Neurodesk: build interactive examples to learn about neuroimaging analysis

[iishiishii]

Title

Neurodesk: build interactive examples to learn about neuroimaging analysis

Leaders

Thuy Dao (Mattermost @thuy)

Collaborators

Steffen Bollmann (Mattermost @sbollmann_mri), Andrew Jahn, Monika Doerig

Brainhack Global 2024 Event

Brainhack Aus

Project Description

This project aims to build, test, and maintain interactive neuroimaging analysis examples using Jupyter notebooks, GitHub Actions, and Neurodesk. Although resources like Andy’s Brainbook provide excellent learning material, they lack interactivity and can quickly become outdated as software functionalities and parameters evolve, often breaking tutorials.

By leveraging Neurodesk’s containerized environment, we can create reliable, reproducible examples that allow users to explore parameters interactively and build a foundation for their own analyses. These notebooks will also serve as open materials for workshops, facilitating hands-on learning and collaborative projects. Additionally, automating testing with GitHub Actions will ensure examples remain functional and up-to-date.

This project also has potential for community growth: extending the notebook collection through contributions from global Brainhack events would enrich the resource pool with diverse analysis techniques, supporting a broad range of neuroimaging needs.

Link to project repository/sources

https://github.com/NeuroDesk/example-notebooks

Goals for Brainhack Global

• Build examples from Andy's brainbook

Good first issues

1. AFNI_01_DataDownload

2. AFNI_04_Preprocessing

Communication channels

Mattermost
Github Discussion

Skills

• Knowledge of analysis procedures.
• Bash
• Python

Onboarding documentation

README
Existing examples

What will participants learn?

• Neurodesk
• Github
• The toolkit they want to document, learn, or share their own pipeline

Data to use

OpenNeuro or other openly available dataset

Number of collaborators

2

Credit to collaborators

Project contributors will be listed in their notebooks and Neurodesk documentation and offered co-authorship in the global OHBM 2025 abstract describing this work.

Image

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Type

data_management, pipeline_development, tutorial_recording

Development status

2_releases_existing

Topic

connectome, data_visualisation, MR_methodologies, physiology, reproducible_scientific_methods, statistical_modelling, systems_neuroscience, tractography

Tools

AFNI, ANTs, BIDS, Brainstorm, CPAC, Datalad, FieldTrip, fMRIPrep, Freesurfer, FSL, Jupyter, MNE, MRtrix, Nipype, SPM

Programming language

Python, shell_scripting, unix_command_line

Modalities

fMRI, MRI

Git skills

0_no_git_skills, 1_commit_push

Anything else?

No response

Things to do after the project is submitted and ready to review.

• Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
• Twitter-sized summary of your project pitch.

[iishiishii]

Hi @brainhackorg/project-monitors my project is ready!

[iishiishii]

Twitter-sized summary:
Building interactive neuroimaging analysis examples with Jupyter, GitHub Actions, and Neurodesk for hands-on learning.

[crnolan]

Looks good!