An Interactive Neuroimaging Learning Platform
Poster No:
1844
Submission Type:
Abstract Submission
Authors:
Monika Dörig1, Thuy Dao2, Ashley Stewart2, Fernanda Ribeiro3, Marla Pinkert4, Michele Masson-Trottier5, Michael Meier6, Thomas Close7, Anna Behler8, Christian Behler9, Jahn Andrew10, Steffen Bollmann2
Institutions:
1Integrative Spinal Research, Department of Chiropractic Medicine, Balgrist University Hospital, Zurich, Zurich, 2University of Queensland, Brisbane, Queensland, 3Justus-Liebig University Giessen, Giessen, Hessen, 4University of Vienna, Vienna, NA, 5Johns Hopkins School of Medecine, Baltimore, MD, 6Integrative Spinal Research, Department of Chiropractic Medicine, Balgrist University Hospital, Univ, Zurich, Zurich, 7The University of Sydney, Sydney, New South Wales, 8The University of Newcastle, Challaghan, NSW, 9The University of Newcastle, Australia, NEW LAMBTON, New South Wales, 10University of Michigan, Ann Arbor, MI
First Author:
Monika Dörig
Integrative Spinal Research, Department of Chiropractic Medicine, Balgrist University Hospital
Zurich, Zurich
Integrative Spinal Research, Department of Chiropractic Medicine, Balgrist University Hospital
Zurich, Zurich
Co-Author(s):
Michael Meier
Integrative Spinal Research, Department of Chiropractic Medicine, Balgrist University Hospital, Univ
Zurich, Zurich
Integrative Spinal Research, Department of Chiropractic Medicine, Balgrist University Hospital, Univ
Zurich, Zurich
Introduction:
Training in neuroimaging analysis is crucial for researchers. Although there are valuable resources available, such as Andy's Brain Book (Jahn, 2022), many examples lack interactivity. As software tools and parameters change periodically, existing tutorials often become outdated or broken, limiting users' ability to learn and apply neuroimaging techniques effectively. To address these challenges, we have developed an open repository of interactive examples, which present analyses using open data and are automatically tested for functionality.
Methods:
Our approach employs Jupyter notebooks to create interactive examples of various neuroimaging tools available in Neurodesk (Renton, 2024), including ANTs, AFNI, FreeSurfer, and FSL. These notebooks are designed to run seamlessly in any Neurodesk installation or Google Colab, where the Neurodesk environment is automatically set up through integrated commands in a notebook cell. We implemented GitHub Actions to automate the testing and rendering of these notebooks with Jupyter Book ensuring that users have reliable, up-to-date resources for their neuroimaging analyses across computing environments. By leveraging the Neurodesk platform, users can easily access and modify these notebooks, allowing interactive exploration and experimentation using neuroimaging parameters (Figure 1).
Results:
The collection of example notebooks (Figure 2), available at the Neurodesk website (https://www.neurodesk.org/example-notebooks/intro.html), provides an interactive learning environment. Users can engage in examples demonstrating the use of various tools, which serve as open educational materials for workshops and collaborative learning opportunities. This approach ensures the continuous functionality of the examples and provides a foundation for users to develop their understanding of neuroimaging techniques and conduct their own analyses as this novel tool facilitates hands-on learning and empowers users to adapt content to their specific needs.
Conclusions:
This initiative represents a significant step toward enhancing the learning environment in neuroimaging analysis, making it more accessible to individuals from less technical backgrounds. Our comprehensive platform for neuroimaging education continues to grow and evolve, supported by resources such as Andy's Brain Book. We invite the community to contribute their own examples, thereby expanding this valuable resource and ensuring that it meets the evolving needs of researchers in the field.
Neuroinformatics and Data Sharing:
Workflows 1
Informatics Other 2
Keywords:
Data analysis
Open-Source Code
Open-Source Software
Other - Interactive learning, Jupyter notebooks, Educational resources, Software testing
1|2Indicates the priority used for review
Abstract Information
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Was this research conducted in the United States?
Were any human subjects research approved by the relevant Institutional Review Board or ethics panel? NOTE: Any human subjects studies without IRB approval will be automatically rejected.
Were any animal research approved by the relevant IACUC or other animal research panel? NOTE: Any animal studies without IACUC approval will be automatically rejected.
Please indicate which methods were used in your research:
Provide references using APA citation style.
Renton, A.I. (2024). Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nature Methods, 21(5). https://doi.org/10.1038/s41592-023-02145-x