A Modular End-to-End Open-Source Software Pipeline to Simulate the Entire MRI Experiment

Motivation: To democratize magnetic resonance (MR) imaging research by developing an open-source software simulation platform where researchers can test new technology, and radiologists can optimize clinical protocols without operating an actual MR scanner. Goal(s): To demonstrate the first comprehensive pipeline to simulate all stages of MR imaging experiments, from coil modeling to spin excitation and image reconstruction. Approach: Six open-source stand-alone software modules, implemented in various programming languages, were interconnected to simulate MR experiments using three head coils. Results: Realistic T1-weighted and T2-weighted brain MR images were successfully generated from the synthetic MR signal produced by a simulated spin-echo sequence. Impact: The comprehensive cloud-compatible simulation pipeline will make MR research freely accessible via internet. By enabling virtual experiments, this tool will allow users to generate synthetic data to train neural networks and will constitute a valuable tool for education and training.