Thanks Rick!

Yes, this was our first thought too so we made a clean directory. Just to confirm I re-ran it with 2 new folders called "affine" and "NL" where one has the -tlrc_NL_warp setting and the other don't.

My current AFNI-version:

afni -version
Precompiled binary linux_ubuntu_16_64: Feb 18 2020 (Version AFNI_20.0.10 'Galba')

My ubuntu-version

lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 18.04.2 LTS
Release:	18.04
Codename:	bionic

Both these clean new directories, using the script I sent you with and without tlrc_NL_warp runt to completion. But I realized that only the NL script gave me the error message:

#++ Aligning /home/robka/upload/NL/test_NL.results/awpy/base.nii data to /home/robka/upload/NL/test_NL.results/awpy/anat.un.nii data
#Script is running (command trimmed):
  @auto_tlrc -base ./base.nii -input ./anat.un.nii -suffix .aff -no_ss -no_pre -init_xform CENTER 
Copying NIFTI volume to ./anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA
++ 3dcopy: AFNI version=AFNI_20.0.10 (Feb 18 2020) [64-bit]

Performing center alignment with @Align_Centers

++ 3dcopy: AFNI version=AFNI_20.0.10 (Feb 18 2020) [64-bit]
++ 3drefit: AFNI version=AFNI_20.0.10 (Feb 18 2020) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig
 + deoblique
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_20.0.10 (Feb 18 2020) [64-bit]
++ THD_rename_dataset_files: rename anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD -> __ats_tmp__anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD
++ THD_rename_dataset_files: rename anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK -> __ats_tmp__anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK
** THD_rename_dataset_files: old header anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+acpc.HEAD doesn't exist!
** THD_rename_dataset_files: old header anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+tlrc.HEAD doesn't exist!
++ 3dWarp: AFNI version=AFNI_20.0.10 (Feb 18 2020) [64-bit]
++ Authored by: RW Cox
++ 3dcopy: AFNI version=AFNI_20.0.10 (Feb 18 2020) [64-bit]
[7m** FATAL ERROR:[0m Output dataset ./pre.anat.un_XYZ_OYmeqfZ3JqF7n9LNC7gDAA+orig.HEAD already exists! - EXIT
** Program compile date = Feb 18 2020
Center distance of 0.000032 mm
Padding ...

The script I sent you was with no -tlrc_NL_warp option so that means if you get it wihen you add the -tlrc_NL_warp option we are on the same page?
Also I did find the anat_final (warped dataset) to look a little more grainy than usual but perhaps that's a concidense or due to me remote login.