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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, FreeSurfer and HALFpipe, available 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, ANTs or HALFpipe images, please contact the RCS team, to have them enabled for you.

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

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.

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:​

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

HALFpipe​

A Ubuntu 22.04 LTS workspace with an LXDE desktop accessible in your browser, co-deployed with HALFpipe for fMRI preprocessing pipelines. HALFpipe is CLI only — connect via oc exec to run it (see Technical Configuration below).

  • Tested version: 1.3.2 (other versions can be specified at instantiation)
  • Note: CLI-only tool. Search for Ubuntu with desktop interface and HALFPipe in the template catalog.

Connecting to the HALFpipe pod​

After the pods are deployed, get the pod name first:

oc get pods -n <project name>

Then connect to the pod and start HALFpipe:

oc exec -it <pod name> -- bash
halfpipe

Data Persistence​

The HALFpipe pod saves data persistently in /home/fmriprep/data. Make sure to select this directory when starting HALFpipe. The co-deployed Ubuntu workspace uses the same Persistent Volume Claim (PVC) via the root/persistent directory.