Hi Rick,

Thanks for your reply. Now I am using afni_proc.py following example 11, as suggested. We get this error message and can't figure out what is causing the problem here.

** error: option -tshift_opts_ts follows unknown arg #11 (-anat_follower_ROI)
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** failed command (get_user_opts):

Below is the command I ran. Note that this is for event-related fMRI (not resting state).

afni_proc.py -subj_id afni_proc_Results \
-blocks despike tshift align volreg regress \
-copy_anat anat+orig \
-anat_follower_ROI Ventricles epi aseg_Ventricles+orig \
-anat_follower_ROI WM epi wm_eroded+orig \ #we eroded the wm ourselves.
-dset fm_run1+orig.HEAD \
-tcat_remove_first 0 \
-tshift_opts_ts 'ignore 5' \
-volreg_align_e2a \
-volreg_align_to first \
-master_epi_dxyz 3.0 \
-regress_ROI_PC Ventricles 3 \
-regress_ROI WM \
-regress_anaticor_fast \
-regress_anaticor_label WM \
-regress_censor_motion 0.2 \
-regress_censor_outliers 0.1 \
-regress_skip_first_outliers 5 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_errts \
-regress_run_clustsim no

Any idea what is the problem here? Thanks a lot!

Best,
Marina