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

Project info

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

Project lead: Steffen Bollmann, @sbollmann_mri

Project collaborators: Aswin Narayanan Oren Civier @OrenCivier Christopher Nolan @cnolanAU Jakub Kaczmarzyk @JakubKaczmarzyk Martin Grignard @grignard_martin MEJ Campbell @MegaEJ_Campbell Thom Shaw @thomcat992 Tom Johnstone @itjohnstone

Registered Brainhack Global 2020 Event: https://brainhack-ankara.github.io/

Project Description: Installing neuroimaging software is hard. Running neuroimaging software on Windows, Mac and HPCs is difficult. Moving analyses between platforms is a pain. Reproducing an analysis stack on a different computer is almost impossible. We are attempting to help with this and we are building an analysis environment for Neuroimaging with the goal to make it very easy to run a variety of neuroimaging tools on any operating system. The project aims to make reproducible and scalable neuroimaging analysis as easy as possible. With this we are not just helping beginners to get access to the tools they need without waiting for their administrators to compile them, but we are also aiming to build good habits by making it easy to document and control software versions, and we enable power users to quickly scale up their analyses and run identical software on a variety of compute platforms.

All skill levels can work on our project, from improving the documentation, testing or adding their favourite tool, working on the underlying container infrastructure or developing CI and CD to make our workflows as robust and easy as possible.

Link to project repository/sources: https://github.com/NeuroDesk

Goals for Brainhack Global 2020: Easy:

• test neurodesk on a variety of platforms and gather feedback: what works, what doesn’t, what tools are missing
• improve documentation

Medium:

• build new software containers with currently missing applications
• develop documentation for analysis workflows
• improve our CI/CD (how to test GUI applications?, how to test workflows?)
• improve handling of licenses (e.g. freesurfer …)

Hard:

• add support for flexible screen resolutions,
• fix user-id mapping when running inside docker container,
• work on the “Inception Mode”: Execute unprivileged containers inside unprivileged containers … we know it’s possible, but we need a container guru to help us getting it to work
• enable a persistent homedirectory so that user settings can persist across container update

Good first issues:

• test neurodesk on a variety of platforms and gather feedback: what works, what doesn’t, what tools are missing
• build new software containers with currently missing applications

Skills:

• making documentation beginner friendly
• testing our current version - what works, what doesn’t?
• python development: refactoring of code currently in shell scripts
• sys-admin skills: improve desktop experience
• CI/CD: better tests, more coverage

Tools/Software/Methods to Use:

• docker and visual studio code

Communication channels:

Project labels

• Type of project: #coding_methods, #data_management, #documentation, #method_development, #pipeline_development, tutorial_recording, visualization

• Project development status: 0_concept_no_content, 1_basic structure, #2_releases_existing

• Topic of the projet: Bayesian_approaches, causality, connectome, data_visualisation, deep_learning, diffusion, diversity_inclusivity_equality, EEG_EventRelatedResponseModelling, EEG_source_modelling, Granger_causality, hypothesis_testing, ICA, information_theory, machine_learning, #MR_methodologies, neural_decoding, neural_encoding, neural_networks, PCA, physiology, reinforcement_learning, #reproducible_scientific_methods, single_neuron_models, statistical_modelling, systems_neuroscience, tractography

• Tools used in the project: #AFNI, #ANTs, #BIDS, Brainstorm, CPAC, #Datalad, DIPY, FieldTrip, #fMRIPrep, #Freesurfer, #FSL, Jupyter, MNE, #MRtrix, #Nipype, NWB, #SPM

• Tools skill level required to enter the project (more than one possible): #comfortable, #expert, #familiar, #no_skills_required

• Programming language used in the project: #no_programming_involved, C++, #containerization, #documentation, Java, Julia, Matlab, #Python, R, #shell_scripting, #Unix_command_line, #Web, #workflows

• Modalities involved in the project (if any): behavioral, #DWI, ECG, ECOG, #EEG, eye_tracking, #fMRI, fNIRS, #MEG, #MRI, PET, TDCS, TMS

• Git skills reuired to enter the project (more than one possible): #0_no_git_skills, #1_commit_push, #2_branches_PRs, #3_continuous_integration

• I added all of the labels I want an associate to my project

Project Submission

Submission checklist

Once the issue is submitted, please check items in this list as you add under ‘Additional project info’

• Link to your project: could be a code repository, a shared document, etc.
• Goals for Brainhack Global 2020: describe what you want to achieve during this brainhack.
• Flesh out at least 2 “good first issues”: those are tasks that do not require any prior knowledge about your project, could be defined as issues in a GitHub repository, or in a shared document.
• Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill. Use the issue labels for this purpose.

Optionally, you can also include information about:

• Number of participants required.
• Twitter-sized summary of your project pitch. NeuroDesk - A flexible, scalable, and easy to use data analysis environment for reproducible neuroimaging
• Provide an image of your project for the Brainhack Global 2020 website.

We would like to think about how you will credit and onboard new members to your project. If you’d like to share your thoughts with future project participants, you can include information about:

• Specify how you will acknowledge contributions (e.g. listing members on a contributing page). contribution page + paper co-authorship once in a publishable state
• Provide links to onboarding documents if you have some: