Yes, I'm trying to remove the residual motion effects from the original signal and pass that data to another program as well. Here's the 3dDeconvolve script:

# regress out the motion
3dDeconvolve -input $finput \
-polort 0 -jobs 2 -nodmbase \
-num_stimts 6 \
-stim_file 1 $mfile'[0]' -stim_label 1 roll -stim_minlag 1 0 -stim_maxlag 1 0 \
-stim_file 2 $mfile'[1]' -stim_label 2 pitch -stim_minlag 2 0 -stim_maxlag 2 0 \
-stim_file 3 $mfile'[2]' -stim_label 3 yaw -stim_minlag 3 0 -stim_maxlag 3 0 \
-stim_file 4 $mfile'[3]' -stim_label 4 IS -stim_minlag 4 0 -stim_maxlag 4 0 \
-stim_file 5 $mfile'[4]' -stim_label 5 RL -stim_minlag 5 0 -stim_maxlag 5 0 \
-stim_file 6 $mfile'[5]' -stim_label 6 AP -stim_minlag 6 0 -stim_maxlag 6 0 \
-errts mcres4-${run}

# now do up the the glm stuff
3dDeconvolve -input mcres4-$run+tlrc \
-mask $fmask \
-CENSORTR 0-5 195-206 \
-jobs 2\
-polort 3 -num_stimts 2 \
-stim_file 1 $file'[0]' -stim_label 1 mom -stim_minlag 1 0 -stim_maxlag 1 0 \
-stim_file 2 $file'[1]' -stim_label 2 stranger -stim_minlag 2 0 -stim_maxlag 2 0 \
-sresp 1 sd-$run-res4-mom \
-sresp 2 sd-$run-res4-stranger \
-fout -tout -rout -bout \
-bucket $run-res4-func -fitts $run-res4-fit -errts $run-res4-errts