Hi Dianne,

I admit I'm not sure why you're getting that output in the nii to dicom step. It's not finding the original dicom during that last nii2dicom step of the process, but of course it found them earlier in the process, so it's rather confusing. If you want to otherwise de-identify the dicom and send them to me, we can test it on our end and see if we can reproduce your error, but I understand that you likely wouldn't be able to do this. You could try running the programs inside the Docker interactively, either to troubleshoot or to pick up with running ADIR_nii2dicom on the de-faced nii with the original dicom. If you have the defaced nifti and it looks good, you also could try something like this to run just the nii2dicom step inside the docker, from outside the docker:

docker run -ti --mount type=bind,src\=,target=/nifti_dir type=bind,src\=,target=/output_dir type=bind,src\=,target=/original_dicom_dir mri_reface /usr/bin/mlrtapp/ADIR_nii2dicom /nifti_dir/ /output_dir /original_dicom_dir -v

where , , , and are replaced with the paths to your files.  The output directory will need to be writable by everyone.  The ownership of the files in will likely need to be changed after running.

As a different workaround, you could also download the non-docker version of mri_reface and install just the included nii2dicom and markDicomDeidentified programs on your mac. Those have relatively minimal dependencies, so if the nifti de-facing steps work inside the docker, you could finish the last part in your python environment outside the docker, if you have to. 

Does any of that help?
Best,

Chris