Hi all,

I’m running recon-all inside a Docker container, but it fails with the following error when launched programmatically through an SDK:

ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,

make sure to source the standard environment.

The command used by the SDK looks like this:

docker run -v /usr/local/lib/python3.10/dist-packages/xxxx/execution/communication.patch:/usr/local/lib/python3.11/dist-packages/xxxx/sdk/communication.py:ro \
  --cap-drop=NET_RAW -dt --name analysis_1420668 --entrypoint /bin/bash \
  --cpus=4 --memory=16384m \
  europe-west3-docker.pkg.dev/xxxx/freesurfer_530:dev-1.0 \
  /xxxx/entrypoint.sh --project 2289 --analysis 1420668 \
  --token xxxx --url https://xxxxx.com/ \

--tool-path tool:run

However, when I start the container manually (e.g., docker run -it ... /bin/bash) and run recon-all inside it directly, the license is detected and validated correctly. So the license.txt file at /usr/local/freesurfer/license.txt itself appears to be valid.

This suggests the issue is related to how the container is executed by the SDK or entrypoint, possibly involving the entrypoint script /xxx/entrypoint.sh altering the environment before recon-all starts.

The Docker container has:

Ubuntu 22.04
Python 3.11

Has anyone seen a similar issue where FreeSurfer fails to validate the license only when invoked non-interactively?

Are there specific environment variables or checks that recon-all performs which might differ when running under /bin/bash -c or through an SDK wrapper?

Any insights or debugging suggestions would be greatly appreciated.

Thanks!