arXiv subjects

Markus Huemer

Publications and source records attributed to Markus Huemer.

3 recordsLinked to original sources

arXiv2026

BART Online Open-Source Sequence Toolbox for Computational MRI

Purpose In advanced computational MRI techniques, acquisition and reconstruction techniques are jointly designed. For reproducibility, it is therefore important to provide an open implementation of both. At the same time, any use in a clinical environment usually requires a close integration with the MRI scanner. Ensuring long-time reproducibility and maintenance then poses additional challenges. In this work, we aim to provide a fully integrated open-source framework that can meet these demands. Methods A software framework to develop pulse sequences is added to the BART toolbox. In addition, a vendor-specific driver sequence is developed that can be used to run the sequence on a clinical MRI scanner enabling online adjustment of all relevant sequence parameters. Using the Pulseq format, the exact same sequence can also be reproduced offline. As proof-of-concept, quantitative MRI methods for T1 and joint water/fat R2*, B0 mapping using radial FLASH and model-based reconstruction are implemented in the proposed framework. Consistency between online and offline acquisition is validated in phantom and in vivo experiments. Results Quantitative MRI methods consisting of acquisition and reconstruction were successfully implemented in BART. Acquisition parameters and FOV can be adapted online on a clinical MRI system. Quantitative parameter maps from model-based reconstruction agree for online and offline regenerated Pulseq acquisitions. Conclusion This work enables reproducibility of advanced computational MRI methods within a comprehensive end-to-end open-source framework.

physics.med-ph↗

arXiv2025

Dynamic transitions for fast joint acquisition and reconstruction of CEST-Rex and T1

Purpose: This work proposes a method for the simultaneous estimation of the exchange-dependent relaxation rate Rex and the longitudinal relaxation time T1 from a single acquisition. Methods: A novel acquisition scheme was developed that combines CEST saturation with an inversion pulse and a Look-Locker readout to capture the magnetization evolution starting from the inverse transient Z-spectrum. The corresponding signal model, derived from the Bloch-McConnell equations, describes both the transient Z-spectrum and the Look-Locker dynamics. A model-based reconstruction approach is employed to jointly estimate Rex and T1. The proposed method was validated using a numerical phantom and benchmarked against conventional CEST and Look-Locker T1 mapping in phantom and in vivo on a clinical 3T scanner. Results: The joint estimation approach demonstrated strong agreement with ground truth and conventional methods across a wide range of T1 and CEST parameters. The acquisition time was reduced by 20-30% compared to standard CEST protocols, while providing higher signal-to-noise ratio (SNR) in parameter maps. Conclusion: The proposed technique enables robust and efficient simultaneous quantification of CEST Rex and T1 in a single acquisition. It improves parameter map quality and reduces scan time, making it suitable for both phantom and in vivo imaging across a wide range of physiological conditions.

physics.med-ph↗

arXiv2024

Enhanced and Robust Contrast in CEST MRI: Saturation Pulse Shape Design via Optimal Control

Purpose: To employ optimal control for the numerical design of CEST saturation pulses to maximize contrast and stability against $B_0$ inhomogeneities. Theory and Methods: We applied an optimal control framework for the design pulse shapes for CEST saturation pulse trains. The cost functional minimized both the pulse energy and the discrepancy between the corresponding CEST spectrum and the target spectrum based on a continuous RF pulse. The optimization is subject to hardware limitations. In measurements on a 7 T preclinical scanner, the optimal control pulses were compared to continuous-wave and Gaussian saturation methods. We conducted a comparison of the optimal control pulses were compared to with Gaussian, block pulse trains, and adiabatic spin-lock pulses. Results: The optimal control pulse train demonstrated saturation levels comparable to continuous-wave saturation and surpassed Gaussian saturation by up to 50 \% in phantom measurements. In phantom measurements at 3 T the optimized pulses not only showcased the highest CEST contrast, but also the highest stability against field inhomogeneities. In contrast, block pulse saturation resulted in severe artifacts. Dynamic Bloch-McConnell simulations were employed to identify the source of these artifacts, and underscore the $B_0$ robustness of the optimized pulses. Conclusion: In this work, it was shown that a substantial improvement in pulsed saturation CEST imaging can be achieved by using Optimal Control design principles. It is possible to overcome the sensitivity of saturation to B0 inhomogeneities while achieving CEST contrast close to continuous wave saturation.

physics.med-ph↗