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- #!/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
- # 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 \
- -anat_follower_ROI aaseg anat $sdir/aparc.a2009s+aseg.nii \
- -anat_follower_ROI aeseg epi $sdir/aparc.a2009s+aseg.nii \
- -anat_follower_ROI FSvent epi $sdir/FT_vent.nii \
- -anat_follower_ROI FSWe epi $sdir/FT_white.nii \
- -dsets $top_dir/FT_epi_r?+orig.HEAD \
- -tcat_remove_first_trs 2 \
- -tlrc_base MNI_caez_N27+tlrc \
- -tlrc_NL_warp \
- -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 FSWe \
- -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 0.1 \
- -regress_apply_mot_types demean deriv \
- -regress_est_blur_epits \
- -regress_est_blur_errts \
- -regress_run_clustsim no
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