Dianne,

Thanks for posting the steps you followed. I followed your steps to create the updated image and I called it mri_reface2, as you did. I then exited and went into mri_reface2 in a new terminal and verified that the updated copy of ADIR_nii2dicom.py was still there.

$ docker run -ti mri_reface2
root@55793afdac4c:/usr/bin/mlrtapp/image_handling# grep xml ADIR_nii2dicom.py 
            dcmfiles_temp = [i for i in dcmfiles_temp if not re.search(r'\.xml$', i) ]

The above grep result matches the code I added newly in the revision I attached previously. 

I created a new run_mri_reface_docker.sh 
$ cp run_mri_reface_docker.sh run_mri_reface2_docker.sh

Which I then edited to replace mri_reface with mri_reface2 in BOTH docker lines:
96 docker run -ti --mount type=bind,src\=$tmpdir,target=$tmpdir mri_reface2 run_mri_reface.sh $input $output_tmp ${input_array[@]:2 }
97 
98 docker run -ti --mount type=bind,src=$tmpdir,target=$tmpdir mri_reface2 chmod =777 -R $tmpdi

From there I ran it two ways. One was using run_mri_reface2_docker.sh:

$ ./run_mri_reface2_docker.sh dcm_t1 outExternal -imType T1

[...]
ADIR_ReFace finished in: 17.9749 minutes
Finished writing 176 dcm files to outDir: /tmp/tmp.A1n3Oz3nih/outputs/dcm
Including custom code sequence: code: "replace_recognizable" meaning: "Replace face, ears, and artifacts in air" designator: "mri_reface" version: "0.3.2"
Finished.
De-faced DICOM was written to /tmp/tmp.A1n3Oz3nih/outputs/dcm. This DICOM metadata is NOT otherwise de-identified. Only de-facing was performed. If you need the meta-data de-identified also, you should run it through your preferred DICOM de-identification software.

When it completed, I opened outExternal/dcm and the files are present and successful.

I also tried running the whole thing inside docker, rather than using run_mri_reface2_docker.sh

$ chmod a+wrX .
$ docker run -ti --mount type=bind,src=${PWD},target=/host mri_reface2
root@23aadd07062d:/usr/bin/mlrtapp/image_handling# cd /host
root@23aadd07062d:/host# run_mri_reface.sh dcm_t1 out2 -imType T1

[...]
ADIR_ReFace finished in: 17.8532 minutes
Finished writing 176 dcm files to outDir: out2/dcm
Including custom code sequence: code: "replace_recognizable" meaning: "Replace face, ears, and artifacts in air" designator: "mri_reface" version: "0.3.2"
Finished.
De-faced DICOM was written to out2/dcm. This DICOM metadata is NOT otherwise de-identified. Only de-facing was performed. If you need the meta-data de-identified also, you should run it through your preferred DICOM de-identification software.
root@23aadd07062d:/host# exit

Then I checked out2/dcm. The dcm files are present and valid.

I tried again using your dicom directory name, just in case that had something to do with it:

$ ./run_mri_reface2_docker.sh T1_mprage_1mm_13/ out -imType T1

And that was also successful. 

From here, I was at a bit of a loss. My best guess was that there's a mistake in one of the steps you didn't show me. Maybe you could verify that your mri_reface2 image has the updated code (via the above grep example), and you could verify that your run_mri_reface2_docker.sh replaced 'mri_reface' in BOTH 'docker' commands with 'mri_reface2'? 

Toward that hypothesis, I looked back at the start of your pdf and I think you may not have replaced the correct file/path. 
/usr/bin/mlrtapp has ADIR_nii2dicom, a program. It also has a subdirectory called image_handling. Inside image_handling is ADIR_nii2dicom.py. I intended for you to replace /usr/bin/mlrtapp/image_handling/ADIR_nii2dicom.py, NOT /usr/bin/mlrtapp/ADIR_nii2dicom, but it looks like you replaced ADIR_nii2dicom. I surprised that didn't up with a new error message when you tried to run it that way, but otherwise I think this explains why it's now working for me, but not you. 

Can you please try starting again from the original mri_reface image and copy the new ADIR_nii2dicom.py into image_handling, this time? From there, I hope it will work for you. Please let me know. Sorry my original instructions weren't clear enough about which file to replace. 

Thanks,
Chris