✦ Docker Setup

Step 1: Install Docker

• macOS / Windows: Download Docker Desktop
• Linux: Install Docker Engine via your package manager (apt, yum, etc.)

Step 2: Check Installation

• Verify installation by running:

docker --version

---

✦ Freesurfer 6.0 Docker Container Setup

Step 1: Download This Repo

• Download the zip file by navigating to the green Code button and selecting Download ZIP
• Or install via CLI by doing

git clone https://github.com/muscbridge/freesurfer-6.0-docker.git

• Unzip the folder and, move it to the location of your choice -- This could be Desktop, Applications, or any other folder on your machine where you would like to store git repositories

Step 2: Build the Docker image and install

• Open a Terminal window and change your directory to location you chose in the previous step -- Replace /path/to/freesurfer-6.0-docker with your freesurfer-6.0-docker folder path

cd /path/to/freesurfer-6.0-docker
docker build -t freesurfer:6.0 .
./install.sh

---

✦ Run Freesurfer on your data

• Input the following command into your terminal, being sure to change the paths to your preferred input and output paths

freesurfer-docker /path/to/BIDS /path/to/output