Overview

Teaching: 0 min
Exercises: 15 min

Questions

Objectives

• Pull (download) an image from Docker Hub

• Run shell inside a container

• Mount local folders

• Apply software from the image to analyze local data

Pulling and image

Let’s pull (download) an image: docker pull bids/base_fsl

Where is this image coming from? From Docker Hub.

Getting inside a container

Let’s go inside the container (an instance of an image) and poke around: docker run -ti --rm bids/base_fsl

A Linux shell prompt should appear (independently of your host operating system!). Play around. Can you answer the following questions:

• What user are you inside the container? Is it the same user as on your host computer?
• Can you run FSL tools such as bet?
• Can you access files from your host computer?
• Create some files inside the container. Get out of the container (type exit). Run the container again. Are the files still there?
• Is there a ‘/data’ folder inside the container?

Accessing local files

Before we try to access files from the localhost lets get some example data

1. Create a folder on your local machine. I went with /home/me/docker_tutorial
2. Go to NeuroVault.org pick a map (for example this one and download it to the example folder.

Let’s mount this folder so it will be accessible from the container when we run it docker run -ti --rm -v /home/me/docker_tutorial:/data bids/base_fsl

Excercises:

1. Can you see the downloaded map in /data folder inside the container?
2. Can you use tools installed in the container on the files in the /data folder? For example fslmaths /data/tfMRI_SOCIAL_TOM-RANDOM_zstat1.nii.gz -kernel gauss 10 -fmean /data/smoothed.nii.gz
3. After getting out of the container can you see the modified files on your host system?

Key Points

• Container images are downloaded from Docker Hub.

• You can run shell inside the container.

• Only explicitly mounted host folder are accessible inside the container.

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