Objective To visualize the encoding capability of magnetic resonance fingerprinting (MRF) dictionaries. Materials and methods High-dimensional MRF dictionaries were simulated and embedded into a... Show moreObjective To visualize the encoding capability of magnetic resonance fingerprinting (MRF) dictionaries. Materials and methods High-dimensional MRF dictionaries were simulated and embedded into a lower-dimensional space using t-distributed stochastic neighbor embedding (t-SNE). The embeddings were visualized via colors as a surrogate for location in low-dimensional space. First, we illustrate this technique on three different MRF sequences. We then compare the resulting embeddings and the color-coded dictionary maps to these obtained with a singular value decomposition (SVD) dimensionality reduction technique. We validate the t-SNE approach with measures based on existing quantitative measures of encoding capability using the Euclidean distance. Finally, we use t-SNE to visualize MRF sequences resulting from an MRF sequence optimization algorithm. Results t-SNE was able to show clear differences between the color-coded dictionary maps of three MRF sequences. SVD showed smaller differences between different sequences. These findings were confirmed by quantitative measures of encoding. t-SNE was also able to visualize differences in encoding capability between subsequent iterations of an MRF sequence optimization algorithm. Discussion This visualization approach enables comparison of the encoding capability of different MRF sequences. This technique can be used as a confirmation tool in MRF sequence optimization. Show less
Dong, Y.M.; Koolstra, K.; Riedel, M.; Osch, M.J.P. van; Bornert, P. 2021
Purpose To develop a new water-fat separation and B-0 estimation algorithm to effectively suppress the multiple resonances of fat signal in EPI. This is especially relevant for DWI where fat is... Show morePurpose To develop a new water-fat separation and B-0 estimation algorithm to effectively suppress the multiple resonances of fat signal in EPI. This is especially relevant for DWI where fat is often a confounding factor. Methods Water-fat separation based on chemical-shift encoding enables robust fat suppression in routine MRI. However, for EPI the different chemical-shift displacements of the multiple fat resonances along the phase-encoding direction can be problematic for conventional separation algorithms. This work proposes a suitable model approximation for EPI under B-0 and fat off-resonance effects, providing a feasible multi-peak water-fat separation algorithm. Simulations were performed to validate the algorithm. In vivo validation was performed in 6 volunteers, acquiring spin-echo EPI images in the leg (B-0 homogeneous) and head-neck (B-0 inhomogeneous) regions, using a TE-shifted interleaved EPI sequence with/without diffusion sensitization. The results are numerically and statistically compared with voxel-independent water-fat separation and fat saturation techniques to demonstrate the performance of the proposed algorithm. Results The reference separation algorithm without the proposed spatial shift correction caused water-fat ambiguities in simulations and in vivo experiments. Some spectrally selective fat saturation approaches also failed to suppress fat in regions with severe B-0 inhomogeneities. The proposed algorithm was able to achieve improved fat suppression for DWI data and ADC maps in the head-neck and leg regions. Conclusion The proposed algorithm shows improved suppression of the multi-peak fat components in multi-shot interleaved EPI applications compared to the conventional fat saturation approaches and separation algorithms. Show less
Riedel, M.; Setsompop, K.; Mertins, A.; Bornert, P. 2021
Purpose To improve the robustness of diffusion-weighted imaging (DWI) data acquired with segmented simultaneous multi-slice (SMS) echo-planar imaging (EPI) against in-plane and through-plane rigid... Show morePurpose To improve the robustness of diffusion-weighted imaging (DWI) data acquired with segmented simultaneous multi-slice (SMS) echo-planar imaging (EPI) against in-plane and through-plane rigid motion.Theory and Methods The proposed algorithm incorporates a 3D rigid motion correction and wavelet denoising into the image reconstruction of segmented SMS-EPI diffusion data. Low-resolution navigators are used to estimate shot-specific diffusion phase corruptions and 3D rigid motion parameters through SMS-to-volume registration. The shot-wise rigid motion and phase parameters are integrated into a SENSE-based full-volume reconstruction for each diffusion direction. The algorithm is compared to a navigated SMS reconstruction without gross motion correction in simulations and in vivo studies with four-fold interleaved 3-SMS diffusion tensor acquisitions.Results Simulations demonstrate high fidelity was achieved in the SMS-to-volume registration, with submillimeter registration errors and improved image reconstruction quality. In vivo experiments validate successful artifact reduction in 3D motion-compromised in vivo scans with a temporal motion resolution of approximately 0.3 s.Conclusion This work demonstrates the feasibility of retrospective 3D rigid motion correction from shot navigators for segmented SMS DWI. Show less
Purpose Non-Cartesian imaging sequences involve sampling during rapid variation of the encoding field gradients. The quality of the reconstructed images often suffers from insufficient knowledge of... Show morePurpose Non-Cartesian imaging sequences involve sampling during rapid variation of the encoding field gradients. The quality of the reconstructed images often suffers from insufficient knowledge of the exact dynamics of the actual fields applied during sampling.Methods We propose determination of the accurate field dynamics by measuring the currents at the gradient amplifier outputs using the amplifiers' internal sensors concurrently with imaging. The actual dynamic field evolution is then determined by convolution with the measured current-to-field impulse response function of the gradient coil. Integration of the gradient field evolution allows derivation of the k-space trajectory for reconstruction.Results The current-based approach is investigated in spiral and ultrashort TE phantom imaging. In comparison with the model-based product reconstruction as well as a correction approach based on the conventional input waveform-to-field impulse response function, it provides slightly improved image quality. The improvement is ascribed to a better representation of eddy current and amplifier nonlinearity effects.Conclusion Trajectory calculation based on measured amplifier output currents offers a robust, purely measurement-based alternative to conventional model-based approaches. The implementation can mitigate gradient amplifier imperfections with no or little additional hardware effort. Show less
Koolstra, K.; O'Reilly, T.; Bornert, P.; Webb, A. 2021
Objective To correct for image distortions produced by standard Fourier reconstruction techniques on low field permanent magnet MRI systems with strong B-0 inhomogeneity and gradient field... Show moreObjective To correct for image distortions produced by standard Fourier reconstruction techniques on low field permanent magnet MRI systems with strong B-0 inhomogeneity and gradient field nonlinearities. Materials and methods Conventional image distortion correction algorithms require accurate Delta B-0 maps which are not possible to acquire directly when the B-0 inhomogeneities also produce significant image distortions. Here we use a readout gradient time-shift in a TSE sequence to encode the B-0 field inhomogeneities in the k-space signals. Using a non-shifted and a shifted acquisition as input, Delta B-0 maps and images were reconstructed in an iterative manner. In each iteration, Delta B-0 maps were reconstructed from the phase difference using Tikhonov regularization, while images were reconstructed using either conjugate phase reconstruction (CPR) or model-based (MB) image reconstruction, taking the reconstructed field map into account. MB reconstructions were, furthermore, combined with compressed sensing (CS) to show the flexibility of this approach towards undersampling. These methods were compared to the standard fast Fourier transform (FFT) image reconstruction approach in simulations and measurements. Distortions due to gradient nonlinearities were corrected in CPR and MB using simulated gradient maps. Results Simulation results show that for moderate field inhomogeneities and gradient nonlinearities, Delta B-0 maps and images reconstructed using iterative CPR result in comparable quality to that for iterative MB reconstructions. However, for stronger inhomogeneities, iterative MB reconstruction outperforms iterative CPR in terms of signal intensity correction. Combining MB with CS, similar image and Delta B-0 map quality can be obtained without a scan time penalty. These findings were confirmed by experimental results. Discussion In case of B-0 inhomogeneities in the order of kHz, iterative MB reconstructions can help to improve both image quality and Delta B-0 map estimation. Show less
Purpose To minimize the known biases introduced by fat in rapid T-1 and T-2 quantification in muscle using a single-run magnetic resonance fingerprinting (MRF) water-fat separation sequence.... Show morePurpose To minimize the known biases introduced by fat in rapid T-1 and T-2 quantification in muscle using a single-run magnetic resonance fingerprinting (MRF) water-fat separation sequence. Methods The single-run MRF acquisition uses an alternating in-phase/out-of-phase TE pattern to achieve water-fat separation based on a 2-point DIXON method. Conjugate phase reconstruction and fat deblurring were applied to correct for B-0 inhomogeneities and chemical shift blurring. Water and fat signals were matched to the on-resonance MRF dictionary. The method was first tested in a multicompartment phantom. To test whether the approach is capable of measuring small in vivo dynamic changes in relaxation times, experiments were run in 9 healthy volunteers; parameter values were compared with and without water-fat separation during muscle recovery after plantar flexion exercise. Results Phantom results show the robustness of the water-fat resolving MRF approach to undersampling. Parameter maps in volunteers show a significant (P < .01) increase in T-1 (105 +/- 94 ms) and decrease in T-2 (14 +/- 6 ms) when using water-fat-separated MRF, suggesting improved parameter quantification by reducing the well-known biases introduced by fat. Exercise results showed smooth T-1 and T-2 recovery curves. Conclusion Water-fat separation using conjugate phase reconstruction is possible within a single-run MRF scan. This technique can be used to rapidly map relaxation times in studies requiring dynamic scanning, in which the presence of fat is problematic. Show less
MRI developed during the last half-century from a very basic concept to an indispensable non-ionising medical imaging technique that has found broad application in diagnostics, therapy control and... Show moreMRI developed during the last half-century from a very basic concept to an indispensable non-ionising medical imaging technique that has found broad application in diagnostics, therapy control and far beyond. Due to its excellent soft-tissue contrast and the huge variety of accessible tissue- and physiological-parameters, MRI is often preferred to other existing modalities. In the course of its development, MRI underwent many substantial transformations. From the beginning, starting as a proof of concept, much effort was expended to develop the appropriate basic scanning technology and methodology, and to establish the many clinical contrasts (e.g., T-1, T-2, flow, diffusion, water/fat, etc.) that MRI is famous for today. Beyond that, additional prominent innovations to the field have been parallel imaging and compressed sensing, leading to significant scanning time reductions, and the move towards higher static magnetic field strengths, which led to increased sensitivity and improved image quality. Improvements in workflow and the use of artificial intelligence are among many current trends seen in this field, paving the way for a broad use of MRI. The 125th anniversary of the BJR is a good point to reflect on all these changes and developments and to offer some slightly speculative ideas as to what the future may bring. Show less
Steinhoff, M.; Nehrke, K.; Mertins, A.; Bornert, P. 2019
Magnetic Resonance Imaging (MRI) has become a valuable imaging modality in ophthalmology, especially for the diagnosis and treatment planning of patients with uveal melanoma, the most common... Show moreMagnetic Resonance Imaging (MRI) has become a valuable imaging modality in ophthalmology, especially for the diagnosis and treatment planning of patients with uveal melanoma, the most common primary intra-ocular tumor. We aim to develop and evaluate the value of silent Zero Echo Time (ZTE) MRI to image patients with ocular tumors at 7Tesla. Therefore, ZTE and different types of magnetization-prepared ZTE (FLAIR, SPIR, T2 and Saturation recovery), have been developed. After an initial validation with 7 healthy subjects, nine patients with an eye tumor have been evaluated. The ZTE scans were compared to their Cartesian equivalent in terms of contrast, motion-sensitivity, diagnostic quality and patient comfort. All volunteers and especially the patients reported a more comfortable experience during the ZTE scans, which had at least a 10 dB lower sound pressure. The image contrast in the native ZTE was poor, but in the different magnetization-prepared ZTE, the eye lens, cornea and retina were clearly discriminated. Overall the T2-prepared scan yielded the best contrast, especially between tumor and healthy tissue, and proved to be robust against eye motion. Although the intrinsic 3D nature of the ZTE-technique provides an accurate analysis of the tumor morphology, the quality of the ZTE-images is lower than their Cartesian equivalent. In conclusion, the quality of magnetization-prepared ZTE images is sufficient to assess the 3D tumor morphology, but insufficient for more detailed evaluations. As such this technique can be an option for patients who cannot comply with the sound-levels of Cartesian scans, but for other patients the conventional Cartesian scans offer a better image quality. Show less
Purpose: To explore the feasibility of MR Fingerprinting (MRF) to rapidly quantify relaxation times in the human eye at 7T, and to provide a data acquisition and processing framework for future... Show morePurpose: To explore the feasibility of MR Fingerprinting (MRF) to rapidly quantify relaxation times in the human eye at 7T, and to provide a data acquisition and processing framework for future tissue characterization in eye tumor patients.Methods: In this single-element receive coil MRF approach with Cartesian sampling, undersampling is used to shorten scan time and, therefore, to reduce the degree of motion artifacts. For reconstruction, approaches based on compressed sensing (CS) and matrix completion (MC) were used, while their effects on the quality of the MRF parameter maps were studied in simulations and experiments. Average relaxation times in the eye were measured in 6 healthy volunteers. One uveal melanoma patient was included to show the feasibility of MRF in a clinical context.Results: Simulation results showed that an MC-based reconstruction enables large undersampling factors and also results in more accurate parameter maps compared with using CS. Experiments in 6 healthy volunteers used a reduction in scan time from 7:02 to 1:16 min,producing images without visible loss of detail in the parameter maps when using the MC-based reconstruction. Relaxation times from 6 healthy volunteers are in agreement with values obtained from fully sampled scans and values in literature, and parameter maps in a uveal melanoma patient show clear difference in relaxation times between tumor and healthy tissue.Conclusion: Cartesian-based MRF is feasible in the eye at 7T. High undersampling factors can be achieved by means of MC, significantly shortening scan time and increasing patient comfort, while also mitigating the risk of motion artifacts. Show less
Koolstra, K.; Gemert, J. van; Bornert, P.; Webb, A.; Remis, R. 2019
Purpose: Design of a preconditioner for fast and efficient parallel imaging (PI) and compressed sensing (CS) reconstructions for Cartesian trajectories.Theory: PI and CS reconstructions become time... Show morePurpose: Design of a preconditioner for fast and efficient parallel imaging (PI) and compressed sensing (CS) reconstructions for Cartesian trajectories.Theory: PI and CS reconstructions become time consuming when the problem size or the number of coils is large, due to the large linear system of equations that has to be solved in l(1) and l(2)-norm based reconstruction algorithms. Such linear systems can be solved efficiently using effective preconditioning techniques.Methods: In this article we construct such a preconditioner by approximating the system matrix of the linear system, which comprises the data fidelity and includes total variation and wavelet regularization, by a matrix that is block circulant with circulant blocks. Due to this structure, the preconditioner can be constructed quickly and its inverse can be evaluated fast using only two fast Fourier transformations. We test the performance of the preconditioner for the conjugate gradient method as the linear solver, integrated into the well-established Split Bregman algorithm.Results: The designed circulant preconditioner reduces the number of iterations required in the conjugate gradient method by almost a factor of 5. The speed up results in a total acceleration factor of approximately 2.5 for the entire reconstruction algorithm when implemented in MATLAB, while the initialization time of the pre-conditioner is negligible.Conclusion: The proposed preconditioner reduces the reconstruction time for PI and CS in a Split Bregman implementation without compromising reconstruction stability and can easily handle large systems since it is Fourier-based, allowing for efficient computations. Show less
Koolstra, K.; Bornert, P.; Brink, W.; Webb, A. 2018
PurposeTo explore the effect of using extremely high permittivity (epsilon(r)approximate to 1,000) materials on image quality and power requirements of spine imaging at 3 T.Theory and MethodsA... Show morePurposeTo explore the effect of using extremely high permittivity (epsilon(r)approximate to 1,000) materials on image quality and power requirements of spine imaging at 3 T.Theory and MethodsA linear array of high permittivity dielectric blocks made of lead zirconate titanate (PZT) was designed and characterized by electromagnetic simulations and experiments. Their effect on the transmit efficiency, receive sensitivity, power deposition, and diagnostic image quality was analyzed in vivo in 10 healthy volunteers.ResultsSimulation results showed that for quadrature mode excitation, the PZT blocks improve the transmit efficiency by 75% while reducing the maximum 10g average specific absorption rate (SAR(10)) by 20%. In vivo experiments in 10 healthy volunteers showed statistically significant improvements for the transmit efficiency, and image quality. Compared to active radiofrequency shimming, image quality was similar, but the required system input power was significantly lower for quadrature excitation using the PZT blocks.ConclusionFor single-channel transmit systems, using high permittivity PZT blocks offer a way to improve transmit efficiency and image quality in the spine. Results show that the effect, and therefore optimal design, is body mass index and sex specific. Magn Reson Med 79:1192-1199, 2018. (c) 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. Show less
