arXiv subjects

Martin Blaimer

Publications and source records attributed to Martin Blaimer.

7 recordsLinked to original sources

arXiv2026

OpenMRF: A Modular, Vendor-Neutral Open-Source Framework for Reproducible Magnetic Resonance Fingerprinting using Pulseq

Purpose: Widespread adoption and methodological advancement of Magnetic Resonance Fingerprinting (MRF) are limited by the lack of unified, reproducible implementation frameworks and fragmented open-source tools. To address these barriers, we introduce OpenMRF - a comprehensive Pulseq-based solution - designed to enable consistent, reproducible, and transferable MRF research across vendors, sites, and field strengths. Methods: OpenMRF integrates modular Pulseq-based sequence design, Bloch-simulation-based dictionary creation directly from .seq files, and iterative low-rank subspace reconstruction. The framework was evaluated through digital phantom simulations, a multi-site ISMRM/NIST phantom study on Siemens MRI systems at 0.55 T, 1.5 T, and 3 T as well as GE and United Imaging 3 T platforms, and representative in vivo acquisitions in the liver (0.55 T), myocardium (1.5 T), and brain (3 T). Results: Simulations demonstrated high mapping accuracy in an ISMRM/NIST-like digital phantom, with low-rank reconstruction yielding deviations of 0.03+/-0.32 % (T1) and 0.12+/-1.94 % (T2). The multi-site phantom study yielded relaxation times consistent with reference values at all field strengths, with mean deviations of -0.1+/-2.9 % (T1), -1.5+/-8.7 % (T2), and -4.0+/-7.2 % (T1rho). In vivo acquisitions produced high-quality parameter maps across platforms and field strengths. Conclusion: OpenMRF provides a robust, open-source, end-to-end Pulseq-based solution for MRF that enables reproducible sequence implementation, physics-accurate dictionary simulation, and advanced reconstruction across vendors and field strengths. By providing a unified platform for method development, comparison, and multi-site validation, OpenMRF aims to accelerate reproducible and harmonized quantitative MRI research within the community.

physics.med-ph↗

arXiv2025

Controlling spatial correlation in k-space interpolation networks for MRI reconstruction: denoising versus apparent blurring

Purpose: Interpretability is essential for the clinical adoption of state-of-the-art machine learning (ML) methods in magnetic resonance imaging (MRI). Conventional evaluation of ML reconstructions relies heavily on aggregate image metrics that require fully sampled references. These metrics, inherited from classical image processing and natural image ML, often overlook the critical challenge of noise amplification specific to medical image reconstruction. This study aims to analyze the influence of nonlinear activations on spatial noise variance distribution of k-space interpolation networks (RAKI) and to provide a framework for incorporating variance maps during network training. Methods: We present an analytical framework that decomposes pixel-level noise variance into components reflecting linear and nonlinear characteristics of RAKI. By applying automatic differentiation on the image-space equivalent of the network, variance maps are computed during each training iteration, enabling runtime quality assessment beyond data consistency. We introduce apparent blurring, quantifying nonlinear signal mixing without dependence on reference images. By incorporating variance maps into the traning loss as regularizers, our self-informed RAKI architecture (G-factor-informed RAKI, GIF-RAKI) can directly integrate updated noise characteristics during runtime. Results: Experimental results demonstrate that variance components quantitatively explain network behavior. GIF-RAKI outperforms conventional RAKI variants in image fidelity and noise suppression. Conclusion: Our methodology advances practical and theoretical aspects of ML-based MRI reconstruction by reinstating reconstruction noise characterization as a cornerstone for performance evaluation, eliminating the need for fully sampled references. GIF-RAKI also enables optimization of the trade-off between denoising and apparent blurring.

physics.med-ph↗

arXiv2024

Representation of Classical Data on Quantum Computers

Quantum computing is currently gaining significant attention, not only from the academic community but also from industry, due to its potential applications across several fields for addressing complex problems. For any practical problem which may be tackled using quantum computing, it is imperative to represent the data used onto a quantum computing system. Depending on the application, many different types of data and data structures occur, including regular numbers, higher-dimensional data structures, e.g., n-dimensional images, up to graphs. This report aims to provide an overview of existing methods for representing these data types on gate-based quantum computers.

quant-ph↗

arXiv2024

Controlling sharpness, SNR and SAR for 3D FSE at 7T by end-to-end learning

Purpose: To non-heuristically identify dedicated variable flip angle (VFA) schemes optimized for the point-spread function (PSF) and signal-to-noise ratio (SNR) of multiple tissues in 3D FSE sequences with very long echo trains at 7T. Methods: The proposed optimization considers predefined SAR constraints and target contrast using an end-to-end learning framework. The cost function integrates components for contrast fidelity (SNR) and a penalty term to minimize image blurring (PSF) for multiple tissues. By adjusting the weights of PSF/SNR cost-function components, PSF- and SNR-optimized VFAs were derived and tested in vivo using both the open-source Pulseq standard on two volunteers as well as vendor protocols on a 7T MRI system with parallel transmit extension on three volunteers. Results: PSF-optimized VFAs resulted in significantly reduced image blurring compared to standard VFAs for T2w while maintaining contrast fidelity. Small white and gray matter structures, as well as blood vessels, are more visible with PSF-optimized VFAs. Quantitative analysis shows that the optimized VFA yields 50% less deviation from a sinc-like reference PSF than the standard VFA. The SNR-optimized VFAs yielded images with significantly improved SNR in a white and gray matter region relative to standard (81.2\pm18.4 vs. 41.2\pm11.5, respectively) as trade-off for elevated image blurring. Conclusion: This study demonstrates the potential of end-to-end learning frameworks to optimize VFA schemes in very long echo trains for 3D FSE acquisition at 7T in terms of PSF and SNR. It paves the way for fast and flexible adjustment of the trade-off between PSF and SNR for 3D FSE.

physics.med-ph↗

arXiv2024

Rotary Excitation of non-sinusoidal pulsed magnetic fields: Towards non-invasive direct detection of cardiac conduction

Purpose: In the recent past, spin-locking MRI experiments were successfully applied for the direct detection of sinusoidal magnetic field oscillations in the sub-nT range. In the present study, this detection approach was extended to non-sinusoidal pulsed magnetic fields based on the Rotary Excitation (REX) mechanism. Methods: The new detection concept was examined by means of Bloch simulations, evaluating the interaction effect of spin-locked magnetization and low-frequency pulsed magnetic fields. The REX detection approach was validated under controlled conditions in phantom experiments at 3T. Gaussian and Sinc-shaped stimuli were investigated. In addition, the detection of artificial fields resembling a cardiac QRS complex, which is the most prominent peak visible on a Magnetocardiogram, was tested. Results: Bloch simulations demonstrated that the REX method has a high sensitivity to pulsed fields in the resonance case, which is met when the spin-lock frequency coincides with a non-zero Fourier component of the stimulus field. In the experiments, we found that magnetic stimuli of different durations and waveforms can be distinguished by their characteristic REX response spectrum. The detected REX amplitude was proportional to the stimulus peak amplitude (R2>0.98) and the lowest field detection was 1 nT. Furthermore, the detection of QRS-like fields with varying QRS durations yielded significant results in a phantom setup (p<0.001). Conclusion: REX detection can be transferred to non-sinusoidal pulsed magnetic fields and could provide a non-invasive, quantitative tool for spatially resolved assessment of cardiac biomagnetism. Potential applications include the direct detection and characterization of cardiac conduction.

physics.med-ph↗

arXiv2024

Image space formalism of convolutional neural networks for k-space interpolation

Purpose: Noise resilience in image reconstructions by scan-specific robust artificial neural networks for k-space interpolation (RAKI) is linked to nonlinear activations in k-space. To gain a deeper understanding of this relationship, an image space formalism of RAKI is introduced for analyzing noise propagation analytically, identifying and characterizing image reconstruction features and to describe the role of nonlinear activations in a human readable manner. Methods: The image space formalism for RAKI inference is employed by expressing nonlinear activations in k-space as element-wise multiplications with activation masks, which transform into convolutions in image space. Jacobians of the de-aliased, coil-combined image relative to the aliased coil images can be expressed algebraically, and thus, the noise amplification is quantified analytically (g-factor maps). We analyze the role of nonlinearity for noise resilience by controlling the degree of nonlinearity in the reconstruction model via the negative slope parameter in leaky ReLU. Results: The analytical g-factor maps correspond with those obtained from Monte Carlo simulations and from an auto differentiation approach for in vivo brain images. Apparent blurring and contrast loss artifacts are identified as implications of enhanced noise resilience. These residual artifacts can be traded against noise resilience by adjusting the degree of nonlinearity in the model (Tikhonov-like regularization) in case of limited training data. The inspection of image space activations reveals an autocorrelation pattern leading to a potential center artifact. Conclusion: The image space formalism of RAKI provides the means for analytical quantitative noisepropagation analysis and human-readable visualization of the effects of the nonlinear activation functions in k-space.

cs.CV↗

arXiv2022

Iterative training of robust k-space interpolation networks for improved image reconstruction with limited scan specific training samples

Purpose: To evaluate an iterative learning approach for enhanced performance of Robust Artificial-neural-networks for K-space Interpolation (RAKI), when only a limited amount of training data (auto-calibration signals, ACS) are available for accelerated standard 2D imaging. Methods: In a first step, the RAKI model was optimized for the case of strongly limited training data amount. In the iterative learning approach (termed iterative RAKI), the optimized RAKI model is initially trained using original and augmented ACS obtained from a linear parallel imaging reconstruction. Subsequently, the RAKI convolution filters are refined iteratively using original and augmented ACS extracted from the previous RAKI reconstruction. Evaluation was carried out on 200 retrospectively undersampled in-vivo datasets from the fastMRI neuro database with different contrast settings. Results: For limited training data (18 and 22 ACS lines for R=4 and R=5, respectively), iterative RAKI outperforms standard RAKI by reducing residual artefacts and yields strong noise suppression when compared to standard parallel imaging, underlined by quantitative reconstruction quality metrics. In combination with a phase constraint, further reconstruction improvements can be achieved. Additionally, iterative RAKI shows better performance than both GRAPPA and RAKI in case of pre-scan calibration with varying contrast between training- and undersampled data. Conclusion: The iterative learning approach with RAKI benefits from standard RAKIs well known noise suppression feature but requires less original training data for the accurate reconstruction of standard 2D images thereby improving net acceleration.

eess.IV↗