Matthew Grech-Sollars

arXiv2025

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↗

arXiv2024

DARES: Depth Anything in Robotic Endoscopic Surgery with Self-supervised Vector-LoRA of the Foundation Model

Robotic-assisted surgery (RAS) relies on accurate depth estimation for 3D reconstruction and visualization. While foundation models like Depth Anything Models (DAM) show promise, directly applying them to surgery often yields suboptimal results. Fully fine-tuning on limited surgical data can cause overfitting and catastrophic forgetting, compromising model robustness and generalization. Although Low-Rank Adaptation (LoRA) addresses some adaptation issues, its uniform parameter distribution neglects the inherent feature hierarchy, where earlier layers, learning more general features, require more parameters than later ones. To tackle this issue, we introduce Depth Anything in Robotic Endoscopic Surgery (DARES), a novel approach that employs a new adaptation technique, Vector Low-Rank Adaptation (Vector-LoRA) on the DAM V2 to perform self-supervised monocular depth estimation in RAS scenes. To enhance learning efficiency, we introduce Vector-LoRA by integrating more parameters in earlier layers and gradually decreasing parameters in later layers. We also design a reprojection loss based on the multi-scale SSIM error to enhance depth perception by better tailoring the foundation model to the specific requirements of the surgical environment. The proposed method is validated on the SCARED dataset and demonstrates superior performance over recent state-of-the-art self-supervised monocular depth estimation techniques, achieving an improvement of 13.3% in the absolute relative error metric. The code and pre-trained weights are available at https://github.com/mobarakol/DARES.

cs.CV↗