Good that the information was relevant =).

While I'm waiting to hear from the potential flip-cost-file-read error and for someone else to answer the other 2-3 questions I looked at the output of the follower dataset. I followed the example and the relevant code bits are here:

#Original NIFTI
T1_data=$datapath/T1.nii
#SSWarperCommand
@SSwarper  -input $T1_data -base /usr/local/abin/MNI152_2009_template_SSW.nii.gz  -subid $sub_id -deoblique -giant_move -odir $startdir/pre_warp_$sub_id
#Relevant AFNIproc parts:
    -copy_anat pre_warp_$sub_id/anatSS.$sub_id.nii \
    -anat_has_skull no \
    -tlrc_base MNI152_2009_template_SSW.nii.gz \
    -tlrc_NL_warp \
    -tlrc_NL_warped_dsets \
           pre_warp_$sub_id/anatQQ.$sub_id.nii \
           pre_warp_$sub_id/anatQQ.$sub_id.aff12.1D \
           pre_warp_$sub_id/anatQQ.${sub_id}_WARP.nii \
    -anat_follower anat_w_skull anat $T1_data \

Everything looks amazing, especially the anat_final. I'm not sure what to expect of the follower dataset though? I interoperate the code
anat_follower anat_w_skull anat $T1_data
as that AFNI will also warp the original dataset to MNI-space and create a anat_w_skull dataset that is also warped (only difference between this an anat_final should be the skull?). Even though that is not what AFNI does I feel that something is wrong since the dataset follow_anat_anat_w_skull+tlrc looks faulty. It's not centred in the viewer and the brain is warped in a way that does not look correct:

Why is this? (same script as the first post if the code in this post is not enough). Top row is anat_final bottom row is the follower dataset follow_anat_anat_w_skull.