Hello. I used afni_proc.py to generate the script below.
I have a few questions:

(1) I wanted to remove the first 6 TRs, and so under the autoblock: tcat, you see '[6..179]' .
Moving a little further down, you see the 3dbucket command:
3dbucket -prefix vr_base pb02.$subj.r01.tshift+orig"[0]"
Question: should the sub-brick index be [0] (as generated by afni_proc) or [6]?

(2) Same question for -epi_base option in the align_epi_anat.py command. Should it be -epi_base 0 or -epi_base 6 ?

(3) In the 3dvolreg command, is this option correct -base vr_base+orig ? Is a sub-brick index required, e.g., -base vr_base+orig[6]? Is there any difference between the two, with and without an index?

(4) Instead of doing the e2a registration align_epi_anat.py first with the option -volreg off and then the realignment 3dvolreg, can I do the 3dvolreg first? How should I change the script if I can do so?

Many thanks,
Duong

================= script ==================================
#!/bin/tcsh -xef

echo "auto-generated by afni_proc.py, Fri May 5 16:10:02 2017"
echo "(version 5.13, March 27, 2017)"
echo "execution started: `date`"

# execute via :
# tcsh -xef ./proc_subj1.sh |& tee ./output.proc_subj1.sh

# =========================== auto block: setup ============================
# script setup

# take note of the AFNI version
afni -ver

# check that the current AFNI version is recent enough
afni_history -check_date 23 Sep 2016
if ( $status ) then
echo "** this script requires newer AFNI binaries (than 23 Sep 2016)"
echo " (consider: @update.afni.binaries -defaults)"
exit
endif

# the user may specify a single subject to run with
if ( $#argv > 0 ) then
set subj = $argv[1]
else
set subj = 20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917
endif

# assign output directory name
set output_dir = 20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917.results

# verify that the results directory does not yet exist
if ( -d $output_dir ) then
echo output dir "$subj.results" already exists
exit
endif

# set list of runs
set runs = (`count -digits 2 1 2`)

# create results and stimuli directories
mkdir $output_dir
mkdir $output_dir/stimuli

# copy stim files into stimulus directory
cp ./stim_times/left.txt ./stim_times/right.txt ./stim_times/up.txt \
./stim_times/down.txt $output_dir/stimuli

# copy anatomy to results dir
3dcopy \
20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917/anatHeadBrik/anat.r1+orig \
$output_dir/anat.r1

# ============================ auto block: tcat ============================
# apply 3dTcat to copy input dsets to results dir, while
# removing the first 6 TRs
3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \
20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917/funcHeadBrik/epi.r1+orig'[6..179]'
3dTcat -prefix $output_dir/pb00.$subj.r02.tcat \
20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917/funcHeadBrik/epi.r2+orig'[6..179]'

# and make note of repetitions (TRs) per run
set tr_counts = ( 174 174 )

# -------------------------------------------------------
# enter the results directory (can begin processing data)
cd $output_dir


# ========================== auto block: outcount ==========================
# data check: compute outlier fraction for each volume
touch out.pre_ss_warn.txt
foreach run ( $runs )
3dToutcount -automask -fraction -polort 3 -legendre \
pb00.$subj.r$run.tcat+orig > outcount.r$run.1D

# censor outlier TRs per run, ignoring the first 0 TRs
# - censor when more than 0.1 of automask voxels are outliers
# - step() defines which TRs to remove via censoring
1deval -a outcount.r$run.1D -expr "1-step(a-0.1)" > rm.out.cen.r$run.1D

# outliers at TR 0 might suggest pre-steady state TRs
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
echo "** TR #0 outliers: possible pre-steady state TRs in run $run" \
>> out.pre_ss_warn.txt
endif
end

# catenate outlier counts into a single time series
cat outcount.r*.1D > outcount_rall.1D

# catenate outlier censor files into a single time series
cat rm.out.cen.r*.1D > outcount_${subj}_censor.1D

# ================================ despike =================================
# apply 3dDespike to each run
foreach run ( $runs )
3dDespike -NEW -nomask -prefix pb01.$subj.r$run.despike \
pb00.$subj.r$run.tcat+orig
end

# ================================= tshift =================================
# time shift data so all slice timing is the same
foreach run ( $runs )
3dTshift -slice 17 -quintic -prefix pb02.$subj.r$run.tshift \
-tpattern alt+z \
pb01.$subj.r$run.despike+orig
end

# --------------------------------
# extract volreg registration base
3dbucket -prefix vr_base pb02.$subj.r01.tshift+orig"[0]"

# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new anat will be intermediate, stripped, anat.r1_ns+orig)
align_epi_anat.py -anat2epi -anat anat.r1+orig \
-save_skullstrip -suffix _al_junk \
-epi vr_base+orig -epi_base 0 \
-epi_strip 3dAutomask \
-giant_move \
-volreg off -tshift off

# ================================= volreg =================================
# align each dset to base volume, align to anat

# register and warp
foreach run ( $runs )
# register each volume to the base
3dvolreg -verbose -zpad 1 -base vr_base+orig \
-1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run \
-cubic \
-1Dmatrix_save mat.r$run.vr.aff12.1D \
pb02.$subj.r$run.tshift+orig

# create an all-1 dataset to mask the extents of the warp
3dcalc -overwrite -a pb02.$subj.r$run.tshift+orig -expr 1 \
-prefix rm.epi.all1

# catenate volreg/epi2anat xforms
cat_matvec -ONELINE \
anat.r1_al_junk_mat.aff12.1D -I \
mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D

# apply catenated xform: volreg/epi2anat
3dAllineate -base anat.r1_ns+orig \
-input pb02.$subj.r$run.tshift+orig \
-1Dmatrix_apply mat.r$run.warp.aff12.1D \
-mast_dxyz 3 \
-prefix rm.epi.nomask.r$run

# warp the all-1 dataset for extents masking
3dAllineate -base anat.r1_ns+orig \
-input rm.epi.all1+orig \
-1Dmatrix_apply mat.r$run.warp.aff12.1D \
-mast_dxyz 3 -final NN -quiet \
-prefix rm.epi.1.r$run

# make an extents intersection mask of this run
3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+orig
end

# make a single file of registration params
cat dfile.r*.1D > dfile_rall.1D

# ----------------------------------------
# create the extents mask: mask_epi_extents+orig
# (this is a mask of voxels that have valid data at every TR)
3dMean -datum short -prefix rm.epi.mean rm.epi.min.r*.HEAD
3dcalc -a rm.epi.mean+orig -expr 'step(a-0.999)' -prefix mask_epi_extents

# and apply the extents mask to the EPI data
# (delete any time series with missing data)
foreach run ( $runs )
3dcalc -a rm.epi.nomask.r$run+orig -b mask_epi_extents+orig \
-expr 'a*b' -prefix pb03.$subj.r$run.volreg
end

# warp the volreg base EPI dataset to make a final version
cat_matvec -ONELINE anat.r1_al_junk_mat.aff12.1D -I > mat.basewarp.aff12.1D

3dAllineate -base anat.r1_ns+orig \
-input vr_base+orig \
-1Dmatrix_apply mat.basewarp.aff12.1D \
-mast_dxyz 3 \
-prefix final_epi_vr_base

# create an anat_final dataset, aligned with stats
3dcopy anat.r1_ns+orig anat_final.$subj

# record final registration costs
3dAllineate -base final_epi_vr_base+orig -allcostX \
-input anat_final.$subj+orig |& tee out.allcostX.txt

# -----------------------------------------
# warp anat follower datasets (identity: resample)

# ================================== tlrc ==================================
# warp anatomy to standard space
@auto_tlrc -base TT_icbm452+tlrc -input anat.r1_ns+orig -no_ss \
-init_xform AUTO_CENTER

# store forward transformation matrix in a text file
cat_matvec anat.r1_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D

# ================================== blur ==================================
# blur each volume of each run
foreach run ( $runs )
3dmerge -1blur_fwhm 7 -doall -prefix pb04.$subj.r$run.blur \
pb03.$subj.r$run.volreg+orig
end

# ================================== mask ==================================
# create 'full_mask' dataset (union mask)
foreach run ( $runs )
3dAutomask -dilate 1 -prefix rm.mask_r$run pb04.$subj.r$run.blur+orig
end

# create union of inputs, output type is byte
3dmask_tool -inputs rm.mask_r*+orig.HEAD -union -prefix full_mask.$subj

# ---- create subject anatomy mask, mask_anat.$subj+orig ----
# (resampled from aligned anat)
3dresample -master full_mask.$subj+orig -input anat.r1_ns+orig \
-prefix rm.resam.anat

# convert to binary anat mask; fill gaps and holes
3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+orig \
-prefix mask_anat.$subj

# compute overlaps between anat and EPI masks
3dABoverlap -no_automask full_mask.$subj+orig mask_anat.$subj+orig \
|& tee out.mask_ae_overlap.txt

# note Dice coefficient of masks, as well
3ddot -dodice full_mask.$subj+orig mask_anat.$subj+orig \
|& tee out.mask_ae_dice.txt

# ================================= scale ==================================
# scale each voxel time series to have a mean of 100
# (be sure no negatives creep in)
# (subject to a range of [0,200])
foreach run ( $runs )
3dTstat -prefix rm.mean_r$run pb04.$subj.r$run.blur+orig
3dcalc -a pb04.$subj.r$run.blur+orig -b rm.mean_r$run+orig \
-c mask_epi_extents+orig \
-expr 'c * min(200, a/b*100)*step(a)*step(b)' \
-prefix pb05.$subj.r$run.scale
end

# ================================ regress =================================

# compute de-meaned motion parameters (for use in regression)
1d_tool.py -infile dfile_rall.1D -set_nruns 2 \
-demean -write motion_demean.1D

# compute motion parameter derivatives (just to have)
1d_tool.py -infile dfile_rall.1D -set_nruns 2 \
-derivative -demean -write motion_deriv.1D

# create censor file motion_${subj}_censor.1D, for censoring motion
1d_tool.py -infile dfile_rall.1D -set_nruns 2 \
-show_censor_count -censor_prev_TR \
-censor_motion 0.3 motion_${subj}

# combine multiple censor files
1deval -a motion_${subj}_censor.1D -b outcount_${subj}_censor.1D \
-expr "a*b" > censor_${subj}_combined_2.1D

# note TRs that were not censored
set ktrs = `1d_tool.py -infile censor_${subj}_combined_2.1D \
-show_trs_uncensored encoded`

# ------------------------------
# run the regression analysis
3dDeconvolve -input pb05.$subj.r*.scale+orig.HEAD \
-censor censor_${subj}_combined_2.1D \
-polort 3 \
-local_times \
-num_stimts 10 \
-stim_times 1 stimuli/left.txt 'BLOCK(30,1)' \
-stim_label 1 L \
-stim_times 2 stimuli/right.txt 'BLOCK(30,1)' \
-stim_label 2 R \
-stim_times 3 stimuli/up.txt 'BLOCK(30,1)' \
-stim_label 3 U \
-stim_times 4 stimuli/down.txt 'BLOCK(30,1)' \
-stim_label 4 D \
-stim_file 5 motion_demean.1D'[0]' -stim_base 5 -stim_label 5 roll \
-stim_file 6 motion_demean.1D'[1]' -stim_base 6 -stim_label 6 pitch \
-stim_file 7 motion_demean.1D'[2]' -stim_base 7 -stim_label 7 yaw \
-stim_file 8 motion_demean.1D'[3]' -stim_base 8 -stim_label 8 dS \
-stim_file 9 motion_demean.1D'[4]' -stim_base 9 -stim_label 9 dL \
-stim_file 10 motion_demean.1D'[5]' -stim_base 10 -stim_label 10 dP \
-num_glt 4 \
-gltsym 'SYM: +L' \
-glt_label 1 L-b \
-gltsym 'SYM: +R' \
-glt_label 2 R-b \
-gltsym 'SYM: +L -R' \
-glt_label 3 L-R \
-gltsym 'SYM: +U -D' \
-glt_label 4 U-D \
-jobs 4 \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.$subj \
-errts errts.${subj} \
-bucket stats.$subj


# if 3dDeconvolve fails, terminate the script
if ( $status != 0 ) then
echo '---------------------------------------'
echo '** 3dDeconvolve error, failing...'
echo ' (consider the file 3dDeconvolve.err)'
exit
endif


# display any large pairwise correlations from the X-matrix
1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt

# -- execute the 3dREMLfit script, written by 3dDeconvolve --
tcsh -x stats.REML_cmd

# if 3dREMLfit fails, terminate the script
if ( $status != 0 ) then
echo '---------------------------------------'
echo '** 3dREMLfit error, failing...'
exit
endif


# create an all_runs dataset to match the fitts, errts, etc.
3dTcat -prefix all_runs.$subj pb05.$subj.r*.scale+orig.HEAD

# --------------------------------------------------
# create a temporal signal to noise ratio dataset
# signal: if 'scale' block, mean should be 100
# noise : compute standard deviation of errts
3dTstat -mean -prefix rm.signal.all all_runs.$subj+orig"[$ktrs]"
3dTstat -stdev -prefix rm.noise.all errts.${subj}_REML+orig"[$ktrs]"
3dcalc -a rm.signal.all+orig \
-b rm.noise.all+orig \
-c full_mask.$subj+orig \
-expr 'c*a/b' -prefix TSNR.$subj

# ---------------------------------------------------
# compute and store GCOR (global correlation average)
# (sum of squares of global mean of unit errts)
3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}_REML+orig
3dmaskave -quiet -mask full_mask.$subj+orig rm.errts.unit+orig \
> gmean.errts.unit.1D
3dTstat -sos -prefix - gmean.errts.unit.1D\' > out.gcor.1D
echo "-- GCOR = `cat out.gcor.1D`"

# ---------------------------------------------------
# compute correlation volume
# (per voxel: average correlation across masked brain)
# (now just dot product with average unit time series)
3dcalc -a rm.errts.unit+orig -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP
3dTstat -sum -prefix corr_brain rm.DP+orig

# create ideal files for fixed response stim types
1dcat X.nocensor.xmat.1D'[8]' > ideal_L.1D
1dcat X.nocensor.xmat.1D'[9]' > ideal_R.1D
1dcat X.nocensor.xmat.1D'[10]' > ideal_U.1D
1dcat X.nocensor.xmat.1D'[11]' > ideal_D.1D

# --------------------------------------------------------
# compute sum of non-baseline regressors from the X-matrix
# (use 1d_tool.py to get list of regressor colums)
set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest`
3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D"[$reg_cols]"

# also, create a stimulus-only X-matrix, for easy review
1dcat X.nocensor.xmat.1D"[$reg_cols]" > X.stim.xmat.1D

# ============================ blur estimation =============================
# compute blur estimates
touch blur_est.$subj.1D # start with empty file

# create directory for ACF curve files
mkdir files_ACF

# -- estimate blur for each run in epits --
touch blur.epits.1D

# restrict to uncensored TRs, per run
foreach run ( $runs )
set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \
-show_trs_run $run`
if ( $trs == "" ) continue
3dFWHMx -detrend -mask full_mask.$subj+orig \
-ACF files_ACF/out.3dFWHMx.ACF.epits.r$run.1D \
all_runs.$subj+orig"[$trs]" >> blur.epits.1D
end

# compute average FWHM blur (from every other row) and append
set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` )
echo average epits FWHM blurs: $blurs
echo "$blurs # epits FWHM blur estimates" >> blur_est.$subj.1D

# compute average ACF blur (from every other row) and append
set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` )
echo average epits ACF blurs: $blurs
echo "$blurs # epits ACF blur estimates" >> blur_est.$subj.1D

# -- estimate blur for each run in errts --
touch blur.errts.1D

# restrict to uncensored TRs, per run
foreach run ( $runs )
set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \
-show_trs_run $run`
if ( $trs == "" ) continue
3dFWHMx -detrend -mask full_mask.$subj+orig \
-ACF files_ACF/out.3dFWHMx.ACF.errts.r$run.1D \
errts.${subj}+orig"[$trs]" >> blur.errts.1D
end

# compute average FWHM blur (from every other row) and append
set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` )
echo average errts FWHM blurs: $blurs
echo "$blurs # errts FWHM blur estimates" >> blur_est.$subj.1D

# compute average ACF blur (from every other row) and append
set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` )
echo average errts ACF blurs: $blurs
echo "$blurs # errts ACF blur estimates" >> blur_est.$subj.1D

# -- estimate blur for each run in err_reml --
touch blur.err_reml.1D

# restrict to uncensored TRs, per run
foreach run ( $runs )
set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \
-show_trs_run $run`
if ( $trs == "" ) continue
3dFWHMx -detrend -mask full_mask.$subj+orig \
-ACF files_ACF/out.3dFWHMx.ACF.err_reml.r$run.1D \
errts.${subj}_REML+orig"[$trs]" >> blur.err_reml.1D
end

# compute average FWHM blur (from every other row) and append
set blurs = ( `3dTstat -mean -prefix - blur.err_reml.1D'{0..$(2)}'\'` )
echo average err_reml FWHM blurs: $blurs
echo "$blurs # err_reml FWHM blur estimates" >> blur_est.$subj.1D

# compute average ACF blur (from every other row) and append
set blurs = ( `3dTstat -mean -prefix - blur.err_reml.1D'{1..$(2)}'\'` )
echo average err_reml ACF blurs: $blurs
echo "$blurs # err_reml ACF blur estimates" >> blur_est.$subj.1D


# add 3dClustSim results as attributes to any stats dset
mkdir files_ClustSim

# run Monte Carlo simulations using method 'ACF'
set params = ( `grep ACF blur_est.$subj.1D | tail -n 1` )
3dClustSim -both -mask full_mask.$subj+orig -acf $params[1-3] \
-cmd 3dClustSim.ACF.cmd -prefix files_ClustSim/ClustSim.ACF

# run 3drefit to attach 3dClustSim results to stats
set cmd = ( `cat 3dClustSim.ACF.cmd` )
$cmd stats.$subj+orig stats.${subj}_REML+orig


# ================== auto block: generate review scripts ===================

# generate a review script for the unprocessed EPI data
gen_epi_review.py -script @epi_review.$subj \
-dsets pb00.$subj.r*.tcat+orig.HEAD

# generate scripts to review single subject results
# (try with defaults, but do not allow bad exit status)
gen_ss_review_scripts.py -mot_limit 0.3 -out_limit 0.1 -exit0

# ========================== auto block: finalize ==========================

# remove temporary files
\rm -f rm.*

# if the basic subject review script is here, run it
# (want this to be the last text output)
if ( -e @ss_review_basic ) ./@ss_review_basic |& tee out.ss_review.$subj.txt

# return to parent directory
cd ..

echo "execution finished: `date`"




# ==========================================================================
# script generated by the command:
#
# afni_proc.py -subj_id \
# 20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917 \
# -script ./proc_subj1.sh -out_dir \
# 20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917.results \
# -dsets \
# ./20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917/funcHeadBrik/epi.r1+orig.HEAD \
# ./20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917/funcHeadBrik/epi.r2+orig.HEAD \
# -blocks despike tshift align volreg tlrc blur mask scale regress \
# -anat_has_skull yes -tlrc_base TT_icbm452+tlrc -tcat_remove_first_trs 6 \
# -tcat_remove_last_trs 4 -tshift_opts_ts -tpattern alt+z \
# -tshift_align_to -slice 17 -copy_anat \
# ./20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917/anatHeadBrik/anat.r1+orig \
# -align_opts_aea -giant_move -volreg_align_to first -volreg_align_e2a \
# -tlrc_opts_at -init_xform AUTO_CENTER -blur_size 7 -regress_stim_times \
# ./stim_times/left.txt ./stim_times/right.txt ./stim_times/up.txt \
# ./stim_times/down.txt -regress_stim_labels L R U D -regress_local_times \
# -regress_reml_exec -regress_est_blur_epits -regress_est_blur_errts \
# -regress_basis_multi 'BLOCK(30,1)' 'BLOCK(30,1)' 'BLOCK(30,1)' \
# 'BLOCK(30,1)' -regress_censor_outliers 0.1 -regress_censor_motion 0.3 \
# -regress_opts_3dD -num_glt 4 -gltsym 'SYM: +L -0' -glt_label 1 L-b \
# -gltsym 'SYM: +R -0' -glt_label 2 R-b -gltsym 'SYM: +L -R' -glt_label 3 \
# L-R -gltsym 'SYM: +U -D' -glt_label 3 U-D -jobs 4 -execute