arXiv subjects

Matthias Stuber

Publications and source records attributed to Matthias Stuber.

14 recordsLinked to original sources

arXiv2025

VPAL: A novel method to reduce reconstruction time for 5D free-running imaging

Purpose: Ferumoxytal-enhanced 5D free-running whole heart CMR provides image quality comparable to CTA, but requires hours-long reconstruction time, preventing clinical usage. This study developed a variable projection augmented Lagrangian (VPAL) method for 5D motion-resolved image reconstruction and compared it with alternating direction method of multipliers (ADMM) in five numerical simulations and 15 in-vivo pediatric data set. Approach: Relative error of the reconstructed images against the ground-truth images was assessed in numerical simulations. In-vivo analysis compared reconstruction time, mid-short axis (SA) blood-myocardium sharpness, left ventricular ejection fraction (LVEF), and a radiologist's image quality ratings between VPAL and ADMM. A paired t-test (p<0.05) was used to determine statistical significance, while linear regression and Bland-Altman analysis for agreement assessments. Results: VPAL and ADMM had similar relative errors compared to the ground truth, p = 0.07. In in-vivo datasets, VPAL reduced the reconstruction time from 16.3 +/- 3.6 hours (ADMM) to 4.7 +/- 1.1 hours (VPAL), p=1e-10. Blood-myocardium border sharpness in VPAL closely correlates to ADMM , R^2 = 0.97. The LVEFs values measured by VPAL and ADMM reconstructions are largely similar, 56 +/- 6 % in ADMM and 56 +/- 6 % in VPAL, p=0.55. Both VPAL and ADMM reconstructions have good to excellent diagnostic ratings (VPAL vs. ADMM: 3.9 +/- 0.3 vs. 3.8 +/- 0.4 in 2-chamber; 3.9 +/- 0.4 vs. 3.9 +/- in 4-chamber; 3.7 +/- 0.5 vs. 3.7 +/- 0.5 in mid-SA reformatted views. Conclusion: VPAL enables faster reconstruction than ADMM while maintaining equivalent image quality for functional assessments, supporting its potential for clinical use.

physics.med-ph↗

arXiv2023

Pilot tone-guided focused navigation for free-breathing whole-liver fat-water and T2* quantification

Purpose To achieve whole-liver motion-corrected fat fraction (FF) and R2* quantification with a 3-minute free-breathing (FB) 3D radial isotropic acquisition, for increased organ coverage, ease-of-use, and patient comfort. Methods A FB 3D radial multiecho gradient-echo liver acquisition with integrated Pilot Tone (PT) navigation and NTE=8 echoes was reconstructed with a motion-correction algorithm based on focused navigation and guided by PT signals (PT-fNAV), with and without a denoising step. Fat fraction (FF) and R2* quantification using a graph cut algorithm was performed on the motion-corrected whole-liver multiecho volumes. Volunteer experiments (n=10) at 1.5T included reference 3D and 2D Cartesian breath-hold (BH) acquisitions. Image sharpness was assessed to evaluate the quality of motion correction with PT-fNAV, compared to a motion-resolved reconstruction. Fat-water images and parametric maps were compared to BH reference acquisitions following Cartesian trajectories, and to a routinely used clinical software (MRQuantiF). Results The image sharpness provided by PT-fNAV (with and without denoising) was similar in end-expiratory motion-resolved reconstructions. The 3D radial FB FF maps compared well with reference BH 3D Cartesian maps (bias +0.7%, limits of agreement (LOA) [-2.5; 4.0]%) and with 2D quantification with MRQuantiF (-0.2%, LOA [-1.1; 0.6]%). While expected visual deviations between proposed FB and reference BH R2* maps were observed, no significant differences were found in quantitative analyses. Conclusion A 3D radial technique with retrospective motion correction by PT-fNAV enabled FF and R2* quantification of the whole-liver at 1.5T. The FB whole-liver acquisition at isotropic spatial resolution compared in accuracy with BH techniques, enabling 3D assessment of steatosis in individuals with limited respiratory capabilities.

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arXiv2022

Motion-resolved fat-fraction mapping with whole-heart free-running multiecho gre and pilot tone

PURPOSE To develop free-running multi-echo GRE for cardiac- and respiratory-motion-resolved whole-heart fat fraction quantification. METHODS Multi-echo readouts optimized for water-fat separation and quantification were integrated within a non-ECG-triggered free-breathing 3D radial GRE acquisition. Pilot Tone navigation was used to extract cardiac and respiratory motion states. Following a XD-GRASP based image reconstruction of the separate echoes, fat fraction, water fraction, R2star and B0 maps, as well as fat and water images, were generated with a maximum likelihood fitting algorithm using graph cuts. The acquisition, reconstruction and post-processing framework was tested in 10 healthy volunteers at 1.5T and compared to a free-breathing ECG-triggered 5-echo acquisition. RESULTS The acquisition was successfully validated in vivo, with motion compensation achieved over all collected echoes, in both respiratory and cardiac dimensions. Pilot Tone navigation provided respiratory and cardiac signals in good agreement (r=0.954 and r=0.783, respectively) with self-gating signal extraction based on the MR data of the first echo. The framework enabled pericardial fat imaging and quantification across the cardiac cycle, revealing a decrease in apparent FF at systole across volunteers. 3D motion-resolved fat fraction maps showed good correlation with reference ECG-triggered measurements, as well as significant difference in measurements performed with NTE = 4 and NTE = 8 echoes (P < 0.0001 in chest fat and P < 0.01 in pericardial fat). CONCLUSION Volunteer experiments at 1.5T demonstrated the feasibility of a whole-heart free-running fat-fraction mapping technique for cardiac MRI in a 6 min scan time, with a resolution of 2mm3 isotropic.

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arXiv2021

FaBiAN: A Fetal Brain magnetic resonance Acquisition Numerical phantom

Accurate characterization of in utero human brain maturation is critical as it involves complex and interconnected structural and functional processes that may influence health later in life. Magnetic resonance imaging is a powerful tool to investigate equivocal neurological patterns during fetal development. However, the number of acquisitions of satisfactory quality available in this cohort of sensitive subjects remains scarce, thus hindering the validation of advanced image processing techniques. Numerical phantoms can mitigate these limitations by providing a controlled environment with a known ground truth. In this work, we present FaBiAN, an open-source Fetal Brain magnetic resonance Acquisition Numerical phantom that simulates clinical T2-weighted fast spin echo sequences of the fetal brain. This unique tool is based on a general, flexible and realistic setup that includes stochastic fetal movements, thus providing images of the fetal brain throughout maturation comparable to clinical acquisitions. We demonstrate its value to evaluate the robustness and optimize the accuracy of an algorithm for super-resolution fetal brain magnetic resonance imaging from simulated motion-corrupted 2D low-resolution series as compared to a synthetic high-resolution reference volume. We also show that the images generated can complement clinical datasets to support data-intensive deep learning methods for fetal brain tissue segmentation.

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arXiv2020

Motion Compensated Whole-Heart Coronary Magnetic Resonance Angiography using Focused Navigation (fNAV)

Background: RSN whole-heart CMRA is a technique that estimates and corrects for respiratory motion. However, RSN has been limited to a 1D rigid correction which is often insufficient for patients with complex respiratory patterns. The goal of this work is therefore to improve the robustness and quality of 3D radial CMRA by incorporating both 3D motion information and nonrigid intra-acquisition correction of the data into a framework called focused navigation (fNAV). Methods: We applied fNAV to 500 data sets from a numerical simulation, 22 healthy volunteers, and 549 cardiac patients. We compared fNAV to RSN and respiratory resolved XD-GRASP reconstructions of the same data and recorded reconstruction times. Motion accuracy was measured as the correlation between fNAV and ground truth for simulations, and fNAV and image registration for in vivo data. Vessel sharpness was measured using Soap-Bubble. Finally, image quality analysis was performed by a blinded expert reviewer who chose the best image for each data set. Results The reconstruction time for fNAV images was significantly higher than RSN (6.1 +/- 2.1 minutes vs 1.4 +/- 0.3, minutes, p<0.025) but significantly lower than XD-GRASP (25.6 +/- 7.1, minutes, p<0.025). There is high correlation between the fNAV, and reference displacement estimates across all data sets (0.73 +/- 0.29). For all data, fNAV lead to significantly sharper vessels than all other reconstructions (p < 0.01). Finally, a blinded reviewer chose fNAV as the best image in 239 out of 571 cases (p = 10-5). Conclusion: fNAV is a promising technique for improving free-breathing 3D radial whole-heart CMRA. This novel approach to respiratory self-navigation can derive 3D nonrigid motion estimations from an acquired 1D signal yielding statistically significant improvement in image sharpness relative to 1D translational correction as well as XD-GRASP reconstructions.

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arXiv2020

T2 Mapping from Super-Resolution-Reconstructed Clinical Fast Spin Echo Magnetic Resonance Acquisitions

Relaxometry studies in preterm and at-term newborns have provided insight into brain microstructure, thus opening new avenues for studying normal brain development and supporting diagnosis in equivocal neurological situations. However, such quantitative techniques require long acquisition times and therefore cannot be straightforwardly translated to in utero brain developmental studies. In clinical fetal brain magnetic resonance imaging routine, 2D low-resolution T2-weighted fast spin echo sequences are used to minimize the effects of unpredictable fetal motion during acquisition. As super-resolution techniques make it possible to reconstruct a 3D high-resolution volume of the fetal brain from clinical low-resolution images, their combination with quantitative acquisition schemes could provide fast and accurate T2 measurements. In this context, the present work demonstrates the feasibility of using super-resolution reconstruction from conventional T2-weighted fast spin echo sequences for 3D isotropic T2 mapping. A quantitative magnetic resonance phantom was imaged using a clinical T2-weighted fast spin echo sequence at variable echo time to allow for super-resolution reconstruction at every echo time and subsequent T2 mapping of samples whose relaxometric properties are close to those of fetal brain tissue. We demonstrate that this approach is highly repeatable, accurate and robust when using six echo times (total acquisition time under 9 minutes) as compared to gold-standard single-echo spin echo sequences (several hours for one single 2D slice).

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arXiv2020

Free-running SIMilarity-Based Angiography (SIMBA) for simplified anatomical MR imaging of the heart

Purpose: Whole-heart MRA techniques typically target pre-determined motion states and address cardiac and respiratory dynamics independently. We propose a novel fast reconstruction algorithm, applicable to ungated free-running sequences, that leverages inherent similarities in the acquired data to avoid such physiological constraints. Theory and Methods: The proposed SIMilarity-Based Angiography (SIMBA) method clusters the continuously acquired k-space data in order to find a motion-consistent subset that can be reconstructed into a motion-suppressed whole-heart MRA. Free-running 3D radial datasets from six ferumoxytol-enhanced scans of pediatric cardiac patients and twelve non-contrast scans of healthy volunteers were reconstructed with a non-motion-suppressed regridding of all the acquired data (All Data), our proposed SIMBA method, and a previously published free-running framework (FRF) that uses cardiac and respiratory self-gating and compressed sensing. Images were compared for blood-myocardium interface sharpness, contrast ratio, and visibility of coronary artery ostia. Results: Both the fast SIMBA reconstruction (~20s) and the FRF provided significantly higher blood-myocardium sharpness than All Data (P<0.001). No significant difference was observed among the former two. Significantly higher blood-myocardium contrast ratio was obtained with SIMBA compared to All Data and FRF (P<0.01). More coronary ostia could be visualized with both SIMBA and FRF than with All Data (All Data: 4/36, SIMBA: 30/36, FRF: 33/36, both P<0.001) but no significant difference was found between the first two. Conclusion: The combination of free-running sequences and the fast SIMBA reconstruction, which operates without a priori assumptions related to physiological motion, forms a simple workflow for obtaining whole-heart MRA with sharp anatomical structures.

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arXiv2020

A robust broadband fat suppressing phaser T2 preparation module for cardiac magnetic resonance imaging at 3T

Purpose: Designing a new T2 preparation (T2-Prep) module in order to simultaneously provide robust fat suppression and efficient T2 preparation without requiring an additional fat suppression module for T2-weighted imaging at 3T. Methods: The tip-down RF pulse of an adiabatic T2 preparation (T2-Prep) module was replaced by a custom-designed RF excitation pulse that induces a phase difference between water and fat, resulting in a simultaneous T2 preparation of water signals and the suppression of fat signals at the end of the module (now called a phaser adiabatic T2-Prep). Using numerical simulations, in vitro and in vivo ECG-triggered navigator gated acquisitions of the human heart, the blood, myocardium and fat signal-to-noise ratio and right coronary artery (RCA) vessel sharpness using this approach were compared against previously published conventional adiabatic T2-Prep approaches Results: Numerical simulations predicted an increased fat suppression bandwidth and decreased sensitivity against transmit magnetic field inhomogeneities using the proposed approach, while preserving the water T2 preparation capabilities. This was confirmed by the tissue signals acquired on the phantom and the in vivo MRA, which show similar blood and myocardium SNR and CNR and significantly reduced fat SNR compared to the other methods tested. As a result, the RCA conspicuity was significantly increased and the motion artifacts were visually decreased. Conclusion: A novel fat-suppressing T2-preparation method was developed and implemented that demonstrated robust fat suppression and increased vessel sharpness compared with conventional techniques, while preserving its T2 preparation capabilities.

physics.med-ph↗

arXiv2019

Time-Dependent Deep Image Prior for Dynamic MRI

We propose a novel unsupervised deep-learning-based algorithm for dynamic magnetic resonance imaging (MRI) reconstruction. Dynamic MRI requires rapid data acquisition for the study of moving organs such as the heart. Existing reconstruction methods suffer from restrictions either in the model design or in the absence of ground-truth data, resulting in low image quality. We introduce a generalized version of the deep-image-prior approach, which optimizes the network weights to fit a sequence of sparsely acquired dynamic MRI measurements. Our method needs neither prior training nor additional data. In particular, for cardiac images, it does not require the marking of heartbeats or the reordering of spokes. The key ingredients of our method are threefold: 1) a fixed low-dimensional manifold that encodes the temporal variations of images; 2) a network that maps the manifold into a more expressive latent space; and 3) a convolutional neural network that generates a dynamic series of MRI images from the latent variables and that favors their consistency with the measurements in k-space. Our method outperforms the state-of-the-art methods quantitatively and qualitatively in both retrospective and real fetal cardiac datasets. To the best of our knowledge, this is the first unsupervised deep-learning-based method that can reconstruct the continuous variation of dynamic MRI sequences with high spatial resolution.

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arXiv2019

Compressed Sensing with Signal Averaging for Improved Sensitivity and Motion Artifact Reduction in Fluorine-19 MRI

Fluorine-19 (19F) MRI of injected perfluorocarbon emulsions (PFCs) allows for the non-invasive quantification of inflammation and cell tracking, but suffers from a low signal-to-noise ratio and extended scan time. To address this limitation, we tested the hypothesis that a 19F MRI pulse sequence that combines a specific undersampling regime with signal averaging has increased sensitivity and robustness against motion artifacts compared to a non-averaged fully-sampled dataset, when both are reconstructed with compressed sensing. To this end, numerical simulations and phantom experiments were performed to characterize the point spread function (PSF) of undersampling patterns and the vulnerability to noise of acquisition-reconstruction strategies with paired numbers of x signal averages and acceleration factor x (NAx-AFx). At all investigated noise levels, the DSC of the acquisition-reconstruction strategies strongly depended on the regularization parameters and acceleration factor. In phantoms, motion robustness of an NA8-AF8 undersampling pattern versus NA1-AF1 was evaluated with simulated and real motions. Differences were assessed with Dice similarity coefficients (DSC), and were consistently higher for NA8-AF8 compared to NA1-AF1 strategy, for both simulated and real cyclic motions (P<0.001). Both acquisition-reconstruction strategies were validated in vivo in mice (n=2) injected with perfluoropolyether. These images displayed a sharper delineation of the liver with the NA8-AF8 strategy than with the NA1-AF1 strategy. In conclusion, we validated the hypothesis that in 19F MRI, the combination of undersampling and averaging improves both the sensitivity and the robustness against motion artifacts compared to a non-averaged fully-sampled dataset, when both are reconstructed with compressed sensing.

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arXiv2019

Accelerated Coronary MRI with sRAKI: A Database-Free Self-Consistent Neural Network k-space Reconstruction for Arbitrary Undersampling

This study aims to accelerate coronary MRI using a novel reconstruction algorithm, called self-consistent robust artificial-neural-networks for k-space interpolation (sRAKI). sRAKI performs iterative parallel imaging reconstruction by enforcing coil self-consistency using subject-specific neural networks. This approach extends the linear convolutions in SPIRiT to nonlinear interpolation using convolutional neural networks (CNNs). These CNNs are trained individually for each scan using the scan-specific autocalibrating signal (ACS) data. Reconstruction is performed by imposing the learned self-consistency and data-consistency enabling sRAKI to support random undersampling patterns. Fully-sampled targeted right coronary artery MRI was acquired in six healthy subjects for evaluation. The data were retrospectively undersampled, and reconstructed using SPIRiT, $\ell_1$-SPIRiT and sRAKI for acceleration rates of 2 to 5. Additionally, prospectively undersampled whole-heart coronary MRI was acquired to further evaluate performance. The results indicate that sRAKI reduces noise amplification and blurring artifacts compared with SPIRiT and $\ell_1$-SPIRiT, especially at high acceleration rates in targeted data. Quantitative analysis shows that sRAKI improves normalized mean-squared-error (~44% and ~21% over SPIRiT and $\ell_1$-SPIRiT at rate 5) and vessel sharpness (~10% and ~20% over SPIRiT and $\ell_1$-SPIRiT at rate 5). In addition, whole-heart data shows the sharpest coronary arteries when resolved using sRAKI, with 11% and 15% improvement in vessel sharpness over SPIRiT and $\ell_1$-SPIRiT, respectively. Thus, sRAKI is a database-free neural network-based reconstruction technique that may further accelerate coronary MRI with arbitrary undersampling patterns, while improving noise resilience over linear parallel imaging and image sharpness over $\ell_1$ regularization techniques.

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arXiv2019

Natively Fat-Suppressed 5D Whole-Heart MRI with a Radial Free-Running Fast-Interrupted Steady-State (FISS) Sequence at 1.5T and 3T

Purpose: To implement, optimize and test fast interrupted steady-state (FISS) for natively fat-suppressed free-running 5D whole-heart MRI at 1.5T and 3T. Methods: FISS was implemented for fully self-gated free-running cardiac- and respiratory-motion-resolved radial imaging of the heart at 1.5T and 3T. Numerical simulations and phantom scans were performed to compare fat suppression characteristics and to determine parameter ranges (readouts per FISS module (NR) and repetition time (TR)) for effective fat suppression. Subsequently, free-running FISS data were collected in ten healthy volunteers. All acquisitions were compared with a continuous bSSFP version of the same sequence, and both fat suppression and scan times were analyzed. Results: Simulations demonstrate a variable width and location of suppression bands in FISS that was dependent on TR and NR. For a fat suppression bandwidth of 100Hz and NR below 8, simulations demonstrated that a TR between 2.2ms and 3.0ms is required at 1.5T while a range of 3.0ms to 3.5ms applies at 3T. Fat signal increases with NR. These findings were corroborated in phantom experiments. In volunteers, fat SNR was significantly decreased using FISS compared with bSSPF at both field strengths. After protocol optimization, high-resolution (1.1mm x 1.1mm x 1.1mm) 5D whole-heart free-running FISS can be performed with effective fat suppression in under 8 min at 1.5T and 3T at a modest scan time increase compared to bSSFP.Conclusion: An optimal FISS parameter range was determined enabling natively fat-suppressed 5D whole-heart free-running MRI with a single continuous scan at 1.5T and 3T, demonstrating potential for cardiac imaging and noncontrast angiography.

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arXiv2019

Flexible water excitation for fat-free MRI at 3 Tesla using lipid insensitive binomial off-resonant RF excitation (LIBRE) pulses

Purpose: To develop a robust and flexible low power water excitation pulse that enables effective fat suppression at high magnetic field strength. Methods: A water excitation method that uses spatially non-selective pulses was optimized in numerical simulations, and implemented and tested in phantoms and healthy volunteers at 3T. The lipid insensitive binomial off-resonant excitation (LIBRE) pulse comprises two low power rectangular sub-pulses that have a variable frequency offset, phase offset and duration. The capability and extent of LIBRE fat suppression was quantitatively compared with conventional fat saturation (FS) and water excitation (WE) techniques. Results: LIBRE enables simultaneous water excitation and near complete fat suppression in large volumes at 3T as demonstrated by numerical simulations, and experiments. In phantoms and in human subjects, the frequency responses matched well with those from the numerical simulation. Comparing FS and WE, LIBRE demonstrated an improved robustness to magnetic field inhomogeneities, and a much more effectively suppressed fat signal. This applied for a range of pulse durations and pulses as short as 1.4 ms. Conclusion: A flexible water excitation method was developed that shows robust, near complete fat suppression at 3T.

physics.med-ph↗

arXiv2019

Noncontrast free-breathing respiratory self-navigated coronary artery cardiovascular magnetic resonance angiography at 3 T using lipid insensitive binomial off-resonant excitation (LIBRE)

Robust and homogeneous lipid suppression is mandatory for coronary magnetic resonance angiography (MRA) since coronary arteries are commonly embedded in fat. However, effective large volume lipid suppression becomes challenging when performing radial whole-heart coronary MRA and the problem may even be exacerbated at increasing magnetic field strengths. Incomplete fat suppression also generates artifacts, and may affect advanced motion correction methods. The aim was to evaluate a recently reported lipid insensitive MRI method for self-navigated coronary MRA at 3T. Lipid insensitive binomial off resonant excitation (LIBRE) radiofrequency (RF) excitation pulses were included into a self-navigated 3D radial GRE coronary MRA sequence at 3T. LIBRE was compared against conventional fat saturation (FS) and binomial 1-180{\deg}-1 water excitation (WE). First, fat suppression of all techniques was numerically characterized using Matlab and experimentally validated in phantoms and in legs of human volunteers. Subsequently, free-breathing self-navigated coronary MRA was performed using the LIBRE pulse as well as FS and WE in ten volunteers. Results obtained in the simulations were confirmed by the experimental validations as LIBRE enabled near complete fat suppression for 3D radial imaging in vitro and in vivo. For self-navigated whole-heart coronary MRA at 3T, fat SNR was significantly attenuated using LIBRE compared with conventional FS. LIBRE increased the RCA vessel sharpness significantly (37 +/- 9% (LIBRE) vs. 29 +/- 8% (FS) and 30 +/- 8% (WE), both p<0.05) and led to a significant increase in the measured RCA vessel length to (83 +/- 31 mm (LIBRE) vs. 56 +/- 12 mm (FS) and 59 +/- 27 (WE) p<0.05). LIBRE enables robust large volume fat suppression and significantly improves coronary artery image quality at 3T compared to the use of conventional fat suppression and water excitation.

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