[BrainHack] PET2BIDScoin: BIDScoin and PET conversion

[marcelzwiers]

• Location (Nordic/Massachusetts): Nordic
• Project (what do you want to talk about or work on): BIDScoin and PET conversion
• Presentation (yes/no - assigning time for you to present): yes, 5 min or so

PET2BIDScoin: BIDScoin and PET conversion

Project lead
Cyril Pernet, Anthony Galassi and Marcel Zwiers

Description
PET2BIDS is a Matlab / Python toolkit from OpenNeuroPET meant to format PET data in BIDS. BIDScoin is a Python 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, PET2BIDS lacks data discovery functionality and BIDScoin lacks a formatting backend for PET data. The goal of this Brainhack project is to develop the plugin interface between BIDScoin and PET2BIDS and hence combine their complementary functionality for both projects.

Link to project

• PET2BIDS
• BIDScoin
• Project pitch

Goals for the Brainhack

1. Write a BIDScoin “bidsmapper” data discovery plugin function using PET2BIDS
2. Write a BIDScoin “bidscoiner” data formatting plugin function using PET2bids
3. Create a PET2BIDS bidsmap section with sensible (regexp) heuristics
4. Extra goal: Write a plugin test function

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 PET2BIDS and for BIDScoin

Skills

• Little experience with bidsification and/or PET data, or little experience with, regular expressions, restructuredtext and readthedocs
• git, python