Known Issues

• Using the -t/--tty option in docker run produces non-printable characters in the generated Dockerfile or Singularity recipe (see moby/moby#8513).

  • Solution: do not use the -t/--tty flag, unless using the container interactively.

• Attempting to rebuild into an existing Singularity image may raise an error.

  • Solution: remove the existing image or build a new image file.

• The default apt --install option --no-install-recommends (that aims to minimize container size) can cause unexpected behavior.

  • Solution: use --install opts="--quiet" package1 package2

• FreeSurfer cannot find my license file.

  • Solution: get a free license from FreeSurfer’s website, and copy it into the container. To build the Docker image, please use the form

    docker build .
    

    instead of

    docker build - < Dockerfile
    

    because the latter form will not copy files into the image.