Dear AFNI experts,

I have some question concerning the stimulus timing files of an ER paradigm.

I have 2 runs, each of it 300 volumes with TR=2seconds. In 3dDeconvolve my runs are auto-concatenated and I used the -stim_time option. A few question arised when running 3dDeconvolve.

-) I´m not sure whether I created my stim_times files correctly. Here is an example of one regressor:
First I created a stimulus timing files for each run on a 1 sec grid, so each file had 600 lines. Then I used make_stim_times.py to generate stim_times files which I then concatented so that I have one stim_times file for both runs. Is this done correctly? (The same I did for all regressors)

- ) When looking at the 3dDeconvolve ouput I saw:
-stim_times using TR=2 s for stimulus timing conversion
This I don´t understand as I already created my stim_time file before. Do I have to worry about this message?

-) Do I have to tell 3dDeconvolve that my EPI data are on a 2-second grid but my stimuli are on a 1-second grid (is there any option for this)? I´m just confused because for 2 other paradigms (block designs) where my stim_times files are on a 2-second grid, the 3dDeconvolve options are the same as in this case. Shouldn´t there be a difference? I also want to write a censor file. Has the lenght of the censor correspond to the lenght of the concatenated runs or do I have to generate a file corresponding to a 1-second grid as I did for the stim_times files.

I know these are very basic questions but I really would appreciate if somebody could help me with that.

Thank you very much in advance!

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