Hey guys, I have a theoretical question.

I'm running 3dDeconvolve on simulated data to check out an experimental design. I've read the 3dDeconvolve manual but it's dated 2001 when stim_file was the norm. I had emailed Doug Ward some questions that he was awesome enough to answer and he recommended for my simulations, to use binary stimulus timing files and the stim_file option in 3dDeconvolve.

Long story short I did 3dDeconvolve on my data in 2 ways:
1) With the -stim_times options using a 'BLOCK(12,1)' duration for 12s stimuli.
2) With the -stim_file options using binary stimulus files (only 1 one where the onset was) and a -minlag option of 0 and -maxlag option of 12.

The -stim_times option gives almost perfect results, right on top of my simulated data but the -stim_file option looks vastly different. This isn't a huge problem because I'll just use -stim_times in my actual analysis but I'm curious as to why the results are so different. In both cases I am also inputting shock onsets (again as either stimulus_times or stim_files, respectively) and it looks like in the case of -stim_files the shock is also being modeled as part of the stimulus which makes it look messed up but I'm just not sure why -stim_times would take care of that but stim_file wouldn't. I mostly just want to know the difference between the two analyses. My two commands are below.

1) 3dDeconvolve -input1D simulated_all_cs_all_shock.1D -force_TR 2 -polort 0 -num_stimts 5 -stim_times 1 stim_test_times_one_ones.01.1D 'BLOCK(12,1)' -stim_times 2 stim_test_times_one_ones.02.1D 'BLOCK(12,1)' -stim_times 3 stim_test_times_one_ones.03.1D 'BLOCK(12,1)' -stim_times 4 shock_test_times.01.1D 'BLOCK(1,1)' -stim_times 5 shock_test_times.02.1D 'BLOCK(1,1)' -xout -iresp 1 CSp_sim_iresp_sts -iresp 2 CSm_sim_iresp_sts -iresp 3 CST_sim_iresp_sts -fitts sim_fitts_sts -errts sim_errts_sts

2) 3dDeconvolve -input1D simulated_all_cs_all_shock.1D -force_TR 2 -polort 0 -num_stimts 5 -stim_file 1 CS+_one_ones.1D -stim_file 2 CS-_one_ones.1D -stim_file 3 CST_one_ones.1D -stim_file 4 CS+_shock.1D -stim_file 5 CST_shock.1D -stim_minlag 1 0 -stim_maxlag 1 12 -stim_minlag 2 0 -stim_maxlag 2 12 -stim_minlag 3 0 -stim_maxlag 3 12 -stim_minlag 4 0 -stim_maxlag 4 1 -stim_minlag 5 0 -stim_maxlag 5 1 -xout -nfirst 0 -iresp 1 CSp_sim_iresp_sfile1 -iresp 2 CSm_sim_iresp_sfile1 -iresp 3 CSt_sim_iresp_sfile1

Thanks for any insight!

(P.S. I have also tried using -stim_files where there is a 1 not just at the onset but, but 6 1s in a row for each stimulus representing that it's on screen for 12s (6 TRs) and it looks even worse).