Big Neuroimaging Dataset Phenotype BIDS Tools

[JessyD]

Title

Big Neuroimaging Dataset Phenotype BIDS Tools

Leaders

Jessica Dafflon and Eric Earl

Collaborators

No response

Brainhack Global 2022 Event

Brainhack Washington DC

Project Description

Information about phenotypes (i.e., age, responses to cognitive/clinical questionnaires, blood tests) is hard to share and varies widely in format when shared. For example, some studies share this information in .tsv, .csv, and some even share this information in .pdf files. Building upon the recent guidelines for phenotypic data in BIDS, we created a repository to share the phenotypes in a uniform & machine-readable format for a few commonly used neuroimaging datasets. We have written the code to extract a dictionary.json (a file that contains a list of the phenotypes present and their description) for a few datasets, but this can be extended to other neuroimaging datasets. A list of other possible contributions is present on the github issues.

Link to project repository/sources

• Project repository
• The Phenotypic Data Guidelines for the BIDS extension
• This link contains the OHBM 2022 poster that summarizes the Phenotypic Data Guidelines for the BIDS extension

Goals for Brainhack Global

• Extract HBN data dictionary
• Add other datasets according to the contributor's interest
• Conceptualize and provide a GUI to select phenotype of interests from the dictionary.json

Good first issues

1. issue one: Run the code for one of the provided datasets. See if there are any issues/bugs and if necessary improve their documentation
2. To see more issues check our github issues.

Communication channels

bids-phenotype channel on brainhack DC's slack workspace

Skills

• Python: basic to intermediate
• Git: basic to intermediate to make changes to the current code
• User experience of how it is to run the code

Onboarding documentation

No response

What will participants learn?

• Reading and manipulating pandas dataframes
• Creating a GUI using Python
• Getting familiar and collaborating with Git
• Documenting code

Data to use

No response

Number of collaborators

more

Credit to collaborators

All collaborators will be added to the git repository and will be on the abstract submission of this project to the OHBM conference

Image

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Type

data_management

Development status

0_concept_no_content

Topic

other

Tools

BIDS

Programming language

Python

Modalities

other

Git skills

0_no_git_skills, 1_commit_push, 2_branches_PRs

Anything else?

No response

Things to do after the project is submitted and ready to review.

• [x] Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
• [ ] Twitter-sized summary of your project pitch.

[JessyD]

Hi @brainhackorg/project-monitors my project is ready!

[Remi-Gau]

Your project is now on the website