physiopy/phys2bids use-case documentation

[sangfrois]

Project info

Title:
Physiopy/phys2bids: use-case documentation for the segmentation and conversion of massive amount of physiological data.

Project lead:

François Lespinasse (Twitter handle : franclespinas | Brainhack mattermost handle : @sangfrois)

Project collaborators:

Katie Bottenhorn @62442katieb

Stefano Moia @smoia

Registered Brainhack Global 2020 Event:

Brainhack Global Donostia (from Montreal, Québec)

Project Description:
My goal is to build protocol-like documentation for phys2bids, a tool for automatic segmentation and conversion of physiological files to BIDS format. The intention is share a blueprint for what the physiopy community expects to be a common use-case of phys2bids.

Info on phys2bids:
This tool reduces human error during the concurent collection of physiological (ECG/PPG/EDA/RSP/etc.) and neuroimaging data (fMRI, MEG, etc.). The reason being that recordings often contain unwanted segments as experimenters continue to acquire physiological activity in-between scanning sessions.

The way it works:
phys2bids can take the physiological recording files (such as those provided from BIOPAC-Acqknowledge) and automatically cut the appropriate segments by using the trigger pulse sent by the scanner (see multi-run phys2bids workflow for more info.

Why it's interesting
This tool allows the user to generate BIDS compatible physiological files organized by runs (just like neuroimaging data). It represents a more convenient way to match neuroimaging acquisition with physiological ones.

What we need, now :
What we need now is to provide users with a convenient way to process massive amount of physio data in a time-efficient way.

Data to use:
As I have special access to the Courtois-Neuromod project data, I intend to use the movie10 experiment to exemplify the usefulness of phys2bids multi-run workflow.

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

Goals for Brainhack Global 2020:

Documentation-specific tasks

• Write down some context to describe the interest of using phys2bids for massive amount of phys data
• Specify the information needed and how to get it in order to execute phys2bids workflow
• Specify steps to fetch this info proceduraly from a BIDS neuroimaging dataset

Code-specific tasks

• Code utility functions to fetch information from BIDS dataset
• Build .sh script that uses the information needed to execute phys2bids workflow for a whole subject directory

Good first issues:

1. Review the order and general organization phys2bids documentation (see also with Physiopy/phys2bids: Tackling good first issues #39 as Katie is also upkeeping phys2bids documentation)
2. Assess where to add this use-case/phys2bids tutorial
3. Review my unreleased code and think about its eventual integration to phys2bids (see whether it should get a PR)

Skills:

• knowledge of physiological recording instruments
• markup languages
• Python
• bash script

Communication channels:

We'll discuss where to meet on mattermost

Project labels

• I added all of the labels I want an associate to my project

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