Containerizing BIDSme : A Reproducible Tool for BIDS Conversion
2026-06-08 • Databases
Databases
AI summaryⓘ
The authors explain that BIDS is a popular way to organize brain imaging data, but turning raw data into BIDS format can be hard and slow. They worked on BIDSme, a tool that helps with this conversion, and made it easier to use by packaging it in Docker containers. This containerized version is simpler to install, run, and share, improving how people can work with their brain imaging data. The paper describes how the authors made these improvements and tested the tool to ensure it works well.
BIDSneuroimagingdata standardizationBIDSmeDockercontainerizationDocker ComposeNeurodeskdata reproducibility
Authors
Bradley Spitz, Antoine Jacquemin, Nikita Beliy, Christophe Phillips
Abstract
The "Brain Imaging Data Structure" (BIDS) has become a widely adopted standard for organizing and sharing neuroimaging datasets of various modalities. However, converting raw brain imaging data into BIDS framework remains a complex and time-consuming task. BIDSme is a semi-automated tool developed to streamline this conversion process, but until recently, it lacked the portability and accessibility needed for widespread adoption. This paper presents the containerization of BIDSme using Docker and Docker Compose, improving usability, reproducibility, and integration into existing platforms like Neurodesk. It also details the design choices, iterative refinements, and validation process that led to a flexible, lightweight, and user-friendly containerized application.