pre-processing concatenated runs

Dear AFNI experts,

I am pre-processing data that is concatenated across 3 runs (RANTI.1, 2, 3) using the script below. Although I would like the data aggregated across runs for my subsequent GLTs, I would like to pre-process the data independent (ie apply motion correction and alignment separately for each run) as runs were sometimes separated by a few minutes/movement due to re-positioning of external equipment (eye movement system) between runs. Is this possible? If so, are there specifications I should indicate within a single pre-processing script, or should I develop separate scripts for each run and then concatenate after pre-processing has been completed?

Thanks very much,
Kathryn -subj_id $subj
-script proc.$subj -scr_overwrite
-blocks tshift align tlrc volreg blur mask scale regress
-copy_anat $anat_dir/anatSS.$subj.nii
-tcat_remove_first_trs 0
-align_opts_aea -ginormous_move -deoblique on -cost lpc+ZZ
-volreg_align_to MIN_OUTLIER
-volreg_opts_vr -heptic
-volreg_tlrc_warp -tlrc_base /usr/bin/abin/MNI152_2009_template_SSW.nii.gz
-blur_size 4.0
Catch_Cue_N_Onset Catch_Cue_R_Onset Task_N Task_R
-regress_basis ‘GAM’
-regress_censor_motion 0.5
-regress_apply_mot_types demean deriv
-gltsym ‘SYM: Catch_Cue_R_Onset -Catch_Cue_N_Onset’ -glt_label 1
-gltsym ‘SYM: Task_R - Task_N’ -glt_label 2
-regress_make_ideal_sum sum_ideal.1D

Depending on how much motion and reshimming there is, you may want to add these two parameters:

    -volreg_post_vr_allin yes/no : do cross-run alignment of reg bases

    -volreg_pvra_base_index INDEX : specify per run INDEX for post_vr_allin

These allow each run to have motion correction handled separately and then affinely aligned to a base volume.