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@stawiskm stawiskm released this 06 Aug 11:18
v1.0.0
ab23fc5

GitHub Release for Image to BIDS to SQLite Tools

Release Title: v1.0.0 - Initial Release

Release Date: August 6, 2024

Description:

We are excited to announce the initial release of the Image to BIDS to SQLite Tools repository. This release introduces a comprehensive suite of workflows, pipelines, and tools to transform image data into BIDS format and store metadata in a SQLite database. This toolset provides flexible and customizable solutions for various data sources and target data models.

Features:

  1. File2BIDS App (with GUI)

    • A user-friendly graphical interface for organizing files into BIDS-compliant structures and generating necessary JSON sidecar files.

  2. ETL Workflows:

    • NIFTI to BIDS Conversion (wf_NIFTI2BIDS.py) (under development)
      • Standardizes NIFTI images according to BIDS guidelines and organizes them in a new BIDS-compliant directory.
    • Slicer BIDS Integration (wf_Slicer2BIDS.py) (under development)
      • Processes 3D Slicer scene images and integrates them into a BIDS-compliant directory.
    • BIDS to SQLite (wf_BIDS2SQLite.py) (stable / dockerized)
      • Extracts metadata from BIDS sidecar files and stores it in a SQLite database for efficient data management.

Installation & Setup:

Executables for File2BIDS:

  • Pre-built executables for the File2BIDS GUI application are available as assets in this release. Download the appropriate executable for your operating system and follow the instructions in the README.md to get started.

Docker Setup:

  • Ensure Docker and Docker-compose are installed.
  • Clone the repository and configure using config_docker_example.json.
  • Start the ETL process with docker-compose -f docker-compose_****.yml up.

Python Environment:

  • Requires Python 3.10.x.
  • Create and activate a virtual environment, install dependencies from requirements.txt, and configure using config_example.json.
  • Run ETL processes with the appropriate script.

Folder Structure:

The repository is organized with clear directories for each component, including ETL scripts, Docker setup files, configuration templates, and utility scripts.

Config File Setup:

Define your configuration in a JSON file, specifying paths, process controls, and other necessary parameters. Refer to the provided config_example.json and config_docker_example.json for guidance.

Data Model Definition:

Define the SQLite database schema using SQL scripts, specifying the structure of tables and columns.

License:

This project is licensed under the MIT License. Feel free to use, modify, and distribute the software, with proper attribution.

Contributing:

Contributions, issues, and feature requests are welcome!

Assets:

We hope you find this toolset useful for your data processing needs. Please provide feedback and report any issues you encounter. Enjoy using the Image to BIDS to SQLite Tools!

View on GitHub

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