NARPS Open Pipelines - A codebase to study variability of fMRI analysis workflows

[bclenet]

Title

NARPS Open Pipelines

Leaders

Boris Clénet - R&D Engineer, Empenn Team, INRIA Rennes, France
Mattermost : @bclenet

Collaborators

This project is developed in the Empenn team by Boris Clénet, Elodie Germani, Jérémy Lefort-Besnard and Camille Maumet with contributions by Rémi Gau.

All project contributors are listed in the Credits section of the project !

Brainhack Global 2023 Event

Brainhack Marseille

Project Description

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

We hope this tools will help analysing and understanding variability of fMRI analysis workflows, hence participating in the reproducible research movement.

Find relevant information about how to get started is in the README.md file.

Join us and contribute to an open-source tool for the community !

Link to project repository/sources

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

Goals for Brainhack Global

• start new pipeline reproductions
• contribute to already stared pipelines
• proof read the documentation
• contribute to the documentation
• write tests for existing pipelines

Good first issues

• Contribute to the documentation (give feedback, help organizing)
• Write the pseudo-code for a pipeline
• Debug already implemented pipelines

Communication channels

Mattermost channel

Skills

• fMRI statistical analysis: advanced
• python (+ nipype): advanced
• writing and organizing documentation: basic

Onboarding documentation

General information can be found here: README file
How to contribute: CONTRIBUTING file

What will participants learn?

• using the nipype python library
• lots of fMRI analysis workflow examples
• good practices for (python) coding

Data to use

Although it may not be useful during the brainhack, the project's documentation (see corresponding section) gives information about required data.

Number of collaborators

4

Credit to collaborators

All project contributors are listed in the Credits section of the project.

Image

Link to the image here.

Type

documentation, pipeline_development

Development status

1_basic structure

Topic

reproducible_scientific_methods, statistical_modelling

Tools

AFNI, ANTs, BIDS, Datalad, fMRIPrep, FSL, Nipype, SPM

Programming language

documentation, Python

Modalities

fMRI

Git skills

0_no_git_skills, 1_commit_push, 2_branches_PRs

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.

[bclenet]

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

[Remi-Gau]

Project should now be listed on the project page: http://brainhack.org/global2023/projects/