A subspace approach to high-resolution spectroscopic imaging

High-Dimensional MR Reconstruction Integrating Subspace and Adaptive Generative Models

OBJECTIVE

To develop a new method that integrates subspace and generative image models for high-dimensional MR image reconstruction.

METHODS

We proposed a formulation that synergizes a low-dimensional subspace model of high-dimensional images, an adaptive generative image prior serving as spatial constraints on the sequence of "contrast-weighted" images or spatial coefficients of the subspace model, and a conventional sparsity regularization. A special pretraining plus subject-specific network adaptation strategy was proposed to construct an accurate generative-network-based representation for images with varying contrasts. An iterative algorithm was introduced to jointly update the subspace coefficients and the multi-resolution latent space of the generative image model that leveraged an recently proposed intermediate layer optimization technique for network inversion.

RESULTS

We evaluated the utility of the proposed method for two high-dimensional imaging applications: accelerated MR parameter mapping and high-resolution MR spectroscopic imaging. Improved performance over state-of-the-art subspace-based methods was demonstrated in both cases.

CONCLUSION

The proposed method provided a new way to address high-dimensional MR image reconstruction problems by incorporating an adaptive generative model as a data-driven spatial prior for constraining subspace reconstruction.

SIGNIFICANCE

Our work demonstrated the potential of integrating data-driven and adaptive generative priors with canonical low-dimensional modeling for high-dimensional imaging problems.

Zero-DeepSub: Zero-shot deep subspace reconstruction for rapid multiparametric quantitative MRI using 3D-QALAS

PURPOSE

To develop and evaluate methods for (1) reconstructing 3D-quantification using an interleaved Look-Locker acquisition sequence with T2 preparation pulse (3D-QALAS) time-series images using a low-rank subspace method, which enables accurate and rapid T1 and T2 mapping, and (2) improving the fidelity of subspace QALAS by combining scan-specific deep-learning-based reconstruction and subspace modeling.

THEORY AND METHODS

A low-rank subspace method for 3D-QALAS (i.e., subspace QALAS) and zero-shot deep-learning subspace method (i.e., Zero-DeepSub) were proposed for rapid and high fidelity T1 and T2 mapping and time-resolved imaging using 3D-QALAS. Using an ISMRM/NIST system phantom, the accuracy and reproducibility of the T1 and T2 maps estimated using the proposed methods were evaluated by comparing them with reference techniques. The reconstruction performance of the proposed subspace QALAS using Zero-DeepSub was evaluated in vivo and compared with conventional QALAS at high reduction factors of up to nine-fold.

RESULTS

Phantom experiments showed that subspace QALAS had good linearity with respect to the reference methods while reducing biases and improving precision compared to conventional QALAS, especially for T2 maps. Moreover, in vivo results demonstrated that subspace QALAS had better g-factor maps and could reduce voxel blurring, noise, and artifacts compared to conventional QALAS and showed robust performance at up to nine-fold acceleration with Zero-DeepSub, which enabled whole-brain T1, T2, and PD mapping at 1 mm isotropic resolution within 2 min of scan time.

CONCLUSION

The proposed subspace QALAS along with Zero-DeepSub enabled high fidelity and rapid whole-brain multiparametric quantification and time-resolved imaging.

Romer-EPTI: rotating-view motion-robust super-resolution EPTI for SNR-efficient distortion-free in-vivo mesoscale dMRI and microstructure imaging

Purpose

To overcome the major challenges in dMRI acquisition, including low SNR, distortion/blurring, and motion vulnerability.

Methods

A novel Romer-EPTI technique is developed to provide distortion-free dMRI with significant SNR gain, high motion-robustness, sharp spatial resolution, and simultaneous multi-TE imaging. It introduces a ROtating-view Motion-robust supEr-Resolution technique (Romer) combined with a distortion/blurring-free EPTI encoding. Romer enhances SNR by a simultaneous multi-thick-slice acquisition with rotating-view encoding, while providing high motion-robustness through a motion-aware super-resolution reconstruction, which also incorporates slice-profile and real-value diffusion, to resolve high-isotropic-resolution volumes. The in-plane encoding is performed using distortion/blurring-free EPTI, which further improves effective spatial resolution and motion robustness by preventing not only T2/T2*-blurring but also additional blurring resulting from combining encoded volumes with inconsistent geometries caused by dynamic distortions. Self-navigation was incorporated to enable efficient phase correction. Additional developments include strategies to address slab-boundary artifacts, achieve minimal TE for SNR gain at 7T, and achieve high robustness to strong phase variations at high b-values.

Results

Using Romer-EPTI, we demonstrate distortion-free whole-brain mesoscale in-vivo dMRI at both 3T (500-μm-iso) and 7T (485-μm-iso) for the first time, with high SNR efficiency (e.g., 25 × ), and high image quality free from distortion and slab-boundary artifacts with minimal blurring. Motion experiments demonstrate Romer-EPTI's high motion-robustness and ability to recover sharp images in the presence of motion. Romer-EPTI also demonstrates significant SNR gain and robustness in high b-value (b=5000s/mm2) and time-dependent dMRI.

Conclusion

Romer-EPTI significantly improves SNR, motion-robustness, and image quality, providing a highly efficient acquisition for high-resolution dMRI and microstructure imaging.

Simultaneous high-resolution whole-brain MR spectroscopy and [18F]FDG PET for temporal lobe epilepsy

PURPOSE

Precise lateralizing the epileptogenic zone in patients with drug-resistant mesial temporal lobe epilepsy (mTLE) remains challenging, particularly when routine MRI scans are inconclusive (MRI-negative). This study aimed to investigate the synergy of fast, high-resolution, whole-brain MRSI in conjunction with simultaneous [18F]FDG PET for the lateralization of mTLE.

METHODS

Forty-eight drug-resistant mTLE patients (M/F 31/17, age 12-58) underwent MRSI and [18F]FDG PET on a hybrid PET/MR scanner. Lateralization of mTLE was evaluated by visual inspection and statistical classifiers of metabolic mappings against routine MRI. Additionally, this study explored how disease status influences the associations between altered N-acetyl aspartate (NAA) and FDG uptake using hierarchical moderated multiple regression.

RESULTS

The high-resolution whole-brain MRSI data offers metabolite maps at comparable resolution to [18F]FDG PET. Visual examinations of combined MRSI and [18F]FDG PET showed an mTLE lateralization accuracy rate of 91.7% in a 48-patient cohort, surpassing routine MRI (52.1%). Notably, out of 23 MRI-negative mTLE, combined MRSI and [18F]FDG PET helped detect 19 cases. Logistical regression models combining hippocampal NAA level and FDG uptake improved lateralization performance (AUC=0.856), while further incorporating extrahippocampal regions such as amygdala, thalamus, and superior temporal gyrus increased the AUC to 0.939. Concurrent MRSI/PET revealed a moderating influence of disease duration and hippocampal atrophy on the association between hippocampal NAA and glucose uptake, providing significant new insights into the disease's trajectory.

CONCLUSION

This paper reports the first metabolic imaging study using simultaneous high-resolution MRSI and [18F]FDG PET, which help visualize MRI-unidentifiable lesions and may thus advance diagnostic tools and management strategies for drug-resistant mTLE.

Single-shot Echo Planar Time-resolved Imaging for multi-echo functional MRI and distortion-free diffusion imaging

Purpose

To develop EPTI, a multi-shot distortion-free multi-echo imaging technique, into a single-shot acquisition to achieve improved robustness to motion and physiological noise, increased temporal resolution, and high SNR efficiency for dynamic imaging applications.

Methods

A new spatiotemporal encoding was developed to achieve single-shot EPTI by enhancing spatiotemporal correlation in k-t space. The proposed single-shot encoding improves reconstruction conditioning and sampling efficiency, with additional optimization under various accelerations to achieve optimized performance. To achieve high SNR efficiency, continuous readout with minimized deadtime was employed that begins immediately after excitation and extends for an SNR-optimized length. Moreover, k-t partial Fourier and simultaneous multi-slice acquisition were integrated to further accelerate the acquisition and achieve high spatial and temporal resolution.

Results

We demonstrated that ss-EPTI achieves higher tSNR efficiency than multi-shot EPTI, and provides distortion-free imaging with densely-sampled multi-echo images at resolutions ~1.25-3 mm at 3T and 7T-with high SNR efficiency and with comparable temporal resolutions to ss-EPI. The ability of ss-EPTI to eliminate dynamic distortions common in EPI also further improves temporal stability. For fMRI, ss-EPTI also provides early-TE images (e.g., 2.9ms) to recover signal-intensity and functional-sensitivity dropout in challenging regions. The multi-echo images provide TE-dependent information about functional fluctuations, successfully distinguishing noise-components from BOLD signals and further improving tSNR. For diffusion MRI, ss-EPTI provides high-quality distortion-free diffusion images and multi-echo diffusion metrics.

Conclusion

ss-EPTI provides distortion-free imaging with high image quality, rich multi-echo information, and enhanced efficiency within comparable temporal resolution to ss-EPI, offering a robust and efficient acquisition for dynamic imaging.

Subspace Model-Assisted Deep Learning for Improved Image Reconstruction

Image reconstruction from limited and/or sparse data is known to be an ill-posed problem and a priori information/constraints have played an important role in solving the problem. Early constrained image reconstruction methods utilize image priors based on general image properties such as sparsity, low-rank structures, spatial support bound, etc. Recent deep learning-based reconstruction methods promise to produce even higher quality reconstructions by utilizing more specific image priors learned from training data. However, learning high-dimensional image priors requires huge amounts of training data that are currently not available in medical imaging applications. As a result, deep learning-based reconstructions often suffer from two known practical issues: a) sensitivity to data perturbations (e.g., changes in data sampling scheme), and b) limited generalization capability (e.g., biased reconstruction of lesions). This paper proposes a new method to address these issues. The proposed method synergistically integrates model-based and data-driven learning in three key components. The first component uses the linear vector space framework to capture global dependence of image features; the second exploits a deep network to learn the mapping from a linear vector space to a nonlinear manifold; the third is an unrolling-based deep network that captures local residual features with the aid of a sparsity model. The proposed method has been evaluated with magnetic resonance imaging data, demonstrating improved reconstruction in the presence of data perturbation and/or novel image features. The method may enhance the practical utility of deep learning-based image reconstruction.

Prediction of Stroke Onset Time With Combined Fast High-Resolution Magnetic Resonance Spectroscopic and Quantitative T2 Mapping

OBJECTIVE

The purpose of this work is to develop a multispectral imaging approach that combines fast high-resolution 3D magnetic resonance spectroscopic imaging (MRSI) and fast quantitative T2 mapping to capture the multifactorial biochemical changes within stroke lesions and evaluate its potentials for stroke onset time prediction.

METHODS

Special imaging sequences combining fast trajectories and sparse sampling were used to obtain whole-brain maps of both neurometabolites (2.0 × 3.0 × 3.0 mm3) and quantitative T2 values (1.9 × 1.9 × 3.0 mm3) within a 9-minute scan. Participants with ischemic stroke at hyperacute (0-24 h, n = 23) or acute (24 h-7d, n = 33) phase were recruited in this study. Lesion N-acetylaspartate (NAA), lactate, choline, creatine, and T2 signals were compared between groups and correlated with patient symptomatic duration. Bayesian regression analyses were employed to compare the predictive models of symptomatic duration using multispectral signals.

RESULTS

In both groups, increased T2 and lactate levels, as well as decreased NAA and choline levels were detected within the lesion (all p < 0.001). Changes in T2, NAA, choline, and creatine signals were correlated with symptomatic duration for all patients (all p < 0.005). Predictive models of stroke onset time combining signals from MRSI and T2 mapping achieved the best performance (hyperacute: R2 = 0.438; all: R2 = 0.548).

CONCLUSION

The proposed multispectral imaging approach provides a combination of biomarkers that index early pathological changes after stroke in a clinical-feasible time and improves the assessment of the duration of cerebral infarction.

SIGNIFICANCE

Developing accurate and efficient neuroimaging techniques to provide sensitive biomarkers for prediction of stroke onset time is of great importance for maximizing the proportion of patients eligible for therapeutic intervention. The proposed method provides a clinically feasible tool for the assessment of symptom onset time post ischemic stroke, which will help guide time-sensitive clinical management.

B1 mapping using pre-learned subspaces for quantitative brain imaging

PURPOSE

To develop a machine learning-based method for estimation of both transmitter and receiver B1 fields desired for correction of the B1 inhomogeneity effects in quantitative brain imaging.

THEORY AND METHODS

A subspace model-based machine learning method was proposed for estimation of B1t and B1r fields. Probabilistic subspace models were used to capture scan-dependent variations in the B1 fields; the subspace basis and coefficient distributions were learned from pre-scanned training data. Estimation of the B1 fields for new experimental data was achieved by solving a linear optimization problem with prior distribution constraints. We evaluated the performance of the proposed method for B1 inhomogeneity correction in quantitative brain imaging scenarios, including T1 and proton density (PD) mapping from variable-flip-angle spoiled gradient-echo (SPGR) data as well as neurometabolic mapping from MRSI data, using phantom, healthy subject and brain tumor patient data.

RESULTS

In both phantom and healthy subject data, the proposed method produced high-quality B1 maps. B1 correction on SPGR data using the estimated B1 maps produced significantly improved T1 and PD maps. In brain tumor patients, the proposed method produced more accurate and robust B1 estimation and correction results than conventional methods. The B1 maps were also applied to MRSI data from tumor patients and produced improved neurometabolite maps, with better separation between pathological and normal tissues.

CONCLUSION

This work presents a novel method to estimate B1 variations using probabilistic subspace models and machine learning. The proposed method may make correction of B1 inhomogeneity effects more robust in practical applications.

Predicting the Onset of Ischemic Stroke With Fast High-Resolution 3D MR Spectroscopic Imaging

BACKGROUND

Neurometabolite concentrations provide a direct index of infarction progression in stroke. However, their relationship with stroke onset time remains unclear.

PURPOSE

To assess the temporal dynamics of N-acetylaspartate (NAA), creatine, choline, and lactate and estimate their value in predicting early (<6 hours) vs. late (6-24 hours) hyperacute stroke groups.

STUDY TYPE

Cross-sectional cohort.

POPULATION

A total of 73 ischemic stroke patients scanned at 1.8-302.5 hours after symptom onset, including 25 patients with follow-up scans.

FIELD STRENGTH/SEQUENCE

A 3 T/magnetization-prepared rapid acquisition gradient echo sequence for anatomical imaging, diffusion-weighted imaging and fluid-attenuated inversion recovery imaging for lesion delineation, and 3D MR spectroscopic imaging (MRSI) for neurometabolic mapping.

ASSESSMENT

Patients were divided into hyperacute (0-24 hours), acute (24 hours to 1 week), and subacute (1-2 weeks) groups, and into early (<6 hours) and late (6-24 hours) hyperacute groups. Bayesian logistic regression was used to compare classification performance between early and late hyperacute groups by using different combinations of neurometabolites as inputs.

STATISTICAL TESTS

Linear mixed effects modeling was applied for group-wise comparisons between NAA, creatine, choline, and lactate. Pearson's correlation analysis was used for neurometabolites vs. time. P < 0.05 was considered statistically significant.

RESULTS

Lesional NAA and creatine were significantly lower in subacute than in acute stroke. The main effects of time were shown on NAA (F = 14.321) and creatine (F = 12.261). NAA was significantly lower in late than early hyperacute patients, and was inversely related to time from symptom onset across both groups (r = -0.440). The decrease of NAA and increase of lactate were correlated with lesion volume (NAA: r = -0.472; lactate: r = 0.366) in hyperacute stroke. Discrimination was improved by combining NAA, creatine, and choline signals (area under the curve [AUC] = 0.90).

DATA CONCLUSION

High-resolution 3D MRSI effectively assessed the neurometabolite changes and discriminated early and late hyperacute stroke lesions.

EVIDENCE LEVEL

1.

TECHNICAL EFFICACY

Stage 2.

SLIPMAT: a pipeline for extracting tissue-specific spectral profiles from 1H MR spectroscopic imaging data

¹H Magnetic Resonance Spectroscopy (MRS) is an important non-invasive tool for measuring brain metabolism, with numerous applications in the neuroscientific and clinical domains. In this work we present a new analysis pipeline (SLIPMAT), designed to extract high-quality, tissue-specific, spectral profiles from MR spectroscopic imaging data (MRSI). Spectral decomposition is combined with spatially dependant frequency and phase correction to yield high SNR white and grey matter spectra without partial-volume contamination. A subsequent series of spectral processing steps are applied to reduce unwanted spectral variation, such as baseline correction and linewidth matching, before direct spectral analysis with machine learning and traditional statistical methods. The method is validated using a 2D semi-LASER MRSI sequence, with a 5-minute duration, from data acquired in triplicate across 8 healthy participants. Reliable spectral profiles are confirmed with principal component analysis, revealing the importance of total-choline and scyllo-inositol levels in distinguishing between individuals - in good agreement with our previous work. Furthermore, since the method allows the simultaneous measurement of metabolites in grey and white matter, we show the strong discriminative value of these metabolites in both tissue types for the first time. In conclusion, we present a novel and time efficient MRSI acquisition and processing pipeline, capable of detecting reliable neuro-metabolic differences between healthy individuals, and suitable for the sensitive neurometabolic profiling of in-vivo brain tissue.

Deuterium echo-planar spectroscopic imaging (EPSI) in the human liver in vivo at 7 T

PURPOSE

To demonstrate the feasibility of deuterium echo-planar spectroscopic imaging (EPSI) to accelerate 3D deuterium metabolic imaging in the human liver at 7 T.

METHODS

A deuterium EPSI sequence, featuring a Hamming-weighted k-space acquisition pattern for the phase-encoding directions, was implemented. Three-dimensional deuterium EPSI and conventional MRSI were performed on a water/acetone phantom and in vivo in the human liver at natural abundance. Moreover, in vivo deuterium EPSI measurements were acquired after oral administration of deuterated glucose. The effect of acquisition time on SNR was evaluated by retrospectively reducing the number of averages.

RESULTS

The SNR of natural abundance deuterated water signal in deuterium EPSI was 6.5% and 5.9% lower than that of MRSI in the phantom and in vivo experiments, respectively. In return, the acquisition time of in vivo EPSI data could be reduced retrospectively to 2 min, beyond the minimal acquisition time of conventional MRSI (of 20 min in this case), while still leaving sufficient SNR. Three-dimensional deuterium EPSI, after administration of deuterated glucose, enabled monitoring of hepatic glucose dynamics with full liver coverage, a spatial resolution of 20 mm isotropic, and a temporal resolution of 9 min 50 s, which could retrospectively be shortened to 2 min.

CONCLUSION

In this work, we demonstrate the feasibility of accelerated 3D deuterium metabolic imaging of the human liver using deuterium EPSI. The acceleration obtained with EPSI can be used to increase temporal and/or spatial resolution, which will be valuable to study tissue metabolism of deuterated compounds over time.

A fast MR fingerprinting simulator for direct error estimation and sequence optimization

Magnetic resonance fingerprinting (MRF) is a novel quantitative MR technique that simultaneously provides multiple tissue property maps. When optimizing MRF scans, modeling undersampling errors and field imperfections in cost functions for direct measurement of quantitative errors will make the optimization results more practical and robust. However, optimizing such cost function is computationally expensive and impractical for MRF optimization with tens of thousands of iterations. Here, we introduce a fast MRF simulator to simulate aliased images from actual scan scenarios including undersampling and system imperfections, which substantially reduces computational time and allows for direct error estimation of the quantitative maps and efficient sequence optimization. We evaluate the performance and computational speed of the proposed approach by simulations and in vivo experiments. The simulations from the proposed method closely approximate the signals and MRF maps from in vivo scans, with 158 times shorter processing time than the conventional simulation method using Non-uniform Fourier transform. We also demonstrate the power of applying the fast MRF simulator in MRF sequence optimization. The optimized sequences are validated with in vivo scans to assess the image quality and accuracy. The optimized sequences produce artifact-free T1 and T2 maps in 2D and 3D scans with equivalent mapping accuracy as the human-designed sequence but at shorter scan times. Incorporating the proposed simulator in the MRF optimization framework makes direct estimation of undersampling errors during the optimization process feasible, and provide optimized MRF sequences that are robust against undersampling artifacts and field inhomogeneity.

Joint spectral quantification of MR spectroscopic imaging using linear tangent space alignment-based manifold learning

PURPOSE

To develop a manifold learning-based method that leverages the intrinsic low-dimensional structure of MR Spectroscopic Imaging (MRSI) signals for joint spectral quantification.

METHODS

A linear tangent space alignment (LTSA) model was proposed to represent MRSI signals. In the proposed model, the signals of each metabolite were represented using a subspace model and the local coordinates of the subspaces were aligned to the global coordinates of the underlying low-dimensional manifold via linear transform. With the basis functions of the subspaces predetermined via quantum mechanics simulations, the global coordinates and the matrices for the local-to-global coordinate alignment were estimated by fitting the proposed LTSA model to noisy MRSI data with a spatial smoothness constraint on the global coordinates and a sparsity constraint on the matrices.

RESULTS

The performance of the proposed method was validated using numerical simulation data and in vivo proton-MRSI experimental data acquired on healthy volunteers at 3T. The results of the proposed method were compared with the QUEST method and the subspace-based method. In all the compared cases, the proposed method achieved superior performance over the QUEST and the subspace-based methods both qualitatively in terms of noise and artifacts in the estimated metabolite concentration maps, and quantitatively in terms of spectral quantification accuracy measured by normalized root mean square errors.

CONCLUSION

Joint spectral quantification using linear tangent space alignment-based manifold learning improves the accuracy of MRSI spectral quantification.

High-Dimensional MR Spatiospectral Imaging by Integrating Physics-Based Modeling and Data-Driven Machine Learning: Current progress and future directions

Magnetic resonance spectroscopic imaging (MRSI) offers a unique molecular window into the physiological and pathological processes in the human body. However, the applications of MRSI have been limited by a number of long-standing technical challenges due to high dimensionality and low signal-to-noise ratio (SNR). Recent technological developments integrating physics-based modeling and data-driven machine learning that exploit unique physical and mathematical properties of MRSI signals have demonstrated impressive performance in addressing these challenges for rapid, high-resolution, quantitative MRSI. This paper provides a systematic review of these progresses in the context of MRSI physics and offers perspectives on promising future directions.

Calibrationless reconstruction of uniformly‐undersampled multi‐channel MR data with deep learning estimated ESPIRiT maps

PURPOSE

To develop a truly calibrationless reconstruction method that derives An Eigenvalue Approach to Autocalibrating Parallel MRI (ESPIRiT) maps from uniformly-undersampled multi-channel MR data by deep learning.

METHODS

ESPIRiT, one commonly used parallel imaging reconstruction technique, forms the images from undersampled MR k-space data using ESPIRiT maps that effectively represents coil sensitivity information. Accurate ESPIRiT map estimation requires quality coil sensitivity calibration or autocalibration data. We present a U-Net based deep learning model to estimate the multi-channel ESPIRiT maps directly from uniformly-undersampled multi-channel multi-slice MR data. The model is trained using fully-sampled multi-slice axial brain datasets from the same MR receiving coil system. To utilize subject-coil geometric parameters available for each dataset, the training imposes a hybrid loss on ESPIRiT maps at the original locations as well as their corresponding locations within the standard reference multi-slice axial stack. The performance of the approach was evaluated using publicly available T1-weighed brain and cardiac data.

RESULTS

The proposed model robustly predicted multi-channel ESPIRiT maps from uniformly-undersampled k-space data. They were highly comparable to the reference ESPIRiT maps directly computed from 24 consecutive central k-space lines. Further, they led to excellent ESPIRiT reconstruction performance even at high acceleration, exhibiting a similar level of errors and artifacts to that by using reference ESPIRiT maps.

CONCLUSION

A new deep learning approach is developed to estimate ESPIRiT maps directly from uniformly-undersampled MR data. It presents a general strategy for calibrationless parallel imaging reconstruction through learning from the coil and protocol-specific data.

Manifold Learning via Linear Tangent Space Alignment (LTSA) for Accelerated Dynamic MRI With Sparse Sampling

The spatial resolution and temporal frame-rate of dynamic magnetic resonance imaging (MRI) can be improved by reconstructing images from sparsely sampled k -space data with mathematical modeling of the underlying spatiotemporal signals. These models include sparsity models, linear subspace models, and non-linear manifold models. This work presents a novel linear tangent space alignment (LTSA) model-based framework that exploits the intrinsic low-dimensional manifold structure of dynamic images for accelerated dynamic MRI. The performance of the proposed method was evaluated and compared to state-of-the-art methods using numerical simulation studies as well as 2D and 3D in vivo cardiac imaging experiments. The proposed method achieved the best performance in image reconstruction among all the compared methods. The proposed method could prove useful for accelerating many MRI applications, including dynamic MRI, multi-parametric MRI, and MR spectroscopic imaging.

Emerging MRI techniques for molecular and functional phenotyping of the diseased heart

Recent advances in cardiac MRI (CMR) capabilities have truly transformed its potential for deep phenotyping of the diseased heart. Long known for its unparalleled soft tissue contrast and excellent depiction of three-dimensional (3D) structure, CMR now boasts a range of unique capabilities for probing disease at the tissue and molecular level. We can look beyond coronary vessel blockages and detect vessel disease not visible on a structural level. We can assess if early fibrotic tissue is being laid down in between viable cardiac muscle cells. We can measure deformation of the heart wall to determine early presentation of stiffening. We can even assess how cardiomyocytes are utilizing energy, where abnormalities are often precursors to overt structural and functional deficits. Finally, with artificial intelligence gaining traction due to the high computing power available today, deep learning has proven itself a viable contender with traditional acceleration techniques for real-time CMR. In this review, we will survey five key emerging MRI techniques that have the potential to transform the CMR clinic and permit early detection and intervention. The emerging areas are: (1) imaging microvascular dysfunction, (2) imaging fibrosis, (3) imaging strain, (4) imaging early metabolic changes, and (5) deep learning for acceleration. Through a concerted effort to develop and translate these areas into the CMR clinic, we are committing ourselves to actualizing early diagnostics for the most intractable heart disease phenotypes.

Dynamic Imaging Using Deep Bi-Linear Unsupervised Representation (DEBLUR)

Bilinear models such as low-rank and dictionary methods, which decompose dynamic data to spatial and temporal factor matrices are powerful and memory-efficient tools for the recovery of dynamic MRI data. Current bilinear methods rely on sparsity and energy compaction priors on the factor matrices to regularize the recovery. Motivated by deep image prior, we introduce a novel bilinear model, whose factor matrices are generated using convolutional neural networks (CNNs). The CNN parameters, and equivalently the factors, are learned from the undersampled data of the specific subject. Unlike current unrolled deep learning methods that require the storage of all the time frames in the dataset, the proposed approach only requires the storage of the factors or compressed representation; this approach allows the direct use of this scheme to large-scale dynamic applications, including free breathing cardiac MRI considered in this work. To reduce the run time and to improve performance, we initialize the CNN parameters using existing factor methods. We use sparsity regularization of the network parameters to minimize the overfitting of the network to measurement noise. Our experiments on free-breathing and ungated cardiac cine data acquired using a navigated golden-angle gradient-echo radial sequence show the ability of our method to provide reduced spatial blurring as compared to classical bilinear methods as well as a recent unsupervised deep-learning approach.

Proton metabolic mapping of the brain at 7 T using a two-dimensional free induction decay-echo-planar spectroscopic imaging readout with lipid suppression

The increased signal-to-noise ratio (SNR) and chemical shift dispersion at high magnetic fields (≥7 T) have enabled neuro-metabolic imaging at high spatial resolutions. To avoid very long acquisition times with conventional magnetic resonance spectroscopic imaging (MRSI) phase-encoding schemes, solutions such as pulse-acquire or free induction decay (FID) sequences with short repetition time and inner volume selection methods with acceleration (echo-planar spectroscopic imaging [EPSI]), have been proposed. With the inner volume selection methods, limited spatial coverage of the brain and long echo times may still impede clinical implementation. FID-MRSI sequences benefit from a short echo time and have a high SNR per time unit; however, contamination from strong extra-cranial lipid signals remains a problem that can hinder correct metabolite quantification. L2-regularization can be applied to remove lipid signals in cases with high spatial resolution and accurate prior knowledge. In this work, we developed an accelerated two-dimensional (2D) FID-MRSI sequence using an echo-planar readout and investigated the performance of lipid suppression by L2-regularization, an external crusher coil, and the combination of these two methods to compare the resulting spectral quality in three subjects. The reduction factor of lipid suppression using the crusher coil alone varies from 2 to 7 in the lipid region of the brain boundary. For the combination of the two methods, the average lipid area inside the brain was reduced by 2% to 38% compared with that of unsuppressed lipids, depending on the subject's region of interest. 2D FID-EPSI with external lipid crushing and L2-regularization provides high in-plane coverage and is suitable for investigating brain metabolite distributions at high fields.

Developments in proton MR spectroscopic imaging of prostate cancer

In this paper, we review the developments of 1H-MR spectroscopic imaging (MRSI) methods designed to investigate prostate cancer, covering key aspects such as specific hardware, dedicated pulse sequences for data acquisition and data processing and quantification techniques. Emphasis is given to recent advancements in MRSI methodologies, as well as future developments, which can lead to overcome difficulties associated with commonly employed MRSI approaches applied in clinical routine. This includes the replacement of standard PRESS sequences for volume selection, which we identified as inadequate for clinical applications, by sLASER sequences and implementation of 1H MRSI without water signal suppression. These may enable a new evaluation of the complementary role and significance of MRSI in prostate cancer management.

T 2 ' mapping of the brain from water-unsuppressed 1 H-MRSI and turbo spin-echo data

PURPOSE

To obtain high-quality T 2 ' $$ {\mathrm{T}}_2^{\prime } $$ maps of brain tissues from water-unsuppressed magnetic resonance spectroscopic imaging (MRSI) and turbo spin-echo (TSE) data.

METHODS

T 2 ' $$ {\mathrm{T}}_2^{\prime } $$ mapping can be achieved using T 2 * $$ {\mathrm{T}}_2^{\ast } $$ mapping from water-unsuppressed MRSI data and T 2 $$ {\mathrm{T}}_2 $$ mapping from TSE data. However, T 2 * $$ {\mathrm{T}}_2^{\ast } $$ mapping often suffers from signal dephasing and distortions caused by B 0 $$ {\mathrm{B}}_0 $$ field inhomogeneity; T 2 $$ {\mathrm{T}}_2 $$ measurements may be biased due to system imperfections, especially for T 2 $$ {\mathrm{T}}_2 $$ -weighted image with small number of TEs. In this work, we corrected the B 0 $$ {\mathrm{B}}_0 $$ field inhomogeneity effect on T 2 * $$ {\mathrm{T}}_2^{\ast } $$ mapping using a subspace model-based method, incorporating pre-learned spectral basis functions of the water signals. T 2 $$ {\mathrm{T}}_2 $$ estimation bias was corrected using a TE-adjustment method, which modeled the deviation between measured and reference T 2 $$ {\mathrm{T}}_2 $$ decays as TE shifts.

RESULTS

In vivo experiments were performed to evaluate the performance of the proposed method. High-quality T 2 * $$ {\mathrm{T}}_2^{\ast } $$ maps were obtained in the presence of large field inhomogeneity in the prefrontal cortex. Bias in T 2 $$ {\mathrm{T}}_2 $$ measurements obtained from TSE data was effectively reduced. Based on the T 2 * $$ {\mathrm{T}}_2^{\ast } $$ and T 2 $$ {\mathrm{T}}_2 $$ measurements produced by the proposed method, high-quality T 2 ' $$ {\mathrm{T}}_2^{\prime } $$ maps were obtained, along with neurometabolite maps, from MRSI and TSE data that were acquired in about 9 min. The results obtained from acute stroke and glioma patients demonstrated the feasibility of the proposed method in the clinical setting.

CONCLUSIONS

High-quality T 2 ' $$ {\mathrm{T}}_2^{\prime } $$ maps can be obtained from water-unsuppressed ¹ H-MRSI and TSE data using the proposed method. With further development, this method may lay a foundation for simultaneously imaging oxygenation and neurometabolic alterations of brain disorders.

Single projection driven real-time multi-contrast (SPIDERM) MR imaging using pre-learned spatial subspace and linear transformation

Objective. To develop and test the feasibility of a novel Single ProjectIon DrivEn Real-time Multi-contrast (SPIDERM) MR imaging technique that can generate real-time 3D images on-the-fly with flexible contrast weightings and a low latency. Approach. In SPIDERM, a ‘prep’ scan is first performed, with sparse k-space sampling periodically interleaved with the central k-space line (navigator data), to learn a subject-specific model, incorporating a spatial subspace and a linear transformation between navigator data and subspace coordinates. A ‘live’ scan is then performed by repeatedly acquiring the central k-space line only to dynamically determine subspace coordinates. With the ‘prep’-learned subspace and ‘live’ coordinates, real-time 3D images are generated on-the-fly with computationally efficient matrix multiplication. When implemented based on a multi-contrast pulse sequence, SPIDERM further allows for data-driven image contrast regeneration to convert real-time contrast-varying images into contrast-frozen images at user’s discretion while maintaining motion states. Both digital phantom and in-vivo experiments were performed to evaluate the technical feasibility of SPIDERM. Main results. The elapsed time from the input of the central k-space line to the generation of real-time contrast-frozen 3D images was approximately 45 ms, permitting a latency of 55 ms or less. Motion displacement measured from SPIDERM and reference images showed excellent correlation ( R 2 ≥ 0.983 ). Geometric variation from the ground truth in the digital phantom was acceptable as demonstrated by pancreas contour analysis (Dice ≥ 0.84, mean surface distance ≤ 0.95 mm). Quantitative image quality metrics showed good consistency between reference images and contrast-varying SPIDREM images in in-vivo studies (mean NMRSE = 0.141 , PSNR = 3 0.12 , SSIM = 0.88 ). Significance. SPIDERM is capable of generating real-time multi-contrast 3D images with a low latency. An imaging framework based on SPIDERM has the potential to serve as a standalone package for MR-guided radiation therapy by offering adaptive simulation through a ‘prep’ scan and real-time image guidance through a ‘live’ scan.

Metabolite-cycled echo-planar spectroscopic imaging of the human heart

Purpose

Spectroscopic imaging could provide insights into regional cardiac triglyceride variations, but is hampered by relatively long scan times. It is proposed to synergistically combine echo‐planar spectroscopic imaging (EPSI) with motion‐adapted gating, weighted acquisition and metabolite cycling to reduce scan times to less than 10 min while preserving spatial‐spectral quality. The method is compared to single‐voxel measurements and to metabolite‐cycled EPSI with conventional acquisition for assessing triglyceride‐to‐water (TG/W) ratios in the human heart.

Methods

Measurements were performed on 10 healthy volunteers using a clinical 1.5T system. EPSI data was acquired both without and with motion‐adapted gating in combination with weighted acquisition to assess TG/W ratios and relative Cramér‐Rao lower bounds (CRLB) of TG. For comparison, single‐voxel (PRESS) spectra were acquired in the interventricular septum.

Results

Bland–Altman analyses did not show a significant bias in TG/W when comparing both metabolite‐cycled EPSI methods to PRESS for any of the cardiac segments. Scan time was 8.05 ± 2.06 min and 17.91 ± 3.93 min for metabolite‐cycled EPSI with and without motion‐adapted gating and weighted acquisition, respectively, while relative CRLB of TG did not differ significantly between the two methods for any of the cardiac segments.

Conclusions

Metabolite‐cycled EPSI with motion‐adapted gating and weighted acquisition allows detecting TG/W ratios in different regions of the in vivo human heart. Scan time is reduced by more than 2‐fold to less than 10 min as compared to conventional acquisition, while keeping the quality of TG fitting constant.

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SNR Enhancement for Multi-TE MRSI Using Joint Low-Dimensional Model and Spatial Constraints

We present a novel method to enhance the SNR for multi-TE MR spectroscopic imaging (MRSI) data by integrating learned nonlinear low-dimensional model and spatial constraints. A deep complex convolutional autoen-coder (DCCAE) was developed to learn a nonlinear low-dimensional representation of the high-dimensional multi-TE 1 H spectroscopy signals. The learned model significantly reduces the data dimension thus serving as an effective constraint for noise reduction. A reconstruction formulation was proposed to integrate the spatiospectral encoding model, the learned model, and a spatial constraint for an SNR-enhancing reconstruction from multi-TE data. The proposed method has been evaluated using both numerical simulations and in vivo brain MRSI experiments. The superior denoising performance of the proposed over alternative methods was demonstrated, both qualitatively and quantitatively. In vivo multi-TE data was used to assess the improved metabolite quantification reproducibility and accuracy achieved by the proposed method. We expect the proposed SNR-enhancing reconstruction to enable faster and/or higher-resolution multi-TE 1 H-MRSI of the brain, potentially useful for various clinical applications.

Epigenetic MRI: Noninvasive imaging of DNA methylation in the brain

Dynamic epigenetic activity is a fundamental mechanism underpinning how the brain changes its function during development and aging and in response to environmental and disease stimuli. We developed a technology called epigenetic MRI (eMRI) that enables noninvasive imaging of DNA methylation in the brain, a major epigenetic mechanism. eMRI reveals strong regional differences in global DNA methylation in pig brains, a model with stronger resemblance to human brains than are rodents. Given the noninvasive nature of eMRI, our results pave the way for a DNA-methylation imaging paradigm for living human brains. We expect eMRI to enable many studies to unravel the molecular control of brain function and disease.

Both neuronal and genetic mechanisms regulate brain function. While there are excellent methods to study neuronal activity in vivo, there are no nondestructive methods to measure global gene expression in living brains. Here, we present a method, epigenetic MRI (eMRI), that overcomes this limitation via direct imaging of DNA methylation, a major gene-expression regulator. eMRI exploits the methionine metabolic pathways for DNA methylation to label genomic DNA through ¹³C-enriched diets. A ¹³C magnetic resonance spectroscopic imaging method then maps the spatial distribution of labeled DNA. We validated eMRI using pigs, whose brains have stronger similarity to humans in volume and anatomy than rodents, and confirmed efficient ¹³C-labeling of brain DNA. We also discovered strong regional differences in global DNA methylation. Just as functional MRI measurements of regional neuronal activity have had a transformational effect on neuroscience, we expect that the eMRI signal, both as a measure of regional epigenetic activity and as a possible surrogate for regional gene expression, will enable many new investigations of human brain function, behavior, and disease.

Sensitivity schemes for dynamic glucose-enhanced magnetic resonance imaging to detect glucose uptake and clearance in mouse brain at 3 T

We investigated three dynamic glucose-enhanced (DGE) MRI methods for sensitively monitoring glucose uptake and clearance in both brain parenchyma and cerebrospinal fluid (CSF) at clinical field strength (3 T). By comparing three sequences, namely, Carr-Purcell-Meiboom-Gill (CPMG), on-resonance variable delay multipulse (onVDMP), and on-resonance spin-lock (onSL), a high-sensitivity DGE MRI scheme with truncated multilinear singular value decomposition (MLSVD) denoising was proposed. The CPMG method showed the highest sensitivity in detecting the parenchymal DGE signal among the three methods, while both onVDMP and onSL were more robust for CSF DGE imaging. Here, onVDMP was applied for CSF imaging, as it displayed the best stability of the DGE results in this study. The truncated MLSVD denoising method was incorporated to further improve the sensitivity. The proposed DGE MRI scheme was examined in mouse brain with 50%/25%/12.5% w/w D-glucose injections. The results showed that this combination could detect DGE signal changes from the brain parenchyma and CSF with as low as a 12.5% w/w D-glucose injection. The proposed DGE MRI schemes could sensitively detect the glucose signal change from brain parenchyma and CSF after D-glucose injection at a clinically relevant concentration, demonstrating high potential for clinical translation.

3D Echo Planar Time-resolved Imaging (3D-EPTI) for ultrafast multi-parametric quantitative MRI

Multi-parametric quantitative MRI has shown great potential to improve the sensitivity and specificity of clinical diagnosis and to enhance our understanding of complex brain processes, but suffers from long scan time especially at high spatial resolution. To address this longstanding challenge, we introduce a novel approach termed 3D Echo Planar Time-resolved Imaging (3D-EPTI), which significantly increases the acceleration capacity of MRI sampling, and provides high acquisition efficiency for multi-parametric MRI. This is achieved by exploiting the spatiotemporal correlation of MRI data at multiple timescales through new encoding strategies within and between efficient continuous readouts. Specifically, an optimized spatiotemporal CAIPI encoding within the readouts combined with a radial-block sampling strategy across the readouts enables an acceleration rate of 800 fold in the k-t space. A subspace reconstruction was employed to resolve thousands of high-quality multi-contrast images. We have demonstrated the ability of 3D-EPTI to provide robust and repeatable whole-brain simultaneous T₁, T₂, T₂*, PD and B₁⁺ mapping at high isotropic resolution within minutes (e.g., 1-mm isotropic resolution in 3 minutes), and to enable submillimeter multi-parametric imaging to study detailed brain structures.

Emerging methods and applications of ultra-high field MR spectroscopic imaging in the human brain

Magnetic Resonance Spectroscopic Imaging (MRSI) of the brain enables insights into the metabolic changes and fluxes in diseases such as tumors, multiple sclerosis, epilepsy, or hepatic encephalopathy, as well as insights into general brain functionality. However, the routine application of MRSI is mostly hampered by very low signal-to-noise ratios (SNR) due to the low concentrations of metabolites, about 10000 times lower than water. Furthermore, MRSI spectra have a dense information content with many overlapping metabolite resonances, especially for proton MRSI. MRI scanners at ultra-high field strengths, like 7 T or above, offer the opportunity to increase SNR, as well as the separation between resonances, thus promising to solve both challenges. Yet, MRSI at ultra-high field strengths is challenged by decreased B0- and B1-homogeneity, shorter T2 relaxation times, stronger chemical shift displacement errors, and aggravated lipid contamination. Therefore, to capitalize on the advantages of ultra-high field strengths, these challenges must be overcome. This review focuses on the challenges MRSI of the human brain faces at ultra-high field strength, as well as the possible applications to this date.

Low-Rank and Framelet Based Sparsity Decomposition for Interventional MRI Reconstruction

OBJECTIVE

Interventional MRI (i-MRI) is crucial for MR image-guided therapy. Current image reconstruction methods for dynamic MR imaging are mostly retrospective that may not be suitable for i-MRI in real-time. Therefore, an algorithm to reconstruct images without a temporal pattern as in dynamic imaging is needed for i-MRI.

METHODS

We proposed a low-rank and sparsity (LS) decomposition algorithm with framelet transform to reconstruct the interventional feature with a high temporal resolution. Different from the existing LS based algorithm, the spatial sparsity of both the low-rank and sparsity components was used. We also used a primal dual fixed point (PDFP) method for optimization of the objective function to avoid solving sub-problems. Intervention experiments with gelatin and brain phantoms were carried out for validation.

RESULTS

The LS decomposition with framelet transform and PDFP could provide the best reconstruction performance compared with those without. Satisfying reconstruction results were obtained with only 10 radial spokes for a temporal resolution of 60 ms.

CONCLUSION AND SIGNIFICANCE

The proposed method has the potential for i-MRI in many different application scenarios.

Mapping an Extended Metabolic Profile of Gliomas Using High-Resolution 31P MRSI at 7T

Phosphorus magnetic resonance spectroscopic imaging (³¹P MRSI) is of particular interest for investigations of patients with brain tumors as it enables to non-invasively assess altered energy and phospholipid metabolism in vivo. However, the limited sensitivity of ³¹P MRSI hampers its broader application at clinical field strengths. This study aimed to identify the additional value of ³¹P MRSI in patients with glioma at ultra-high B₀ = 7T, where the increase in signal-to-noise ratio may foster its applicability for clinical research. High-quality, 3D ³¹P MRSI datasets with an effective voxel size of 5.7 ml were acquired from the brains of seven patients with newly diagnosed glioma. An optimized quantification model was implemented to reliably extract an extended metabolic profile, including low-concentrated metabolites such as extracellular inorganic phosphate, nicotinamide adenine dinucleotide [NAD(H)], and uridine diphosphoglucose (UDPG), which may act as novel tumor markers; a background signal was extracted as well, which affected measures of phosphomonoesters beneficially. Application of this model to the MRSI datasets yielded high-resolution maps of 12 different ³¹P metabolites, showing clear metabolic differences between white matter (WM) and gray matter, and between healthy and tumor tissues. Moreover, differences between tumor compartments in patients with high-grade glioma (HGG), i.e., gadolinium contrast-enhancing/necrotic regions (C+N) and peritumoral edema, could also be suggested from these maps. In the group of patients with HGG, the most significant changes in metabolite intensities were observed in C+N compared to WM, i.e., for phosphocholine +340%, UDPG +54%, glycerophosphoethanolamine −45%, and adenosine-5′-triphosphate −29%. Furthermore, a prominent signal from mobile phospholipids appeared in C+N. In the group of patients with low-grade glioma, only the NAD(H) intensity changed significantly by −28% in the tumor compared to WM. Besides the potential of ³¹P MRSI at 7T to provide novel insights into the biochemistry of gliomas in vivo, the attainable spatial resolutions improve the interpretability of ³¹P metabolite intensities obtained from malignant tissues, particularly when only subtle differences compared to healthy tissues are expected. In conclusion, this pilot study demonstrates that ³¹P MRSI at 7T has potential value for the clinical research of glioma.

Distortion-Free Diffusion Imaging Using Self-Navigated Cartesian Echo-Planar Time Resolved Acquisition and Joint Magnitude and Phase Constrained Reconstruction

Echo-planar time resolved imaging (EPTI) is an effective approach for acquiring high-quality distortion-free images with a multi-shot EPI (ms-EPI) readout. As with traditional ms-EPI acquisitions, inter-shot phase variations present a main challenge when incorporating EPTI into a diffusion-prepared pulse sequence. The aim of this study is to develop a self-navigated Cartesian EPTI-based (scEPTI) acquisition together with a magnitude and phase constrained reconstruction for distortion-free diffusion imaging. A self-navigated Cartesian EPTI-based diffusion-prepared pulse sequence is designed. The different phase components in EPTI diffusion signal are analyzed and an approach to synthesize a fully phase-matched navigator for the inter-shot phase correction is demonstrated. Lastly, EPTI contains richer magnitude and phase information than conventional ms-EPI, such as the magnitude and phase correlations along the temporal dimension. The potential of these magnitude and phase correlations to enhance the reconstruction is explored. The reconstruction results with and without phase matching and with and without phase or magnitude constraints are compared. Compared with reconstruction without phase matching, the proposed phase matching method can improve the accuracy of inter-shot phase correction and reduce signal corruption in the final diffusion images. Magnitude constraints further improve image quality by suppressing the background noise and thereby increasing SNR, while phase constraints can mitigate possible image blurring from adding magnitude constraints. The high-quality distortion-free diffusion images and simultaneous diffusion-relaxometry imaging capacity provided by the proposed EPTI design represent a highly valuable tool for both clinical and neuroscientific assessments of tissue microstructure.

Machine Learning-Enabled High-Resolution Dynamic Deuterium MR Spectroscopic Imaging

Deuterium magnetic resonance spectroscopic imaging (DMRSI) has recently been recognized as a potentially powerful tool for noninvasive imaging of brain energy metabolism and tumor. However, the low sensitivity of DMRSI has significantly limited its utility for both research and clinical applications. This work presents a novel machine learning-based method to address this limitation. The proposed method synergistically integrates physics-based subspace modeling and data-driven deep learning for effective denoising, making high-resolution dynamic DMRSI possible. Specifically, a novel subspace model was used to represent the dynamic DMRSI signals; deep neural networks were trained to capture the low-dimensional manifolds of the spectral and temporal distributions of practical dynamic DMRSI data. The learned subspace and manifold structures were integrated via a regularization formulation to remove measurement noise. Theoretical analysis, computer simulations, and in vivo experiments have been conducted to demonstrate the denoising efficacy of the proposed method which enabled high-resolution imaging capability. The translational potential was demonstrated in tumor-bearing rats, where the Warburg effect associated with cancer metabolism and tumor heterogeneity were successfully captured. The new method may not only provide an effective tool to enhance the sensitivity of DMRSI for basic research and clinical applications but also provide a framework for denoising other spatiospectral data.

Whole-brain steady-state CEST at 3 T using MR Multitasking

PURPOSE

To perform fast 3D steady-state CEST (ss-CEST) imaging using MR Multitasking.

METHODS

A continuous acquisition sequence with repetitive ss-CEST modules was developed. Each ss-CEST module contains a single-lobe Gaussian saturation pulse, followed by a spoiler gradient and eight FLASH readouts (one "training line" + seven "imaging lines"). Three-dimensional Cartesian encoding was used for k-space acquisition. Reconstructed CEST images were quantified with four-pool Lorentzian fitting.

RESULTS

Steady-state CEST with whole-brain coverage was performed in 5.6 s per saturation frequency offset at the spatial resolution of 1.7 × 1.7 × 3.0 mm³ . The total scan time was 5.5 min for 55 different frequency offsets. Quantitative CEST maps from multipool fitting showed consistent image quality across the volume.

CONCLUSION

Three-dimensional ss-CEST with whole-brain coverage can be done at 3 T within 5.5 min using MR Multitasking.

High-resolution, 3D multi-TE 1 H MRSI using fast spatiospectral encoding and subspace imaging

PURPOSE

To develop a novel method to achieve fast, high-resolution, 3D multi-TE ¹ H-MRSI of the brain.

METHODS

A new multi-TE MRSI acquisition strategy was developed that integrates slab selective excitation with adiabatic refocusing for better volume coverage, rapid spatiospectral encoding, sparse multi-TE sampling, and interleaved water navigators for field mapping and calibration. Special data processing strategies were developed to interpolate the sparsely sampled data, remove nuisance signals, and reconstruct multi-TE spatiospectral distributions with high SNR. Phantom and in vivo experiments have been carried out to demonstrate the capability of the proposed method.

RESULTS

The proposed acquisition can produce multi-TE ¹ H-MRSI data with three TEs at a nominal spatial resolution of 3.4 × 3.4 × 5.3 mm³ in around 20 min. High-SNR brain metabolite spatiospectral reconstructions can be obtained from both a metabolite phantom and in vivo experiments by the proposed method.

CONCLUSION

High-resolution, 3D multi-TE ¹ H-MRSI of the brain can be achieved within clinically feasible time. This capability, with further optimizations, could be translated to clinical applications and neuroscience studies where simultaneously mapping metabolites and neurotransmitters and TE-dependent molecular spectral changes are of interest.

High-Resolution Magnetic Resonance Spectroscopic Imaging using a Multi-Encoder Attention U-Net with Structural and Adversarial Loss

Common to most medical imaging techniques, the spatial resolution of Magnetic Resonance Spectroscopic Imaging (MRSI) is ultimately limited by the achievable SNR. This work presents a deep learning method for 1H-MRSI spatial resolution enhancement, based on the observation that multi-parametric MRI images provide relevant spatial priors for MRSI enhancement. A Multi-encoder Attention U-Net (MAU-Net) architecture was constructed to process a MRSI metabolic map and three different MRI modalities through separate encoding paths. Spatial attention modules were incorporated to automatically learn spatial weights that highlight salient features for each MRI modality. MAU-Net was trained based on in vivo brain imaging data from patients with high-grade gliomas, using a combined loss function consisting of pixel, structural and adversarial loss. Experimental results showed that the proposed method is able to reconstruct high-quality metabolic maps with a high-resolution of 64×64 from a low-resolution of 16 × 16, with better performance compared to several baseline methods.

High-Resolution Label-Free Molecular Imaging of Brain Tumor

Molecular imaging has long been recognized as an important tool for diagnosis, characterization, and monitoring of treatment responses of brain tumors. Magnetic resonance spectroscopic imaging (MRSI) is a label-free molecular imaging technique capable of mapping metabolite distributions non-invasively. Several metabolites detectable by MRSI, including Choline, Lactate and N-Acetyl Aspartate, have been proved useful biomarkers for brain tumor characterization. However, clinical application of MRSI has been limited by poor resolution, small spatial coverage, low signal-to-noise ratio and long scan time. This work presents a novel MRSI method for fast, high-resolution metabolic imaging of brain tumor. This method synergistically integrates fast acquisition sequence, sparse sampling, subspace modeling and machine learning to enable 3D mapping of brain metabolites with a spatial resolution of 2.0×3.0×3.0 mm³ in a 7-minute scan. Experimental results obtained from patients with diagnosed brain tumor showed great promise for capturing small-size tumors and revealing intra-tumor metabolic heterogeneities.Clinical Relevance - This paper presents a novel technique for label-free molecular imaging of brain tumor. With further development, this technology may enable many potential clinical applications, from tumor detection, characterization, to assessment of treatment efficacy.

Simultaneous pure T2 and varying T2'-weighted BOLD fMRI using Echo Planar Time-resolved Imaging for mapping cortical-depth dependent responses

Spin-echo (SE) BOLD fMRI has high microvascular specificity, and thus provides a more reliable means to localize neural activity compared to conventional gradient-echo BOLD fMRI. However, the most common SE BOLD acquisition method, SE-EPI, is known to suffer from T₂′ contrast contamination with undesirable draining vein bias. To address this, in this study, we extended a recently developed distortion/blurring-free multi-shot EPI technique, Echo-Planar Time-resolved Imaging (EPTI), to cortical-depth dependent SE-fMRI at 7T to test whether it could provide purer SE BOLD contrast with minimal T₂′ contamination for improved neuronal specificity. From the same acquisition, the time-resolved feature of EPTI also provides a series of asymmetric SE (ASE) images with varying T₂′ weightings, and enables extraction of data equivalent to conventional SE EPI with different echo train lengths (ETLs). This allows us to systematically examine how T₂′-contribution affects different SE acquisition strategies using a single dataset. A low-rank spatiotemporal subspace reconstruction was implemented for the SE-EPTI acquisition, which incorporates corrections for both shot-to-shot phase variations and dynamic B₀ drifts. SE-EPTI was used in a visual task fMRI experiment to demonstrate that i) the pure SE image provided by EPTI results in the highest microvascular specificity; ii) the ASE EPTI series, with a graded introduction of T₂′ weightings at time points farther away from the pure SE, show a gradual sensitivity increase along with increasing draining vein bias; iii) the longer ETL seen in conventional SE EPI acquisitions will induce more draining vein bias. Consistent results were observed across multiple subjects, demonstrating the robustness of the proposed technique for SE-BOLD fMRI with high specificity.

Uncertainty in denoising of MRSI using low-rank methods

PURPOSE

Low-rank denoising of MRSI data results in an apparent increase in spectral SNR. However, it is not clear if this translates to a lower uncertainty in metabolite concentrations after spectroscopic fitting. Estimation of the true uncertainty after denoising is desirable for downstream analysis in spectroscopy. In this work, the uncertainty reduction from low-rank denoising methods based on spatiotemporal separability and linear predictability in MRSI are assessed. A new method for estimating metabolite concentration uncertainty after denoising is proposed. Automatic rank threshold selection methods are also assessed in simulated low SNR regimes.

METHODS

Assessment of denoising methods is conducted using Monte Carlo simulation of proton MRSI data and by reproducibility of repeated in vivo acquisitions in 5 subjects.

RESULTS

In simulated and in vivo data, spatiotemporal based denoising is shown to reduce the concentration uncertainty, but linear prediction denoising increases uncertainty. Uncertainty estimates provided by fitting algorithms after denoising consistently underestimate actual metabolite uncertainty. However, the proposed uncertainty estimation, based on an analytical expression for entry-wise variance after denoising, is more accurate. It is also shown automated rank threshold selection using Marchenko-Pastur distribution can bias the data in low SNR conditions. An alternative soft-thresholding function is proposed.

CONCLUSION

Low-rank denoising methods based on spatiotemporal separability do reduce uncertainty in MRS(I) data. However, thorough assessment is needed as assessment by SNR measured from residual baseline noise is insufficient given the presence of non-uniform variance. It is also important to select the right rank thresholding method in low SNR cases.

Accelerated MR spectroscopic imaging-a review of current and emerging techniques

Over more than 30 years in vivo MR spectroscopic imaging (MRSI) has undergone an enormous evolution from theoretical concepts in the early 1980s to the robust imaging technique that it is today. The development of both fast and efficient sampling and reconstruction techniques has played a fundamental role in this process. State-of-the-art MRSI has grown from a slow purely phase-encoded acquisition technique to a method that today combines the benefits of different acceleration techniques. These include shortening of repetition times, spatial-spectral encoding, undersampling of k-space and time domain, and use of spatial-spectral prior knowledge in the reconstruction. In this way in vivo MRSI has considerably advanced in terms of spatial coverage, spatial resolution, acquisition speed, artifact suppression, number of detectable metabolites and quantification precision. Acceleration not only has been the enabling factor in high-resolution whole-brain 1 H-MRSI, but today is also common in non-proton MRSI (31 P, 2 H and 13 C) and applied in many different organs. In this process, MRSI techniques had to constantly adapt, but have also benefitted from the significant increase of magnetic field strength boosting the signal-to-noise ratio along with high gradient fidelity and high-density receive arrays. In combination with recent trends in image reconstruction and much improved computation power, these advances led to a number of novel developments with respect to MRSI acceleration. Today MRSI allows for non-invasive and non-ionizing mapping of the spatial distribution of various metabolites' tissue concentrations in animals or humans, is applied for clinical diagnostics and has been established as an important tool for neuro-scientific and metabolism research. This review highlights the developments of the last five years and puts them into the context of earlier MRSI acceleration techniques. In addition to 1 H-MRSI it also includes other relevant nuclei and is not limited to certain body regions or specific applications.

Variable flip angle echo planar time-resolved imaging (vFA-EPTI) for fast high-resolution gradient echo myelin water imaging

Myelin water imaging techniques based on multi-compartment relaxometry have been developed as an important tool to measure myelin concentration in vivo, but are limited by the long scan time of multi-contrast multi-echo acquisition. In this work, a fast imaging technique, termed variable flip angle Echo Planar Time-Resolved Imaging (vFA-EPTI), is developed to acquire multi-echo and multi-flip-angle gradient-echo data with significantly reduced acquisition time, providing rich information for multi-compartment analysis of gradient-echo myelin water imaging (GRE-MWI). The proposed vFA-EPTI method achieved 26 folds acceleration with good accuracy by utilizing an efficient continuous readout, optimized spatiotemporal encoding across echoes and flip angles, as well as a joint subspace reconstruction. An approach to estimate off-resonance field changes between different flip-angle acquisitions was also developed to ensure high-quality joint reconstruction across flip angles. The accuracy of myelin water fraction (MWF) estimate under high acceleration was first validated by a retrospective undersampling experiment using a lengthy fully-sampled data as reference. Prospective experiments were then performed where whole-brain MWF and multi-compartment quantitative maps were obtained in 5 min at 1.5 mm isotropic resolution and 24 min at 1 mm isotropic resolution at 3T. Additionally, ultra-high resolution data at 600 μm isotropic resolution were acquired at 7T, which show detailed structures within the cortex such as the line of Gennari, demonstrating the ability of the proposed method for submillimeter GRE-MWI that can be used to study cortical myeloarchitecture in vivo.

On the use of low-dimensional temporal subspace constraints to reduce reconstruction time and improve image quality of accelerated 4D-MRI

BACKGROUND AND PURPOSE

The purpose of this work is to investigate the use of low-dimensional temporal subspace constraints for 4D-MRI reconstruction from accelerated data in the context of MR-guided online adaptive radiation therapy (MRgOART).

MATERIALS AND METHODS

Subspace basis functions are derived directly from the accelerated golden angle radial stack-of-stars 4D-MRI data. The reconstruction times, image quality, and motion estimates are investigated as a function of the number of subspace coefficients and compared with a conventional frame-by-frame reconstruction. These experiments were performed in five patients with four 4D-MRI scans per patient on a 1.5T MR-Linac.

RESULTS

If two or three subspace coefficients are used, the iterative reconstruction time is reduced by 32% and 18%, respectively, compared to conventional parallel imaging with compressed sensing reconstructions. No significant difference was found between motion estimates made with the subspace-constrained reconstructions (p > 0.08). Qualitative improvements in image quality included reduction in apparent noise and reductions in streaking artifacts from the radial k-space coverage.

CONCLUSION

Incorporating subspace constraints for accelerated 4D-MRI reconstruction reduces noise and residual undersampling artifacts in the images while reducing computation time, making it a strong candidate for use in clinical MRgOART workflows.

Fast high-resolution metabolic imaging of acute stroke with 3D magnetic resonance spectroscopy

Impaired oxygen and cellular metabolism is a hallmark of ischaemic injury in acute stroke. Magnetic resonance spectroscopic imaging (MRSI) has long been recognized as a potentially powerful tool for non-invasive metabolic imaging. Nonetheless, long acquisition time, poor spatial resolution, and narrow coverage have limited its clinical application. Here we investigated the feasibility and potential clinical utility of rapid, high spatial resolution, near whole-brain 3D metabolic imaging based on a novel MRSI technology. In an 8-min scan, we simultaneously obtained 3D maps of N-acetylaspartate and lactate at a nominal spatial resolution of 2.0 × 3.0 × 3.0 mm3 with near whole-brain coverage from a cohort of 18 patients with acute ischaemic stroke. Serial structural and perfusion MRI was used to define detailed spatial maps of tissue-level outcomes against which high-resolution metabolic changes were evaluated. Within hypoperfused tissue, the lactate signal was higher in areas that ultimately infarcted compared with those that recovered (P < 0.0001). Both lactate (P < 0.0001) and N-acetylaspartate (P < 0.001) differed between infarcted and other regions. Within the areas of diffusion-weighted abnormality, lactate was lower where recovery was observed compared with elsewhere (P < 0.001). This feasibility study supports further investigation of fast high-resolution MRSI in acute stroke.

High-sensitivity CEST mapping using a spatiotemporal correlation-enhanced method

PURPOSE

To obtain high-sensitivity CEST maps by exploiting the spatiotemporal correlation between CEST images.

METHODS

A postprocessing method accomplished by multilinear singular value decomposition (MLSVD) was used to enhance the CEST SNR by exploiting the correlation between the Z-spectrum for each voxel and the low-rank property of the overall CEST data. The performance of this method was evaluated using CrCEST in ischemic mouse brain at 11.7 tesla. Then, MLSVD CEST was applied to obtain Cr, amide, and amine CEST maps of the ischemic mouse brain to demonstrate its general applications.

RESULTS

Complex-valued Gaussian noise was added to CEST k-space data to mimic a low SNR situation. MLSVD CEST analysis was able to suppress the noise, recover the degraded CEST peak, and provide better CrCEST quality compared to the smoothing and singular value decomposition (SVD)-based denoising methods. High-resolution Cr, amide, and amine CEST maps of an ischemic stroke using MLSVD CEST suggest that CrCEST is also a sensitive pH mapping method, and a wide range of pH changes can be detected by combing CrCEST with amine CEST at high magnetic fields.

CONCLUSION

MLSVD CEST provides a simple and efficient way to improve the SNR of CEST images.

Accelerating Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry Imaging Using a Subspace Approach

We present a subspace method that accelerates data acquisition using Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry imaging (MSI). For MSI of biological tissue samples, there is a finite number of heterogeneous tissue types with distinct chemical profiles that introduce redundancy in the high-dimensional measurements. Our subspace model exploits the redundancy in data measured from whole-slice tissue samples by decomposing the transient signals into linear combinations of a set of basis transients with the desired spectral resolution. This decomposition allowed us to design a strategy that acquires a subset of long transients for basis determination and short transients for the remaining pixels, drastically reducing the acquisition time. The computational reconstruction strategy can maintain high-mass-resolution and spatial-resolution MSI while providing a 10-fold improvement in throughput. We validated the capability of the subspace model using a rat sagittal brain slice imaging data set. Comprehensive evaluation of the quality of the mass spectral and ion images demonstrated that the reconstructed data produced by the reported method required only 15% of the typical acquisition time and exhibited both qualitative and quantitative consistency when compared to the original data. Our method enables either higher sample throughput or higher-resolution images at similar acquisition lengths, providing greater flexibility in obtaining FT-ICR MSI measurements.

An integrated RF-receive/B0-shim array coil boosts performance of whole-brain MR spectroscopic imaging at 7 T

Metabolic imaging of the human brain by in-vivo magnetic resonance spectroscopic imaging (MRSI) can non-invasively probe neurochemistry in healthy and disease conditions. MRSI at ultra-high field (≥ 7 T) provides increased sensitivity for fast high-resolution metabolic imaging, but comes with technical challenges due to non-uniform B0 field. Here, we show that an integrated RF-receive/B0-shim (AC/DC) array coil can be used to mitigate 7 T B0 inhomogeneity, which improves spectral quality and metabolite quantification over a whole-brain slab. Our results from simulations, phantoms, healthy and brain tumor human subjects indicate improvements of global B0 homogeneity by 55%, narrower spectral linewidth by 29%, higher signal-to-noise ratio by 31%, more precise metabolite quantification by 22%, and an increase by 21% of the brain volume that can be reliably analyzed. AC/DC shimming provide the highest correlation (R2 = 0.98, P = 0.001) with ground-truth values for metabolite concentration. Clinical translation of AC/DC and MRSI is demonstrated in a patient with mutant-IDH1 glioma where it enables imaging of D-2-hydroxyglutarate oncometabolite with a 2.8-fold increase in contrast-to-noise ratio at higher resolution and more brain coverage compared to previous 7 T studies. Hence, AC/DC technology may help ultra-high field MRSI become more feasible to take advantage of higher signal/contrast-to-noise in clinical applications.

Simultaneous QSM and metabolic imaging of the brain using SPICE: Further improvements in data acquisition and processing

PURPOSE

To achieve high-resolution mapping of brain tissue susceptibility in simultaneous QSM and metabolic imaging.

METHODS

Simultaneous QSM and metabolic imaging was first achieved using SPICE (spectroscopic imaging by exploiting spatiospectral correlation), but the QSM maps thus obtained were at relatively low-resolution (2.0 × 3.0 × 3.0 mm³ ). We overcome this limitation using an improved SPICE data acquisition method with the following novel features: 1) sampling (k, t)-space in dual densities, 2) sampling central k-space fully to achieve nominal spatial resolution of 3.0 × 3.0 × 3.0 mm³ for metabolic imaging, and 3) sampling outer k-space sparsely to achieve spatial resolution of 1.0 × 1.0 × 1.9 mm³ for QSM. To keep the scan time short, we acquired spatiospectral encodings in echo-planar spectroscopic imaging trajectories in central k-space but in CAIPIRINHA (controlled aliasing in parallel imaging results in higher acceleration) trajectories in outer k-space using blipped phase encodings. For data processing and image reconstruction, a union-of-subspaces model was used, effectively incorporating sensitivity encoding, spatial priors, and spectral priors of individual molecules.

RESULTS

In vivo experiments were carried out to evaluate the feasibility and potential of the proposed method. In a 6-min scan, QSM maps at 1.0 × 1.0 × 1.9 mm³ resolution and metabolic maps at 3.0 × 3.0 × 3.0 mm³ nominal resolution were obtained simultaneously. Compared with the original method, the QSM maps obtained using the new method reveal fine-scale brain structures more clearly.

CONCLUSION

We demonstrated the feasibility of achieving high-resolution QSM simultaneously with metabolic imaging using a modified SPICE acquisition method. The improved capability of SPICE may further enhance its practical utility in brain mapping.

Accelerated J-resolved 1 H-MRSI with limited and sparse sampling of ( k , t 1 , t 2 -space

PURPOSE

To accelerate the acquisition of J-resolved proton magnetic resonance spectroscopic imaging (¹ H-MRSI) data for high-resolution mapping of brain metabolites and neurotransmitters.

METHODS

The proposed method used a subspace model to represent multidimensional spatiospectral functions, which significantly reduced the number of parameters to be determined from J-resolved ¹ H-MRSI data. A semi-LASER-based (Localization by Adiabatic SElective Refocusing) echo-planar spectroscopic imaging (EPSI) sequence was used for data acquisition. The proposed data acquisition scheme sampled k , t 1 , t 2 -space in variable density, where t₁ and t₂ specify the J-coupling and chemical-shift encoding times, respectively. Selection of the J-coupling encoding times (or, echo time values) was based on a Cramer-Rao lower bound analysis, which were optimized for gamma-aminobutyric acid (GABA) detection. In image reconstruction, parameters of the subspace-based spatiospectral model were determined by solving a constrained optimization problem.

RESULTS

Feasibility of the proposed method was evaluated using both simulated and experimental data from a spectroscopic phantom. The phantom experimental results showed that the proposed method, with a factor of 12 acceleration in data acquisition, could determine the distribution of J-coupled molecules with expected accuracy. In vivo study with healthy human subjects also showed that 3D maps of brain metabolites and neurotransmitters can be obtained with a nominal spatial resolution of 3.0 × 3.0 × 4.8 mm³ from J-resolved ¹ H-MRSI data acquired in 19.4 min.

CONCLUSIONS

This work demonstrated the feasibility of highly accelerated J-resolved ¹ H-MRSI using limited and sparse sampling of k , t 1 , t 2 -space and subspace modeling. With further development, the proposed method may enable high-resolution mapping of brain metabolites and neurotransmitters in clinical applications.

High-Resolution 3D Spin-Echo MRSI Using Interleaved Water Navigators, Sparse Sampling and Subspace-Based Processing

This work presents a new method to achieve accelerated, high-resolution magnetic resonance spectroscopic imaging (MRSI) with spin-echo excitations. A new data acquisition strategy is proposed that integrates adiabatic refocusing, elimination of lipid suppression, rapid spatiospectral encoding with sparse (k,t)-space sampling, and interleaved water navigators. This integration leads to a significantly improved combination of volume coverage, spatial resolution (approximately 3 × 3.4 × 4 mm³) and speed (< 10 minutes), while eliminating additional scans for field mapping and coil sensitivity estimation. A data processing strategy that integrates parallel imaging reconstruction and subspace-based processing is devised to produce high-SNR spatiospectral reconstruction from the sparsely sampled, noisy and highresolution MRSI data. Promising in vivo results have been obtained to demonstrate the potential of the proposed method.Clinical relevance- The proposed method enabled volumetric MRSI with a nominal resolution of 3 × 3.4 × 4 mm³ in less than 10 minutes. With further developments and optimizations, the proposed method is expected to be useful for providing molecular-level information of brain functions and diseases, and has the potential to provide new biomarkers for disease diagnosis and treatment monitoring.