Project Timeline

Day 1

• The day the ideas for BIDSInspec was born!
• A.P. lay the foundation for BIDSInspec when she pitched her hackproject idea to the NeuroHackademy attendees, at the time the hackproject was called bids-reports and a Slack channel was created for members to join.
• N.O. joined the #bids-reports channel and met with A.P. over Zoom to brainstorm ideas and start the journey towards the creation of BIDSInspec.
• Members were assigned tasks based on expertise.

Implementation discussions

• Option #1: Should this tool be added to a new BIDS app?
• Option #2: Should this tool be added to a BIDS conversion tool (i.e., d2b or dsm2bids)?

Reports

Discussed where the report should be saved. Can we save the report in the root of the BIDS directory? Will this cause BIDS validation to fail? Will this report interfere with BIDS prep apps?

Protocol validation

The idea behind this is similar to having a BIDS config file

Preliminary testing

• Python bids validator only validates file name (not full bids directory validation)

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Helpful resources for beginners to review:

Brain Imaging Data Structure (BIDS)

• Specification
• Validator
• Starter kit
• more BIDS introduction

BIDS Converter Tools

• d2b
• HeuDiConv
• dcm2bids
• entire list

Day 2

Naming our project

• Named our project/Github: BIDSInspec
• Agreed that the purpose of our tool is to inspect BIDS directories

Implementation

• Decided to proceed with the idea to make a stand alone tool that is going to be a BIDS app that will be published on PyPi. Poetry will be used to manage dependencies and publish on PyPi.

Minimally Viable Product (MVP)

• This hackathon project will consist of two end products: 1. BIDS directory report, 2. BIDS protocol validator
• Due to time constraints we will focus on creating the BIDS directory report app

Create Github Repository

Initialize Poetry setup

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Learn more about:

• Argparse for the command line tool that will be used to specify inputs for our tool
• Toml files (ex. Pyproject.toml in the geometry repo)

Day 3

Identify testing dataset from OpenNEURO

• Accession Number ds004730 [N=10]
• Accession Number ds001705 [N=5]

Create Wiki

Establish milestones and issues

Explore report creation implementation

Day 4

• Work on creating report components and a report using nireports
• Get test datasets onto repository
• Use BIDS validator (via command line) to validate test datasets
• Complete pybids tutorial to learn about it's functionality and how we can draw from it to begin steps towards protocol validation

Day 5

• Finalize scripts!
• Push all work to repository!
• Present BIDSInspec to Neurohackademy 2024 audience!