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Neuroimaging and Neuroscience Research on DSRI

We provide specialized environments on the DSRI optimized for neuroimaging analysis. These images include standard tools like FSL, ANTs, and FreeSurfer, aavailable as integrated graphical workstations or standalone environments.

Accessing Neuroimaging Tools

Please note that these specialized neuroimaging templates are not activated by default in the DSRI catalog.

If you require access to the Integrated Ubuntu fMRI Workstation, Freesurfer, FSL, or ANTs images, please contact the Research Computing Support team to have them enabled for your specific project:

Email us directly: rcs-ub@maastrichtuniversity.nl

Ubuntu VNC for fMRI Preprocessing​

A complete Ubuntu 22.04 LTS desktop environment pre-loaded with FSL, ANTs, and JupyterLab. Perfect for interactive fMRI preprocessing workflows that require both scripting and visualization.

What's Included​

  • FSL 6.0.7 - Full suite including FSLeyes for visualization
  • ANTs 2.6.4 - Advanced normalization tools
  • JupyterLab - Pre-installed and accessible via a desktop icon

Standalone Workspaces​

For workflows that don't require a full desktop, we provide lightweight JupyterLab environments:

JupyterLab with FreeSurfer​

  • Version: 8.1.0

JupyterLab with FSL​

Standalone FSL environment for command-line workflows.

  • Version: 6.0.7
  • Note: This is a CLI-only image. For FSL GUI tools like FSLeyes, use the Ubuntu VNC fMRI environment.

JupyterLab with ANTs​

Standalone ANTs environment optimized for registration and segmentation.

  • Version: 2.6.4

Technical Configuration​

Data Persistence​

When instantiating the template you can provide a few parameters similar to the standard JupyterLab, such as:

  • Password to access the notebook
  • Optionally you can provide a git repository to be automatically cloned in the JupyterLab (if there is a requirements.txt packages will be automatically installed with pip)
  • Your git username and email to automatically configure git

The DSRI will automatically create a persistent volume to store data you will put in the /home/jovyan/work folder (the folder used by the notebook interface). You can find the persistent volumes in the DSRI web UI, go to the Administrator view > Storage > Persistent Volume Claims

You can also link your git repository to the project for automatic deployment see using git in JupyterLab

Firefox in VNC Desktop with the fMRI tools​

Firefox inside the Ubuntu VNC environment is configured with sandboxing disabled for compatibility with DSRI's security model. You may see a security warning in the browser, this can be safely ignored as your pod is already isolated at the Kubernetes level.