The courtois-neuromod physiological data as a use-case for phys2bids

[sangfrois]

Project info

Project Title:
phys2bids use-case: Segmentation and conversion of CNeuroMod Movie10

Project lead:
François Lespinasse @sangfrois

Timezone:
UTC-4

Description:
Phys2bids provides a way to convert physiological recording files to bids format. This brainhack project acts as user testing for the software by applying its workflow to a large-scale dataset. The Courtois Neuromod project is a longitudinal program which collects massive amounts of multimodal data (neuroimaging, peripheral physiologicals signal and eye-tracking) with the same 6 subjects throughout different tasks. We want to apply the phys2bids workflow to the entire physiological signals (electrocardiographic, electrodermal, respiration and pulse) dataset.

Link to project:
phys2bids
Courtois-Neuromod website
Courtois-Neuromod github
Courtois-Neuromod github PR in development
Mattermost handle:

• @sangfrois

Goals for the OHBM Brainhack:

1. Write documentation on dataset used : Provide description of file and folder structure of sourcedata, and detail the conversion workflow + expected output
2. Use dataset information to validate phys2bids’s output (dataset information is fetched using home-brewed code already written in courtois-neuromod/ds_prep repo)
3. Assess the reproducibility of testing (get home-brewed code reviewed by one internal [courtois-neuromod] and one external [physiopy] reviewer)

Good first issues:

1. Write documentation for sourcedata and conversion workflow
2. Share and adapt this documentation/code with the physiopy community create a pull request to merge it in.

Skills:
python coding for review
physiological signal processing
Chat channel:

~hbm-physiopy

Image for the OHBM brainhack website

Twitter size summary:
@franclespinas
@cneuromod uses phys2bids conversion tool to share its physiological data along with its neuroimaging data under BIDS format. A community-driven effort to promote the shareability of peripheral physiological signals.

Number of participants: I don’t know (less than 5)

Acknowledge contributions: Physiopy adopts the all-contributors system to recognise contributions. Contributors will be recognised as such in the relevant library README (e.g. here) and as authors during outreach (conference posters, talks, ...).

Documentation
physiopy's contributors guidelines
physiopy's code of conduct

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.
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• Provide an image of your project for the OHBM brainhack website

You can also include information about (all optional):

• Someone co-leading the project in the timeslot you have not selected to provide additional visibility.
• Number of participants, cf. here
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• 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.

QMENTA has agreed to sponsor the event and provide computational resources through their platform.

• Get in touch with QMENTA through their Brain Innovation Hub Slack space, if you think your project would benefit from their support.

[tiborauer]

Thank you for the submission. It is almost ready, however, an image is still missing.

[sangfrois]

@tiborauer Thank you for seeing this through. Error in copy paste is the reason why.