Integration of EEG inside Connectome-Mapper 3

[sebastientourbier]

Project info

Title: Integration of EEG inside Connectome-Mapper 3

Project lead: Sebastien Tourbier (sebastientourbier)

Timezone: UTC/GMT +2 hours (CEST)

Hub: Europe, Middle East and Africa

Description:

Flexible pipelines for both diffusion MRI and functional MRI have been implemented in different software such as the Connectome Mapper 3, an open-source pipeline software, released as a BIDS App, for mapping hierarchical multi-scale connectomes from multi-modal datasets, but solutions for EEG and MEG are still lacking. This project intents to extends Connectome Mapper 3 to EEG.

Link to project: https://github.com/connectomicslab/connectomemapper3/tree/ohbm-brainhack-2020

Mattermost handle: sebastientourbier

Goals for the OHBM Brainhack

1. Creation of a sample BIDS dataset with EEG derivatives (computed inverse solutions):

• Decide a sample dataset (open-source) to use (ultimately with T1w, DWI, rfMRI, EEG modality)
• Organize the sample dataset according to BIDS MRI/EEG standard
• EEG analysis (computes the inverse solution) by an open-source EEG analysis software such as MNE, EGGLab,... depending of the expertise in the team
• Organization of EEG analysis outputs into the derivatives of the dataset according to new derivatives specs introduced in BIDS 1.4.0 (https://bids-specification.readthedocs.io/en/stable/05-derivatives/01-introduction.html)

2. Implementation of Nipype interfaces that:

• loads the inverse solutions and their respective x,y,z locations
• computes ROI source dipoles using the SVD technique
• computes single source dipoles per ROI based on SVD decomposition [Rubega et al. 2018] using pycartool (https://github.com/Functional-Brain-Mapping-Laboratory/PyCartool)
• computes diverse common functional connectivity metrics (Imaginary coherence, ...) using MNE - See how it integrates BIDS Connectivity data schema #203

3. Implementation of EEG pipeline in the Connectome Mapper 3

• Implementation of the EEG processing pipeline (cmp/pipelines/functional/eeg.py)
• Extension with graphical components (cmp/bidsappmanager/pipelines/functional/eeg.py)

Good first issues:

• Get familiar to the Brain Imaging Data Structures: https://bids-specification.readthedocs.io/en/stable/
• Get familiar to the BIDS App framework: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005209
• Get familiar with Nipype: https://miykael.github.io/nipype_tutorial/

Skills:

• Brain Imaging Data Structure
• EEG analysis
• Nipype dataflow library

Chat channel: https://mattermost.brainhack.org/brainhack/channels/hbm-eeginsidecmp3

Image for the OHBM brainhack website

Project submission

Submission checklist

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

Please include the following above (all required):

• Link to your project: could be a code repository, a shared document, etc. See here
• Include your Mattermost handle (i.e. your username). If you do not have an account, please sign up here.
• Goals for the OHBM Brainhack: describe what you want to achieve during this brainhack. See here.
• 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, cf here.
• Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill, cf. here.
• Chat channel: A link to a chat channel that will be used during the OHBM Brainhack. This can be an existing channel or a new one. We recommend using the Brainhack space on mattermost, cf. here.
• Video channel: Please create a video channel that will be used during the OHBM Brainhack and share it in your chat channel above. This can be an existing channel or a new one. For instance a jitsi meet room, cf. here.
• Provide an image of your project for the OHBM brainhack website

You can also include information about (all optional):

• Number of participants, cf. here
• Twitter-size summary of your project pitch, cf. here
• Set up a kanban board on your repository to better divide the work and keep track of things, cf here
• Project snippet for the OHBM Brainhack website, cf. here

We would like to think about how you will credit and onboard new members to your project. We recommend reading references from this section. If you'd like to share your thoughts with future project participants, you can include information about (recommended):

• Specify how will you acknowledge contributions (e.g. listing members on a contributing page).
• Provide links to onboarding documents if you have some.

[welcome]

(Image: CC-BY license, The Turing Way Community, & Scriberia. Zenodo. http://doi.org/10.5281/zenodo.3332808)
🎉 Welcome to the 2020 OHBM Hackathon! 🎉 We're really excited to have your input on this repository and welcome your idea! 💖 If you haven't done so already, please make sure you check out our Code of Conduct. Did you issue a new hackathon project? Please check if you have provided all relevant information and an image for the website.

[DorienHuijser]

Hi @sebastientourbier, can you provide us with an image for the hackathon website? Thanks in advance!

[complexbrains]

Dear @@sebastientourbier, would you mind setting up a Mattermost channel and sharing here please. Also would you mind creating a video chat link and sharing it in your Mattermost channel only please. Once you are done with those, please give us a shout then we will finish with the revision of your project! Thank you 🤗

[cmaumet]

Hey @sebastientourbier. Thanks for your project. Unless I am mistaken, In think you are not registered yet to the event. Can you please do this asap over here? Thank you!

[sebastientourbier]

Hey cmaumet. Yes here is the information about when I registered:

OHBM Brainhack
Registration Date: 05/22/2020
Invoice #: 95980 

Now I just completed the other registration form at the link you set a few days ago and I got the submission identifier HACK2020-5614690

[sebastientourbier]

hi @ohbm/project-monitors: My project is ready!'

[complexbrains]

Dear @sebastientourbier Thank you very much. As it seems your project is ready! So welcome aboard! 🤗 🎊

[cmaumet]

Thank you @sebastientourbier! All good now :D