Phys2BIDScoin: Integrating BIDScoin and phys2bids for a user-friendly GUI based BIDS conversion of physiological files

[marcelzwiers]

Project info

Title
Phys2BIDScoin: Integrating BIDScoin and phys2bids for a user-friendly GUI based BIDS conversion of physiological files

Project lead
Stefano Moia (@smoia) and Marcel Zwiers (@marcelzwiers)

Timezone
Brussels UTC+2

Description
Phys2bids is a python3 toolkit meant to format physiological files in BIDS. BIDScoin is also a python3 toolkit that is meant to format MRI source files in BIDS. BIDScoin comes with data discovery functionality and a graphical interface to customize the formatting heuristics. The actual interaction with the source data is done using plugins and the BIDScoin framework itself is therefore agnostic about the source data modality. Currently, phys2bids lacks data discovery functionality and BIDScoin lacks a formatting backend for physiological data. The goal of this brainhack project is to develop the plugin interface between BIDScoin and phys2bids and hence combine their complementary functionality for both projects

Link to project

• Initial post
• phys2bids
• BIDScoin
• Brainhack pitch

Mattermost handle

• @smoia
• @mpzwiers

Goals for the OHBM Brainhack

1. Move part of the main phys2bids workflow to a phys2bids.info function:
   a. to test if a source file is supported
   b. to retrieve attributes from source files
2. Add YAML support for heuristics in phys2bids
3. Write a BIDScoin “bidsmapper” data discovery plugin function using (1) and (2)
4. Write a BIDScoin “bidscoiner” data formatting plugin / wrapper around phys2bids
5. Create a phys2bids bidsmap section with sensible (regexp) heuristics
6. Extra goal: Add YAML support for system call configuration in phys2bids
7. Extra goal: Expand the attribute dictionary retrieved by phys2bids
8. Extra goal: Write a plugin test function
9. Extra goal: Move SIEMENS physiological files conversion to phys2bids

Good first issues

1. User testing (toward the end of the hackathon), e.g. by creating a test / example data-set
2. Documentation (toward the end of the hackathon), both for phys2bids and for BIDScoin

Skills

• Mandatory for good first issue: none
• Plus for good first issue: little experience with bidsification and/or physiological recordings, or little experience with restructuredtext and readthedocs
• Mandatory for other part of the project: git, python

Number of participants
5-15

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

Chat channel
~hbm-physiopy

Image for the OHBM brainhack website

Project submission

Submission checklist

• 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.
• Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill, cf. here.
• Chat channel: A link to a chat channel that will be used during the OHBM Brainhack. This can be an existing channel or a new one. We recommend using the Brainhack space on mattermost, cf. here.
• Provide an image of your project for the OHBM brainhack website
• Someone co-leading the project in the timeslot you have not selected to provide additional visibility.
• Number of participants, cf. here
• Twitter-size summary of your project pitch, cf. here
• Set up a kanban board on your repository to better divide the work and keep track of things, cf here
• Project snippet for the OHBM Brainhack website, cf. here

[smoia]

Link for project pitch presentation:
https://docs.google.com/presentation/d/13IY2NolS9PRQe0ktw5Jzy2D1gEzqwbcTePJ45l9Vqjw/edit?usp=sharing