I'll try to use 3ddeconvolve then. That's probably the best thing to do like you said.

I'm not sure how I would do that however. I assume I want to use the errts file (from modeling out movement, etc..) from where I'm extracting my time course as my input. And of course I have to feed in my time course somehow. I'm trying something like this:

3dDeconvolve -input ../errts.T01.tproject+tlrc \
-polort -1 \
-num_stimts 1 \
-stim_file 1 TimeCourse01.txt -stim_base 1 -stim_label 1 TC \
-fout \
-tout \
-fitts B1_F1_fitts \
-errts B1_F1_errts \
-bucket B1_F1_stats


It gets me an empty output though... any advice?

Thanks.