#!/usr/bin/env tcsh

# ------------------------------------------------------------
# ------------ pretend this is resting state data ------------
#
# apply Example 10 from "afni_proc.py -help"
# ------------------------------------------------------------

set top_dir   = FT
set subj      = FT.rest

# run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id $subj                                      \
        -script proc.$subj -scr_overwrite                        \
        -blocks despike tshift align tlrc volreg blur mask regress \
        -copy_anat $top_dir/FT_anat+orig                         \
        -tcat_remove_first_trs 2                                 \
        -dsets                                                   \
            $top_dir/FT_epi_r1+orig.HEAD                         \
            $top_dir/FT_epi_r2+orig.HEAD                         \
            $top_dir/FT_epi_r3+orig.HEAD                         \
        -volreg_align_to MIN_OUTLIER                             \
        -volreg_align_e2a                                        \
        -volreg_tlrc_warp                                        \
        -blur_size 4.0                                           \
        -mask_segment_anat yes                                   \
        -mask_segment_erode yes                                  \
        -regress_motion_per_run                                  \
        -regress_censor_motion 0.2                               \
        -regress_censor_outliers 0.1                             \
        -regress_bandpass 0.01 0.1                               \
        -regress_apply_mot_types demean deriv                    \
        -regress_ROI WMe                                         \
        -regress_run_clustsim no                                 \
        -regress_est_blur_errts