I am using make_random_timing.py to make stimulus timing files. I would like to then test the efficiency of the timing files with the 3dDeconvolve -nodata command. I added a ‘save_3dd_cmd’ when i ran make_random_timing and it generated a command for running 3dDeconvolve. It automatically assumed my TR was 1 second because in the first line it put into the command was: 3dDeconvolve -nodata 202 1.000. My thought is to use the rest of the command but just replace the TR with the appropriate TR, but I wanted to make sure I wasn’t misunderstanding anything? Is this an appropriate action?
Sorry for being slow here…
Add a -tr option to the make_random_timing.py command.
Thanks for your help with that. One last question is that the 3dDeconvolve command that got generated includes a polort flag with ‘3’ after it. I’m used to specifiying 1, or 2, and I don’t know why it would deem 3 appropriate for my model. Can you advise?
The make_random_timing command was:
make_random_timing.py -num_stim 2 -num_runs 1 -run_time 317.14 -stim_dur 1.57 -num_reps 48 -min_rest 0.785 -prefix stimes -pre_stim_rest 7.85 -post_stim_rest 7.85 -tr_locked -tr 0.785 -stim_labels congruent incongruent
Thanks so much!
Our (Bob’s) rule of thumb on polort is to use 1+ceil(duration/150s).
Since your run duration is >= 300 s (and less than 450 s), the
suggested polort is 3.