An Open-Source, Reproducible MRI Data Acquisition and Reconstruction Workflow Using Pulseq: Multi-Site and...

Area of Science:

• Medical Imaging
• Magnetic Resonance Imaging (MRI)
• Open Science

Background:

• MRI reproducibility is hindered by variations in data acquisition, formatting, and reconstruction across different sites and vendors.
• Standardization efforts are crucial for reliable and comparable MRI research outcomes.

Purpose of the Study:

• To develop and validate an open-source, vendor-independent workflow to mitigate MRI reproducibility challenges.
• To harmonize MRI data acquisition, formatting, and reconstruction processes.

Main Methods:

• Utilized Pulseq with advanced features for harmonized data acquisition and k-space description.
• Converted Pulseq-generated data to MRD format using metadata.
• Performed open-source, vendor-independent image reconstruction and post-processing with Gadgetron.
• Enabled vendor-native online reconstructions on Siemens platforms for Pulseq-based sequences.
• Validated the workflow with MPRAGE and EPI protocols on nine scanners across five sites and four vendors, comparing against vendor-native protocols.

Main Results:

• Pulseq-based sequences executed successfully on all tested systems, with seamless data conversion and reconstruction.
• Pulseq-based, Gadgetron-reconstructed images showed good agreement with vendor-native images, though minor differences persisted.
• Vendor-native protocols exhibited subtle cross-platform differences in sequence execution and reconstruction.
• The proposed workflow demonstrated highly consistent sequence execution and standardized reconstruction across scanners.

Conclusions:

• An open-source MRI workflow harmonizing acquisition, formatting, and reconstruction across sites and vendors has been established.
• This workflow is a significant advancement toward fully open and reproducible MRI research.
• The system promotes transparency, standardization, and collaboration within the MRI research community.