Hi Steven,
Thanks for your help! I think I understand. Although since I’m running on docker alone instead singularity, I think the command would be different. Maybe something like:
dcm2niix_path=$(which dcm2niix) \ # Make sure this points to the correct version
docker run -rm -it -v ${dcm2niix_path}:/opt/dcm2niix-v1.0.20220720/bin/dcm2niix (REST OF COMMAND)
Am I on the right track?