AFNI Class 04: 09/06/2019

afni_proc.py for Resting and Nonlinear
#!/bin/csh
# Example 11b. Similar to 11, but without FreeSurfer.
# 3dcalc -a /rpool/apps/AFNI/abin_201710/TT_desai_dd_mpm+tlrc -expr 'amongst(a,152,170)' -prefix template_ventricle
# 3dresample -dxyz 4 4 4 -inset template_ventricle+tlrc -prefix template_ventricle_4mm.nii.gz
# Be explicit with 2.5mm, using '-volreg_warp_dxyz 2.5'.
# Use template TT_N27+tlrc, to be aligned with the desai atlas.
# No -anat_follower options, but use -mask_import to import the
# template_ventricle_2.5mm dataset (and call it Tvent).
# Use -mask_intersect to intersect ventricle mask with the subject's
# CSFe mask, making a more reliable subject ventricle mask (Svent).
# Ventrile principle components are created as per-run regressors.
# Make WMe and Svent correlation volumes, which are just for
# entertainment purposes anyway.
# Run the cluster simulation.

afni_proc.py -subj_id VNS_01RS_fm_NL_RSFC \
 -blocks despike tshift align tlrc volreg mask blur regress \
 -copy_anat VNS_01.nii.gz  -dsets VNS_01RestingVNS_fm.nii.gz  \
 -tcat_remove_first_trs 2  -align_opts_aea -cost lpc+ZZ \
 -tlrc_base MNI_avg152T1+tlrc  -tlrc_NL_warp  -volreg_align_to MIN_OUTLIER  -volreg_align_e2a \
 -volreg_tlrc_warp  -volreg_warp_dxyz 4  -mask_segment_anat yes  -mask_segment_erode yes \
 -mask_import Tvent /rpool/home/asimmons/data/VNS1/AFNI_RS/file/template_ventricle_4mm.nii.gz \
 -mask_intersect Svent CSFe Tvent  -blur_to_fwhm -blur_size 6 -blur_in_mask yes -regress_motion_per_run \
 -regress_ROI_PC Svent 3 -regress_ROI_PC_per_run Svent \
 -regress_make_corr_vols WMe Svent \
 -regress_anaticor_fast  -regress_censor_outliers 0.1 \
 -regress_apply_mot_types demean deriv \
 -regress_est_blur_epits  -regress_est_blur_errts \
 -regress_RSFC  -regress_bandpass 0.01 0.1 \
 -regress_run_clustsim yes

Which creates: proc.VNS_01RS_fm_NL_RSFC

NL with task and @SSwarper:
   first strip data:
      @SSwarper ${subj}.nii.gz ${subj}
   then you can add to your afni_proc.py the following:
    -tlrc_NL_warp -tlrc_NL_warped_dsets anatQQ.${subj}.nii anatQQ.aff12.1D anatQQ.${subj}_WARP.nii
   an example of a proc script: