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Purpose: To harmonize the use of color for MR relaxometry maps and therefore recommend the use of specific color-maps for representing T1 and T2 maps. Methods: Perceptually linearized color-maps were chosen to have similar color settings as those proposed by Griswold et al. in 2018. A Delphi process, polling the opinion of a panel of 81 experts, was used to generate consensus on the suitability of these maps. Results: Consensus was reached on the suitability of the logarithm-processed Lipari color-map for T1 and the logarithm-processed Navia color-map for T2. There was consensus on color bars being mandatory and on the use of a specific value indicating invalidity. There was no consensus on whether the ranges should be fixed per anatomy. Conclusion: The authors recommend the use of the logarithm-processed Lipari color map for displaying quantitative T1 maps and R1 maps; likewise, the authors recommend the logarithm-processed Navia color-map for displaying T2, T2*, R2 and R2* maps., Comment: 22 pages; embedded are 5 figures and 5 tables; contact the first author for supplementary material. Submitted to Magnetic Resonance in Medicine

The high speed of cardiorespiratory motion introduces a unique challenge for cardiac stereotactic radio-ablation (STAR) treatments with the MR-linac. Such treatments require tracking myocardial landmarks with a maximum latency of 100 ms, which includes the acquisition of the required data. The aim of this study is to present a new method that allows to track myocardial landmarks from few readouts of MRI data, thereby achieving a latency sufficient for STAR treatments. We present a tracking framework that requires only few readouts of k-space data as input, which can be acquired at least an order of magnitude faster than MR-images. Combined with the real-time tracking speed of a probabilistic machine learning framework called Gaussian Processes, this allows to track myocardial landmarks with a sufficiently low latency for cardiac STAR guidance, including both the acquisition of required data, and the tracking inference. The framework is demonstrated in 2D on a motion phantom, and in vivo on volunteers and a ventricular tachycardia (arrhythmia) patient. Moreover, the feasibility of an extension to 3D was demonstrated by in silico 3D experiments with a digital motion phantom. The framework was compared with template matching - a reference, image-based, method - and linear regression methods. Results indicate an order of magnitude lower total latency (<10 ms) for the proposed framework in comparison with alternative methods. The root-mean-square-distances and mean end-point-distance with the reference tracking method was less than 0.8 mm for all experiments, showing excellent (sub-voxel) agreement. The high accuracy in combination with a total latency of less than 10 ms - including data acquisition and processing - make the proposed method a suitable candidate for tracking during STAR treatments.

In this study, we develop a physics-informed deep learning-based method to synthesize multiple brain magnetic resonance imaging (MRI) contrasts from a single five-minute acquisition and investigate its ability to generalize to arbitrary contrasts to accelerate neuroimaging protocols. A dataset of fifty-five subjects acquired with a standard MRI protocol and a five-minute transient-state sequence was used to develop a physics-informed deep learning-based method. The model, based on a generative adversarial network, maps data acquired from the five-minute scan to "effective" quantitative parameter maps, here named q*-maps, by using its generated PD, T1, and T2 values in a signal model to synthesize four standard contrasts (proton density-weighted, T1-weighted, T2-weighted, and T2-weighted fluid-attenuated inversion recovery), from which losses are computed. The q*-maps are compared to literature values and the synthetic contrasts are compared to an end-to-end deep learning-based method proposed by literature. The generalizability of the proposed method is investigated for five volunteers by synthesizing three non-standard contrasts unseen during training and comparing these to respective ground truth acquisitions via contrast-to-noise ratio and quantitative assessment. The physics-informed method was able to match the high-quality synthMRI of the end-to-end method for the four standard contrasts, with mean \pm standard deviation structural similarity metrics above 0.75 \pm 0.08 and peak signal-to-noise ratios above 22.4 \pm 1.9 and 22.6 \pm 2.1. Additionally, the physics-informed method provided retrospective contrast adjustment, with visually similar signal contrast and comparable contrast-to-noise ratios to the ground truth acquisitions for three sequences unused for model training, demonstrating its generalizability and potential application to accelerate neuroimaging protocols., Comment: 23 pages, 7 figures, 1 table. Presented at ISMRM 2022. Will be submitted to NMR in biomedicine

MR-STAT is an emerging quantitative magnetic resonance imaging technique which aims at obtaining multi-parametric tissue parameter maps from single short scans. It describes the relationship between the spatial-domain tissue parameters and the time-domain measured signal by using a comprehensive, volumetric forward model. The MR-STAT reconstruction solves a large-scale nonlinear problem, thus is very computationally challenging. In previous work, MR-STAT reconstruction using Cartesian readout data was accelerated by approximating the Hessian matrix with sparse, banded blocks, and can be done on high performance CPU clusters with tens of minutes. In the current work, we propose an accelerated Cartesian MR-STAT algorithm incorporating two different strategies: firstly, a neural network is trained as a fast surrogate to learn the magnetization signal not only in the full time-domain but also in the compressed lowrank domain; secondly, based on the surrogate model, the Cartesian MR-STAT problem is re-formulated and split into smaller sub-problems by the alternating direction method of multipliers. The proposed method substantially reduces the computational requirements for runtime and memory. Simulated and in-vivo balanced MR-STAT experiments show similar reconstruction results using the proposed algorithm compared to the previous sparse Hessian method, and the reconstruction times are at least 40 times shorter. Incorporating sensitivity encoding and regularization terms is straightforward, and allows for better image quality with a negligible increase in reconstruction time. The proposed algorithm could reconstruct both balanced and gradient-spoiled in-vivo data within 3 minutes on a desktop PC, and could thereby facilitate the translation of MR-STAT in clinical settings., Comment: 12 pages, 7 figures, accepted by IEEE Transactions on Medical Imaging (in press)

Magnetic resonance-electrical properties tomography (MR-EPT) is a technique used to estimate the conductivity and permittivity of tissues from MR measurements of the transmit magnetic field. Different reconstruction methods are available, however all these methods present several limitations which hamper the clinical applicability. Standard Helmholtz based MR-EPT methods are severely affected by noise. Iterative reconstruction methods such as contrast source inversion-EPT (CSI-EPT) are typically time consuming and are dependent on their initialization. Deep learning (DL) based methods require a large amount of training data before sufficient generalization can be achieved. Here, we investigate the benefits achievable using a hybrid approach, i.e. using MR-EPT or DL-EPT as initialization guesses for standard 3D CSI-EPT. Using realistic electromagnetic simulations at 3 T and 7 T, the accuracy and precision of hybrid CSI reconstructions are compared to standard 3D CSI-EPT reconstructions. Our results indicate that a hybrid method consisting of an initial DL-EPT reconstruction followed by a 3D CSI-EPT reconstruction would be beneficial. DL-EPT combined with standard 3D CSI-EPT exploits the power of data driven DL-based EPT reconstructions while the subsequent CSI-EPT facilitates a better generalization by providing data consistency., Comment: 8 pages, 4 figures, 1 table

Purpose: To investigate deep learning electrical properties tomography (EPT) for application on different simulated and in-vivo datasets including pathologies for obtaining quantitative brain conductivity maps. Methods: 3D patch-based convolutional neural networks were trained to predict conductivity maps from B1 transceive phase data. To compare the performance of DLEPT networks on different datasets, three datasets were used throughout this work, one from simulations and two from in-vivo measurements from healthy volunteers and cancer patients, respectively. At first, networks trained on simulations are tested on all datasets with different levels of homogeneous Gaussian noise introduced in training and testing. Secondly, to investigate potential robustness towards systematical differences between simulated and measured phase maps, in-vivo data with conductivity labels from conventional EPT is used for training. Results: High quality of reconstructions from networks trained on simulations with and without noise confirms the potential of deep learning for EPT. However, artifact encumbered results in this work uncover challenges in application of DLEPT to in-vivo data. Training DLEPT networks on conductivity labels from conventional EPT improves quality of results. This is argued to be caused by robustness to artifacts from image acquisition. Conclusions: Networks trained on simulations with added homogeneous Gaussian noise yield reconstruction artifacts when applied to in-vivo data. Training with realistic phase data and conductivity labels from conventional EPT allows for severely reducing these artifacts.

Magnetic resonance imaging (MRI) based electrical properties tomography (EPT) is the quantification of the conductivity and permittivity of different tissues. These electrical properties can be obtained through different reconstruction methods and can be used as a contrast mechanism. The work presented here continues from the two-dimensional CSI-EPT algorithm which was shown to work with two-dimensional Matlab based simulations. The existing CSI-EPT algorithm is reformulated to use the transceive phase rather than relying on the transceive phase assumption. This is achieved by implementing a forward problem, computing the receive phase, into the inverse minimization problem, i.e. retrieving the electrical properties. Furthermore, the radio frequency (RF) shield is numerically implemented to model the RF fields inside the MRI more accurately. Afterwards, the algorithm is tested with three-dimensional FDTD simulations to investigate if the two-dimensional CSI-EPT can retrieve the electrical properties for three-dimensional RF fields. Finally, an MR experiment with a phantom is performed to show the potential for this method. From the results of the two-dimensional Matlab simulations it is seen that CSI-EPT can reconstruct the electrical properties using MRI accessible quantities. In the three-dimensional simulations it is observed that the electrical properties are underestimated, nonetheless, CSI-EPT is more precise than the standard Helmholtz based methods. Finally, the first CSI-EPT results using measured data are shown. The results for the reconstruction using measured data were of the same quality as the results from the FDTD simulation.

Electrical properties (EPs) of tissues, conductivity and permittivity, are modulated by the ionic and water content, which change in presence of pathologies. Information on tissues EPs can be used e.g. as an endogenous biomarker in oncology. MR-Electrical Properties Tomography (MR-EPT) aims to reconstruct tissue EPs by solving an electromagnetic inverse problem relating MR measurements of the transmit radiofrequency RF field to the EPs. However, MR-EPT reconstructions highly suffer from noise in the RF field maps, which limits the clinical applicability. Instead of employing electromagnetic models posing strict requirements on the measured quantities, we propose a data driven approach where the inverse transformation is learned by means of a neural network. Supervised training of a conditional generative adversarial neural network was performed using simulated realistic RF field maps and realistic human head dielectric models. Deep learning EPT (DL-EPT) reconstructions are presented for in-silica MR data and MR measurements at 3 Tesla on phantoms and human brains. DL-EPT shows high quality EP maps, demonstrating good accuracy and greatly improved precision compared to conventional MR-EPT. Moreover, DL-EPT allows permittivity reconstructions at 3 Tesla, which is not possible with state-of-art MR-EPT techniques. The supervised learning-based approach leverages the strength of tailored electromagnetic simulations, allowing inclusion of a priori information (e.g. coil setup) and circumvention of inaccessible MR electromagnetic quantities. Since DL-EPT is highly noise-robust, the requirements for MRI data acquisitions can be relaxed, allowing faster acquisitions and higher resolutions. We believe that DL-EPT greatly improves the quality and applicability of EPT opening a new window for an endogenous biomarker in MRI diagnostics that reflects differences in ionic tissue content.