arXiv subjects

Florian Wiesinger

Publications and source records attributed to Florian Wiesinger.

8 recordsLinked to original sources

arXiv2026

Neural Fields for Highly Accelerated 2D Cine Phase Contrast MRI

2D cine phase contrast (CPC) MRI provides quantitative information on blood velocity and flow within the human vasculature. However, data acquisition is time-consuming, motivating the reconstruction of the velocity field from undersampled measurements to reduce scan times. In this work, neural fields are proposed as a continuous spatiotemporal parametrization of complex-valued images, jointly modeling magnitude and phase across multiple echoes to enable velocity estimation, and leveraging their inductive bias for the reconstruction of the velocity data. Additionally, to compensate for the oversmoothing tendency observed in neural-field reconstructions under severe undersampling, a simple voxel-based postprocessing step is introduced. The method is validated numerically in Cartesian and radial k-space with both high and low temporal resolution data. This approach achieves accurate reconstructions at high acceleration factors, with low errors even at 32$\times$ and 64$\times$ undersampling for the high temporal resolution data, and 16$\times$ for the low temporal resolution data, and consistently outperforms classical locally low-rank regularized voxel-based methods in both flow estimates and anatomical depiction.

eess.IV↗

arXiv2025

Self-Supervised Weighted Image Guided Quantitative MRI Super-Resolution

Object: To present and evaluate Self-supervised Weighted Image Guided quantitative MRI Super-Resolution (SWIG qMRI SR), a physics-informed framework recovering high-resolution (HR) qMRI from a rapid low-resolution (LR) acquisition guided by routine weighted images (wMRI), without HR training targets. Materials and Methods: A CNN matches acquired wMRI to images synthesized from predicted maps through forward signal models, while anchoring those maps to the acquired LR qMRI. Training and ablation used synthetic data (n = 27); cross-sequence generalizability was tested in three volunteers scanned with silent 3D MuPa-ZTE at 1 and 5min, with clinical T1w/T2w guides. Results: In synthetic data, dual-guide SR reduced the T1 high-frequency error norm 45.4% below baseline; removing the LR qMRI anchor raised gray-matter T1 error from 63 to 110ms. In vivo, super-resolved 1-min maps synthesized T1w images (SSIM 0.93, PSNR 27.3dB) surpassing synthesis from 5-min maps (SSIM 0.83), and improved synthesis of T2-FLAIR, never used as a guide (SSIM 0.69 to 0.75). Discussion: HR detail was recovered without HR supervision, and the network transferred across a different qMRI sequence. Because the guides are already acquired, adding a 1-min qMRI scan to a standard exam offers a practical route to routine clinical qMRI integration.

cs.CV↗

arXiv2025

q3-MuPa: Quick, Quiet, Quantitative Multi-Parametric MRI using Physics-Informed Diffusion Models

The 3D fast silent multi-parametric mapping sequence with zero echo time (MuPa-ZTE) is a novel quantitative MRI (qMRI) acquisition that enables nearly silent scanning by using a 3D phyllotaxis sampling scheme. MuPa-ZTE improves patient comfort and motion robustness, and generates quantitative maps of T1, T2, and proton density using the acquired weighted image series. In this work, we propose a diffusion model-based qMRI mapping method that leverages both a deep generative model and physics-based data consistency to further improve the mapping performance. Furthermore, our method enables additional acquisition acceleration, allowing high-quality qMRI mapping from a fourfold-accelerated MuPa-ZTE scan (approximately 1 minute). Specifically, we trained a denoising diffusion probabilistic model (DDPM) to map MuPa-ZTE image series to qMRI maps, and we incorporated the MuPa-ZTE forward signal model as an explicit data consistency (DC) constraint during inference. We compared our mapping method against a baseline dictionary matching approach and a purely data-driven diffusion model. The diffusion models were trained entirely on synthetic data generated from digital brain phantoms, eliminating the need for large real-scan datasets. We evaluated on synthetic data, a NISM/ISMRM phantom, healthy volunteers, and a patient with brain metastases. The results demonstrated that our method produces 3D qMRI maps with high accuracy, reduced noise and better preservation of structural details. Notably, it generalised well to real scans despite training on synthetic data alone. The combination of the MuPa-ZTE acquisition and our physics-informed diffusion model is termed q3-MuPa, a quick, quiet, and quantitative multi-parametric mapping framework, and our findings highlight its strong clinical potential.

physics.med-ph↗

arXiv2025

Evaluation of a Novel Quantitative Multiparametric MR Sequence for Radiation Therapy Treatment Response Assessment

Purpose: To evaluate a Deep-Learning-enhanced MUlti-PArametric MR sequence (DL-MUPA) for treatment response assessment for brain metastases patients undergoing stereotactic radiosurgery (SRS) and head-and-neck (HnN) cancer patients undergoing conventionally fractionation adaptive radiation therapy. Methods: DL-MUPA derives quantitative T1 and T2 maps from a single 4-6-minute scan denoised via DL method using dictionary fitting. Phantom benchmarking was performed on a NIST-ISMRM phantom. Longitudinal patient data were acquired on a 1.5T MR-simulator, including pre-treatment (PreTx) and every 3 months after SRS (PostTx) in brain, and PreTx, mid-treatment and 3 months PostTx in HnN. Changes of mean T1 and T2 values were calculated within gross tumor volumes (GTVs), residual disease (RD, HnN), parotids, and submandibular glands (HnN) for treatment response assessment. Uninvolved normal tissues (normal appearing white matter in brain, masseter in HnN) were evaluated to as control. Results: Phantom benchmarking showed excellent inter-session repeatability (coefficient of variance <1% for T1, <7% for T2). Uninvolved normal tissue suggested acceptable in-vivo repeatability (brain |$Δ$|<6%, HnN |$Δ$T1|<7%, |$Δ$T2|<18% (4ms)). Remarkable changes were noted in resolved brain metastasis ($Δ$T1=14%) and necrotic settings ($Δ$T1=18-40%, $Δ$T2=9-41%). In HnN, two primary tumors showed T2 increase (PostTx GTV $Δ$T2>13%, RD $Δ$T2>18%). A nodal disease resolved PostTx (GTV $Δ$T1=-40%, $Δ$T2=-33%, RD $Δ$T1=-29%, $Δ$T2=-35%). Enhancement was found in involved parotids (PostTx $Δ$T1>12%, $Δ$T2>13%) and submandibular glands (PostTx $Δ$T1>15%, $Δ$T2>35%) while the uninvolved organs remained stable. Conclusions: DL-MUPA shows promise for treatment response assessment and identifying potential endpoints for functional sparing.

physics.med-ph↗

arXiv2025

Algebraic Methods and Computational Strategies for Pseudoinverse-Based MR Image Reconstruction (Pinv-Recon)

Image reconstruction in Magnetic Resonance Imaging (MRI) is fundamentally a linear inverse problem, such that the image can be recovered via explicit pseudoinversion of the encoding matrix by solving $\textbf{data} = \textbf{Encode} \times \textbf{image}$ - a method referred to here as Pinv-Recon. While the benefits of this approach were acknowledged in early studies, the field has historically favored fast Fourier transforms (FFT) and iterative techniques due to perceived computational limitations of the pseudoinversion approach. This work revisits Pinv-Recon in the context of modern hardware, software, and optimized linear algebra routines. We compare various matrix inversion strategies, assess regularization effects, and demonstrate incorporation of advanced encoding physics into a unified reconstruction framework. While hardware advances have already significantly reduced computation time compared to earlier studies, our work further demonstrates that leveraging Cholesky decomposition leads to a two-order-of-magnitude improvement in computational efficiency over previous Singular Value Decomposition-based implementations. Moreover, we demonstrate the versatility of Pinv-Recon on diverse $\textit{in vivo}$ datasets encompassing a range of encoding schemes, starting with low- to medium-resolution functional and metabolic imaging and extending to high-resolution cases. Our findings establish Pinv-Recon as a versatile and robust reconstruction framework that aligns with the increasing emphasis on open-source and reproducible MRI research.

physics.med-ph↗

arXiv2022

Region of Interest focused MRI to Synthetic CT Translation using Regression and Classification Multi-task Network

In this work, we present a method for synthetic CT (sCT) generation from zero-echo-time (ZTE) MRI aimed at structural and quantitative accuracies of the image, with a particular focus on the accurate bone density value prediction. We propose a loss function that favors a spatially sparse region in the image. We harness the ability of a multi-task network to produce correlated outputs as a framework to enable localisation of region of interest (RoI) via classification, emphasize regression of values within RoI and still retain the overall accuracy via global regression. The network is optimized by a composite loss function that combines a dedicated loss from each task. We demonstrate how the multi-task network with RoI focused loss offers an advantage over other configurations of the network to achieve higher accuracy of performance. This is relevant to sCT where failure to accurately estimate high Hounsfield Unit values of bone could lead to impaired accuracy in clinical applications. We compare the dose calculation maps from the proposed sCT and the real CT in a radiation therapy treatment planning setup.

eess.IV↗

arXiv2022

Unsupervised-learning-based method for chest MRI-CT transformation using structure constrained unsupervised generative attention networks

The integrated positron emission tomography/magnetic resonance imaging (PET/MRI) scanner facilitates the simultaneous acquisition of metabolic information via PET and morphological information with high soft-tissue contrast using MRI. Although PET/MRI facilitates the capture of high-accuracy fusion images, its major drawback can be attributed to the difficulty encountered when performing attenuation correction, which is necessary for quantitative PET evaluation. The combined PET/MRI scanning requires the generation of attenuation-correction maps from MRI owing to no direct relationship between the gamma-ray attenuation information and MRIs. While MRI-based bone-tissue segmentation can be readily performed for the head and pelvis regions, the realization of accurate bone segmentation via chest CT generation remains a challenging task. This can be attributed to the respiratory and cardiac motions occurring in the chest as well as its anatomically complicated structure and relatively thin bone cortex. This paper presents a means to minimise the anatomical structural changes without human annotation by adding structural constraints using a modality-independent neighbourhood descriptor (MIND) to a generative adversarial network (GAN) that can transform unpaired images. The results obtained in this study revealed the proposed U-GAT-IT + MIND approach to outperform all other competing approaches. The findings of this study hint towards possibility of synthesising clinically acceptable CT images from chest MRI without human annotation, thereby minimising the changes in the anatomical structure.

cs.CV↗

arXiv2021

Attenuation Coefficient Estimation for PET/MRI With Bayesian Deep Learning pseudo-CT and Maximum Likelihood Estimation of Activity and Attenuation

A major remaining challenge for magnetic resonance-based attenuation correction methods (MRAC) is their susceptibility to sources of MRI artifacts (e.g. implants, motion) and uncertainties due to the limitations of MRI contrast (e.g. accurate bone delineation and density, and separation of air/bone). We propose using a Bayesian deep convolutional neural network that, in addition to generating an initial pseudo-CT from MR data, also produces uncertainty estimates of the pseudo-CT to quantify the limitations of the MR data. These outputs are combined with MLAA reconstruction that uses the PET emission data to improve the attenuation maps. With the proposed approach (UpCT-MLAA), we demonstrate accurate estimation of PET uptake in pelvic lesions and show recovery of metal implants. In patients without implants, UpCT-MLAA had acceptable but slightly higher RMSE than Zero-echo-time and Dixon Deep pseudo-CT when compared to CTAC. In patients with metal implants, MLAA recovered the metal implant; however, anatomy outside the implant region was obscured by noise and crosstalk artifacts. Attenuation coefficients from the pseudo-CT from Dixon MRI were accurate in normal anatomy; however, the metal implant region was estimated to have attenuation coefficients of air. UpCT-MLAA estimated attenuation coefficients of metal implants alongside accurate anatomic depiction outside of implant regions.

physics.med-ph↗