#!/usr/bin/env tcsh

# ------------------------------------------------------------
# ------------ pretend this is resting state data ------------
#
# apply Example 11 from "afni_proc.py -help"
# This is considered to be a very modern example.
# Just process one run.
# ------------------------------------------------------------

set top_dir   = FT
set sdir      = $top_dir/SUMA
set subj      = FT.rest.11

# note: we might use the Qwarp NL results from @SSwarper, but
#       that means changing from TT space to MNI, if we care

# 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 scale regress \
        -radial_correlate_blocks tcat volreg regress                     \
        -copy_anat Qwarp/anat_warped/anatSS.FT.nii                       \
        -anat_follower anat_w_skull anat $top_dir/FT_anat+orig           \
        -anat_has_skull no                                               \
        -anat_follower_ROI aaseg  anat $sdir/aparc.a2009s+aseg.nii.gz    \
        -anat_follower_ROI aeseg  epi  $sdir/aparc.a2009s+aseg.nii.gz    \
        -anat_follower_ROI FSvent epi  $sdir/fs_ap_latvent.nii.gz        \
        -anat_follower_ROI FSWe   epi  $sdir/fs_ap_wm.nii.gz             \
        -anat_follower_erode FSvent FSWe                                 \
        -dsets $top_dir/FT_epi_r?+orig.HEAD                              \
        -tcat_remove_first_trs 2                                         \
        -align_opts_aea -cost lpc+ZZ -giant_move -check_flip             \
        -tlrc_base MNI152_2009_template_SSW.nii.gz                       \
        -tlrc_NL_warp                                                    \
        -tlrc_NL_warped_dsets                                            \
           Qwarp/anat_warped/anatQQ.FT.nii                               \
           Qwarp/anat_warped/anatQQ.FT.aff12.1D                          \
           Qwarp/anat_warped/anatQQ.FT_WARP.nii                          \
        -volreg_align_to MIN_OUTLIER                                     \
        -volreg_align_e2a                                                \
        -volreg_tlrc_warp                                                \
        -blur_size 4.0                                                   \
        -mask_epi_anat yes                                               \
        -regress_ROI_PC FSvent 3                                         \
        -regress_ROI_PC_per_run FSvent                                   \
        -regress_make_corr_vols aeseg FSvent                             \
        -regress_anaticor_fast                                           \
        -regress_anaticor_label FSWe                                     \
        -regress_motion_per_run                                          \
        -regress_censor_motion 0.2                                       \
        -regress_censor_outliers 0.05                                    \
        -regress_apply_mot_types demean deriv                            \
        -regress_est_blur_epits                                          \
        -regress_est_blur_errts                                          \
        -regress_run_clustsim no                                         \
        -html_review_style pythonic