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troubleshooting_docker.rst

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Docker

|question| MIRACL's GUI (miraclGUI) is not working

Access control might be enabled on your host machine. Change your xhost access control on your host machine (not within your :program:`Docker` container). Exit the running :program:`Docker` container and type:

xhost +

Log back in to your container. Reset xhost after you are done with using the :program:`MIRACL` GUI using:

xhost -

The above will enable/disable access for all users. If this is not the desired behavior, access can be granted in a more fine grained manner.

Example:

xhost +SI:localsuer:<yourusername>

Note

Replace <yourusername> with the actual user name of your host system

|question| The GUI worked before but does not work anymore

Navigate to the directory that contains your docker-compose.yml and restart the container with docker compose down followed by docker compose up -d. The GUI should work again.

|question| I cannot run X or Y with Docker because of permission denied errors

If you have not set up a :program:`Docker` user you might need to run :program:`Docker` commands with sudo. While this should work, setting up a :program:`Docker` user is the prefered.

|question| Processes that require TrackVis or Diffusion Toolkit are not working

|question| STA workflow fails when trying to create tracts

Make sure that the :program:`TrackVis` and :program:`Diffusion Toolkit` binaries are available to :program:`MIRACL`. See the previous question for details.

|question| I need to install or make changes to apps in the MIRACL container but my user is not authorized to do so

The user in the container is the user of your host machine. This is done to avoid issues with the :program:`MIRACL` GUI and X11. If you need to make changes that require sudo privileges, just log out of your container and log back in as root:

$ docker exec -it -u root miracl bash

After making your changes, log out and log back in with your regular user:

$ docker exec -it miracl bash

Attention!

Always remembert that changes to the container are not persistent. If you need to make permanent changes as sudo, add them to the Dockerfile instead.

|question| MIRACL's GUI (miraclGUI) does not work anymore after my ssh connection has been broken

Assuming you logged back in with ssh and are in the container, exit the container and restart it using docker compose down and docker compose up -d .

Shell back into the container and the GUI should work again.

|question| I do not want to create the image using the provided script

You can build the image yourself, not using the script we provide. However, the build script makes sure that the GUI version of :program:`MIRACL` works with :program:`Docker` and it is therefore recommended to use it. Build the image with:

$ docker build -t mgoubran/miracl .

Note

Do not forget the . at the end of the command. It is required to point docker build to the Dockerfile.

To run the container use:

$ docker run -it mgoubran/miracl bash

Attention!

If you make changes in the container that are not stored on a volume, make sure to use the same container the next time you run :program:`MIRACL` as changes made to a container will only apply to this specific container. If you run :program:`MIRACL` again from the same image using docker run -it mgoubran/miracl bash, a new container will be created that does not contain the changes you made to the first container.

Warning

The :program:`MIRACL` GUI will be unlikely to work out-of-the-box but you can try the troubleshooting steps in the following section to make it work.

|question| I get either or both of the following errors whenever I try to run the GUI from within a Docker container that was build without the provided build script

Authorization required, but no authorization protocol specified
qt.qpa.xcb: could not connect to display :1

Note

The number for the display could be different in your case

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Exit your running :program:`Docker` container and run the following to mount an X11 socket from the host system in a new :program:`Docker` container:

docker run -it -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix mgoubran/miracl bash

If you still receive the above error, you may have to change your xhost access control. See previous troubleshooting step above.