Physiopy: open development solutions for physiology in MRI

Project title: Physiopy: open development solutions for physiology in MRI



Topic: Data visualization, Physiology, Reproducible scientific methods

Project description: Physiopy is a community developing open science software for physiological files (e.g. vital signs, respiration, eye tracking, skin conductance, …) handling and processing. Currently maintaining three libraries to format physiological files into BIDS (phys2bids), clean physiological traces and find their peaks (peakdet), and use physiological traces to compute nuisance regressors for fMRI denoising (phys2denoise), this (meta-)project aims to provide challenges for all levels of contributors within physiopy’s environment, its three libraries, and its documentation.Collaborators of all levels of experience with git, GitHub, python, and physiology are welcome. Depending on the level of experience, we’ll match collaborators and tasks, and help filling gaps and acquire the necessary skills to finish them.

Data to use: Most tasks do not require data. For those that do, we provide minimal physiological and BOLD fMRI data to work with.

Link to project repository:

Goals for Brainhack Donostia 2021:

First tasks:

Communication channels:

Video channel: Jitsi

Number of collaborators: More

Credit to collaborators: We follow the all-contributors specification in recognising each and all contributions.

Type of project: Coding methods, Data management, Documentation, Pipeline development, Visualization, literature review

Development status: Releases existing

Programming languages: Python, Shell scripting, markdown, if it counts as programming language

Necessary Programming skills level for the project: None

Necessary git skills level for the project: None

Modality: fMRI, physiology

Software suites: BIDS


What will participants learn: Depending on the task, participants might learn:

Jan 1, 0001 12:00 AM