Justin,
We're going to have to take some time to look into this and get back to you. Your post was news to me that Docker images are not cross-architecture, but producing the mri_reface Docker was really the first forray into containers for me and my team. Our docker build is a little unusual because of the Matlab runtime. We have to use Matlab's own Docker-building functionality to build a working image containing the Matlab runtime, and then use that output as the base for us to add additional layers with our program  and the rest of its dependencies. Installing the off-the-shelf Matlab runtime in our Docker environments produces OpenGL errors in some of the function calls we use, and this only seems to happen inside Docker images (you can find old messages about that on this board). The one installed by Matlab's own docker-builder avoids this; it seems to be a special version somehow. I suspect that these issues will make it a lot tougher to build an image for arm64 that also contains the Matlab runtimes for arm64. One of my colleagues has an M2 laptop and has offered to help test. In short, I want to help you and other arm64/Apple users, but I think it will be a bigger undertaking than the average Docker image. Please be patient, and I will get back to you. In the meantime, my best suggestion is to use our corresponding not-Docker release. You can install the appropriate Matlab runtime, compile niftyreg and ANTs, and hopefully that would work around your issue. For your hardware, the Docker solution may be creating more issues than it is solving.

Best,
Chris