The SSwarper seemed to work perfectly (see attached picture). I modified the cmd file as you suggested (I think i did this correctly) but the final outputted images are as warped as before (see attached picture of anat_final). Maybe the deskulling was not the problem or maybe I did something else wrong. Can you advise me?

Here is my modifed cmd file:

afni_proc.py -subj_id $subj \
-script proc.$subj -scr_overwrite \
-blocks tshift align tlrc volreg blur mask scale regress \
-copy_anat ${anat_dir}/SSW/anatSS.${subj}.nii \
-tcat_remove_first_trs 0 \
-dsets \
$epi_dir/MID+orig.HEAD \
-anat_has_skull no \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-tlrc_base ${template} \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets \
${anat_dir}/SSW/anatQQ.${subj}.nii \
${anat_dir}/SSW/anatQQ.${subj}.aff12.1D \
${anat_dir}/SSW/anatQQ.${subj}_WARP.nii \
-dsets \
$epi_dir/MID+orig.HEAD \
-blur_size 4.0 \
-regress_stim_times \
$stim_dir/CII1085_ATNtd.txt \
$stim_dir/CII1085_ATRHtd.txt \
$stim_dir/CII1085_ATRLtd.txt \
$stim_dir/CII1085_ATLHtd.txt \
$stim_dir/CII1085_ATLLtd.txt \
$stim_dir/CII1085_FRHHtd.txt \
$stim_dir/CII1085_FRHMtd.txt \
$stim_dir/CII1085_FRLHtd.txt \
$stim_dir/CII1085_FRLMtd.txt \
$stim_dir/CII1085_FLLHtd.txt \
$stim_dir/CII1085_FLLMtd.txt \
$stim_dir/CII1085_FLHHtd.txt \
$stim_dir/CII1085_FLHMtd.txt \
$stim_dir/CII1085_FNHtd.txt \
$stim_dir/CII1085_FNMtd.txt \
-regress_opts_3dD \
-num_glt 12 \
-gltsym 'SYM:ATRHtd -ATNtd' \
-glt_label 1 AntTarg_RewHi-Neu \
-gltsym 'SYM:ATRLtd -ATNtd' \
-glt_label 2 AntTarg_RewLow-Neu \
-gltsym 'SYM:ATLHtd -ATNtd' \
-glt_label 3 AntTarg_LossHi-Neu \
-gltsym 'SYM:ATLLtd -ATNtd' \
-glt_label 4 AntTarg_LossLow-Neu \
-gltsym 'SYM:FRHHtd -FNHtd' \
-glt_label 5 FbHit_RewHi-Neu \
-gltsym 'SYM:FRHMtd -FNMtd' \
-glt_label 6 FbMiss_RewHi-Neu \
-gltsym 'SYM:FRLHtd -FNHtd' \
-glt_label 7 FbHit_RewLo-Neu \
-gltsym 'SYM:FRLMtd -FNMtd' \
-glt_label 8 FbMiss_RewLo-Neu \
-gltsym 'SYM:FLHHtd -FNHtd' \
-glt_label 9 FbHit_LossHi-Neu \
-gltsym 'SYM:FLHMtd -FNMtd' \
-glt_label 10 FbMiss_LossHi-Neu \
-gltsym 'SYM:FLLHtd -FNHtd' \
-glt_label 11 FbHit_LossLow-Neu \
-gltsym 'SYM:FLLMtd -FNMtd' \
-glt_label 12 FbMiss_LossLow-Neu \
-regress_stim_labels \
ATNtd ATRHtd ATRLtd ATLHtd ATLLtd FRHHtd FRHMtd FRLHtd FRLMtd FLLHtd FLLMtd FLHHtd FLHMtd FNHtd FNMtd \
-regress_basis 'dmBLOCK(1)' \
-regress_stim_types AM2 \
-regress_censor_motion 0.3 \
-regress_apply_mot_types demean deriv \
-regress_reml_exec \
-regress_compute_fitts \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_make_cbucket yes