PhysioQC: A physiological data Quality Control toolbox with physiopy

[smoia]

Title

PhysioQC: A physiological data Quality Control toolbox with physiopy

Short description and the goals for the OHBM BrainHack

Physiopy is a community formed around developing solutions to operate physiological files in neuroimaging setups. We manage a few physiology-oriented toolboxes to process physiological data, and we would like to add a new toolbox to help quality assurance of physiological data through (automatised) quality control. If you are familiar with MRIQC, or afni proc quality control - we want to do something similar, but for physiological data.

During previous hackathons and meetings we planned the toolbox, and during these upcoming three days we'll implement a workflow to automatise it and get textual and image-based outputs, in order to get a starting point to report valuable QC information.

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/physioqc

Image for the OHBM brainhack website

https://github.com/physiopy/phys2bids/blob/master/docs/_static/physiopy_logo_1280x640.png?raw=true

Project lead

Stefano Moia, Github Username: smoia, Discord Username: smoia

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 skillset and level.
We are big believers in learning-by-doing!
No prior git knowledge necessary, if willing to learn on the spot!
Basic knowledge of python, toolbox set up, and/or signal processing are helpful, but not necessary.

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

• Write simple functions to compute basic signal properties
• Select data to test the library

Twitter summary

PhysioQC: A physiological data Quality Control toolbox with physiopy @stemoia
#OHBMHackathon #Brainhack #OHBM2023 #Physiopy

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

physiopy-qc

Please read and follow the OHBM Code of Conduct

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