How to Run FreeSurfer(GUI) on Windows with Docker

Docker Desktop for Windows, WSL2 must be installed to follow the practice below.

1. Obtain a FreeSurfer License Key

Obtain a license key from the FreeSurfer homepage.

2. Place license key

I placed a license key in C:\nsimg\freesurfer

3. Create a Dockerfile

# Pull cgvalle/freesurfer_vnc:latest

FROM cgvalle/freesurfer_vnc:latest

# Copy the license.txt to the docker's /root/freesurfer

COPY license.txt /root/freesurfer

4. Build an Image with Dockerfile

Open a command prompt or powershell to run command below (in blue letter).

You should build where Dockerfile and license.txt are.

docker build -t fs_vnc .

docker images

5. Run fs_vnc image as a container

Run command below (in blue letters) at the command prompt or in the power shell.

docker run -d --name fs_vnc -e VNC_PASSWORD=fsvnc -e SUBJECTS_DIR=/root/persistent/subjects -v C:\\nsimg\\freesurfer:/root/persistent -p 6080:80 -p 5900:5900 cgvalle/freesurfer_vnc:latest

# --name : Container name
# -e : Set container environment variable
# -v : Volume mount (persistent disk settings, local storage to container storage)
# -p : Port forwarding (local port to container port)
# fs_vnc : Image name