Hi All,
After talking to another AFNI user, I am now questioning my understanding of what the baseline reference is when using 3dDeconvolve.
It was suggested that I might need to use base_file to ensure that I am getting the baseline I want.

I thought that if you had multiple stim_files all variance associated with each defined stimulus would be excluded from the baseline estimate, even if you are only looking at one of the effects (a sub-brik). (This would be similar to oridinary multiple regression analyses based upon Type III sums of squares.)
In other words, only those time points set to zero in all the different stim_file references would be used to estimate your baseline value.
Is this correct?


Below is the 3dDeconvolve command I have used.

3dDeconvolve \
-input ${id2}concatB216+orig \
-censor ${id2}B216_censor.1D \
-num_stimts 15 \
-concat san_cat.1D \
-stim_file 1 faceswav01.1D -stim_label 1 R1neu \
-stim_file 2 faceswavneg1.1D -stim_label 2 R1neg \
-stim_file 3 faceswav03.1D -stim_label 3 R1hap \
-stim_file 4 faceswav06.1D -stim_label 4 R2neu \
-stim_file 5 faceswavneg2.1D -stim_label 5 R2neg \
-stim_file 6 faceswav08.1D -stim_label 6 R2hap \
-stim_file 7 faceswav11.1D -stim_label 7 R3neu \
-stim_file 8 faceswavneg3.1D -stim_label 8 R3neg \
-stim_file 9 faceswav13.1D -stim_label 9 R3hap \
-stim_file 10 ${id2}f123Mparam.1D'[0]' -stim_label 10 1Roll \
-stim_file 11 ${id2}f123Mparam.1D'[1]' -stim_label 11 1Pit \
-stim_file 12 ${id2}f123Mparam.1D'[2]' -stim_label 12 1Yaw \
-stim_file 13 ${id2}B216.1D'[1]' -stim_label 13 2Rol \
-stim_file 14 ${id2}B216.1D'[2]' -stim_label 14 2Pit \
-stim_file 15 ${id2}B216.1D'[3]' -stim_label 15 2Yaw \
-fout -tout \
-bucket {$id2}HabitNegPosDifmv2.buc