This repository contains scripts, Flywheel gears, and viewer protocols that support the processing, quality control, and visualization of Advanced MRI data, including MEGRE, ASL, and vNAV sequences. It provides a centralized, version-controlled workspace for developing, testing, and deploying tools used across CLARiTI, SCAN, and related imaging workflows.
Contents Scripts Utilities for data preparation, DICOM metadata extraction, automated classification, reprocessing, and workflow orchestration. Flywheel Gears Containerized analysis tools ready for execution within the Flywheel platform, including: Sequence-specific QC pipelines MEGRE → QSM workflows ASL quantification and derived metrics Reprocessing utilities for updated analysis methods Viewer Protocols Standardized configurations for image inspection and QC in popular viewers (e.g., Flywheel’s built-in viewer, ITK-SNAP, 3D Slicer).
Purpose Advanced MRI techniques evolve rapidly, and this repository provides a shared home for: Reproducible analysis workflows Standardized QC tools Rapid prototyping of new methods Seamless integration with Flywheel for multisite studies Reprocessing capabilities when new algorithms or updates become available
Usage Each component includes its own documentation in subdirectories. Typical uses include: Running automated QC on new uploads Deploying or updating Flywheel gears Testing new analysis approaches prior to production release Organizing viewer presets for consistent manual review across sites