So in addition to other issues relating to copyfile, apparently there isn't an option to copy a symbolic link as a file, instead it just copies the link itself.
This is problematic if you anatomical images are symbolic links, as they'll be copied as links and the coregistration will modify the original file.
I suspect a solution would need to just avoid using copyfile. For now I'm going to add a warning in the comment to make sure that anatomical image paths aren't pointing at symbolic links.
So in addition to other issues relating to copyfile, apparently there isn't an option to copy a symbolic link as a file, instead it just copies the link itself.
This is problematic if you anatomical images are symbolic links, as they'll be copied as links and the coregistration will modify the original file.
I suspect a solution would need to just avoid using copyfile. For now I'm going to add a warning in the comment to make sure that anatomical image paths aren't pointing at symbolic links.