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.