Hi Rick,

Thanks so much for your reply and suggestions!

0. TR is .72 with 667 volumes
1. Initially we were completing it twice, but are no longer trimming the masks
2. It does look like valid time series
3. We think the regressors did not project out based on the results of the one-sample and paired-samples t-test, we are still finding signal in the ventricles, WM, cerebellum etc.,
4. Yes, we first ran nuisance regression and then band pass filtered that processed functional file

In that case if we include -x1D_stop, is the script below correct?
##STEP4##
# echo
# cd ${subjectsDirectory}/

# echo "Removing nuisance regressors..."
# 3dDeconvolve -float -input rest/rest_mcf_MNI_b6.nii.gz \
# -nfirst 0 -polort 4 \
# -mask rest/automask_MNI.nii.gz \
# -GOFORIT 5 \
# -num_stimts 16 \
# -stim_file 1 rest/qualitycontrol/motion/${subj}_fMRI_vr_motion.1D'[0]' -stim_label 1 roll -stim_base 1 \
# -stim_file 2 rest/qualitycontrol/motion/${subj}_fMRI_vr_motion.1D'[1]' -stim_label 2 pitch -stim_base 2 \
# -stim_file 3 rest/qualitycontrol/motion/${subj}_fMRI_vr_motion.1D'[2]' -stim_label 3 yaw -stim_base 3 \
# -stim_file 4 rest/qualitycontrol/motion/${subj}_fMRI_vr_motion.1D'[3]' -stim_label 4 x -stim_base 4 \
# -stim_file 5 rest/qualitycontrol/motion/${subj}_fMRI_vr_motion.1D'[4]' -stim_label 5 y -stim_base 5 \
# -stim_file 6 rest/qualitycontrol/motion/${subj}_fMRI_vr_motion.1D'[5]' -stim_label 6 z -stim_base 6 \
# -stim_file 7 rest/qualitycontrol/motion/${subj}_fMRI_vr_motion_deriv.1D'[0]' -stim_label 7 droll -stim_base 7 \
# -stim_file 8 rest/qualitycontrol/motion/${subj}_fMRI_vr_motion_deriv.1D'[1]' -stim_label 8 dpitch -stim_base 8 \
# -stim_file 9 rest/qualitycontrol/motion/${subj}_fMRI_vr_motion_deriv.1D'[2]' -stim_label 9 dyaw -stim_base 9 \
# -stim_file 10 rest/qualitycontrol/motion/${subj}_fMRI_vr_motion_deriv.1D'[3]' -stim_label 10 dx -stim_base 10 \
# -stim_file 11 rest/qualitycontrol/motion/${subj}_fMRI_vr_motion_deriv.1D'[4]' -stim_label 11 dy -stim_base 11 \
# -stim_file 12 rest/qualitycontrol/motion/${subj}_fMRI_vr_motion_deriv.1D'[5]' -stim_label 12 dz -stim_base 12 \
# -stim_file 13 ${subj}_wm_regressor.1D'[0]' -stim_label 13 wm -stim_base 13 \
# -stim_file 14 ${subj}_vent_regressor.1D'[0]' -stim_label 14 vent -stim_base 14 \
# -stim_file 15 ${subj}_wm_regressor_deriv.1D'[0]' -stim_label 15 dwm -stim_base 15 \
# -stim_file 16 ${subj}_vent_regressor_deriv.1D'[0]' -stim_label 16 dvent -stim_base 16 \
# -jobs 2 \
# -errts X.xmat.1D
# -x1D_stop

##STEP6##
# rm Decon*
cd ${subjectsDirectory}
echo
echo "Filtering..."
3dTproject -input Decon.xmat.1D -passband 0.008 0.08 -quiet -prefix rest/${subj}_rest_mcf_MNI_b6_nuisreg_bp.nii.gz

Able to complete 3dDeconvolve and generate a .1D file, but 3dTproject doesn't run.

If you can please assist, thank you so much!