Advancing RF pulse design using an open-competition format: Report from the 2015 ISMRM challenge

Reproducibility of arterial spin labeling cerebral blood flow image processing: A report of the ISMRM open science initiative for perfusion imaging (OSIPI) and the ASL MRI challenge

PURPOSE

Arterial spin labeling (ASL) is a widely used contrast-free MRI method for assessing cerebral blood flow (CBF). Despite the generally adopted ASL acquisition guidelines, there is still wide variability in ASL analysis. We explored this variability through the ISMRM-OSIPI ASL-MRI Challenge, aiming to establish best practices for more reproducible ASL analysis.

METHODS

Eight teams analyzed the challenge data, which included a high-resolution T1-weighted anatomical image and 10 pseudo-continuous ASL datasets simulated using a digital reference object to generate ground-truth CBF values in normal and pathological states. We compared the accuracy of CBF quantification from each team's analysis to the ground truth across all voxels and within predefined brain regions. Reproducibility of CBF across analysis pipelines was assessed using the intra-class correlation coefficient (ICC), limits of agreement (LOA), and replicability of generating similar CBF estimates from different processing approaches.

RESULTS

Absolute errors in CBF estimates compared to ground-truth synthetic data ranged from 18.36 to 48.12 mL/100 g/min. Realistic motion incorporated into three datasets produced the largest absolute error and variability between teams, with the least agreement (ICC and LOA) with ground-truth results. Fifty percent of the submissions were replicated, and one produced three times larger CBF errors (46.59 mL/100 g/min) compared to submitted results.

CONCLUSIONS

Variability in CBF measurements, influenced by differences in image processing, especially to compensate for motion, highlights the significance of standardizing ASL analysis workflows. We provide a recommendation for ASL processing based on top-performing approaches as a step toward ASL standardization.

Actual patient position versus safety models: Specific Absorption Rate implications of initial head position for Ultrahigh Field Magnetic Resonance Imaging

Specific absorption rate (SAR) relates power absorption to tissue heating, and therefore is used as a safety constraint in magnetic resonance imaging (MRI). This study investigates the implications of initial head positioning on local and whole-head SAR. A virtual body model was simulated at 161 positions inside an eight-channel parallel-transmit (pTx) array. On-axis displacements and rotations of up to 20 mm/degrees and off-axis axial/coronal translations were investigated. Single-channel, radiofrequency (RF) shimming (i.e., single-spoke pTx) and multispoke pTx pulses were designed for seven axial, five coronal and five sagittal slices at each position (the slices were consistent across all positions). Whole-head and local SAR were calculated using safety models consisting of a single (centred) body position, multiple representative positions and all simulated body positions. Positional mismatches between safety models and actual positions cause SAR underestimation. For axial imaging, the actual peak local SAR was up to 4.2-fold higher for both single-channel and 5-spoke pTx, 3.5-fold higher for 3-/4-spoke pTx, and 2-fold higher for RF shimming and 2-spoke pTx, compared with that calculated using the centred body position. For sagittal and coronal imaging, the underestimation of peak local SAR was up to 5.2-fold and 3.8-fold, respectively. Using all body positions to estimate SAR prevented SAR underestimation but yielded up to 11-fold SAR overestimation for RF shimming. Local SAR of single-channel and pTx multispoke pulses showed considerable dependence on the initial patient position. RF shimming yielded much lower sensitivity to positional mismatches for axial imaging but not for sagittal and coronal imaging. This was deemed attributable to the higher degrees-of-freedom of control offered by the investigated coil array for axial imaging. Whole-head SAR is less sensitive to positional mismatches compared with local SAR. Nevertheless, whole-head SAR increased by up to 80% for sagittal imaging. Local and whole-head SAR were observed to be more sensitive to positional mismatches in the axial plane, because of larger variations in coil-tissue proximity. Using all possible body positions in the safety model may become substantially over-conservative and limit imaging performance, especially for the RF shimming mode for axial imaging.

Evaluating of the Quality of Hepatic Diffusion Weighted Imaging Using Multiband Imaging With Variable-Rate Selective Excitation

OBJECTIVE

To assess the image quality of diffusion-weighted imaging (DWI) using multiband (MB) imaging with variable-rate selective excitation (VERSE) and compare it to conventional DWI.

METHODS

We retrospectively evaluated hepatic DWI images of patients (n = 76) according to either the conventional method (SENSE, acceleration factor = 2) (n = 38) or fast scanning method (MB imaging with VERSE, acceleration factor = 2 × 2) (n = 38). We also conducted a volunteer study (n = 15) for those scanning methods. During quantitative analysis, the signal-to-noise ratio (SNR), apparent diffusion coefficient values, and contrast in the liver, spleen, and spinal cord were compared between the 2 groups. During qualitative analysis, all images were independently and blindly evaluated by 2 board-certified radiologists. The image contrast, noise, artifacts, and sharpness were assessed, and the performance of classification was measured using receiver operating characteristic curve analysis.

RESULTS

In the retrospective study, the SNRs of the hepatic parenchyma and spinal cord between the 2 protocols were significantly different (liver, 8.9 [interquartile range {IQR}, 7.6-12.2] vs 13.0 [IQR, 10.0-16.7]; P < 0.001 and spinal cord, 6.0 [IQR, 4.7-9.4] vs 4.3 [IQR, 3.8-6.8]; P < 0.02). No significant differences between the 2 protocols in the other retrospective analyses were noted. In the receiver operating characteristic curve analysis, area under the curve was 0.49 (95% confidence intervals, 0.40-0.58).

CONCLUSION

Multiband VERSE reduced scan time and SNR of hepatic DWI; however, subjective image quality parameters were not significantly impacted.

Rigid motion-resolved B1+ prediction using deep learning for real-time parallel-transmission pulse design

PURPOSE

Tailored parallel-transmit (pTx) pulses produce uniform excitation profiles at 7 T, but are sensitive to head motion. A potential solution is real-time pulse redesign. A deep learning framework is proposed to estimate pTx B 1 + distributions following within-slice motion, which can then be used for tailored pTx pulse redesign.

METHODS

Using simulated data, conditional generative adversarial networks were trained to predict B 1 + distributions in the head following a displacement. Predictions were made for two virtual body models that were not included in training. Predicted maps were compared with ground-truth (simulated, following motion) B1 maps. Tailored pTx pulses were designed using B1 maps at the original position (simulated, no motion) and evaluated using simulated B1 maps at displaced position (ground-truth maps) to quantify motion-related excitation error. A second pulse was designed using predicted maps (also evaluated on ground-truth maps) to investigate improvement offered by the proposed method.

RESULTS

Predicted B 1 + maps corresponded well with ground-truth maps. Error in predicted maps was lower than motion-related error in 99% and 67% of magnitude and phase evaluations, respectively. Worst-case flip-angle normalized RMS error due to motion (76% of target flip angle) was reduced by 59% when pulses were redesigned using predicted maps.

CONCLUSION

We propose a framework for predicting B 1 + maps online with deep neural networks. Predicted maps can then be used for real-time tailored pulse redesign, helping to overcome head motion-related error in pTx.

B1 field map synthesis with generative deep learning used in the design of parallel-transmit RF pulses for ultra-high field MRI

Spoke trajectory parallel transmit (pTX) excitation in ultra-high field MRI enables B₁⁺ inhomogeneities arising from the shortened RF wavelength in biological tissue to be mitigated. To this end, current RF excitation pulse design algorithms either employ the acquisition of field maps with subsequent non-linear optimization or a universal approach applying robust pre-computed pulses. We suggest and evaluate an intermediate method that uses a subset of acquired field maps combined with generative machine learning models to reduce the pulse calibration time while offering more tailored excitation than robust pulses (RP). The possibility of employing image-to-image translation and semantic image synthesis machine learning models based on generative adversarial networks (GANs) to deduce the missing field maps is examined. Additionally, an RF pulse design that employs a predictive machine learning model to find solutions for the non-linear (two-spokes) pulse design problem is investigated. As a proof of concept, we present simulation results obtained with the suggested machine learning approaches that were trained on a limited data-set, acquired in vivo. The achieved excitation homogeneity based on a subset of half of the B₁⁺ maps acquired in the calibration scans and half of the B₁⁺ maps synthesized with GANs is comparable with state of the art pulse design methods when using the full set of calibration data while halving the total calibration time. By employing RP dictionaries or machine-learning RF pulse predictions, the total calibration time can be reduced significantly as these methods take only seconds or milliseconds per slice, respectively.

Joint Design of RF and Gradient Waveforms via Auto-differentiation for 3D Tailored Excitation in MRI

This paper proposes a new method for joint design of radiofrequency (RF) and gradient waveforms in Magnetic Resonance Imaging (MRI), and applies it to the design of 3D spatially tailored saturation and inversion pulses. The joint design of both waveforms is characterized by the ODE Bloch equations, to which there is no known direct solution. Existing approaches therefore typically rely on simplified problem formulations based on, e.g., the small-tip approximation or constraining the gradient waveforms to particular shapes, and often apply only to specific objective functions for a narrow set of design goals (e.g., ignoring hardware constraints). This paper develops and exploits an auto-differentiable Bloch simulator to directly compute Jacobians of the (Bloch-simulated) excitation pattern with respect to RF and gradient waveforms. This approach is compatible with arbitrary sub-differentiable loss functions, and optimizes the RF and gradients directly without restricting the waveform shapes. For computational efficiency, we derive and implement explicit Bloch simulator Jacobians (approximately halving computation time and memory usage). To enforce hardware limits (peak RF, gradient, and slew rate), we use a change of variables that makes the 3D pulse design problem effectively unconstrained; we then optimize the resulting problem directly using the proposed auto-differentiation framework. We demonstrate our approach with two kinds of 3D excitation pulses that cannot be easily designed with conventional approaches: Outer-volume saturation (90° flip angle), and inner-volume inversion.

Results of the 2020 fastMRI Challenge for Machine Learning MR Image Reconstruction

Accelerating MRI scans is one of the principal outstanding problems in the MRI research community. Towards this goal, we hosted the second fastMRI competition targeted towards reconstructing MR images with subsampled k-space data. We provided participants with data from 7,299 clinical brain scans (de-identified via a HIPAA-compliant procedure by NYU Langone Health), holding back the fully-sampled data from 894 of these scans for challenge evaluation purposes. In contrast to the 2019 challenge, we focused our radiologist evaluations on pathological assessment in brain images. We also debuted a new Transfer track that required participants to submit models evaluated on MRI scanners from outside the training set. We received 19 submissions from eight different groups. Results showed one team scoring best in both SSIM scores and qualitative radiologist evaluations. We also performed analysis on alternative metrics to mitigate the effects of background noise and collected feedback from the participants to inform future challenges. Lastly, we identify common failure modes across the submissions, highlighting areas of need for future research in the MRI reconstruction community.

Minimum TR radiofrequency-pulse design for rapid gradient echo sequences

PURPOSE

A framework to design radiofrequency (RF) pulses specifically to minimize the TR of gradient echo sequences is presented, subject to hardware and physiological constraints.

METHODS

Single-band and multiband (MB) RF pulses can be reduced in duration using variable-rate selective excitation (VERSE) VERSE for a range of flip angles; however, minimum-duration pulses do not guarantee minimum TR because these can lead to a high specific absorption rate (SAR). The optimal RF pulse is found by meeting spatial encoding, peripheral nerve stimulation (PNS) and SAR constraints. A TR reduction for a range of designs is achieved and an application of this in an MB cardiac balanced steady-state free-precession (bSSFP) experiment is presented. Gradient imperfections and their imaging effects are also considered.

RESULTS

Sequence TR with low-time bandwidth product (TBP) pulses, as used in bSSFP, was reduced up to 14%, and the TR when using high TBP pulses, as used in slab-selective imaging, was reduced by up to 72%. A breath-hold cardiac exam was reduced by 46% using both MB and the TR-optimal framework. The importance of RF-based correction of gradient imperfections is demonstrated. PNS was not a practical limitation.

CONCLUSION

The TR-optimal framework designs RF pulses for a range of pulse parameters, specifically to minimize sequence TR.

Application of Evolution Strategies to the Design of SAR Efficient Parallel Transmit Multi-Spoke Pulses for Ultra-High Field MRI

We present an evolution-strategy based approach to solve the magnitude least squares (MLS) design problem of low flip-angle slice-selective parallel transmit RF pulses for ultra-high field MRI using SAR and peak-RF-constraints. A combined transmit k-space trajectory and RF pulse weight optimization is proposed in two algorithmic steps. The first step is a coarse grid search to find an initial solution that fulfills all constraints for the subsequent multistage optimization. This avoids convergence to the next nearest local minimum. The second step attempts to refine the results using multiple evolution strategies. We compare the performance of our approach with the non-convex optimization methods described in the literature. The proposed algorithm converges for phantom and in vivo data and only requires an initial estimate of the range of suitable regularization parameters. It demonstrates improved excitation homogeneity compared to published spoke-design methods and allows optimization for homogeneity with a subsequent reduction in the SAR burden. Moreover, excitation homogeneity and the SAR burden can be balanced against each other, enabling a further reduction in SAR at the cost of minor relaxations in excitation homogeneity. This feature makes the algorithm a good candidate for SAR limited sequences in ultra-high field imaging. The algorithm is validated using phantom and in vivo measurements obtained with a 16-channel transmit array at 9.4T.

Advancing machine learning for MR image reconstruction with an open competition: Overview of the 2019 fastMRI challenge

PURPOSE

To advance research in the field of machine learning for MR image reconstruction with an open challenge.

METHODS

We provided participants with a dataset of raw k-space data from 1,594 consecutive clinical exams of the knee. The goal of the challenge was to reconstruct images from these data. In order to strike a balance between realistic data and a shallow learning curve for those not already familiar with MR image reconstruction, we ran multiple tracks for multi-coil and single-coil data. We performed a two-stage evaluation based on quantitative image metrics followed by evaluation by a panel of radiologists. The challenge ran from June to December of 2019.

RESULTS

We received a total of 33 challenge submissions. All participants chose to submit results from supervised machine learning approaches.

CONCLUSIONS

The challenge led to new developments in machine learning for image reconstruction, provided insight into the current state of the art in the field, and highlighted remaining hurdles for clinical adoption.

Accelerated spin-echo functional MRI using multisection excitation by simultaneous spin-echo interleaving (MESSI) with complex-encoded generalized slice dithered enhanced resolution (cgSlider) simultaneous multislice echo-planar imaging

PURPOSE

Spin-echo functional MRI (SE-fMRI) has the potential to improve spatial specificity when compared with gradient-echo fMRI. However, high spatiotemporal resolution SE-fMRI with large slice-coverage is challenging as SE-fMRI requires a long echo time to generate blood oxygenation level-dependent (BOLD) contrast, leading to long repetition times. The aim of this work is to develop an acquisition method that enhances the slice-coverage of SE-fMRI at high spatiotemporal resolution.

THEORY AND METHODS

An acquisition scheme was developed entitled multisection excitation by simultaneous spin-echo interleaving (MESSI) with complex-encoded generalized slice dithered enhanced resolution (cgSlider). MESSI uses the dead-time during the long echo time by interleaving the excitation and readout of 2 slices to enable 2× slice-acceleration, while cgSlider uses the stable temporal background phase in SE-fMRI to encode/decode 2 adjacent slices simultaneously with a "phase-constrained" reconstruction method. The proposed cgSlider-MESSI was also combined with simultaneous multislice (SMS) to achieve further slice-acceleration. This combined approach was used to achieve 1.5-mm isotropic whole-brain SE-fMRI with a temporal resolution of 1.5 s and was evaluated using sensory stimulation and breath-hold tasks at 3T.

RESULTS

Compared with conventional SE-SMS, cgSlider-MESSI-SMS provides 4-fold increase in slice-coverage for the same repetition time, with comparable temporal signal-to-noise ratio. Corresponding fMRI activation from cgSlider-MESSI-SMS for both fMRI tasks were consistent with those from conventional SE-SMS. Overall, cgSlider-MESSI-SMS achieved a 32× encoding-acceleration by combining Rinplane × MB × cgSlider × MESSI = 4 × 2 × 2 × 2.

CONCLUSION

High-quality, high-resolution whole-brain SE-fMRI was acquired at a short repetition time using cgSlider-MESSI-SMS. This method should be beneficial for high spatiotemporal resolution SE-fMRI studies requiring whole-brain coverage.

Specific absorption rate implications of within-scan patient head motion for ultra-high field MRI

PURPOSE

This study investigates the implications of all degrees of freedom of within-scan patient head motion on patient safety.

METHODS

Electromagnetic simulations were performed by displacing and/or rotating a virtual body model inside an 8-channel transmit array to simulate 6 degrees of freedom of motion. Rotations of up to 20° and displacements of up to 20 mm including off-axis axial/coronal translations were investigated, yielding 104 head positions. Quadrature excitation, RF shimming, and multi-spoke parallel-transmit excitation pulses were designed for axial slice-selection at 7T, for seven slices across the head. Variation of whole-head specific absorption rate (SAR) and 10-g averaged local SAR of the designed pulses, as well as the change in the maximum eigenvalue (worst-case pulse) were investigated by comparing off-center positions to the central position.

RESULTS

In their respective worst-cases, patient motion increased the eigenvalue-based local SAR by 42%, whole-head SAR by 60%, and the 10-g averaged local SAR by 210%. Local SAR was observed to be more sensitive to displacements along right-left and anterior-posterior directions than displacement in the superior-inferior direction and rotation.

CONCLUSION

This is the first study to investigate the effect of all 6 degrees of freedom of motion on safety of practical pulses. Although the results agree with the literature for overlapping cases, the results demonstrate higher increases (up to 3.1-fold) in local SAR for off-axis displacement in the axial plane, which had received less attention in the literature. This increase in local SAR could potentially affect the local SAR compliance of subjects, unless realistic within-scan patient motion is taken into account during pulse design.

Time optimal control-based RF pulse design under gradient imperfections

Purpose

This study incorporates a gradient system imperfection model into an optimal control framework for radio frequency (RF) pulse design.

Theory and Methods

The joint design of minimum‐time RF and slice selective gradient shapes is posed as an optimal control problem. Hardware limitations such as maximal amplitudes for RF and slice selective gradient or its slew rate are included as hard constraints to assure practical applicability of the optimized waveforms. In order to guarantee the performance of the optimized waveform with possible gradient system disturbances such as limited system bandwidth and eddy currents, a measured gradient impulse response function (GIRF) for a specific system is integrated into the optimization.

Results

The method generates optimized RF and pre‐distorted slice selective gradient shapes for refocusing that are able to fully compensate the modeled imperfections of the gradient system under investigation. The results nearly regenerate the optimal results of an idealized gradient system. The numerical Bloch simulations are validated by phantom and in‐vivo experiments on 2 3T scanners.

Conclusions

The presented design approach demonstrates the successful correction of gradient system imperfections within an optimal control framework for RF pulse design.

Parallel Transmission for Ultrahigh Field MRI

Magnetic resonance imaging (MRI) has been driven toward ultrahigh magnetic fields (UHF) in order to benefit from correspondingly higher signal-to-noise ratio and spectral resolution. Technological challenges associated with UHF, such as increased radiofrequency (RF) energy deposition and RF excitation inhomogeneity, limit realization of the full potential of these benefits. Parallel RF transmission (pTx) enables decreases in the inhomogeneity of RF excitations and in RF energy deposition by using multiple-transmit RF coils driven independently and operating simultaneously. pTx plays a fundamental role in UHF MRI by bringing the potential applications of UHF into reality. In this review article, we review the recent developments in pTx pulse design and RF safety in pTx. Simultaneous multislice imaging and inner volume imaging using pTx are reviewed with a focus on UHF applications. Emerging pTx design approaches using improved pTx design frameworks and calibrations are reviewed together with calibration-free approaches that remove the necessity of time-consuming calibrations necessary for successful pTx. Lastly, we focus on the safety of pTx that is improved by using intersubject variability analysis, proactively managing pTx and temperature-based pTx approaches.

Multiband RF pulse design for realistic gradient performance

PURPOSE

Simultaneous multi-slice techniques are reliant on multiband RF pulses, for which conventional design strategies result in long pulse durations, lengthening echo-times so lowering SNR for spin-echo imaging, and lengthening repetition times for gradient echo sequences. Pulse durations can be reduced with advanced RF pulse design methods that use time-variable selection gradients. However, the ability of gradient systems to reproduce fast switching pulses is often limited and can lead to image artifacts when ignored. We propose a time-efficient pulse design method that inherently produces gradient waveforms with lower temporal bandwidth.

METHODS

Efficient multiband RF pulses with time-variable gradients were designed using time-optimal VERSE. Using VERSE directly on multiband pulses leads to gradient waveforms with high temporal bandwidth, whereas VERSE applied first to singleband RF pulses and then modulated to make them multiband, significantly reduces this. The relative performance of these approaches was compared using simulation and experimental measurements.

RESULTS

Applying VERSE before multiband modulation was successful at removing out-of-band slice distortion. This effectively removes the need for high frequency modulation in the gradient waveform while preserving the benefit of time-efficiency inherited from VERSE.

CONCLUSION

We propose a time-efficient RF pulse design that produces gradient pulses with lower temporal bandwidth, reducing image artifacts associated with finite temporal bandwidth of gradient systems.

Pulse sequences and parallel imaging for high spatiotemporal resolution MRI at ultra-high field

The SNR and CNR benefits of ultra-high field (UHF) have helped push the envelope of achievable spatial resolution in MRI. For applications based on susceptibility contrast where there is a large CNR gain, high quality sub-millimeter resolution imaging is now being routinely performed, particularly in fMRI and phase imaging/QSM. This has enabled the study of structure and function of very fine-scale structures in the brain. UHF has also helped push the spatial resolution of many other MRI applications as will be outlined in this review. However, this push in resolution comes at a cost of a large encoding burden leading to very lengthy scans. Developments in parallel imaging with controlled aliasing and the move away from 2D slice-by-slice imaging to much more SNR-efficient simultaneous multi-slice (SMS) and 3D acquisitions have helped address this issue. In particular, these developments have revolutionized the efficiency of UHF MRI to enable high spatiotemporal resolution imaging at an order of magnitude faster acquisition. In addition to describing the main approaches to these techniques, this review will also outline important key practical considerations in using these methods in practice. Furthermore, new RF pulse design to tackle the B1+ and SAR issues of UHF and the increased SAR and power requirement of SMS RF pulses will also be touched upon. Finally, an outlook into new developments of smart encoding in more dimensions, particularly through using better temporal/across-contrast encoding and reconstruction will be described. Just as controlled aliasing fully exploits spatial encoding in parallel imaging to provide large multiplicative gains in accelerations, the complimentary use of these new approaches in temporal and across-contrast encoding are expected to provide exciting opportunities for further large gains in efficiency to further push the spatiotemporal resolution of MRI.

Magnetic Resonance RF Pulse Design by Optimal Control With Physical Constraints

Optimal control approaches have proved useful in designing RF pulses for large tip-angle applications. A typical challenge for optimal control design is the inclusion of constraints resulting from physiological or technical limitations that assure the realizability of the optimized pulses. In this paper, we show how to treat such inequality constraints, in particular, amplitude constraints on the B1 field, the slice-selective gradient, and its slew rate, as well as constraints on the slice profile accuracy. For the latter, a pointwise profile error and additional phase constraints are prescribed. Here, a penalization method is introduced that corresponds to a higher order tracking instead of the common quadratic tracking. The order is driven to infinity in the course of the optimization. We jointly optimize for the RF and slice-selective gradient waveform. The amplitude constraints on these control variables are treated efficiently by semismooth Newton or quasi-Newton methods. The method is flexible, adapting to many optimization goals. As an application, we reduce the power of refocusing pulses, which is important for spin echo-based applications with a short echo spacing. Here, the optimization method is tested in numerical experiments for reducing the pulse power of simultaneous multislice refocusing pulses. The results are validated by phantom and in-vivo experiments.