Connectome Workbench

A Dockerfile that sets up the HCP Connectome Workbench (via NeuroDebian) on top of linuxserver/webtop (Ubuntu 24.04 + XFCE), accessible through your browser.

Quick start (docker compose)

cp .env.example .env        # then edit to taste (see Configuration below)
docker compose up -d --build

Then open http://127.0.0.1:3000 (or https://127.0.0.1:3001 for HTTPS).

Launching Connectome Workbench

Once the desktop loads in your browser, launch wb_view either way:

• Apps menu: click the menu icon in the top-left corner of the desktop → Science → Connectome Workbench.
• Terminal: right-click the desktop → Open Terminal Here (or use the terminal icon in the taskbar) → type wb_view and hit enter.

Your host data mount is at /data inside the container — point Workbench's file browser there to load scenes, CIFTI files, etc.

Other useful commands:

docker compose logs -f      # watch output
docker compose down         # stop and remove
docker compose pull         # update the webtop base image
docker compose up -d --build  # rebuild on top of a fresh base

Configuration

Settings live in .env (copied from .env.example). All have sensible defaults — only override what you need.

Variable	Default	Purpose
HTTP_PORT	3000	Host port mapped to the container's HTTP web UI
HTTPS_PORT	3001	Host port mapped to the container's HTTPS web UI
DATA_DIR	./data	Host path mounted at /data inside the container
PUID	1000	Numeric user ID the desktop runs as — set to $(id -u) so files written to /data are owned by you
PGID	1000	Numeric group ID — set to $(id -g)
TZ	America/New_York	Container timezone (IANA format, e.g. Europe/Berlin)

Example: run on non-default ports with a specific dataset directory:

HTTP_PORT=8080
HTTPS_PORT=8443
DATA_DIR=/mnt/hcp/tutorial

Running without compose

docker run -d --rm \
  -p 3000:3000 -p 3001:3001 \
  -v /dev/shm:/dev/shm \
  -v /path/to/your/data:/data \
  --name cwb \
  connectome-workbench:latest

Tutorial data: the HCP Tutorial dataset is a good first thing to point /data at.

Notes

• The webtop terminal has passwordless sudo. Don't expose the container to untrusted networks without setting CUSTOM_USER and PASSWORD env vars — see the webtop docs.
• PUID/PGID in .env should match your host user (id -u / id -g) so files written to /data are owned by you.