arXiv subjects

Jon Cleary

Publications and source records attributed to Jon Cleary.

3 recordsLinked to original sources

arXiv2025

An Automated Framework for Large-Scale Graph-Based Cerebrovascular Analysis

We present CaravelMetrics, a computational framework for automated cerebrovascular analysis that models vessel morphology through skeletonization-derived graph representations. The framework integrates atlas-based regional parcellation, centerline extraction, and graph construction to compute fifteen morphometric, topological, fractal, and geometric features. The features can be estimated globally from the complete vascular network or regionally within arterial territories, enabling multiscale characterization of cerebrovascular organization. Applied to 570 3D TOF-MRA scans from the IXI dataset (ages 20-86), CaravelMetrics yields reproducible vessel graphs capturing age- and sex-related variations and education-associated increases in vascular complexity, consistent with findings reported in the literature. The framework provides a scalable and fully automated approach for quantitative cerebrovascular feature extraction, supporting normative modeling and population-level studies of vascular health and aging.

cs.CV↗

arXiv2025

From Offline to Inline Without Pain: A Practical Framework for Translating Offline MR Reconstructions to Inline Deployment Using the Gadgetron Platform

Purpose: To develop and validate a practical framework to overcome common issues in inline deployment of established offline MR reconstruction, including (1) delay from lengthy reconstructions, (2) limited support for multi-scan input reconstructions, (3) the need to adapt scripts for different raw formats, and (4) limited guidance and experience in retaining scanner reconstructions and applying scanner-based post-processing to custom outputs. Methods: The framework builds upon the Gadgetron platform and includes: (1) an input converter to transform ISMRMRD format raw into a Siemens format raw structure, facilitating reuse of existing code; (2) an asynchronous trigger-and-retrieve mechanism enabling long reconstructions without delaying scanner processes; (3) resource-aware scheduling for parallel execution; (4) integrated file management to support multi-scan inputs; and (5) preservation of scanner-based reconstructions and post-processing. The framework was validated on 2 Siemens scanners for SENSE, AlignedSENSE, and NUFFT reconstructions, and in a large-cohort study. Results: Minimum code modification for inline deployment has been shown, and all reconstructions were successfully executed inline without disrupting scanner workflows. Images were retrieved via automated or retro-reconstruction, with scanner-based post-processing applied to custom outputs. Multi-scan input reconstructions were executed using GPU-aware scheduling, confirming feasibility for routine and large-scale applications. In 480 consecutive examinations, inline reconstructions were retrieved in 99% of cases without disruptions. Conclusion: The framework lowers the technical barrier to inline deployment of offline reconstructions, enabling robust, scalable, and post-processing-compatible integration. It is openly available with documentation and demonstration cases to support reproducibility and community adoption.

physics.med-ph↗

arXiv2024

3D distortion-free, reduced field of view diffusion-prepared GRE at 3T

Purpose: To develop a 3D distortion-free reduced-FOV diffusion-prepared GRE sequence and demonstrate its in-vivo application for diffusion imaging of the spinal cord in healthy volunteers. Methods: A 3D multi-shot reduced-FOV diffusion-prepared GRE (RFOV-DP-GRE) acquisition is achieved using a slice-selective tip-down pulse in the phase encoding direction in the diffusion preparation, combined with magnitude stabilisers. The efficacy of the developed reduced FOV approach and accuracy of ADC estimates were evaluated in a phantom. In addition, 5 healthy volunteers were enrolled and scanned at 3T using the proposed sequence and a standard spin echo diffusion-weighted single-shot EPI sequence (DW-SS-EPI) for spinal cord imaging. Image quality, perceived SNR and image distortion were assessed by two expert readers and quantitative measurements of apparent SNR were performed. Results: The phantom scan demonstrates the efficacy of the proposed reduced FOV approach. Consistent ADC estimates were measured with RFOV-DP-GRE when compared with DW-SS-EPI. In-vivo, RFOV-DP-GRE demonstrated improved image quality and reduced perceived distortion, while maintaining perceived SNR compared to DW-SS-EPI. Conclusion: 3D Distortion-free diffusion-prepared imaging can be achieved using the proposed sequence

physics.med-ph↗