Publications by authors named "Maxim Zaitsev"

106 Publications

MR-compatible optical microscope for in-situ dual-mode MR-optical microscopy.

PLoS One 2021 10;16(5):e0250903. Epub 2021 May 10.

Department of Microsystemes Engineering (IMTEK), Laborarory for Microactuators, University of Freiburg, Freiburg, Germany.

We present the development of a dual-mode imaging platform that combines optical microscopy with magnetic resonance microscopy. Our microscope is designed to operate inside a 9.4T small animal scanner with the option to use a 72mm bore animal RF coil or different integrated linear micro coils. With a design that minimizes the magnetic distortions near the sample, we achieved a field inhomogeneity of 19 ppb RMS. We further integrated a waveguide in the optical layout for the electromagnetic shielding of the camera, which minimizes the noise increase in the MR and optical images below practical relevance. The optical layout uses an adaptive lens for focusing, 2 × 2 modular combinations of objectives with 0.6mm to 2.3mm field of view and 4 configurable RGBW illumination channels and achieves a plano-apochromatic optical aberration correction with 0.6μm to 2.3μm resolution. We present the design, implementation and characterization of the prototype including the general optical and MR-compatible design strategies, a knife-edge optical characterization and different concurrent imaging demonstrations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0250903PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8109821PMC
May 2021

Pulseq-CEST: Towards multi-site multi-vendor compatibility and reproducibility of CEST experiments using an open-source sequence standard.

Magn Reson Med 2021 Oct 7;86(4):1845-1858. Epub 2021 May 7.

Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany.

Purpose: As the field of CEST grows, various novel preparation periods using different parameters are being introduced. At the same time, large, multisite clinical studies require clearly defined protocols, especially across different vendors. Here, we propose a CEST definition standard using the open Pulseq format for a shareable, simple, and exact definition of CEST protocols.

Methods: We present the benefits of such a standard in three ways: (1) an open database on GitHub, where fully defined, human-readable CEST protocols can be shared; (2) an open-source Bloch-McConnell simulation to test and optimize CEST preparation periods in silico; and (3) a hybrid MR sequence that plays out the CEST preparation period and can be combined with any existing readout module.

Results: The exact definition of the CEST preparation period, in combination with the flexible simulation, leads to a good match between simulations and measurements. The standard allowed finding consensus on three amide proton transfer-weighted protocols that could be compared in healthy subjects and a tumor patient. In addition, we could show coherent multisite results for a sophisticated CEST method, highlighting the benefits regarding protocol sharing and reproducibility.

Conclusion: With Pulseq-CEST, we provide a straightforward approach to standardize, share, simulate, and measure different CEST preparation schemes, which are inherently completely defined.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mrm.28825DOI Listing
October 2021

Combining prospective and retrospective motion correction based on a model for fast continuous motion.

Magn Reson Med 2021 09 8;86(3):1284-1298. Epub 2021 Apr 8.

Center for Diagnostic and Therapeutic Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.

Purpose: Prospective motion correction (PMC) and retrospective motion correction (RMC) have different advantages and limitations. The present work aims to combine the advantages of both for rigid body motion, aiming at correcting for faster motions than was previously achievable. Additionally, it provides insights into the effects of motion on pulse sequences and MR signals with a goal of further improving motion correction in the future.

Methods: The effective encoding trajectory and a global phase offset in a moving object are calculated based on complete gradient waveforms of an arbitrary sequence and a continuous motion model. These data are used to feed the forward signal model, which is then used in iterative image reconstruction to suppress the artifacts still present after the PMC.

Results: Verification experiments with a rotation phantom and in vivo were performed. Predictions of simulated motion artifacts for PMC based on sequence waveforms are very accurate. The performance at combined PMC+RMC is limited by Nyquist violations in the sampled k-space and can be compensated by oversampling.

Conclusion: The combined correction results in better images than pure PMC in the presence of fast motion. The predictions of artifacts are very accurate, allowing for comparing sequences or protocols in simulations. The observed artifacts due to Nyquist violations are expected to be corrected by utilizing parallel imaging.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mrm.28783DOI Listing
September 2021

Strategies to improve intratrain prospective motion correction for turbo spin-echo sequences with constant flip angles.

Magn Reson Med 2021 08 16;86(2):852-865. Epub 2021 Mar 16.

Department of Radiology, Medical Physics, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.

Purpose: To investigate the effects of prospective motion correction on turbo spin echo sequences and optimize motion correction approaches, mitigating signal dropout artifacts caused by the imperfections of motion tracking data.

Methods: Signal dropout artifacts caused by undesired phase deviations introduced by tracking errors are analyzed theoretically. To reduce the adverse effect of such deviations, two approaches are proposed: (1) freezing the correction for example, for even-numbered or higher number of echoes and (2) shifting the correction event prior to the left crusher gradient preceding the refocusing pulse. A comprehensive analysis is presented, including both signal simulations and experimental verifications in phantoms and in vivo. Performance of the proposed approach is validated in two healthy volunteers imaged under two types of motion conditions simulating inadvertent fast motions associated with discomfort and continuous large motions.

Results: The results show that the proposed optimization is able to efficiently correct for the motion artifacts and at the same time avoid signal dropout artifacts. Specifically, performing correction every 4 echo prior to the left crusher gradient was shown to improve image quality.

Conclusion: An optimization approach is proposed to exploit the potential of external tracking for intra-echo-train motion artifact correction for turbo spin echo sequences.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mrm.28763DOI Listing
August 2021

Three-dimensional spatially resolved phase graph framework.

Magn Reson Med 2021 07 19;86(1):551-560. Epub 2021 Feb 19.

Department of Radiology, Medical Physics, Medical Center University of Freiburg, University of Freiburg, Freiburg, Germany.

Purpose: An open-source spatially resolved phase graph framework is proposed for simulating arbitrary pulse sequences in the presence of piece-wise constant gradients with arbitrary orientations in three dimensions. It generalizes the extended phase graph algorithm for analysis of nonperiodic sequences while preserving its efficiency, and is able to estimate the signal modulation in the 3D spatial domain.

Methods: The framework extends the recursive magnetization-evolution algorithm to account for anisotropic diffusion and exploits a novel 3D k-space grid-merging method to balance the computational effort and memory requirements against acceptable simulation errors. A new postsimulation module is proposed to track and visualize the signal evolution both in the k-space and in the image domain, which can be used for simulating image artifacts or finding frequency-response profiles. To illustrate the developed technique, three examples are presented: (1) fast off-resonance calculation for dictionary building in MR fingerprinting, (2) validation of a steady-state sequence with quasi-isotropic diffusion weighting, and (3) investigation of the magnetization evolution in PRESS-based spectroscopic imaging.

Results: The grid-merging algorithm of the proposed framework demonstrates high calculation efficiency exemplified by frequency-response simulation of pseudo steady-state or diffusion-weighted steady-state sequences. It further helps to visualize the signal evolution in PRESS-based sequences.

Conclusions: The proposed simulation framework has been validated based on several different example applications for analyzing signal evolution in the frequency and spatial domain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mrm.28732DOI Listing
July 2021

Magnetic modeling of actively shielded rotating MRI magnets in the presence of environmental steel.

Phys Med Biol 2021 02 2;66(4):045004. Epub 2021 Feb 2.

Innovation, Advanced Therapies, Siemens Healthineers GmbH, Forchheim, Germany. ACRF Image X Institute, Sydney School of Health Sciences, University of Sydney, Australia.

Rotating MRI systems could enable novel integrated medical devices such as MRI-Linacs, MRI-xray-angiography systems, and MRI-proton therapy systems. This work aimed to investigate the feasibility of rotating actively shielded superconducting MRI magnets in the presence of environmental steel-in particular, construction steel in the floor of the installation site. Two magnets were investigated: a 1.0 T split bore magnet, and a 1.5 T closed bore magnet. Each magnet was scaled to emulate field strengths of 0.5, 1.0, and 1.5 T. Finite Element Modeling was used to simulate these magnets in the presence of a 3 × 4 m steel plate located 1250 mm or 1400 mm below the isocenter. There are two possible rotation directions: around the longitudinal (z) axis or around the transverse (x) axis. Each model was solved for rotation angles between 0 and 360° in 30° intervals around each of these axes. For each simulation, a 300 mm DSV was extracted and decomposed into spherical harmonics. For the closed-bore magnet, total induced perturbation for the zero degree rotation angle was 223, 432, and 562 μT peak-to-peak (pk-pk) for the 0.5, 1.0, and 1.5 T models respectively (steel at 1250 mm). For the split-bore magnet, the same numbers were 1477, 16747, and 1766 μT. The substantially higher perturbation for the split-bore magnet can be traced to its larger fringe field. For rotation around the z-axis, total perturbation does not change as a function of angle but is exchanged between different harmonics. For rotation around the x-axis, total perturbation is different at each rotation angle. For the closed bore magnet, maximum perturbations occurred for a 90° rotation around the transverse axis. For the split-bore magnet, the opposite was observed, with the same 90° rotation yielding total perturbation lower than the conventional position. In all cases, at least 95% of the total perturbation was composed of 1st and 2nd order harmonics. The presence of environmental steel poses a major challenge to the realization of an actively shielded rotating superconducting MRI system, requiring some novel form of shimming. Possible shimming strategies are discussed at length.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/1361-6560/abd010DOI Listing
February 2021

Frequency-adjustable magnetic field probes.

Magn Reson Med 2021 02 3;85(2):1123-1133. Epub 2020 Aug 3.

Faculty of Medicine, Department of Radiology, Medical Physics, Medical Center-University of Freiburg, Freiburg, Germany.

Purpose: Nuclear Magnetic Resonance field probes provide exciting possibilities for enhancing MR image quality by allowing for calibration of k-space trajectories and/or dynamic measurement of local field changes. The purpose of this study is to design and build field probes, which are easier to manufacture and more flexible to use than existing probes.

Methods: A new manufacturing method is presented based on light-activated resin to encase the coil assembly and the 1H sample. This method allows for realizing field probes with tightly integrated orthogonal coils, whereby the local resonance frequency of protons can be adjusted during the MR experiment, by applying a DC current to the integrated -field modification coil.

Results: The apparent field probe position in a gradient echo experiment was shifted within the field of view by changing its Larmor frequency using an integrated micro-coil with 5.5 windings. The measured frequency modulation induced by the -field modification coil was 113 Hz/mA. The probe was tested with currents up to 100 mA. The DC current in the local field modification coil did not introduce visible artifacts in the MR images. Furthermore selective off-resonant excitation of the new field probes at 2 kHz above the main RF frequency was demonstrated. Gradient impulse response functions measured with a traditional and proposed probe show similar gradient imperfections.

Conclusions: The presented approach opens up new possibilities for concurrent field monitoring during MR experiments using standard RF capabilities of clinical scanners.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mrm.28444DOI Listing
February 2021

Corrigendum to "Design and implementation of a low-cost, tabletop MRI scanner for education and research prototyping" [J. Magn. Reson. 310 (2020) 106625].

J Magn Reson 2020 Aug 28;317:106764. Epub 2020 Jun 28.

A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA; Harvard-MIT Division of Health Sciences Technology, Cambridge, MA, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmr.2020.106764DOI Listing
August 2020

Design and implementation of a low-cost, tabletop MRI scanner for education and research prototyping.

J Magn Reson 2020 01 22;310:106625. Epub 2019 Oct 22.

A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA; Harvard-MIT Division of Health Sciences Technology, Cambridge, MA, USA.

While access to a laboratory MRI system is ideal for teaching MR physics as well as many aspects of signal processing, providing multiple MRI scanners can be prohibitively expensive for educational settings. To address this need, we developed a small, low-cost, open-interface tabletop MRI scanner for academic use. We constructed and tested 20 of these scanners for parallel use by teams of 2-3 students in a teaching laboratory. With simplification and down-scaling to a 1 cm FOV, fully-functional scanners were achieved within a budget of $10,000 USD each. The design was successful for teaching MR principles and basic signal processing skills and serves as an accessible testbed for more advanced MR research projects. Customizable GUIs, pulse sequences, and reconstruction code accessible to the students facilitated tailoring the scanner to the needs of laboratory exercise. The scanners have been used by >800 students in 6 different courses and all designs, schematics, sequences, GUIs, and reconstruction code is open-source.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmr.2019.106625DOI Listing
January 2020

Design of a shim coil array matched to the human brain anatomy.

Magn Reson Med 2020 04 30;83(4):1442-1457. Epub 2019 Sep 30.

Department of Radiology, Medical Physics, Faculty of Medicine, Medical Center University of Freiburg, University of Freiburg, Freiburg, Germany.

Purpose: The purpose of this study is to introduce a novel design method of a shim coil array specifically optimized for whole brain shimming and to compare the performance of the resulting coils to conventional spherical harmonic shimming.

Methods: The proposed design approach is based on the stream function method and singular value decomposition. Eighty-four field maps from 12 volunteers measured in seven different head positions were used during the design process. The cross validation technique was applied to find an optimal number of coil elements in the array. Additional 42 field maps from 6 further volunteers were used for an independent validation. A bootstrapping technique was used to estimate the required population size to achieve a stable coil design.

Results: Shimming using 12 and 24 coil elements outperforms fourth- and fifth-order spherical harmonic shimming for all measured field maps, respectively. Coil elements show novel coil layouts compared to the conventional spherical harmonic coils and existing multi-coils. Both leave-one-out and independent validation demonstrate the generalization ability of the designed arrays. The bootstrapping analysis predicts that field maps from approximately 140 subjects need to be acquired to arrive at a stable design.

Conclusions: The results demonstrate the validity of the proposed method to design a shim coil array matched to the human brain anatomy, which naturally satisfies the laws of electrodynamics. The design method may also be applied to develop new shim coil arrays matched to other human organs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mrm.28016DOI Listing
April 2020

A 32-channel multi-coil setup optimized for human brain shimming at 9.4T.

Magn Reson Med 2020 02 4;83(2):749-764. Epub 2019 Sep 4.

High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany.

Purpose: A multi-coil shim setup is designed and optimized for human brain shimming. Here, the size and position of a set of square coils are optimized to improve the shim performance without increasing the number of local coils. Utilizing such a setup is especially beneficial at ultrahigh fields where B inhomogeneity in the human brain is more severe.

Methods: The optimization started with a symmetric arrangement of 32 independent coils. Three parameters per coil were optimized in parallel, including angular and axial positions on a cylinder surface and size of the coil, which were constrained by cylinder size, construction consideration, and amplifiers specifications. B maps were acquired at 9.4T in 8 healthy volunteers for use as training data. The global and dynamic shimming performance of the optimized multi-coil were compared in simulations and measurements to a symmetric design and to the scanner's second-order shim setup, respectively.

Results: The optimized multi-coil performs better by 14.7% based on standard deviation (SD) improvement with constrained global shimming in comparison to the symmetric positioning of the coils. Global shimming performance was comparable with a symmetric 65-channel multi-coil and full fifth-order spherical harmonic shim coils. On average, an SD of 48.4 and 31.9 Hz was achieved for in vivo measurements after global and dynamic slice-wise shimming, respectively.

Conclusions: An optimized multi-coil shim setup was designed and constructed for human whole-brain shimming. Similar performance of the multi-coils with many channels can be achieved with a fewer number of channels when the coils are optimally arranged around the target.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mrm.27929DOI Listing
February 2020

Diffusion kurtosis imaging does not improve differentiation performance of breast lesions in a short clinical protocol.

Magn Reson Imaging 2019 11 16;63:205-216. Epub 2019 Aug 16.

Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Maximiliansplatz 3, 91054 Erlangen, Germany. Electronic address:

Background: Diffusion weighted magnetic resonance imaging (DWI) is known to differentiate between malignant and benign lesions via the apparent diffusion coefficient (ADC). Here, the value of diffusion kurtosis imaging (DKI) for differentiation and further characterization of benign and malignant breast lesions and their subtypes in a clinically feasible protocol is investigated.

Material And Methods: This study included 85 patients (with 68 malignant and 73 benign lesions) who underwent 3 T breast DWI using three b values (50, 750, 1500 s/mm), with a total measurement time < 5 min. ADC maps were calculated from b values 50, 750 s/mm. The diffusion kurtosis model was fitted to the diffusion weighted images, yielding in each lesion the average kurtosis-corrected diffusion coefficient D and mean kurtosis K. Histopathology was obtained of radiologically suspicious lesions; follow-up scans were used as a standard of reference for benign appearing lesions. Receiver operating characteristic curves were used to evaluate the parameters' diagnostic performance for differentiation of lesion types and grades. The difference in diffusion parameters between subgroups was analysed statistically using the Wilcoxon rank sum test and Kruskal-Wallis test, applying a Bonferroni correction for multiple testing where necessary.

Results: ADC, D and K showed significant differences between malignant and benign lesions (p < 10). All parameters had similar areas under the curve (AUC) (ADC: 0.92, D: 0.91, K: 0.89) for differentiation of malignant and benign lesions. Sensitivity was highest for ADC (ADC: 0.96, D: 0.94, K: 0.93), as well as specificity (ADC: 0.85, D: 0.82, K: 0.82). ADC and D showed significant differences between tumor histologic grades (p = 6.8⋅10, p = 6.6 · 10, respectively), whereas K did not (p = 0.99). All three parameters differed significantly between subtypes of benign lesions (ADC: p < 10, D: p< 10, K: p = 4.1·10), but not between subtypes of malignant lesions (ADC: p = 0.21, D: p = 0.25, K: p = 0.08).

Conclusion: DKI parameters and conventional ADC can differentiate between malignant and benign lesions. Differentiation performance was best for ADC. Different tumor grades were significantly different in ADC and D, which may have an impact on therapy planning and monitoring. In our study, K did not add value to the diagnostic performance of DWI in a clinical setting.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mri.2019.08.007DOI Listing
November 2019

Switching Circuit Optimization for Matrix Gradient Coils.

Tomography 2019 06;5(2):248-259

Department of Radiology, Medical Physics, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany and.

Matrix gradient coils with up to 84 coil elements were recently introduced for magnetic resonance imaging. Ideally, each element is driven by a dedicated amplifier, which may be technically and financially infeasible. Instead, several elements can be connected in series (called a "cluster") and driven by a single amplifier. In previous works, a set of clusters, called a "configuration," was sought to approximate a target field shape. Because a magnetic resonance pulse sequence requires several distinct field shapes, a mechanism to switch between configurations is needed. This can be achieved by a hypothetical switching circuit connecting all terminals of all elements with each other and with the amplifiers. For a predefined set of configurations, a switching circuit can be designed to require only a limited amount of switches. Here we introduce an algorithm to minimize the number of switches without affecting the ability of the configurations to accurately create the desired fields. The problem is modeled using graph theory and split into 2 sequential combinatorial optimization problems that are solved using simulated annealing. For the investigated cases, the results show that compared to unoptimized switching circuits, the reduction of switches in optimized circuits ranges from 8% to up to 44% (average of 31%). This substantial reduction is achieved without impeding circuit functionality. This study shows how technical effort associated with implementation and operation of a matrix gradient coil is related to different hardware setups and how to reduce this effort.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.18383/j.tom.2018.00056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6588200PMC
June 2019

Quantification of patellofemoral cartilage deformation and contact area changes in response to static loading via high-resolution MRI with prospective motion correction.

J Magn Reson Imaging 2019 11 23;50(5):1561-1570. Epub 2019 Mar 23.

Department of Orthopedic and Trauma Surgery, Medical Center - Albert-Ludwigs-University of Freiburg, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany.

Background: Higher-resolution MRI of the patellofemoral cartilage under loading is hampered by subject motion since knee flexion is required during the scan.

Purpose: To demonstrate robust quantification of cartilage compression and contact area changes in response to in situ loading by means of MRI with prospective motion correction and regularized image postprocessing.

Study Type: Cohort study.

Subjects: Fifteen healthy male subjects.

Field Strength: 3 T.

Sequence: Spoiled 3D gradient-echo sequence augmented with prospective motion correction based on optical tracking. Measurements were performed with three different loads (0/200/400 N).

Assessment: Bone and cartilage segmentation was performed manually and regularized with a deep-learning approach. Average patellar and femoral cartilage thickness and contact area were calculated for the three loading situations. Reproducibility was assessed via repeated measurements in one subject.

Statistical Tests: Comparison of the three loading situations was performed by Wilcoxon signed-rank tests.

Results: Regularization using a deep convolutional neural network reduced the variance of the quantified relative load-induced changes of cartilage thickness and contact area compared to purely manual segmentation (average reduction of standard deviation by ∼50%) and repeated measurements performed on the same subject demonstrated high reproducibility of the method. For the three loading situations (0/200/400 N), the patellofemoral cartilage contact area as well as the mean patellar and femoral cartilage thickness were significantly different from each other (P < 0.05). While the patellofemoral cartilage contact area increased under loading (by 14.5/19.0% for loads of 200/400 N), patellar and femoral cartilage thickness exhibited a load-dependent thickness decrease (patella: -4.4/-7.4%, femur: -3.4/-7.1% for loads of 200/400 N).

Data Conclusion: MRI with prospective motion correction enables quantitative evaluation of patellofemoral cartilage deformation and contact area changes in response to in situ loading. Regularizing the manual segmentations using a neural network enables robust quantification of the load-induced changes.

Level Of Evidence: 2 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2019;50:1561-1570.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jmri.26724DOI Listing
November 2019

Clinical Potential of a New Approach to MRI Acceleration.

Sci Rep 2019 02 13;9(1):1912. Epub 2019 Feb 13.

Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT, 06520, USA.

Fast ROtary Nonlinear Spatial ACquisition (FRONSAC) was recently introduced as a new strategy that applies nonlinear gradients as a small perturbation to improve image quality in highly undersampled MRI. In addition to experimentally showing the previously simulated improvement to image quality, this work introduces the insight that Cartesian-FRONSAC retains many desirable features of Cartesian imaging. Cartesian-FRONSAC preserves the existing linear gradient waveforms of the Cartesian sequence while adding oscillating nonlinear gradient waveforms. Experiments show that performance is essentially identical to Cartesian imaging in terms of (1) resilience to experimental imperfections, like timing errors or off-resonance spins, (2) accommodating scan geometry changes without the need for recalibration or additional field mapping, (3) contrast generation, as in turbo spin echo. Despite these similarities to Cartesian imaging, which provides poor parallel imaging performance, Cartesian-FRONSAC consistently shows reduced undersampling artifacts and better response to advanced reconstruction techniques. A final experiment shows that hardware requirements are also flexible. Cartesian-FRONSAC improves accelerated imaging while retaining the robustness and flexibility critical to real clinical use.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-36802-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6374397PMC
February 2019

Direct matching methods for coils and preamplifiers in MRI.

J Magn Reson 2018 05 16;290:85-91. Epub 2018 Mar 16.

Dept. of Radiology, Medical Physics, University Medical Center Freiburg, Freiburg, Germany.

In this paper, direct matching methods for coils and preamplifiers in receiver arrays are presented. Instead of compensating the reactance of the input impedance of preamplifiers, in our method, the reactance was used to resonate with the coil matching networks and thus to decouple the coils. Furthermore, coil matching networks and preamplifier input matching networks were combined, meaning the coil loop can be matched to the transistor in the preamplifier directly. These matching methods and, for comparison, the conventional matching method were implemented with custom-made preamplifiers and coils. Decoupling and noise-matching performance were compared between these three configurations. Phase shifting networks between coils and preamplifiers are not necessary in our matching methods. With fewer components, these matching networks showed lower noise factors, while similar preamplifier-decoupling performance was found for all three methods.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmr.2018.03.009DOI Listing
May 2018

Pulseq-Graphical Programming Interface: Open source visual environment for prototyping pulse sequences and integrated magnetic resonance imaging algorithm development.

Magn Reson Imaging 2018 10 11;52:9-15. Epub 2018 Mar 11.

Medical Imaging Research Center (MIRC), Dayananda Sagar Institutions, Bangalore, India; Magnetic Resonance Research Program, Columbia University, USA; Dept. of Radiology, Columbia University Medical Center, USA. Electronic address:

Purpose: To provide a single open-source platform for comprehensive MR algorithm development inclusive of simulations, pulse sequence design and deployment, reconstruction, and image analysis.

Methods: We integrated the "Pulseq" platform for vendor-independent pulse programming with Graphical Programming Interface (GPI), a scientific development environment based on Python. Our integrated platform, Pulseq-GPI, permits sequences to be defined visually and exported to the Pulseq file format for execution on an MR scanner. For comparison, Pulseq files using either MATLAB only ("MATLAB-Pulseq") or Python only ("Python-Pulseq") were generated. We demonstrated three fundamental sequences on a 1.5 T scanner. Execution times of the three variants of implementation were compared on two operating systems.

Results: In vitro phantom images indicate equivalence with the vendor supplied implementations and MATLAB-Pulseq. The examples demonstrated in this work illustrate the unifying capability of Pulseq-GPI. The execution times of all the three implementations were fast (a few seconds). The software is capable of user-interface based development and/or command line programming.

Conclusion: The tool demonstrated here, Pulseq-GPI, integrates the open-source simulation, reconstruction and analysis capabilities of GPI Lab with the pulse sequence design and deployment features of Pulseq. Current and future work includes providing an ISMRMRD interface and incorporating Specific Absorption Ratio and Peripheral Nerve Stimulation computations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mri.2018.03.008DOI Listing
October 2018

Optimization of Coil Element Configurations for a Matrix Gradient Coil.

IEEE Trans Med Imaging 2018 01 23;37(1):284-292. Epub 2017 Aug 23.

Recently, matrix gradient coils (also termed multi-coils or multi-coil arrays) were introduced for imaging and B shimming with 24, 48, and even 84 coil elements. However, in imaging applications, providing one amplifier per coil element is not always feasible due to high cost and technical complexity. In this simulation study, we show that an 84-channel matrix gradient coil (head insert for brain imaging) is able to create a wide variety of field shapes even if the number of amplifiers is reduced. An optimization algorithm was implemented that obtains groups of coil elements, such that a desired target field can be created by driving each group with an amplifier. This limits the number of amplifiers to the number of coil element groups. Simulated annealing is used due to the NP-hard combinatorial nature of the given problem. A spherical harmonic basis set up to the full third order within a sphere of 20-cm diameter in the center of the coil was investigated as target fields. We show that the median normalized least squares error for all target fields is below approximately 5% for 12 or more amplifiers. At the same time, the dissipated power stays within reasonable limits. With a relatively small set of amplifiers, switches can be used to sequentially generate spherical harmonics up to third order. The costs associated with a matrix gradient coil can be lowered, which increases the practical utility of matrix gradient coils.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/TMI.2017.2743463DOI Listing
January 2018

Design of a shielded coil element of a matrix gradient coil.

J Magn Reson 2017 08 9;281:217-228. Epub 2017 Jun 9.

Dept. of Radiology, Medical Physics, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 60a, 79106 Freiburg, Germany.

The increasing interest in spatial encoding with non-linear magnetic fields has intensified the need for coils that generates such fields. Matrix coils consisting of multiple coil elements appear to offer a high flexibility in generating customized encoding fields and are particularly promising for localized high resolution imaging applications. However, coil elements of existing matrix coils were primarily designed and constructed for better shimming and therefore are not expected to achieve an optimal performance for local spatial encoding. Moreover, eddy current properties of such coil elements were not fully explored. In this work, an optimization problem is formulated based on the requirement of local non-linear encoding and eddy current reduction that results in novel designs of coil elements for an actively-shielded matrix gradient coil. Two metrics are proposed to assess the performance of different coil element designs. The results are analyzed to reveal new insights into coil element design.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmr.2017.06.006DOI Listing
August 2017

Development and implementation of an 84-channel matrix gradient coil.

Magn Reson Med 2018 02 25;79(2):1181-1191. Epub 2017 Apr 25.

Department of Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.

Purpose: Design, implement, integrate, and characterize a customized coil system that allows for generating spatial encoding magnetic fields (SEMs) in a highly-flexible fashion.

Methods: A gradient coil with a high number of individual elements was designed. Dimensions of the coil were chosen to mimic a whole-body gradient system, scaled down to a head insert. Mechanical shape and wire layout of each element were optimized to increase the local gradient strength while minimizing eddy current effects and simultaneously considering manufacturing constraints.

Results: Resulting wire layout and mechanical design is presented. A prototype matrix gradient coil with 12 × 7 = 84 elements consisting of two element types was realized and characterized. Measured eddy currents are <1% of the original field. The coil is shown to be capable of creating nonlinear, and linear SEMs. In a DSV of 0.22 m gradient strengths between 24 mT∕m and 78 mT∕m could be realized locally with maximum currents of 150 A. Initial proof-of-concept imaging experiments using linear and nonlinear encoding fields are demonstrated.

Conclusion: A shielded matrix gradient coil setup capable of generating encoding fields in a highly-flexible manner was designed and implemented. The presented setup is expected to serve as a basis for validating novel imaging techniques that rely on nonlinear spatial encoding fields. Magn Reson Med 79:1181-1191, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mrm.26700DOI Listing
February 2018

Comparative T and T mapping of patellofemoral cartilage under in situ mechanical loading with prospective motion correction.

J Magn Reson Imaging 2017 08 3;46(2):452-460. Epub 2017 Feb 3.

Department of Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany.

Purpose: To demonstrate improved T and T mapping of patellofemoral cartilage with in situ loading by means of prospective motion correction and to assess load-induced changes in healthy subjects.

Materials And Methods: Established T and T mapping sequences were augmented with prospective motion correction based on optical tracking. Protocols were optimized for robust imaging of the patellofemoral cartilage at a field strength of 3T. Subjects were positioned in the scanner with knee flexion and in situ loading of the patellofemoral joint was performed with a pneumatic loading device. In a pilot study on a cohort of 10 healthy subjects, load-induced T and T changes were evaluated through measurements with axial loads of 0/20/40 kg.

Results: With prospective motion correction and additional lipid saturation, motion artifacts in patellofemoral cartilage magnetic resonance imaging (MRI) with in situ loading could be notably decreased, as demonstrated for T mapping. The acquired relaxation maps suggested a T /T decrease in superficial cartilage and a T /T increase in deep cartilage under loading. However, in the quantitative group evaluation of the lateral patellar facet, only T in superficial cartilage was significantly changed by loading (P ≤ 0.05), while no significant T differences for the three loading conditions were observed (P ≥ 0.3).

Conclusion: Prospective motion correction enables T and T mapping of patellofemoral cartilage with in situ loading and a comparison of the two contrasts in terms of their response to mechanical loading. T is a more sensitive marker for load-induced patellar cartilage changes than T .

Level Of Evidence: 3 Technical Efficacy: Stage 1 J. MAGN. RESON. IMAGING 2017;46:452-460.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jmri.25574DOI Listing
August 2017

One-second MRI of a three-dimensional vocal tract to measure dynamic articulator modifications.

J Magn Reson Imaging 2017 07 9;46(1):94-101. Epub 2016 Dec 9.

University Medical Center Freiburg, Department of Radiology, Medical Physics, Freiburg, Germany.

Purpose: To enable three-dimensional (3D) vocal tract imaging of dynamic singing or speech tasks at voxel sizes of 1.6 × 1.6 × 1.3 mm at 1.3 s per image.

Materials And Methods: A Stack-of-Stars method was implemented and enhanced to allow for fast and efficient k-space sampling of the box-shaped vocal tract using a 3 Tesla MRI system. Images were reconstructed using an off-line image reconstruction using compressed sensing theory, leading to the abovementioned spatial and temporal resolutions. To validate spatial resolution, a phantom with holes of defined sizes was measured. The applicability of the imaging method was validated in an eight-subject study of amateur singers that were required to sustain phonation at a constant pitch, past their comfortable expiratory level. A segmentation of the vocal tract over all phonation time steps was done for one subject. Anatomical distances (larynx position and pharynx width) were calculated and compared for all subjects.

Results: Analysis of the phantom study revealed that the imaging method could provide at least 1.6 mm isotropic resolution. Visual inspection of the segmented vocal tract during phonation showed modifications of the lips, tongue, and larynx position in all three dimensions. The mean larynx position per subject amounted to 52-85 mm, deviating up to 5% over phonation time. Parameter pharynx width was 32-181 mm on average per subject, deviating up to 16% over phonation time. Visual inspection of the parameter course revealed no common compensation strategy for long sustained phonation.

Conclusion: The results of both phantom and in vivo measurements show the applicability of the fast 3D imaging method for voice research and indicate that modifications in all three dimensions can be observed and quantified.

Level Of Evidence: 2 Technical Efficacy: Stage 1 J. MAGN. RESON. IMAGING 2017;46:94-101.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jmri.25561DOI Listing
July 2017

Prospective motion correction in functional MRI.

Neuroimage 2017 07 11;154:33-42. Epub 2016 Nov 11.

Department of Radiology - Medical Physics, University of Freiburg, Faculty of Medicine, University of Freiburg - Medical Centre, Freiburg, Germany.

Due to the intrinsic low sensitivity of BOLD-fMRI long scanning is required. Subject motion during fMRI scans reduces statistical significance of the activation maps and increases the prevalence of false activations. Motion correction is therefore an essential tool for a successful fMRI data analysis. Retrospective motion correction techniques are now commonplace and are incorporated into a wide range of fMRI analysis toolboxes. These techniques are advantageous due to robustness, sequence independence and have minimal impact on the fMRI study setup. Retrospective techniques however, do not provide an accurate intra-volume correction, nor can these techniques correct for the spin-history effects. The application of prospective motion correction in fMRI appears to be effective in reducing false positives and increasing sensitivity when compared to retrospective techniques, particularly in the cases of substantial motion. Especially advantageous in this regard is the combination of prospective motion correction with dynamic distortion correction. Nevertheless, none of the recent methods are able to recover activations in presence of motion that are comparable to no-motion conditions, which motivates further research in the area of adaptive dynamic imaging.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.neuroimage.2016.11.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5427003PMC
July 2017

The noise factor of receiver coil matching networks in MRI.

Magn Reson Imaging 2017 Apr 2;37:252-259. Epub 2016 Nov 2.

Dept. of Radiology, Medical Physics, University Medical Center Freiburg, Freiburg, Germany.

In typical MRI applications the dominant noise sources in the received signal are the sample, the coil loop and the preamplifier. We hypothesize that in some cases (e.g. for very small receiver coils) the matching network noise has to be considered explicitly. Considering the difficulties of direct experimental determinations of the noise factor of matching networks with sufficient accuracy, it is helpful to estimate the noise factor by calculation. A useful formula of the coil matching network is obtained by separating commonly used coil matching network into different stages and calculating their noise factor analytically by a combination of the noise from these stages. A useful formula of the coil matching network is obtained. ADS simulations are performed to verify the theoretical predictions. Thereafter carefully-designed proof-of-concept phantom experiments are carried out to qualitatively confirm the predicted SNR behavior. The matching network noise behavior is further theoretically investigated for a variety of scenarios. It is found that in practice the coil matching network noise can be improved by adjusting the coil open port resonant frequency.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mri.2016.10.032DOI Listing
April 2017

EEG-fMRI Gradient Artifact Correction by Multiple Motion-Related Templates.

IEEE Trans Biomed Eng 2016 12 21;63(12):2647-2653. Epub 2016 Jul 21.

Objectives: In simultaneous electroencephalography (EEG) and functional magnetic resonance imaging (fMRI), artifacts on the EEG arise from the switching of magnetic field gradients in the MR scanner. These artifacts depend on head position, and are, therefore, difficult to remove in the presence of subject motion. In this study, gradient artifacts are modeled by multiple templates extracted from externally recorded motion information.

Methods: Gradient artifact correction was performed in EEG-fMRI recordings by estimating artifactual templates modulated by slowly varying splines, as well as head position information. The EEG signal quality was then compared following two common methods: averaged artifact subtraction (AAS) and optimal basis sets (OBS).

Results: Artifact correction using multiple templates estimated from splines or motion time courses outperformed the existing AAS and OBS approaches, as quantified by root-mean-square power across gradient epochs. Improvements were mostly seen in posterior EEG channels, where most of the residual artifacts are seen following the AAS and OBS methods. Residual spectral power was comparable to that of EEG signals recorded without fMRI scanning.

Conclusion: Gradient artifacts can be well modeled by multiple templates estimated from head position information, resulting in an effective artifact removal.

Significance: This method can facilitate EEG-fMRI of uncooperative subjects in whom motion is inevitable, for example, to investigate high-frequency EEG activity in which gradient artifacts are particularly prominent.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/TBME.2016.2593726DOI Listing
December 2016

Marker-based ballistocardiographic artifact correction improves spike identification in EEG-fMRI of focal epilepsy patients.

Clin Neurophysiol 2016 08 8;127(8):2802-2811. Epub 2016 Jun 8.

Dept. Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany.

Objectives: Ballistocardiographic (BCG) artifacts resemble interictal epileptic discharges (IEDs) and can lead to incorrect IED identification in EEG-fMRI. This study investigates IEDs marked in EEGs corrected using information from a moiré phase tracking (MPT) marker.

Methods: EEG-fMRI from 18 patients was processed with conventional methods for BCG removal, while 9 patients used a MPT marker. IEDs were marked first without ECG information. In a second review, suspicious IEDs synchronous with the BCG were discarded. After each review, an event-related fMRI analysis was performed on the marked IEDs.

Results: No difference was found in the proportion of suspicious IEDs in the 2 patient groups. However, the distribution of IED timings was significantly related to the cardiac cycle in 11 of 18 patients recorded without MPT marker, but only 2 of 9 patients with marker. In patients recorded without marker, failing to discard suspicious IEDs led to more inaccurate fMRI maps and more distant activations.

Conclusions: BCG artifact correction based on MPT recordings allowed a more straightforward identification of IEDs that did not require ECG information in the large majority of patients.

Significance: Marker-based ballistocardiographic artifact correction greatly facilitates the study of the generators of interictal discharges with EEG-fMRI.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.clinph.2016.05.361DOI Listing
August 2016

High resolution CBV assessment with PEAK-EPI: k-t-undersampling and reconstruction in echo planar imaging.

Magn Reson Med 2017 06 25;77(6):2153-2166. Epub 2016 Jun 25.

Department of Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.

Purpose: Achieving higher spatial resolution and improved brain coverage while mitigating in-plane susceptibility artifacts in the assessment of perfusion parameters, such as cerebral blood volume, in echo planar imaging (EPI)-based dynamic susceptibility contrast weighted cerebral perfusion measurements.

Methods: PEAK-EPI, an EPI sequence with interleaved readout trajectories and three different strategies for autocalibration-signal acquisition (inplace, dynamic extra and extra) is presented. Performance of each approach is analyzed in vivo based on flip angle variation induced dynamics, assessing temporal fidelity, temporal SNR and g-factors. All approaches are compared with conventional GRAPPA reconstructions. PEAK-EPI with inplace autocalibration-signal at R = 5 is then compared with the standard clinical EPI protocol in six patients, using two half-dose dynamic susceptibility contrast weighted cerebral perfusion measurements per subject.

Results: PEAK-EPI acquisition facilitates a substantial increase of spatial resolution at a higher number of slices per TR and provides improved SNR compared to conventional GRAPPA. High dependency of the resulting reconstruction quality on the type of autocalibration-signal acquisition is observed. PEAK-EPI with inplace autocalibration-signal achieves high temporal fidelity and initial feasibility is shown.

Conclusion: The obtained high resolution cerebral blood volume maps reveal more detailed information than in corresponding standard EPI measurements and facilitate detailed delineation of tumorous tissue. Magn Reson Med 77:2153-2166, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mrm.26298DOI Listing
June 2017

Pulseq: A rapid and hardware-independent pulse sequence prototyping framework.

Magn Reson Med 2017 04 7;77(4):1544-1552. Epub 2016 Jun 7.

Department of Radiology, Medical Physics, University Medical Center Freiburg, Freiburg, BW, Germany.

Purpose: Implementing new magnetic resonance experiments, or sequences, often involves extensive programming on vendor-specific platforms, which can be time consuming and costly. This situation is exacerbated when research sequences need to be implemented on several platforms simultaneously, for example, at different field strengths. This work presents an alternative programming environment that is hardware-independent, open-source, and promotes rapid sequence prototyping.

Methods: A novel file format is described to efficiently store the hardware events and timing information required for an MR pulse sequence. Platform-dependent interpreter modules convert the file to appropriate instructions to run the sequence on MR hardware. Sequences can be designed in high-level languages, such as MATLAB, or with a graphical interface. Spin physics simulation tools are incorporated into the framework, allowing for comparison between real and virtual experiments.

Results: Minimal effort is required to implement relatively advanced sequences using the tools provided. Sequences are executed on three different MR platforms, demonstrating the flexibility of the approach.

Conclusion: A high-level, flexible and hardware-independent approach to sequence programming is ideal for the rapid development of new sequences. The framework is currently not suitable for large patient studies or routine scanning although this would be possible with deeper integration into existing workflows. Magn Reson Med 77:1544-1552, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mrm.26235DOI Listing
April 2017

Design of a 3T preamplifier which stability is insensitive to coil loading.

J Magn Reson 2016 Apr 26;265:215-23. Epub 2016 Feb 26.

Dept. of Radiology, Medical Physics, University Medical Center Freiburg, Freiburg, Germany.

In MRI (magnetic resonance imaging), preamplifiers are needed to amplify signals obtained from MRI receiver coils. Under various loading conditions of the corresponding receiver coils, preamplifiers see different source impedance at their input and may become unstable. Therefore preamplifiers which stability is not sensitive to coil loading are desirable. In this article, a coil-loading-insensitive preamplifier for MRI is presented, derived from an unstable preamplifier. Different approaches to improve stability were used during this derivation. Since a very low noise factor is essential for MRI preamplifiers, noise contributions from passive components in the MRI preamplifier have to be considered during the stabilization process. As a result, the initially unstable preamplifier became stable with regard to coil loading, while other MRI requirements, as the extremely low noise factor, were still fulfilled. The newly designed preamplifier was manufactured, characterized and tested in the MRI spectrometer. Compared to a commercially available preamplifier, the newly designed preamplifier has similar imaging performance but other advantages like smaller size and better stability. Furthermore, presented stabilization approaches can be generalized to stabilize other unstable low-noise amplifiers.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmr.2016.02.012DOI Listing
April 2016

Performance evaluation of matrix gradient coils.

MAGMA 2016 Feb 14;29(1):59-73. Epub 2015 Dec 14.

Medical Physics, Department of Radiology, University Medical Center Freiburg, Breisacher Str. 60a, 79106, Freiburg, Germany.

Objective: In this paper, we present a new performance measure of a matrix coil (also known as multi-coil) from the perspective of efficient, local, non-linear encoding without explicitly considering target encoding fields.

Materials And Methods: An optimization problem based on a joint optimization for the non-linear encoding fields is formulated. Based on the derived objective function, a figure of merit of a matrix coil is defined, which is a generalization of a previously known resistive figure of merit for traditional gradient coils.

Results: A cylindrical matrix coil design with a high number of elements is used to illustrate the proposed performance measure. The results are analyzed to reveal novel features of matrix coil designs, which allowed us to optimize coil parameters, such as number of coil elements. A comparison to a scaled, existing multi-coil is also provided to demonstrate the use of the proposed performance parameter.

Conclusions: The assessment of a matrix gradient coil profits from using a single performance parameter that takes the local encoding performance of the coil into account in relation to the dissipated power.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10334-015-0519-yDOI Listing
February 2016