Hi!
A)
I'll change
-blur_size SOMETHING
-anat_has_skull YES_OR_NO
To be explicit
B)
I'll remove
-regress_apply_mot_types demean deriv \
C)
Yes, I have realized that is a good idea. I'll change the first steps accordingly:
# Once the TR is registered
cd $afni_dir/all_TRs
name=TR$last_brik
mkdir $name
cd $name
#changing this
cp $nii_dir/${last_brik}.nii.gz .
#to
3dcopy $nii_dir/${last_brik}.nii.gz ${last_brik}
#and changing this
3drefit -oblique_recenter ${last_brik}.nii.gz
3drefit -deoblique ${last_brik}.nii.gz
#to this
3drefit -oblique_recenter ${last_brik}+orig.
3drefit -deoblique ${last_brik}+orig.
But that won't help with my problem, or do you think it will?
