The BIDS connectivity project - current state and next steps of the BEPs

[PeerHerholz]

Title

The BIDS connectivity project - current state and next steps of the BEPs

Short description and the goals for the OHBM BrainHack

Besides BIDS' success, expansion, and description of multiple data modalities, gaps still exist in developing the standard to effectively support the process of scientific results reporting. Among others, this prominently refers to data obtained through and during connectivity analyses. This comprises brain parcellations, connectivity maps, structural and functional connections, major white matter tracts, diffusion signal models, white matter tractograms and tractometry, as well as networks based on dimensionality reduction. Sharing processed data and features in addition to raw and minimally-processed data is critical to accelerating scientific discovery. This is because substantial effort, software, and hardware instrumentation, and know-how are required to bring raw data to a usable state. The aim of the present project is to extend the BIDS standard to encompass derivatives resulting from experiments related to macroscopic brain connectivity (U.S. National Institutes of Health NIMH R01-MH126699). During the Brainhack, we would like to

1. Gather feedback from experts, users, tool developers, ie everyone!
2. Work on the respective BEPs
3. Convert BEPs from GoogleDocs to GitHub PRs

Link to the Project

https://pestillilab.github.io/bids-connectivity/

Image for the OHBM brainhack website

https://pestillilab.github.io/bids-connectivity/img/logo.svg

Project lead

Peer Herholz, GitHub: peerherholz, discord: peerherholz
Franco Pestilli, GitHub: francopestilli, discord:
Ariel Rokem, GitHub: arokem, discord

Main Hub

Montreal

Other Hub covered by the leaders

• Montreal
• Asia / Pacific
• Europe / Middle East / Africa
• Americas

Skills

Experience with one of our covered data modalities and respective analysis software packages would be helpful: s/fMRI, dMRI, PET, MEG, i/EEG. Additionally, knowledge of BIDS would come in handy.
However, these are not requirements: we're happy to welcome everyone interested.

Recommended tutorials for new contributors

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

Good first issues

No response

Twitter summary

Interested in Brain connectivity and FAIR data? The BIDS connectivity project might be of interest to you! During the Brainhack we will discuss work on the different connectivity-related BIDS Extension Proposals (BEPs) and welcome support from all interested parties!

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

bids-connectivity

Please read and follow the OHBM Code of Conduct

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

[eduff]

Hi - I won't be at OHBM or in timezone, but is there somewhere other than the BEPs that we might follow/contribute? @PeerHerholz

[PeerHerholz]

Hi @eduff,

thanks for reaching out! Yeah, I prepared a presentation and a GoogleDoc that hopefully should allow folks to follow/contribute. You can find the presentation here and the GoogleDoc here. We are also reachable via the usual slack channels and this jitsi room.

There's also the BIDS town hall that will provide general and BEP-specific updates. The BIDS Connectivity Project will have a slot towards the end of the presentation.

Please let me know if you have any questions and/or run into problems.
Thanks again.

Cheers, Peer

[eduff]

Great - happy to help get BEP017 onto github.

…

On Tue, 18 Jul 2023 at 13:46, Peer Herholz ***@***.***> wrote: Hi @eduff <https://github.com/eduff>, thanks for reaching out! Yeah, I prepared a presentation and a GoogleDoc that hopefully should allow folks to follow/contribute. You can find the presentation here <https://docs.google.com/presentation/d/1KTyiMWRI8ML6nzJB_uHeQh5lPD9iEAWL-tf02mZMILE/preview> and the GoogleDoc here <https://docs.google.com/document/d/1ETGgN7RiTi5sloCMi-YFWY1eQQl7CsNsjyJ7uhR0yPo/edit?usp=sharing>. We are also reachable via the usual slack channels and this jitsi room <https://meet.jit.si/BIDS_connectivity_project_meeting>. Please let me know if you have any questions and/or run into problems. Thanks again. Cheers, Peer — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG4KVEPJIU6VLYKSA3UZM3XQ2AUBANCNFSM6AAAAAAYKM52PQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>