2. Installation

2.1. Using Docker

2.1.1. Install Docker

If you have not yet installed Docker, install Docker from here. Docker is available on all platforms. For Linux, you may have to perform additional post-installation steps.

2.1.2. Pulling pre-built Docker image

After installing Docker, you can directly pull the BrainSuite BIDS App from the Docker Hub repository by running the following command in the terminal:

docker pull bids/brainsuite:v21a

The above command will pull all layers of the Docker image (15 GB total) and may take a while depending on your download speed.

2.1.3. Building from source

To build from source (not recommended due to constantly changing third party repos), you can clone our BrainSuite BIDS App Github repo by running:

git clone https://github.com/bids-apps/BrainSuite.git
cd BrainSuite
docker build -t brainsuite .

where brainsuite is modifiable and is the name used for the Docker image that will be built.

2.2. Using Singularity

Converting the Docker version of BrainSuite BIDS App to Singularity is optional but is often required for multi-user systems with shared resources due to security reasons. Docker requires admin privileges, which can pose risks and Singularity handles this this issue by restricting escalated privileges.

2.2.1. Converting Docker image to Singularity image

  1. Define the directory where you want to store the Singularity-converted image:

  2. Define the name of the built BrainSuite BIDS App image. If you have pulled the pre-built version from Docker Hub, then you can run:


However, if you have built it from the source, you will set $CMD with the name you have given it.

  1. Now, using Docker, you will convert the Docker version of the BrainSuite BIDS App by running the following in the terminal:

    docker run -v /var/run/docker.sock:/var/run/docker.sock \
        -v $outputDirectory:/output \
        --privileged -t --rm \
        quay.io/singularity/docker2singularity \

This may take a while and will create a 5.3 GB image.

2.2.2. Install Singularity

To run the converted Singularity-compatible BrainSuite BIDS App, you will need to install Singularity on the system where you will be running the Singularity image. You (or your IT support) can install Singularity as described here.