Hi all, thanks for this forum and all the helpful posts!
I was looking up afni commands to compute the nuisance matrix and residuals for doing resting fc-MRI and found this thread; just wondered if somebody had actually followed up on whether the 3dDeconvolve + 3dREMLfit steps shown below produce results similar to the ones produced using the nitrc script #5? Below are commands from my script:($file is the preprocessed resting func file, $cor is the type of correction with or w/out motion, wm/csf/glob etc); wonder if anyone has used something similar?

3dDeconvolve \
     -input $file+orig -polort 0 \
     -mask Mask.Brain.$file+orig \
     -num_stimts $n \
     -stim_file 1 $nuisance/dm.0.$MotionFile -stim_label 1 mot0    -stim_base 1 \
     -stim_file 2 $nuisance/dm.1.$MotionFile -stim_label 2 mot1    -stim_base 2 \
     -stim_file 3 $nuisance/dm.2.$MotionFile -stim_label 3 mot2    -stim_base 3 \
     -stim_file 4 $nuisance/dm.3.$MotionFile -stim_label 4 mot3    -stim_base 4 \
     -stim_file 5 $nuisance/dm.4.$MotionFile -stim_label 5 mot4    -stim_base 5 \
     -stim_file 6 $nuisance/dm.5.$MotionFile -stim_label 6 mot5    -stim_base 6 \
     -stim_file 7 $nuisance/ts.WM.$sid.rest.oxrtfsd.1D -stim_label 7 WM -stim_base 7 \
     -stim_file 8 $nuisance/ts.CSF.$sid.rest.oxrtfsd.1D -stim_label 8 CSF -stim_base 8 \
    # -stim_file 9 $nuisance/ts.global.$sid.rest.oxrtfsd.1D -stim_label 10 global -stim_base 9 \
     -x1D $nuisance/nuisance.$cor.$file \
     -x1D_stop

echo "Running 3dREMlfit to get residuals"
3dREMLfit -input $file+orig \
    -matrix $nuisance/nuisance.$cor.$file.xmat.1D \
    -mask Mask.Brain.$file+orig \
    -Rerrts $nuisance/res4d.$cor.nii.gz \
    -GOFORIT

echo "Demeaning residuals and adding 100"
3dTstat -mean -prefix $nuisance/res4d_mean.$cor.nii.gz $nuisance/res4d.$cor.nii.gz
3dcalc -a $nuisance/res4d.$cor.nii.gz -b $nuisance/res4d_mean.$cor.nii.gz -expr '(a-b)+100' -prefix $file.$cor.nii

echo "Resampling residuals to TLRC space"
@auto_tlrc -apar $sid.brain+tlrc -suffix res2std -input $file.$cor.nii

-thanks,
veena