Docker is an open-source project that automates the deployment of applications inside software containers. Those containers wrap up a piece of software in a complete filesystem that contains everything it needs to run: code, system tools, software libraries, such as Python, FSL, AFNI, SPM, FreeSurfer, ANTs, etc. This guarantees that it will always run the same, regardless of the environment it is running in.
Important: You don't need Docker to run Nipype on your system. For Mac and Linux users, it probably is much simpler to install Nipype directly on your system. For more information on how to do this see the Installation Section of this tutorial. But for Windows user, or users that don't want to setup all the dependencies themselves, Docker is the way to go.
If you want to run this Nipype Tutorial with the example dataset locally on your own system, you need to use the docker image, provided under miykael/nipype_course. This docker image sets up a Linux environment on your system, with functioning Python, Nipype, FSL, AFNI, ANTs and SPM12 software package, some example data and all the tutorial notebooks to learn Nipype.
Before you can do anything, you first need to install Docker on your system. The installation process differes per system. Luckily, the docker homepage has nice instructions for...
Once Docker is installed, open up the docker terminal and test it works with the command:
docker run hello-world
Note: Mac and Linux users might need to use sudo to run docker commands.
miykael/nipype_courseAfter installing docker on your system and making sure that the hello-world example was running, we are good to go to start the Nipype Course image. The exact implementation is a bit different for Windows user, but the general command looks as follows:
docker run -ti --rm -p 8888:8888 -v /home/username/results:/output miykael/nipype_course
But what do those flags mean?
-ti flag tells docker that it should open an interactive container instance.--rm flag tells docker that the container should automatically be removed after we close docker.-p flag specifies which port we want to make available for docker.-v flag tells docker which folder (here: /home/username/results it should mount to make it accesible inside the container. The second part of the -v flag (here: /output) specifies under which path the mounted folder can be found inside the container. This means that we can use the folder /output inside the tutorial to save data outside the docker container under /home/username/results. Important: To use the results folder, you first need to create it on your system!miykael/nipype_course tells docker that we want to run this docker image.To run a docker image, docker will look for the specified image on Docker Hub. If the docker image was already download to your system, it will be directly opened. Otherwise, it first needs to download all containers, which might take some time.
Running a docker image on a Linux or Mac OS is very simple. Make sure that you've created a results folder on your system (e.g. mkdir -p /home/username/results). Then just open a new terminal and use the command from above:
docker run -ti --rm -p 8888:8888 -v /home/username/results:/output miykael/nipype_course
Once the docker image is downloaded, open the shown URL link in your browser and you are good to go. The URL will look something like:
http://localhost:8888/?token=0312c1ef3b61d7a44ff5346d3d150c23249a548850e13868
Running a docker image on Windows is a bit trickier than on Ubuntu. Assuming you've installed the DockerToolbox, open the Docker Quickstart Terminal (encircled in red).
Once the docker terminal is ready (when you see the whale), we can execute the following steps (see also figure):
We need to check the IP adress of your docker machine. For this, use the command:
docker-machine ip
In my case, this returned 192.168.99.100
If you haven't already created a new folder to store your container output into, do so. You can create the folder either in the explorer as usual or do it with the command mkdir -p in the docker console. For example like this:
mkdir -p /c/Users/username/results
Please replace username with the name of the current user on your system. Pay attention that the folder paths in the docker terminal are not backslash (\) as we usually have in Windows. Also, C:\ needs to be specified as /c/.
Now, we can open run the container with the command from above:
docker run -ti --rm -p 8888:8888 -v /c/Users/username/outputs:/output miykael/nipype_course
Once the docker image is downloaded, it will show you an URL that looks something like this:
http://localhost:8888/?token=0312c1ef3b61d7a44ff5346d3d150c23249a548850e13868
This URL will not work on a Windows system. To make it work, you need to replace the string localhost with the IP address of your docker machine, that we acquired under step 1. Afterwards, your URL should look something like this:
http://192.168.99.100:8888/?token=0312c1ef3b61d7a44ff5346d3d150c23249a548850e13868
Copy this link into your webbrowser and you're good to go!
bash or ipythonYou don't have to open a jupyter notebook when you run miykael/nipype_course. You can also access the docker container directly with bash or ipython by adding it to the end of your command, i.e.:
docker run -ti --rm -v /home/username/results:/output miykael/nipype_course bash
This also works with other software commands, such as bet etc.
To stop a running docker container, either close the docker terminal or select the terminal and uste the Ctrl-C shortcut multiple times.
To see a list of all installed docker images use:
docker images
To delete a specific docker image, first use the docker images command to list all installed containers and than use the IMAGE ID and the rmi instruction to delete the container:
docker rmi -f 7d9495d03763
If you don't want to depend on a internet connection, you can also export an already downloaded docker image and than later on import it on another PC. To do so, use the following two commands:
# Export docker image miykael/nipype_course
docker save -o nipype_course.tar miykael/nipype_course
# Import docker image on another PC
docker load --input nipype_course.tar
It might be possible that you run into administrator privileges isssues because you ran your docker command with sudo. This means that òther users don't have access rights to nipype_course.tar. To avoid this, just change the rights of nipype_course.tar with the command:
sudo chmod 777 nipype_course.tar