It looks like the shell isn't reading your entire afni_proc.py command for whatever reason. You can see that the generated script says what call it received. It happens to cut off when it hits the first commented out (#-copy_anat ${subfolder}/${subject}/p*/e*/${subject}.${study}.spgr+orig \) line in your script.
# script generated by the command:
#
# afni_proc.py -subj_id sub11 -script \
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Scripts/Imagery/sub11_imagery_proc_script \
# -out_dir \
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery.results \
# -dsets \
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.PTSD_Conditioning.Neutral+orig.HEAD \
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.PTSD_Conditioning.Trauma+orig.HEAD \
# -copy_anat \
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/p532/e542/sub11.PTSD_Conditioning.spgr+orig
From here I would suggest you check all of your lines to see if there is a space after any continuation backslash (\). You can also use file_tool:
file_tool -test -infiles my_scripts_*.txt
Alternatively you can put all of you script into a single line for testing!
