Claudia A. M. Gandini Wheeler-Kingshott

arXiv2026

Real-time, inline quantitative MRI enabled by scanner-integrated machine learning: a proof of principle with NODDI

Purpose: The clinical feasibility and translation of many advanced quantitative MRI (qMRI) techniques are inhibited by their restriction to 'research mode', due to resource-intensive, offline parameter estimation. This work aimed to achieve 'clinical mode' qMRI, by real-time, inline parameter estimation with a trained neural network (NN) fully integrated into a vendor's image reconstruction environment, therefore facilitating and encouraging clinical adoption of advanced qMRI techniques. Methods: The Siemens Image Calculation Environment (ICE) pipeline was customised to deploy trained NNs for advanced diffusion MRI parameter estimation with Open Neural Network Exchange (ONNX) Runtime. Two fully-connected NNs were trained offline with data synthesised with the neurite orientation dispersion and density imaging (NODDI) model, using either conventionally estimated (NNMLE) or ground truth (NNGT) parameters as training labels. The strategy was demonstrated online in two healthy volunteers (one rescanned) and evaluated offline with synthetic data, testing two diffusion protocols. Results: NNs were successfully integrated and deployed natively in ICE, performing inline, whole-brain, in vivo NODDI parameter estimation in <10 seconds. The proposed workflow was reproducible across protocols, volunteers and rescans. DICOM parametric maps were exported from the scanner for further analyses. Comparisons between NNMLE and NNGT suggested NNMLE parameter estimates to be more consistent with conventional fitting, a finding supported by offline evaluations. Conclusion: Real-time, inline parameter estimation with the proposed generalisable framework resolves a key practical barrier to the potential clinical uptake of advanced qMRI methods, enabling their efficient integration into clinical workflows. Next steps include incorporation of pre-processing methods and evaluation in pathology.

physics.med-ph↗

arXiv2023

Machine-learning-informed parameter estimation improves the reliability of spinal cord diffusion MRI

Purpose: We address the challenge of inaccurate parameter estimation in diffusion MRI when the signal-to-noise ratio (SNR) is very low, as in the spinal cord. The accuracy of conventional maximum-likelihood estimation (MLE) depends highly on initialisation. Unfavourable choices could result in suboptimal parameter estimates. Current methods to address this issue, such as grid search (GS) can increase computation time substantially. Methods: We propose a machine learning (ML) informed MLE approach that combines conventional MLE with ML approaches synergistically. ML-based methods have been developed recently to improve the speed and precision of parameter estimation. However, they can generate high systematic bias in estimated parameters when SNR is low. In the proposed ML-MLE approach, an artificial neural network model is trained to provide sensible initialisation for MLE efficiently, with the final solution determined by MLE, avoiding biases typically affecting pure ML estimations. Results: Using parameter estimation of neurite orientation dispersion and density imaging as an example, simulation and in vivo experiments suggest that the ML-MLE method can reduce outlier estimates from conventional MLE in white matter voxels affected by CSF contamination. It also accelerates computation compared to GS-MLE. Conclusion: The ML-MLE method can improve the reliability of parameter estimation with reduced computation time compared to GS-MLE, making it a practical tool for diffusion dataset with low SNR.

physics.med-ph↗