. 2017 Dec 7;39(3):1187–1206. doi: 10.1002/hbm.23909

Table 5.

A compact tcsh script that contains the succinct, selected afni_proc.py command used to generate the full processing pipeline ( $> 500$ lines) in AFNI for this study

#!/bin/tcsh

# Set top level directory structure

set subjID = $1

set currDir = 'pwd’

set anatDir =./freesurfer.anat/${subjID}/mri

set epiDir = afni

set stimDir = stim.files

# miscellaneous parameters or options

set motion_max = 1.0; set delete_nfirst = 4; set costfunc = lpc+zz

# run afni_proc.py to create a single subject processing script

afni_proc.py ‐subj_id ${subjID}\

‐script proc.script.FINAL.1.20.17.${subjID} ‐scr_overwrite\

‐blocks despike tshift align tlrc volreg blur mask scale regress\

‐copy_anat $anatDir/brainmask.nii\

‐tcat_remove_first_trs $delete_nfirst\

‐dsets $epiDir/r01+orig $epiDir/r02+orig $epiDir/r03+orig\

‐blur_size 5 ‐out_dir NL.results\

‐anat_unif_GM no ‐anat_has_skull no ‐tlrc_NL_warp\

‐volreg_align_e2a ‐volreg_align_to MIN_OUTLIER ‐volreg_tlrc_warp\

‐align_opts_aea ‐cost $costfunc ‐giant_move ‐AddEdge\

‐regress_stim_times\

$stimDir/${subjID}n_A_timing.1D\

$stimDir/${subjID}a50_timing.1D\

$stimDir/${subjID}a100_timing.1D\

$stimDir/${subjID}a150_timing.1D\

$stimDir/${subjID}n_F_timing.1D\

$stimDir/${subjID}f50_timing.1D\

$stimDir/${subjID}f100_timing.1D\

$stimDir/${subjID}f150_timing.1D\

$stimDir/${subjID}n_H_timing.1D\

$stimDir/${subjID}h50_timing.1D\

$stimDir/${subjID}h100_timing.1D\

$stimDir/${subjID}h150_timing.1D\

$stimDir/${subjID}w_timing.1D\

‐regress_stim_labels\

n_A a50 a100 a150 n_F f50 f100 f150 n_H h50 h100 h150 w\

‐regress_local_times ‐regress_censor_outliers 0.1\

‐regress_basis 'BLOCK(2,1)’ ‐regress_censor_motion $motion_max\

‐regress_est_blur_epits ‐regress_est_blur_errts\

‐regress_reml_exec ‐regress_compute_fitts ‐regress_opts_3dD\

‐allzero_OK ‐regress_opts_reml ‐GOFORIT\

‐regress_make_ideal_sum sum_ideal.1D\

‐gltsym 'SYM: +n_A +a50 +a100 +a150 +n_F +f50 +f100 +f150 +n_H +h50 +h100 +h150 ’\

‐glt_label 1 Positive_Control

tcsh ‐xef proc.script.${subjID} |& tee proc.script.${subjID}.output

Note. To implement across the group, one simply loops through a list of subjects, entering the given file name as the sole command line argument, which is passed to the variable $subjID. Here, stimulus variables are encoded as: h = happy, n = neutral, f = fearful, w = wrong; and each is followed by the duration (50, 100, 150 s).