Poppy & Bagel: How to FAIRly curate, process, and share your neuroimaging datasets

[nikhil153]

Title

Poppy & Bagel: How to FAIRly curate, process, and share your neuroimaging datasets

Short description and the goals for the OHBM BrainHack

Curating data, running reproducible pipelines, creating data dictionaries, integrating data from collaborators, making sensitive data FAIR - these tasks are hard; and we all have to deal with them every day. Here we aim to serve Nipoppy and Neurobagel - a set of protocols and tools with modular framework that one can adopt as needed to simplify common data organization, processing, harmonization, and sharing tasks on neuroimaging datasets.

We cover BIDSification, containerized processing with completion tracking, annotation of phenotypic data, and generation of knowledge graphs for distributed data discovery and sharing.

This is a useful project for those who:

• Feel frustrated replicating work by others or even reproducing your own work from 6 months ago
• Struggle with BIDSification of data
• Spend endless hours trying to match column names in tabular data files
• Work with multi-site datasets
• Support open-science but work with datasets that have privacy issues
• Want to create a community to build a common ecosystem

We have experienced all these issues ourselves in the past, and so we are here to prevent future grief to newcomers!

Link to the Project

https://nipoppy.readthedocs.io/en/latest/index.html

Image/Logo for the OHBM brainhack website

https://raw.githubusercontent.com/neurobagel/documentation/main/docs/imgs/logo/neurobagel_logo.png

Project lead

Michelle Wang: michellewang
Brent McPherson: bcmcpher
Sebastian Urchs: surchs
Nikhil Bhagwat: nikhil153

Main Hub

Seoul

Link to the Project pitch

https://docs.google.com/presentation/d/10cXPlcPPVaShkpH-Mw1vNuk-iNA4ruDfoYrMAA6Llmg/edit?usp=sharing

Other hubs covered by the leaders

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

Skills

This is for anyone looking to adopt and contribute to the best practices for neuroimaging data workflows. If you wrangle with data, you can contribute! Technical skills are useful but not a strong prerequisite.

Technical

• Bash - familiarity with Terminal
• Python - familiarity with pandas
• Containers - familiarity with running Singularity/Apptainer containers (no need to build them)
• BIDS: familiarly with the specification Neurobagel_high_level_overview

Non-technical

• Belief in reproducible and open science!

Recommended tutorials for new contributors

No response

Good first issues

No response

Twitter summary

Poppy & Bagel: How to FAIRly curate, process, and share your neuroimaging datasets
https://github.com/neurodatascience/nipoppy
@michelle__wang
#OHBMHackathon #Brainhack #OHBM2024 #OHBM_Brainhack_2024

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

poppy_bagel

Please read and follow the OHBM Code of Conduct

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

[sina-mansour]

@nikhil153 Thanks for submitting this amazing project. We encourage including a short Twitter summary along with your project submission for us to be able to promote the project during the brainhack. Apart from that, all is good to go!

Looking forward to seeing you in Seoul.

[nikhil153]

@sina-mansour - I have added the Twitter summary based on the guidelines.
Let me know if anything else comes up! Thanks!

[sina-mansour]

Thanks for the quick response @nikhil153 . All looks good to me, looking forward to seeing you in Seoul!