The NARPS open pipelines project

[elodiegermani]

Title

The NARPS open pipelines project

Short description and the goals for the OHBM BrainHack

NARPS is an fMRI many-analyst study in which 70 research teams were asked to analyze the same fMRI dataset with their favorite pipeline. We would like to take advantage of this wide range of pipelines to build a repository of existing fMRI pipelines that could be used to investigate the impact of analytical variability. Thus, we aim at reproducing these pipelines (for now, 8 were fully reproduced and validated) and to do so, we have access to a file containing textual descriptions of the pipelines as well as the original code for some of the pipelines.

Our project can be split into several goals:

• Facilitate the access, the use and the contributions to the database with good documentation, the development of a standard way of contributing and the use of tools like Docker/Singularity to store data and directly execute the pipeline ;
• Decoding of the textual descriptions of the NARPS pipelines to understand what choices were made by researchers at each step of the analysis ;
• Code adaptation of each step using NiPype interface with the original software packages to build the workflow of the pipeline ;
• Computation of results and validation of the reproduction using original unthresholded and thresholded group level statistical maps published in NeuroVault ;
• Creation of a link with NeuroVault to directly publish the results on the platform.

Link to the Project

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

Image for the OHBM brainhack website

https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/static/images/project_illustration.png

Project lead

Project leaders: Elodie Germani and Camille Maumet Github login: project managed by Inria-Empenn, personal accounts are elodiegermani and cmaumet Discord login: elodiegermani and cmaumet

Main Hub

Glasgow

Other Hub covered by the leaders

• [X] Glasgow
• [ ] Asia / Pacific
• [X] Europe / Middle East / Africa
• [ ] Americas

Skills

We welcome all sorts of contributions. However, knowledge and practice in reproducibility and code sharing practices could help. One or more of the specific skills below would be greatly appreciated:

• Theoretical knowledge in fMRI data analysis pipelines
• Practical skills in fMRI data analysis pipelines with the software packages SPM, FSL and/or AFNI (others also appreciated)
• BIDS format
• Python programming language
• Experience with NiPype interface
• Docker/Singularity: installation and use of a Docker container, sharing images with Docker hub…
• Use of Git and Github

Recommended tutorials for new contributors

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

Good first issues

• Improve Docker containerisation with pre-downloaded data and good documentation for new Docker users: Issue #1
• Creation of a standard template that contributors could use to reproduce a new pipeline: Issue #2 ;
• Debug the pipelines for which a first non-validated workflow was implemented (SPM and FSL based): Issue #3 ;
• Facilitate the link with public databases to download and upload data: Issue #4.

Twitter summary

NARPSOpenPipelinesProject

Come and help @ElodieGermani and @cmaumet build a public fMRI pipeline database! On the menu 🍽️: discussion on good code sharing practices 📋 and reproducibility issues 📝, fMRI workflows 🧠 and development of a shared, sustainable and easy to use repository 📂 #OHBMHackathon #Brainhack #OHBM2022

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

narps-open-pipelines

Please read and follow the OHBM Code of Conduct

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

[djarecka]

Thank you for submitting the project! We have 35 projects right now, woohoo! But that means the projects pitches will have to be short. We will give you tomorrow 2 minutes to pitch your project, you can have one slide or no slides! If you decide to use a slide, please include the link to the slide here.

And don't worry, you will still have more time to talk about your project during the BrainHack :-)

[github-actions[bot]]

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