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UQ XNAT

Jupyter environment

You can start a Jupyter notebook server directly from XNAT and analyse your project data without downloading it. The environment is built on Neurodesk, which provides a large suite of containerised neuroimaging tools alongside the usual Python and Jupyter stack.

RCC support sets up access on request.

Request access to the Jupyter environment

Section titled “Request access to the Jupyter environment”

  1. Open a ticket with RCC support. Fill in the XNAT projects that should be accessible from the Jupyter environment, then copy the generated email into your mail client.

  2. The support ticket will inform you when your access is set up. Jupyter access setup typically takes around ~24 hours from ticket submission.

Start an interactive session

Section titled “Start an interactive session”

  1. Open the project you want to work with.

    Select a project

  2. Select Start Jupyter Notebook from the Actions menu.

    Start Jupyter action

  3. Choose a Jupyter Environment and Hardware, then select Start Notebook.

    The environment determines which software is available. neurodesk-latest gives you the Neurodesk toolset. The hardware option sets the memory and CPU available to the server, so pick a size that matches the analysis you are running.

    Jupyter settings

  4. Open the Jupyter window once the server has started.

    Open Jupyter window

Using interactive session

Section titled “Using interactive session”

The project data will be accessible as read-only at:

/data/projects

Next steps

Section titled “Next steps”

Your notebook server runs Neurodesk, so its documentation covers the tools themselves.

Find a toolBrowse the neuroimaging applications available in the environment.
Neurodesk on XNATHow the XNAT-hosted Neurodesk environment is put together.

UQ XNAT is operated by the Research Computing Centre at The University of Queensland, as part of the National Imaging Facility and the Australian Imaging Service.