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Working With Your Neurodesk For Neuroimaging Data

Published:

As a data analyst or a student needing to perform complex neuroimaging tasks or workflows, you may be interested in accessing a wide array of specialized neuroimaging tools without the headache of manual installation.

In this post, we will explore how Neurodesk provides a streamlined, containerized environment to run powerful neuroimaging tools seamlessly. We will walk through the setup process and show you how to get your environment ready for analysis.

By Lookman Jamad, Mehdi Ketata, Sandrine Muller

Neurodesk Installation Guide

Neurodesk is an open-source platform that provides ready-to-use neuroscience tools in a reproducible environment. It uses containers (via Docker or other engines) so you don’t need to manually install complex dependencies.

Learn more about it at: https://neurodesk.org/

Overview

Neurodesk simplifies neuroscience workflows by providing everything pre-configured and reproducible. It is primarily used for:

  • Neuroimaging analysis: (MRI, fMRI, diffusion imaging, etc.)
  • Tool management: Running software like FSL, SPM, and others without manual installation.
  • Reproducible research: Ensuring the same environment across different machines.
  • Education: Teaching and tutorials in neuroscience.
  • Flexibility: Working both locally or remotely with the same setup.

System Requirements & Prerequisites

Before you begin, ensure your system meets the following criteria:

  • Disk Space: At least 5GB of free space.
  • System Privileges:
    • With Privileged Access (Admin): Docker (recommended) or Podman.
    • Without Privileged Access: TinyRange Engine (included with Neurodesk App) and QEMU (macOS only).

[!IMPORTANT] Docker must be running before starting Neurodesk.

Installation Guide

Choose the section corresponding to your operating system.

🍎 macOS/Linux

1. Checking system privileges

On macOS, Docker is the standard and easiest option. Ensure you have admin rights to install Docker Desktop.

2. Docker Installation

  1. Go to the official Docker website: https://www.docker.com/
  2. Download Docker Desktop for Mac.
  3. Install it like a normal application.
  4. Launch Docker and ensure it is running (look for the Docker icon in the menu bar).

3. Neurodesk Installation

  1. Go to https://neurodesk.org/.
  2. Click on Install Locally.
  3. Follow the macOS installation prompts.

🪟 Windows

1. Checking system privileges

Check whether your system has administrative rights.

  • With Admin Access: Use Docker (recommended) or Podman.
  • Without Admin Access: Use TinyRange Engine or a remote Neurodesk instance.

2. Docker Installation

  1. Go to the official Docker website: https://www.docker.com/
  2. Download Docker Desktop for Windows.
  3. Install it like a normal application.
  4. Launch Docker and ensure it is running (the icon should appear in the system tray).

Troubleshooting Windows Docker:

3. Neurodesk Installation

  1. Go to https://neurodesk.org/.
  2. Click on Install Locally.
  3. Install the application and launch it.

Running Neurodesk

Once installed, follow these steps to start your environment:

  1. Launch the Neurodesk App.
  2. Click on “Start a local Neurodesk server”.

What happens in the background?

Neurodesk starts a local server and uses Docker to pull and run the required containers. It then connects you to the environment through your web browser.

Interacting with the interface

Once the JupyterLab interface opens, you have two ways to interact:

  • NeurodeskApp Icon: Click the icon on the right sidebar to launch a dedicated Neurodesk interface where you can easily launch tools.
  • Module Loading: Use the left sidebar to load containers as modules. You can interact with these modules via the command line interface.

[!NOTE] The first launch may take some time as the necessary containers and data need to be downloaded.

Useful Resources