https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev.pkg

We don’t really support running/debugging X-Windows applications like freeview thru docker back to the host. For the case where freeview does not run natively, many people choose a VM image with its own built in X-server, e.g., run VirtualBox on Windows.

There are however ubuntu debian package installers located in the same directory as the mac package listed above, i,.e., there is an Ubuntu 22 .deb installer. If you don't use the linux install tools to install the .deb package, then you will likely be missing system libraries.

- R.

On Sep 20, 2024, at 14:36, Belakovski, Nickolai <nickolai.belakovski@mssm.edu> wrote:

External Email - Use Caution
Hello all,

I'm just getting started with Freesurfer so please forgive me if I'm missing something basic, but basically my setup is like this:

I'm on an M3 Mac and I'd like to run FreeSurfer. Since there's arm/x86 compatibility issues I'm trying to run it inside of an x86_64 docker image of Ubuntu 22.04. I've downloaded the relevant .tar.gz, mounted it inside my docker and I've installed all the various packages I need to run freeview (basically I tried to run freeview and every time it complained about a shared lib not found I'd install the relevant package), but now I've gotten to a point where I try to run freeview and it just says "Aborted" and that's it.

I have a license.txt at FREESURFER_HOME and I've run source SetUpFreeSurfer.sh, but basically I'm stuck at this point. I can run freeview -h and get the help message. I can run freeview --verbose, but this also just results in an "Aborted" message and that's it.

Is there anything else I can do to debug? The "Aborted" message unfortunately doesn't give me much to go on 🙁

For the sake of completeness I'll just make a note that I should be able to run this through Docker. I've installed x11-apps and run xeyes in the same container in which I'm trying to run freeview and it works, so I don't think that's the part it's choking on. Also for completeness here's a list of the packages I had to apt-get install: libgomp1, libgl1, libglib2.0-0, libqt5gui5, and I also had to export LIBGL_ALWAYS_INDIRECT=1 for some reason.

Thanks very much for your help,
Nickolai Belakovski
Biomedical Software Engineer
BioMedical Engineering and Imaging Institute (BMEII)
Icahn School of Medicine at Mount Sinai

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