NeuroDesk - A flexible, scalable, and easy to use data analysis environment for reproducible neuroimaging

Title

NeuroDesk - A flexible, scalable, and easy to use data analysis environment for reproducible neuroimaging

Leaders

• Steffen Bollmann (Twitter: @sbollmann_MRI; Mattermost: @sbollmann_mri)

Collaborators

• Aswin Narayanan (Twitter: @aswinn89; Mattermost: @aswinnarayanan)
• Oren Civer (Twitter: @OrenCivier; Mattermost: @orenciv)
• Tom Johnstone (Twitter: @itjohnstone; Mattermost: @tom_johnstone)
• David White (Twitter: @davidjwhite_33; Mattermost: n/a)
• Angela Renton (Twitter: @angier2310; Mattermost: @angier23)
• Ryan Sullivan (Twitter: @ryans343; Mattermost: @ryan)

Brainhack Global 2021 Event

Brainhack Australasia

Project Description

• What are you doing, for whom, and why? Neurodesk provides a containerised data analysis environment to facilitate reproducible analysis of neuroimaging data.

• What makes your project special and exciting? Analysis pipelines for neuroimaging data typically rely on specific versions of packages and software, and are dependent on their native operating system. These dependencies mean that a working analysis pipeline may fail or produce different results on a new computer, or even on the same computer after a software update. Neurodesk provides a platform in which anyone, anywhere, using any computer can reproduce your original research findings given the original data and analysis code.

• How to get started? Head over to https://neurodesk.github.io/ and try it out :)

• Where to find key resources? https://neurodesk.github.io/docs/

Link to project repository/sources

https://github.com/NeuroDesk

Goals for Brainhack Global

Warm-up goals:

1. Add your favorite workflow to our workflow collection: https://neurodesk.github.io/tutorials/ and benchmark how long it takes to run on Neurodesk vs your standard setup

2. Add your favorite tools to Neurodesk as a new container: https://neurodesk.github.io/developers/new_tools/add_tool/ (already existing tools: https://github.com/orgs/NeuroDesk/packages)

3. Test Neurodesk for your work - let us know what works and what doesn’t work :) https://github.com/NeuroDesk/neurodesk.github.io/discussions

4. Test Neurodesk on free cloud tiers of amazon AWS, google cloud, Alibaba

Stretch goals:

5. Find a way how we can run automatic unit tests of our workflow documentation

6. Build a cross-platform graphical user interface for launching and managing neurodesk (Go/Electron) app

Good first issues

1. issue one: Test Neurodesk for your work - let us know what works and what doesn’t work :) https://github.com/NeuroDesk/neurodesk.github.io/discussions

2. issue two: Add your favorite workflow to our workflow collection: https://neurodesk.github.io/tutorials/

Communication channels

https://mattermost.brainhack.org/brainhack/channels/virtual-neuro-machine-vnm

Skills

• Interest in Neuroimaging Analyses (FSL, Freesurfer, AFNI, EEGlab, MNE, ….)
• Knowhow on installing applications
• running, building and testing docker containers
• writing documentation using Markdown
• advanced: go or javascript for cross-platform development

Onboarding documentation

No response

What will participants learn?

containers, github workflows

Data to use

No response

Number of collaborators

more

Credit to collaborators

Project contributors will be listed on the website and be part of publications originating from the project.

Image

https://neurodesk.github.io/neurodesk.svg

Type

coding_methods, data_management, documentation, method_development, pipeline_development, visualization

Development status

2_releases_existing

Topic

data_visualisation, diffusion, EEG_EventRelatedResponseModelling, EEG_source_modelling, MR_methodologies, reproducible_scientific_methods, tractography

Tools

AFNI, ANTs, BIDS, Brainstorm, CPAC, Datalad, DIPY, FieldTrip, fMRIPrep, Freesurfer, FSL, Jupyter, MNE, MRtrix, Nipype, NWB, SPM, other

Programming language

containerization, documentation, Java, Python, shell_scripting, unix_command_line, html_css

Modalities

DWI, ECOG, EEG, fMRI, MEG, MRI, PET

Git skills

0_no_git_skills, 1_commit_push, 2_branches_PRs, 3_continuous_integration

Anything else?

No response

Things to do after the project is submitted.

• Add a comment saying: Hi @Brainhack-Global/project-monitors: my project is ready!
• Twitter-sized summary of your project pitch.