A Centralized Project Gallery

The Brainhack Global team aims to create a (de)centralized collaborative working platform that would facilitate & increase across-site collaborations and interactions while also giving visibility to the projects run under Brainhack Global as much as possible. We encourage sharing ideas, experiences and knowledge across parties, removing the barriers and allowing contributions by researchers from all around the globe and a myriad of disciplines.

If you would like to submit a project, please do so by opening an issue here or reading the submission guidelines down below the gallery to get more details.

Projects

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All Git level: 0 none Git level: 1 commit push Git level: 2 branches PRs Git level: 3 continuous integration behavioral DWI ECG ECOG EEG eye tracking fMRI fNIRS MEG MRI PET TDCS TMS C++ containerization documentation Java Julia Matlab none Python R shell scripting Unix command line Web workflows Skills: comfortable Skills: expert Skills: familiar Skills: none coding methods data management documentation method development pipeline development tutorial recording visualisation AFNI ANTs BIDS Brainstorm CPAC Datalad DIPY FieldTrip fMRIPrep Freesurfer FSL Jupyter MNE MRtrix Nipype NWB SPM 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

Interested in submitting a project?

There is still time to submit a project!

 Project URL Submit a project Brainhack global Be nice Hackathon project No knowledge required

Baby Steps Towards De-Sci (Decentralized Science) with Datalad + git annex + IPFS (Interplanetary File Storage System)

A substantial barrier to open science practice is the sharing and accessibility of datasets. Often datasets are stored in a …

 Project URL reproducible scientific methods BIDS Datalad Jupyter Python Web Unix command line shell scripting Skills: none Skills: familiar Git level: 2 branches PRs coding methods data management

Bayesian Hierarchical Microstructure Modelling in the Brain

AIM: Implement a hierarchical Bayesian fitting procedure for a range of brain microstructural models.

Typically microstructural …

 Project URL Bayesian approaches diffusion statistical modelling DWI MRI Jupyter Python Unix command line Skills: familiar Skills: comfortable Skills: expert Git level: 0 none Git level: 1 commit push Git level: 2 branches PRs coding methods method development

Brainhack Proceedings – an open & free journal for Brainhack project outcomes

We are building the Brainhack Proceedings Journal – an open free publishing platform for the community to publish Brainhack …

 Project URL Web none Git level: 1 commit push coding methods

CleanBibImpact: Do papers with a Citation Diversity Statement have more diverse citations?

Gender imbalance is a big problem in academic research, and it is even reflected in our citation behavior. Our goal is to assess …

causality data visualisation diversity inclusivity equality Python none Git level: 1 commit push Git level: 2 branches PRs

Development of the SLAM -Surface anaLysis And Modeling- python package

Slam (https://gauzias.github.io/slam/) is an open source python package dedicated to the representation of neuroanatomical …

 Project URL data visualisation reproducible scientific methods Python Unix command line documentation Skills: none Skills: familiar Skills: comfortable Skills: expert Git level: 0 none Git level: 1 commit push Git level: 2 branches PRs Git level: 3 continuous integration coding methods documentation method development

eCobidas: because methods writing is too important (and boring) to let humans do it!

The main aim of this project is to improve reporting methods and results in neuroimaging (f/MRI, i/EEG, MEG, PET…) in order …

 Project URL MR methodologies reproducible scientific methods EEG eye tracking fMRI MEG MRI PET Python Web documentation none Skills: none Skills: comfortable Git level: 0 none Git level: 1 commit push Git level: 2 branches PRs Git level: 3 continuous integration documentation

eeg-notebooks: a Python library for mobile EEG experiments and analysis

eeg-notebooks is a Python library that allows you to run cognitive neuroscience experiments with a simple mobile EEG device and …

 Project URL data visualisation EEG EventRelatedResponseModelling machine learning reproducible scientific methods statistical modelling behavioral EEG MNE Jupyter Python documentation Skills: familiar Git level: 2 branches PRs coding methods documentation data management method development

Fantastic measures and how to repeat them: tractography-based test retest reproducibility of microstructural MRI

The goal of our project is to investigate novel approaches to assess repeatability and reproducibility in MRI research. As ‘open …

 Project URL connectome data visualisation diffusion hypothesis testing MR methodologies reproducible scientific methods statistical modelling tractography DWI MRI FSL MRtrix Matlab R Skills: familiar Skills: comfortable Git level: 0 none coding methods

Implementation of soma and neurite density imaging (SANDI) in the accelerated microstructure imaging via convex optimization (AMICO) framework

AIM

The aim of the project is to implement an algorithm for fast and robust fitting of complex microstructure imaging methods, …

 Project URL diffusion MR methodologies DWI MRI FSL DIPY Jupyter Python Skills: familiar Git level: 0 none coding methods pipeline development

macapype: segmentation to mesh pipeline

MR methodologies MRI SPM FSL Freesurfer AFNI ANTs Nipype BIDS CPAC Python Matlab Unix command line workflows containerization documentation Skills: none Skills: familiar Skills: comfortable Skills: expert Git level: 2 branches PRs pipeline development documentation

Make Brainhack Accessible WorldWide: Translation of Brainhack Glossary into Different Languages

The project aims to bring together Brainhack and Open Science terminologies together in one glossary to help the newcomers to …

 Project URL documentation Skills: none Skills: familiar Git level: 0 none Git level: 1 commit push Git level: 2 branches PRs Git level: 3 continuous integration documentation data management

Making Of BrainWeb

BrainWeb is a permanent virtual space for online collaborations on projects related to neuroscience. Inspired by initiatives such …

 Project URL data visualisation diversity inclusivity equality Git level: 2 branches PRs

Matplotlib surface plotting

There are lots of nice tools to plot brain meshes in python, but many come with dependencies that can be tricky to install. This …

 Project URL data visualisation fMRI Jupyter Python documentation Skills: familiar Skills: comfortable Git level: 0 none Git level: 1 commit push Git level: 2 branches PRs documentation

Microstructural variations on a theme: a bottom-up approach to diffusion models

The goal of this project is to quantify in practical terms the differences between different microstructural models focusing on …

diffusion MR methodologies reproducible scientific methods DWI FSL DIPY Datalad Python Unix command line shell scripting containerization Skills: familiar Skills: comfortable Git level: 0 none Git level: 1 commit push pipeline development

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

Installing neuroimaging software is hard. Running neuroimaging software on Windows, Mac and HPCs is difficult. Moving analyses …

 Project URL MR methodologies reproducible scientific methods DWI EEG fMRI MEG MRI SPM FSL Freesurfer AFNI ANTs Nipype MRtrix BIDS Datalad fMRIPrep Python Web Unix command line shell scripting workflows containerization documentation none Skills: none Skills: familiar Skills: comfortable Skills: expert Git level: 0 none Git level: 1 commit push Git level: 2 branches PRs Git level: 3 continuous integration coding methods pipeline development documentation data management method development

Neuroimaging Cookbook 🧠🍳📓

Anyone ever Google how to accomplish a task for neuroimaging data more than once? For example, I’ve Googled “how to extract …

 Project URL Bayesian approaches causality connectome data visualisation deep learning diffusion EEG EventRelatedResponseModelling Granger causality ICA machine learning neural decoding neural encoding neural networks PCA reinforcement learning reproducible scientific methods statistical modelling tractography behavioral DWI ECOG EEG fMRI fNIRS MEG MRI PET SPM FSL Freesurfer AFNI ANTs Nipype DIPY MRtrix FieldTrip Brainstorm BIDS NWB Datalad CPAC fMRIPrep MNE Jupyter Python Matlab Julia Web Java C++ R Unix command line shell scripting documentation none Skills: none Skills: familiar Skills: comfortable Git level: 0 none Git level: 1 commit push Git level: 2 branches PRs Git level: 3 continuous integration coding methods documentation data management

OpenMentalizing: leveraging open neurological data for uncovering the differences in mentalizing/empathy capabilities

Mentalizing is a higher cognitive ability that is vital for the social life of an individual. New brain imaging techniques have …

 Project URL causality hypothesis testing neural decoding PCA physiology statistical modelling systems neuroscience MRI PET DIPY BIDS Datalad Python Matlab Julia Web R shell scripting workflows Skills: expert Git level: 1 commit push pipeline development method development

Optimization and GPU porting of information flow implementation

Frites is a recent pure Python package (https://github.com/brainets/frites) to analyse neurophysiological data within the …

 Project URL causality information theory physiology MNE Jupyter Python Skills: familiar Skills: expert Git level: 1 commit push Git level: 2 branches PRs method development

physiopy/phys2bids use-case documentation

My goal is to build protocol-like documentation for phys2bids, a tool for automatic segmentation and conversion of physiological …

 Project URL physiology ECG fMRI BIDS Python shell scripting workflows documentation Git level: 1 commit push Git level: 2 branches PRs coding methods pipeline development documentation data management method development

Physiopy/phys2bids: Tackling good first issues

The aim of this project is to address some issues in phys2bids. Specifically, we’d like to address some good first issues, …

 Project URL physiology ECG fMRI BIDS Python containerization documentation Skills: none Skills: familiar Git level: 0 none coding methods documentation

Physiopy/phys2denoise: Automated pipeline to create BIDS-formatted physiological regressors for neuroimaging denoising

The aim of this project is to restart the development of physiopy/phys2denoise, an automated pipeline to create BIDS-formatted …

 Project URL physiology reproducible scientific methods fMRI BIDS fMRIPrep Python documentation none Git level: 0 none coding methods pipeline development documentation

Prediction of Personality using Diffusion MRI Local Connectome Fingerprints

Local connectome fingerprints (LCF) are voxel-based metrics derived from diffusion MRI to provide a subject-specific …

 Project URL connectome deep learning diffusion machine learning MR methodologies neural decoding statistical modelling behavioral DWI MRI Python Matlab R Skills: familiar Skills: comfortable Skills: expert Git level: 0 none coding methods data management method development

Pydesperate times call for Pydrastic measures

Nipype is a Python library that provides a uniform interface to existing neuroimaging software and facilitates interaction between …

 Project URL reproducible scientific methods behavioral DWI ECG ECOG EEG eye tracking fMRI fNIRS MEG MRI PET TDCS TMS SPM FSL Freesurfer AFNI ANTs Nipype DIPY MRtrix FieldTrip Brainstorm BIDS Datalad MNE Python Unix command line shell scripting workflows containerization documentation Skills: familiar Skills: comfortable Skills: expert Git level: 1 commit push Git level: 2 branches PRs Git level: 3 continuous integration pipeline development documentation method development

Relating EEG eye-tracking data to attention network subsystems

This project involves analysis eye-tracking EEG data that was recorded during the Attention Network Task, a paradigm used to …

EEG EventRelatedResponseModelling hypothesis testing physiology statistical modelling behavioral EEG eye tracking Jupyter Python Matlab Unix command line Skills: none Skills: familiar Skills: comfortable Skills: expert Git level: 1 commit push Git level: 2 branches PRs data management

Standardized denoising strategies with fMRIprep

abels There are many strategies that have been proposed in the literature to denoise fMRI time series, and fMRIprep implements …

 Project URL reproducible scientific methods fMRI fMRIPrep Python shell scripting workflows documentation Skills: familiar coding methods documentation

Task-based connectivity analysis for functional NIRS data

The aim of this project is to learn, comprehend and implement implement two types of task-based connectivity analyses for …

 Project URL connectome fNIRS SPM Matlab Skills: familiar Git level: 0 none Git level: 1 commit push Git level: 2 branches PRs coding methods method development

Towards the Queer Neuroscience&STEM

Towards the Queer Neuroscience & STEM is a project inspired by Queer Theory and Being Queer in Academia Unconference at …

 Project URL none Skills: none Git level: 0 none

TR-OPEN “Getting Started”, Introducing Open Ethical Committee Permissions as an early first step of Open Science

Brainhack Ankara Project For Introducing Open Ethical Committee Permissions as an introductory step of open science. Goal is to …

 Project URL documentation Skills: none Git level: 0 none documentation

Try BioImage Suite Web, a modern and powerful software for neuroscience

BioImage Suite Web (BISWeb) is a point-and-click app that runs in any modern web browser without any installation necessary, yet …

 Project URL connectome data visualisation MR methodologies reproducible scientific methods fMRI MRI C++ documentation none Skills: none Git level: 0 none documentation

Try Data Carpentry Neuroimaging Project

A group of us have been building a set of BIDS/neuroimaging curriculum for the carpentries. The lessons cover intro to …

 Project URL reproducible scientific methods DWI fMRI MRI BIDS fMRIPrep Jupyter Python documentation Skills: none Git level: 0 none documentation

What to do with sh***y (clinical) data? How to apply your perfect estimator/model/method to data that contains outliers?

1 Aim: Modify existing brain structure modeling algorithms and estimators to adjust for outliers in the measurements to enable …

 Project URL Git level: 0 none Git level: 1 commit push Git level: 2 branches PRs DWI MRI Matlab Python R Unix command line shell scripting Skills: familiar Skills: none coding methods method development DIPY Freesurfer MRtrix Nipype SPM MR methodologies diffusion reproducible scientific methods statistical modelling tractography

Brainhack Global 2020 Project Submission Guideline

Why a Centralised Project Submission?

As the Brainhack Global team, we aim to create a (de)centralized collaborative working platform that would facilitate & increase across-site collaborations and interactions while also giving visibility to the projects run under Brainhack Global as much as possible. Creating such a (de)centralized platform and workflow, we aim to encourage sharing ideas, experiences and knowledge across parties, removing the barriers and allowing contributions by researchers from all around the globe and a myriad of disciplines.

Given that this year Brainhack Global will be run virtually, (de)centralized project submission and listing platform will allow you to submit your initial project call to gather interests from researchers from every single Brainhack Global event location.

The ideal project should convey ideas with respect to the development of tools, methodologies, guidelines and begets to brainstorming new ideas that would facilitate the implementation of open science practices in neuroscience and create more opportunities for collaborative work and information exchange within the community.

If you would like to get more ideas about:

  • how to design your project and what to expect from a Brainhack experience,
  • how to lead a project,
  • how to be an attendee of a project

Please read our How to Guideline for Leading and Attending to Brainhack Projects!

How will it work?

Where to start?

In order to submit a project to the Brainhack Global 2020 Project Gallery, please follow these steps:

  1. Register with an event listed in the Brainhack Global 2020 Events.
  2. Create a GitHub account.
  3. Go to the Brainhack 2020 GitHub Repository.
  4. Click on the New Issue button on the up right.
  5. Create a new issue by clicking on the Get Started button beside Project submission template.
  6. Fill in the necessary/required information as requested.
  7. Please make sure that the information about your project is as clear and brief as possible sharing the necessary links that point reviewers/attendees to the right resources/repository and more detailed information about your project.
  8. Please make sure to follow the instructions in the How to Guideline for Leading and Attending to Brainhack Projects to increase the diversity and inclusivity in your project work and define the tasks, roles and the skills that you are expecting from your attendees accordingly. Make sure that you have room for newcomers to give them a chance to learn from more seniored colleagues and share their own experiences.
  9. Choose/create the label that is pointing to the event location that you are registered with.
  10. Follow the instructions given in the issue template on how to choose the labels that defines the scope of your project best. By assinging the labels, you will increase the visibility of your project to curate attendees' attention to your project and will help us to match your event with the attendees having the requested/matching skill sets and interests.
  11. After you are done filling in the necessary/required information, open the issue to submit your project to be reviewed.
  12. Do not forget that you can make amendments in your issue template as necessary/required to do so along with and after the reviewing process.

What happens next?

Once you have submitted your project, a reviewer from the event that you have registered with will follow up with you and will review the information in your issue. They may request some changes if deemed necessary. If all necessary/required information is in place, the project will be marked as ‘status:web_ready’ and will be listed on the Brainhack Global 2020 Projects page after a short delay. A subpage dedicated to your own project will be automatically created. In the meantime, you can still continue to make changes in/to your issue.

This year, Brainhack Global also offers a new feature to assign event attendees to projects across the globe based on the matching between expertise/skill sets that attendees want to acquire and the projects are looking for. Once the attendee registrations are completed, the matching algorithm will be run by the local organizers themselves based on the information provided by the attendees in the participant registration form. The attendees will be automatically sent an email that is listing the best fitting projects with their expertise and interests. However, the preference of the project the attendees will participate will be based on the attendees own decision. They could either go with the suggested options or they could choose among the other projects listed in the Brainhack Global 2020 Projects page. Based on the communication channels listed in the project issues, the attendees will contact the project leaders as necessary.

Please be aware that, at the very early stage of the interactions, attendees might just want to contact you for more information to make sure that the project is a good fit to the aims they want to achieve from a Brainhack. Therefore, please make sure that you welcome all attentions and explain your project with care and guide them as necessary.