physiopy/phys2bids: BIDS formatting of physiological recordings

[smoia]

Guidelines

We are very excited to meet you at the 2020 OHBM Brainhack 🎉 To submit a project, you need to be an attendee of the 2020 OHBM Brainhack. We ask you to register first over here. Thank you!

We have prepared a checklist to help with your project submission. Here is how to proceed:

1. Before filling in any part, please submit this issue
2. Check items in the checklist below as you go through them
3. Once you are done (at least all 'required' items must be provided), please delete the "Guidelines" section add a comment saying 'hi @ohbm/project-monitors: My project is ready!'

Thank you!

After step 1 (issue submitted), we will assign a 'project monitor' to follow your submission. If at any time you need help or anything is unclear, please add a comment and ping your project monitor. Our team is here to help!

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Project info

Title: physiopy/phys2bids: BIDS formatting of physiological recordings

Project lead: Vicente Ferrer @vinferrer (EMEA), Eneko Uruñuela @eurunuela (EMEA), François Lespinasse @sangfrois (The Americas), Stefano Moia @smoia (EMEA, The Americas)

Timezone: Berlin, Brussels UTC+2

Hub: EMEA / The Americas

Description: Physiopy is a github organisation maintained by (at the moment) 12 volunteers that aims to offer open development solutions for physiology in MRI. phys2bids is the flagship library of physiopy, and consists in a python3 library meant to format physiological (cardiac, respiratory, or gas signals) files in BIDS. It was born for AcqKnowledge (BIOPAC) files, and at the moment it also supports LabChart (ADInstruments). It doesn’t support physiological files recorded with the MRI (yet). Next to phys2bids, we’re starting the development of phys2denoise, a library dedicated to prepare physiological signal for fMRI denoising.

Link to project: https://github.com/physiopy/phys2bids

Mattermost handle: @smoia

Goals for the OHBM Brainhack We have different proposals for Brainhack participants, that can be seen here. Between the contributors, we have very different background, but one that is lacking is knowledge in pattern recognition or ML. We’d be thrilled if someone that has experience in that field could help us set up an automatic recognition of the file contents! We would also like to start supporting eyetracking bidsification, so if anyone with background (and recordings) in eyetracking wants to help out, it would be a great opportunity to work together. We’re always looking forward for collaboration with other bidsificators. At the moment, we’re working together with bidscoin to integrate the two solutions together, and we’d be happy to start a dialogue with heudiconv contributors and other bidsificators too!

Good first issues: See them here

Skills: Depending on the issue that you want to tackle!

• Good First Issues: willingness to learn python/git/github/restructured text. We’ll help you out with those!
• Automatic recognition of physiological signal: knowledge of pattern recognition in python is welcomed.
• Eyetracking integration: knowledge of eye tracking (python knowledge not necessary).
• Making a report for phys2bids: interest in design or UI/UX or web design skills.
• If you’re a BIDS expert, we’d love to have a chat with you!
• Other required skills are described in the issues themselves.

Chat channel: #hbmhack-physiopy

Video channel: will be provided in the mattermost channel.

Image for the OHBM brainhack website https://github.com/physiopy/phys2bids/blob/master/docs/_static/phys2bids_card.jpg

Contribution recognition: We follow all-contributors specifications! See here

Important documents: Start with this page,

Project submission

Submission checklist

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

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• [x] Link to your project: could be a code repository, a shared document, etc. See here
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• [x] Goals for the OHBM Brainhack: describe what you want to achieve during this brainhack. See here.
• [x] 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.
• [x] Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill, cf. here.
• [x] 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.
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You can also include information about (all optional):

• [ ] Number of participants, cf. here
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[welcome[bot]]

(Image: CC-BY license, The Turing Way Community, & Scriberia. Zenodo. http://doi.org/10.5281/zenodo.3332808) :tada: Welcome to the 2020 OHBM Hackathon! :tada: We're really excited to have your input on this repository and welcome your idea! :sparkling_heart: 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.

[jhlegarreta]

@smoia looks awesome. Could please check that the eye tracking label description matches the type of data that you will be dealing with?

As for the website description, could you please share one that summarizes the goal of the project and its background? You can either do it here or open a PR with the proposal editing the following file: https://github.com/ohbm/hackathon2020/blob/master/_data/projects.yml

If you open the PR, do not forge to add the image to the following folder: https://github.com/ohbm/hackathon2020/tree/master/img/hackathon

[smoia]

@jhlegarreta thank you for your help! Sure thing! Is there a label for physiology (but not electrophysiology) as well? That's more the kind of data we work with. Tomorrow a project lead will make the PR to the website descriptor!

[smoia]

Ah, you ninjaed me! Thank you again!

[Remi-Gau]

hey @smoia

As you have project leads in several hubs, should I put you down for project pitches in both hubs (meaning will there be some who can pitch live for both hubs)?

[smoia]

If it's possible, yes, it would be great!

[Remi-Gau]

If it's possible, yes, it would be great!

OK noted just let us know who we should call on "stage" in each hub. :-)

[smoia]

If it's possible to have two people onstage, @eurunuela and I for EMEA and @sangfrois and I for The Americas!

[smoia]

@jhlegarreta I opened a PR for the snippet in #209

[jhlegarreta]

@smoia the project requirements are complete. Ready to start hacking when the event starts ! Happy hacking :keyboard: !

[smoia]

:tada: :tada: :tada: @eurunuela @sangfrois @vinferrer Let's get ready!

[cmaumet]

Hi @vinferrer! Thanks a lot for your project. Unless I am mistaken, In think that your project co-lead (François Lespinasse) is not registered yet to the event. Can you please ask them to register or list them as project collaborators if they are not joining the event? Thank you!

[smoia]

Hey @cmaumet ! Is he not? I'm going to ask him!

[smoia]

@cmaumet , @sangfrois told me he registered this morning?

[sangfrois]

... sorry for late registration :)

[cmaumet]

Oh @sangfrois, thanks for that! All you need to do now to complete your registration now is to fill in the form here to provide us with important additional info. Thank you!