Hi Rick,

Thanks so much for your help. I work with Kyle (student) which is why I am joining the thread. The input file is a concatenated file. So I have adjusted the script as follows:

3dDeconvolve \
-input 00_Data/s1_norm+tlrc -00_Data/concat.1D \
-polort 2 \
-num_stimts 2 \
-stim_file 1 00_Data/s1_global.1D -stim_label 1 RegNoInt \
-stim_file 2 06_Interaction2/s1_FA_Inter_ts${seed}.1D -stim_label 2 FA \
-rout \
-bucket 07_Deconvolve/s1_R2_FA_${roi}_${seed}

There are 2 runs the first run has 222 TRs, and the 2nd has 235 TRs. Should I still use polort 2?

I would really like a clearer understanding of how the specified polort will affect the results. Is it just based on the length of the file? For example if I am running the 3dDetrend on one of these runs (222TR) or (235TR) what polort would I specify?

Thanks so very much for your help,
Lesley