Thanks so much Rick for your time explaining.

We are running the AP in an online web server where we have to run each AP script manually and cannot loop through subjects to add the stim timing files (it will also take a bit of infrastructure upgrade to add the timing files to this web platform), hence why we would like to run the 3ddeconvolve separately on our computer via bash for example. We do include a regress block to clean up the data in the web-based AP script, see below the command. If we want to run 3ddeconvolve on the output of the AP (with basic regress and preprocessing), do we use the all_runs output file or the eerts?

/root/abin/afni_proc.py -dsets /flywheel/v0/input/fMRI/1003048345.nii.gz -copy_anat /flywheel/v0/input/anat/1003048345.nii.gz -blocks despike tshift align tlrc volreg blur mask scale regress -blur_size 4 -regress_apply_mot_types deriv -regress_bandpass 0.01 0.1 -regress_est_blur_epits -regress_est_blur_errts -regress_motion_per_run -regress_run_clustsim yes -subj_id SUBJ -tcat_remove_first_trs 0 -volreg_align_e2a -volreg_tlrc_warp