Physiopy - Semi-Automated Workflows for Physiological Signals

[m-miedema]

Title

Physiopy - Semi-Automated Workflows for Physiological Signals

Short description and the goals for the OHBM BrainHack

Physiopy is a community formed around developing solutions to acquire, process, and utilize physiological files in neuroimaging contexts. Physiopy is developing or has developed several physiology-oriented modular toolboxes to this end, including 1) phys2bids, a toolbox to standardize physiological files in BIDS format 2) peakdet, a toolbox for automatic detection and manual correction of peaks in physiological data and 3) phys2denoise, a toolbox to prepare derivatives of physiological data for use in fMRI denoising. Currently, we have no complete workflows encompassing all steps of physiological data processing and model estimations. The goal of this project is to facilitate a unified workflow across these toolboxes for semi-automated physiological signal processing.

During this hackathon, we aim to:

• Create a semi-automated workflow based on peakdet and phys2denoise to process respiratory and cardiac signals and obtain models of physiological signal variance for neuroimaging analysis (e.g. RVT, HRV, ...)
• Create a command line interface (CLI) for the workflows
• Update and upgrade the current codebase of peakdet and phys2denoise, including better harmonization between toolboxes

Extra and optional aims could include:

• Create a graphical report of the workflows output
• BIDS-App-lify the workflows: we want to create an entry point to transform the workflow into a BIDS Application
• Pydra-ify the libraries: to learn the strength of Pydra as a workflow manager, we can create a version of the workflow using Pydra.
• Add support for eye-tracking and skin conductance data

All contributions are welcome and accepted, from any level of contribution. We follow the all-contributors specification to report contributions, and adopt physiopy's contributors guide and code of conduct.

Link to the Project

https://github.com/physiopy/

Image for the OHBM brainhack website

https://raw.githubusercontent.com/physiopy/phys2bids/master/docs/_static/physiopy_logo_small.png

Project lead

Mary Miedema (Montreal), Github Username: m-miedema , Discord Username: m-miedema
Roza Gunes Bayrak (Americas), Github Username: rgbayrak Discord Username: @rgbayrak,
Marie-Eve Picard (Montreal), Github Username: me-pic, Discord Username: Marie-Eve Picard (she/her)#4750

Main Hub

Montreal

Other Hub covered by the leaders

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

Skills

We welcome all contributors and contributions, from any skill set and level. Prior work with physiological data would be useful – we’d like to compare how different labs are processing their data. However, we are big believers in learning-by-doing!

No prior git knowledge necessary, if willing to learn on the spot!
Likewise, basic knowledge of python and toolbox set up are helpful, but not necessary.

However, if you are acquainted with bokeh or html reports or pygui or other graphic interfaces, we are looking for you!!!

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

• Add import support for BIDS-format physiological data
• Lay out a sample workflow to process physiological data
• Write documentation about the workflow
• Write a tutorial on the workflow-

Twitter summary

Physiopy - semi-automated workflows for physiological signals
https://github.com/physiopy/
@MaryMiedema @redgreenblues @stemoia
#OHBMHackathon #Brainhack #OHBM2023 #physiopy

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

physiopy-workflows

Please read and follow the OHBM Code of Conduct

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