Fed-BioMed node: Part 1¶
We will be using Fed-BioMed to conduct the federated learning experiment. See this page of the Fed-BioMed website for more information about how it works. Essentially, each site participating in the federated experiment needs to deploy a node, and the person responsible for running the experiment (i.e. training the models) deploys a server (researcher in Fed-BioMed vocabulary) to which all nodes connect to.
Deploy the node¶
Run this to download the images (if needed) and start them:
docker compose up -d
[+] Running 3/3
✔ Network brainflex-node_default Created
✔ Container brainflex-vpn-default Healthy
✔ Container brainflex-node-default Started
The two services are:
vpn: a WireGuard VPN client that connects to the central VPN servernode: the node image distributed by Fed-BioMed
Troubleshooting¶
By default, Docker images are stored on the root disk. If you encounter issues with disk storage quota being exceeded, you can configure Docker to use a different directory for storing data. This can be done by following e.g. this guide.
Check Fed-BioMed node status¶
docker compose exec -u fedbiomed node fedbiomed node -p /fbm-node status
# Using component located at: /fbm-node #
2026-11-03 19:27:17,690 fedbiomed INFO - Syslog configuration is disabled or not found in configuration. Disabling syslog logging.
Node status: NodeState.RUNNING
Add datasets to the node¶
Run the two commands below to register the datasets created by nipoppy2fedbiomed:
docker compose exec -u fedbiomed node fedbiomed node -p /fbm-node dataset add --file /nipoppy_study/derivatives/nipoppy2fedbiomed/0.1.0/output/age/dataset_info.json
docker compose exec -u fedbiomed node fedbiomed node -p /fbm-node dataset add --file /nipoppy_study/derivatives/nipoppy2fedbiomed/0.1.0/output/sex/dataset_info.json
Confirm that they have been added:
docker compose exec -u fedbiomed node fedbiomed node -p /fbm-node dataset list