NARPS Open Pipelines

[bclenet]

Title

NARPS Open Pipelines

Short description and the goals for the OHBM BrainHack

The goal of the NARPS Open Pipelines project is to create a codebase reproducing the 70 pipelines of the NARPS project (Botvinik-Nezer et al., 2020) and share this as an open resource for the community.

In particular, we would like to focus on these tasks during the Brainhack:

• Start reproducing new pipelines, based on the knowledges of participants (i.e.: which fMRI analysis software they are used to, whether they use Python or not, ...) ;
• Improving documentation and accessibility of the project.

Link to the Project

https://github.com/Inria-Empenn/narps_open_pipelines

Image for the OHBM brainhack website

https://raw.githubusercontent.com/Inria-Empenn/narps_open_pipelines/main/assets/images/project_illustration.png

Project lead

Boris Clénet (https://github.com/bclenet) - virtual hub Europe
Camille Maumet (https://github.com/cmaumet) - Montreal
Elodie Germani (https://github.com/elodiegermani) - Montreal

Main Hub

Europe / Middle East / Africa

Other Hub covered by the leaders

• Montreal
• Asia / Pacific
• Europe / Middle East / Africa
• Americas

Skills

• Base knowledge of git and GitHub
• Able to understand Python code
• Understanding of fMRI analysis pipelines
• Ideally but not required : some Nipype knowledge
• Ideally but not required : having used SPM or FSL or AFNI or nistats

Recommended tutorials for new contributors

• Set up a brainhack friendly computing environment
• A introduction to Bash
• Python: Writing a script
• Python: Data analysis with Python
• Python: Visualisation
• Machine learning basics
• BIDS
• Machine learning for neuroimaging
• VCS: Using Git and Github
• VCS: Data management with Datalad
• Virtualization
• High Performance Computing: Oracle cloud resource

Good first issues

• Debug pre-implemented pipelines
• Write the pseudo-code for a pipeline
• Documentation : write a nice summary of NARPS

Twitter summary

NARPS Open Pipelines
https://github.com/Inria-Empenn/narps_open_pipelines
Project leader: Boris Clénet with @cmaumet @elodiegermani
#OHBMHackathon #Brainhack #OHBM2022

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

narps-open

Please read and follow the OHBM Code of Conduct

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

[bclenet]

Hi @anibalsolon ! I will attend the event from the Europe / Middle East / Africa Hub : can I present the project during the project pitches session tomorrow ? Thanks :)

[anibalsolon]

Certainly @bclenet thank you for joining us!