Nipoppy pipeline catalog

[michellewang]

Title

Nipoppy pipeline catalog

Short description and the goals for the OHBM BrainHack

Nipoppy is a neuroinformatics framework for standardized organization and reproducible processing of neuroimaging-clinical pipelines. We have recently launched a community-driven pipeline catalog on the Zenodo data repository. Users can use the Nipoppy command-line interface to search the pipeline catalog, download available pipelines and upload new pipelines. We propose two projects related to the pipeline catalog, as well as an additional project for more advanced brainhackers.

Subproject 1: Improve Zenodo interface
Want to contribute to an open-source software project? Help improve the Nipoppy CLI’s Zenodo interface! We have identified a list of good first issues for newcomers.

Subproject 2: Contribute new pipelines to the pipeline catalog
Have a pipeline you would like to share? Want to use Nipoppy to run a pipeline that is not currently in the pipeline catalog? Help extend the pipeline catalog by adding new pipeline(s) to it! This project does not require any Python programming skills.

Subproject 3: Add telemetry to the Nipoppy CLI
Telemetry allows for the recording of usage statistics for software tools, which can be useful to demonstrate the usage level/impact of a tool. Join this project to help design and implement telemetry to the Nipoppy CLI.

Link to the Project

https://github.com/nipoppy/nipoppy

Image/Logo for the OHBM brainhack website

https://raw.githubusercontent.com/nipoppy/nipoppy/refs/heads/main/logo/logo_square.svg

Project lead

Michelle Wang, @michellewang (GitHub), michelle__wang (Discord)
Nikhil Bhagwat, @nikhil053 (GitHub), nikhil153_ (Discord)

Main Hub

Brisbane

Link to the Project pitch

No response

Other hubs covered by the leaders

• Brisbane
• Hybrid (Asia / Pacific)
• Hybrid (Europe / Middle East / Africa)
• Hybrid (Americas)

Skills

Subproject 1: Improve Zenodo interface

• Familiarity with the command line/Terminal
• Some programming experience with Python

Subproject 2: Contribute new pipelines to the pipeline catalog (no Python programming knowledge needed!)

• Familiarity with the command line/Terminal
• Familiarity with the JSON file format

Subproject 3: Add telemetry to Nipoppy CLI

• Programming experience with Python

Recommended tutorials for new contributors

https://nipoppy.readthedocs.io/en/latest/tutorials/mriqc_from_bids/index.html
https://nbviewer.org/github/boutiques/tutorial/blob/master/notebooks/boutiques-tutorial.ipynb

Good first issues

See Subproject 1 description

Twitter summary

No response

Short name for the Discord chat channel (~15 chars)

nipoppy

Please read and follow the OHBM Code of Conduct

• I agree to follow the OHBM Code of Conduct during the hackathon