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June 14, 2022 09:55AM
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!
Subject Author Posted

regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 09:55AM

Re: regress_stim_times_offset after fmriPREP

Peter Molfese June 14, 2022 10:50AM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 11:01AM

Re: regress_stim_times_offset after fmriPREP

rick reynolds June 14, 2022 11:05AM

Re: regress_stim_times_offset after fmriPREP

rick reynolds June 14, 2022 11:06AM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 12:14PM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 12:23PM

Re: regress_stim_times_offset after fmriPREP

rick reynolds June 14, 2022 02:11PM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 02:14PM

Re: regress_stim_times_offset after fmriPREP

rick reynolds June 14, 2022 03:11PM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 03:18PM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 03:20PM

Re: regress_stim_times_offset after fmriPREP

rick reynolds June 14, 2022 04:05PM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 04:11PM



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