Phase correction for three‐dimensional (3D) diffusion‐weighted interleaved EPI using 3D multiplexed sensitivity encoding and reconstruction (3D‐MUSER)

Motion compensated structured low-rank reconstruction for 3D multi-shot EPI

PURPOSE

The 3D multi-shot EPI imaging offers several benefits including higher SNR and high isotropic resolution compared to 2D single shot EPI. However, it suffers from shot-to-shot inconsistencies arising from physiologically induced phase variations and bulk motion. This work proposed a motion compensated structured low-rank (mcSLR) reconstruction method to address both issues for 3D multi-shot EPI.

METHODS

Structured low-rank reconstruction has been successfully used in previous work to deal with inter-shot phase variations for 3D multi-shot EPI imaging. It circumvents the estimation of phase variations by reconstructing an individual image for each phase state which are then sum-of-squares combined, exploiting their linear interdependency encoded in structured low-rank constraints. However, structured low-rank constraints become less effective in the presence of inter-shot motion, which corrupts image magnitude consistency and invalidates the linear relationship between shots. Thus, this work jointly models inter-shot phase variations and motion corruptions by incorporating rigid motion compensation for structured low-rank reconstruction, where motion estimates are obtained in a fully data-driven way without relying on external hardware or imaging navigators.

RESULTS

Simulation and in vivo experiments at 7T have demonstrated that the mcSLR method can effectively reduce image artifacts and improve the robustness of 3D multi-shot EPI, outperforming existing methods which only address inter-shot phase variations or motion, but not both.

CONCLUSION

The proposed mcSLR reconstruction compensates for rigid motion, and thus improves the validity of structured low-rank constraints, resulting in improved robustness of 3D multi-shot EPI to both inter-shot motion and phase variations.

Improved Value of Multiplexed Sensitivity Encoding DWI with Reversed Polarity Gradients in Diagnosing Prostate Cancer: A Comparison Study with Single-Shot DWI and MUSE DWI

RATIONALE AND OBJECTIVES

This study aimed to investigate the value of multiplexed sensitivity encoding with reversed polarity gradients in improving the quality of diffusion-weighted imaging (DWI) images of the prostate and the diagnostic efficacy of prostate cancer.

MATERIALS AND METHODS

Seventy-three patients with prostate disease underwent multiplexed sensitivity encoding with reversed polarity gradients (RPG-MUSE), multiplexed sensitivity encoding (MUSE), and single-shot echo-planar imaging (ssEPI) DWI. Three radiologists performed a qualitative image analysis of the three DWI sequences. Qualitative image analysis included artifact minimization, anatomical detail, and sharpness of prostate edges. Two radiologists measured the signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), geometric distortion rate, and the apparent diffusion coefficient (ADC) values of the prostate disease tissue. Two radiologists jointly performed Prostate Imaging Reporting and Data System scoring of prostate lesions and compared the diagnostic efficacy of the three DWI sequences for prostate cancer.

RESULTS

There was good agreement among radiologists in the evaluation and measurement of the three DWI sequence images (intraclass correlation coefficient >0.75, P < 0.05). The RPG-MUSE DWI images were rated higher than those of MUSE and ssEPI in terms of artifact minimization, anatomical details, and sharpness of prostate edges (P < 0.05). The SNR and CNR of the RPG-MUSE DWI images were higher than those of MUSE and ssEPI (P < 0.05), and the geometric distortion rate was lower than that of the other two sequences (P < 0.05). There were no statistical differences in ADC values between the three DWI sequences (P > 0.05). The diagnostic efficacy of RPG-MUSE and MUSE DWI was higher than that of ssEPI (P < 0.017).

CONCLUSION

RPG-MUSE can reduce the artifacts and geometric distortion in DWI images of the prostate, improve the SNR and CNR of the images, improve the clarity of anatomical details and boundaries without affecting the measurement of ADC values, has the potential to improve the diagnostic efficacy of prostate lesions, and facilitates the clear display and accurate assessment of prostate lesions.

Three-dimensional echo-shifted EPI with simultaneous blip-up and blip-down acquisitions for correcting geometric distortion

PURPOSE

EPI with blip-up/down acquisition (BUDA) can provide high-quality images with minimal distortions by using two readout trains with opposing phase-encoding gradients. Because of the need for two separate acquisitions, BUDA doubles the scan time and degrades the temporal resolution when compared to single-shot EPI, presenting a major challenge for many applications, particularly fMRI. This study aims at overcoming this challenge by developing an echo-shifted EPI BUDA (esEPI-BUDA) technique to acquire both blip-up and blip-down datasets in a single shot.

METHODS

A 3D esEPI-BUDA pulse sequence was designed by using an echo-shifting strategy to produce two EPI readout trains. These readout trains produced a pair of k-space datasets whose k-space trajectories were interleaved with opposite phase-encoding gradient directions. The two k-space datasets were separately reconstructed using a 3D SENSE algorithm, from which time-resolved B0 -field maps were derived using TOPUP in FSL and then input into a forward model of joint parallel imaging reconstruction to correct for geometric distortion. In addition, Hankel structured low-rank constraint was incorporated into the reconstruction framework to improve image quality by mitigating the phase errors between the two interleaved k-space datasets.

RESULTS

The 3D esEPI-BUDA technique was demonstrated in a phantom and an fMRI study on healthy human subjects. Geometric distortions were effectively corrected in both phantom and human brain images. In the fMRI study, the visual activation volumes and their BOLD responses were comparable to those from conventional 3D echo-planar images.

CONCLUSION

The improved imaging efficiency and dynamic distortion correction capability afforded by 3D esEPI-BUDA are expected to benefit many EPI applications.

3D diffusion MRI with twin navigator-based GRASE and comparison with 2D EPI for tractography in the human brain

PURPOSE

3D pulse sequences enable high-resolution acquisition with a high SNR and ideal slice profiles, which, however, is particularly difficult for diffusion MRI (dMRI) due to the additional phase errors from diffusion encoding.

METHODS

We proposed a twin navigator-based 3D diffusion-weighted gradient spin-echo (GRASE) sequence to correct the phase errors between shots and between odd and even spin echoes for human whole-brain acquisition. We then compared the SNR of 3D GRASE and 2D simultaneous multi-slice EPI within the same acquisition time. We further tested the performance of 2D versus 3D acquisition at equivalent SNR on fiber tracking and microstructural mapping, using the diffusion tensor and high-order fiber orientation density-based metrics.

RESULTS

The proposed twin navigator approach removed multi-shot phase errors to some extent in the whole brain dMRI, and the 2D navigator performed better than the 1D navigator. Comparisons of SNR between the 2D simultaneous multi-slice EPI and 3D GRASE sequences demonstrated that the SNR of the GRASE sequence was 1.4-1.5-fold higher than the EPI sequence at an equivalent scan time. More importantly, we found a significantly higher fiber cross-section in the cerebrospinal tract, as well as richer subcortical fibers (U-fibers) using the 3D GRASE sequence compared to 2D EPI.

CONCLUSION

The twin navigator-based 3D diffusion-weighted-GRASE sequence minimized the multishot phase error and effectively improved the SNR for whole-brain dMRI acquisition. We found differences in fiber tracking and microstructural mapping between 2D and 3D acquisitions, possibly due to the different slice profiles.

High-fidelity mesoscale in-vivo diffusion MRI through gSlider-BUDA and circular EPI with S-LORAKS reconstruction

PURPOSE

To develop a high-fidelity diffusion MRI acquisition and reconstruction framework with reduced echo-train-length for less T2* image blurring compared to typical highly accelerated echo-planar imaging (EPI) acquisitions at sub-millimeter isotropic resolution.

METHODS

We first proposed a circular-EPI trajectory with partial Fourier sampling on both the readout and phase-encoding directions to minimize the echo-train-length and echo time. We then utilized this trajectory in an interleaved two-shot EPI acquisition with reversed phase-encoding polarity, to aid in the correction of off-resonance-induced image distortions and provide complementary k-space coverage in the missing partial Fourier regions. Using model-based reconstruction with structured low-rank constraint and smooth phase prior, we corrected the shot-to-shot phase variations across the two shots and recover the missing k-space data. Finally, we combined the proposed acquisition/reconstruction framework with an SNR-efficient RF-encoded simultaneous multi-slab technique, termed gSlider, to achieve high-fidelity 720 µm and 500 µm isotropic resolution in-vivo diffusion MRI.

RESULTS

Both simulation and in-vivo results demonstrate the effectiveness of the proposed acquisition and reconstruction framework to provide distortion-corrected diffusion imaging at the mesoscale with markedly reduced T2*-blurring. The in-vivo results of 720 µm and 500 µm datasets show high-fidelity diffusion images with reduced image blurring and echo time using the proposed approaches.

CONCLUSIONS

The proposed method provides high-quality distortion-corrected diffusion-weighted images with ∼40% reduction in the echo-train-length and T2* blurring at 500µm-isotropic-resolution compared to standard multi-shot EPI.

Multi-band multi-shot diffusion MRI reconstruction with joint usage of structured low-rank constraints and explicit phase mapping

PURPOSE

To develop a joint reconstruction method for multi-band multi-shot diffusion MRI.

THEORY AND METHODS

Multi-band multi-shot EPI acquisition is an effective approach for high-resolution diffusion MRI, but requires specific algorithms to correct the inter-shot phase variations. The phase correction can be done by first estimating the explicit phase map and then feeding it into the k-space signal formulation model. Alternatively, the phase information can be used indirectly as structured low-rank constraints in k-space. The 2 methods differ in reconstruction accuracy and efficiency. We aim to combine the 2 different approaches for improved image quality and reconstruction efficiency simultaneously, termed "joint usage of structured low-rank constraints and explicit phase mapping" (JULEP). The proposed JULEP reconstruction is tested on both single-band and multi-band, multi-shot diffusion data, with different resolutions and b values. The results of JULEP are compared with conventional methods with explicit phase mapping (i.e., multiplexed sensitivity-encoding [MUSE]) and structured low-rank constraints (i.e., MUSSELS), and another joint reconstruction method (i.e., network estimated artifacts for tempered reconstruction [NEATR]).

RESULTS

JULEP improves the quality of the navigator and subsequently facilitates the reconstruction of final diffusion images. Compared with all 3 other methods (MUSE, MUSSELS, and NEATR), JULEP mitigates residual structural bias and improves temporal SNRs in the final diffusion image, particularly at high multi-band factors. Compared with MUSSELS, JULEP also improves computational efficiency.

CONCLUSION

The proposed JULEP method significantly improves the image quality and reconstruction efficiency of multi-band multi-shot diffusion MRI, which can promote a broader application of high-resolution diffusion MRI.

High-resolution whole-brain diffusion MRI at 3T using simultaneous multi-slab (SMSlab) acquisition

High-resolution diffusion MRI (dMRI) is a crucial tool in neuroscience studies to detect fine fiber structure, depict complex fiber architecture and analyze cortical anisotropy. However, high-resolution dMRI is limited by its intrinsically low SNR due to diffusion attenuation. A series of techniques have been proposed to improve the SNR performance, but most of them are at the cost of long scan time, which in turn sacrifice the SNR efficiency, especially for large FOV imaging, such as whole-brain imaging. Recently, a combination of 3D multi-slab acquisition and simultaneous multi-slice (SMS) excitation, namely simultaneous multi-slab (SMSlab), has been demonstrated to have potential for high-resolution diffusion imaging with high SNR and SNR efficiency. In our previous work, we have proposed a 3D Fourier encoding and reconstruction framework for SMSlab acquisition. In this study, we extend this 3D k-space framework to diffusion imaging, by developing a novel navigator acquisition strategy and exploring a k-space-based phase correction method. In vivo brain data are acquired using the proposed SMSlab method and compared with a series of different acquisitions, including the traditional 3D multi-slab, 2D SMS and 2D single-shot EPI (ss-EPI) acquisitions. The results demonstrate that SMSlab has a better SNR performance compared with 3D multi-slab and 2D SMS. The detection capacity of fine fiber structures is improved using SMSlab, compared with the low-resolution diffusion imaging using conventional 2D ss-EPI.

Distortion-free, high-isotropic-resolution diffusion MRI with gSlider BUDA-EPI and multicoil dynamic B0 shimming

PURPOSE

We combine SNR-efficient acquisition and model-based reconstruction strategies with newly available hardware instrumentation to achieve distortion-free in vivo diffusion MRI of the brain at submillimeter-isotropic resolution with high fidelity and sensitivity on a clinical 3T scanner.

METHODS

We propose blip-up/down acquisition (BUDA) for multishot EPI using interleaved blip-up/blip-down phase encoding and incorporate B₀ forward-modeling into structured low-rank reconstruction to enable distortion-free and navigator-free diffusion MRI. We further combine BUDA-EPI with an SNR-efficient simultaneous multislab acquisition (generalized slice-dithered enhanced resolution ["gSlider"]), to achieve high-isotropic-resolution diffusion MRI. To validate gSlider BUDA-EPI, whole-brain diffusion data at 860-μm and 780-μm data sets were acquired. Finally, to improve the conditioning and minimize noise penalty in BUDA reconstruction at very high resolutions where B₀ inhomogeneity can have a detrimental effect, the level of B₀ inhomogeneity was reduced by incorporating slab-by-slab dynamic shimming with a 32-channel AC/DC coil into the acquisition. Whole-brain 600-μm diffusion data were then acquired with this combined approach of gSlider BUDA-EPI with dynamic shimming.

RESULTS

The results of 860-μm and 780-μm datasets show high geometry fidelity with gSlider BUDA-EPI. With dynamic shimming, the BUDA reconstruction's noise penalty was further alleviated. This enables whole-brain 600-μm isotropic resolution diffusion imaging with high image quality.

CONCLUSIONS

The gSlider BUDA-EPI method enables high-quality, distortion-free diffusion imaging across the whole brain at submillimeter resolution, where the use of multicoil dynamic B₀ shimming further improves reconstruction performance, which can be particularly useful at very high resolutions.

Self-navigation for 3D multishot EPI with data-reference

PURPOSE

In this study, we sought to develop a self-navigation strategy for improving the reconstruction of diffusion weighted 3D multishot echo planar imaging (EPI). We propose a method for extracting the phase correction information from the acquisition itself, eliminating the need for a 2D navigator, further accelerating the acquisition.

METHODS

In-vivo acquisitions at 3T with 0.9 mm and 1.5 mm isotropic resolutions were used to evaluate the performance of the self-navigation strategy. Sensitivity to motion was tested using a large difference in pitch position of the head. Using a multishell diffusion weighted acquisition, tractography results were obtained at (0.9 mm)³ to validate the quality with conventional acquisition.

RESULTS

The use of 3D multislab EPI with self-navigation enables 3D diffusion-weighted spin echo EPI acquisitions that have the same efficiency as 2D single-shot acquisition. For matched acquisition time the image signal-to-noise ratio (SNR) between 3D and 2D acquisition is shown to be comparable for whole-brain coverage with (1.5 mm)³ resolution and for (0.9 mm)³ resolution the 3D acquisition has higher SNR than what can be obtained with 2D acquisitions using current state-of-art multiband techniques. The self-navigation technique was shown to be stable under inter-volume motion. In tractography analysis, the higher resolution afforded by our technique enabled clear delineation of the tapetum and posterior corona radiata.

CONCLUSION

The proposed self-navigation approach utilized a self-consistent phase in 3D diffusion weighted acquisitions. Its efficiency and stability were demonstrated for a plurality of common acquisitions. The proposed self-navigation approach allows for faster acquisition of 3D multishot EPI desirable for large field of view and/or higher resolution.

Qualitative and quantitative comparison of image quality between single-shot echo-planar and interleaved multi-shot echo-planar diffusion-weighted imaging in female pelvis

OBJECTIVES

To qualitatively and quantitatively compare the image quality between single-shot echo-planar (SS-EPI) and multi-shot echo-planar (IMS-EPI) diffusion-weighted imaging (DWI) in female pelvis METHODS: This was a prospective study involving 80 females who underwent 3.0T pelvic magnetic resonance imaging (MRI). SS-EPI and IMS-EPI DWI were acquired with 3 b values (0, 400, 800 s/mm²). Two independent reviewers assessed the overall image quality, artifacts, sharpness, and lesion conspicuity based on a 5-point Likert scale. Regions of interest (ROI) were placed on the endometrium and the gluteus muscles to quantify the signal intensities and apparent diffusion coefficient (ADC). Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and geometric distortion were quantified on both sequences. Inter-rater agreement was assessed using κ statistics and Kendall test. Qualitative scores were compared using Wilcoxon signed-rank test and quantitative parameters were compared with paired t test and Bland-Altman analysis.

RESULTS

IMS-EPI demonstrated better image quality than SS-EPI for all aspects evaluated (SS-EPI vs. IMS-EPI: overall quality 3.04 vs. 4.17, artifacts 3.09 vs. 3.99, sharpness 2.40 vs. 4.32, lesion conspicuity 3.20 vs. 4.25; p < 0.001). Good agreement and correlation were observed between two reviewers (SS-EPI κ 0.699, r 0.742; IMS-EPI κ 0.702, r 0.789). IMS-EPI showed lower geometric distortion, SNR, and CNR than SS-EPI (p < 0.050). There was no significant difference in the mean ADC between the two sequences.

CONCLUSION

IMS-EPI showed better image quality with lower geometric distortion without affecting the quantification of ADC, though the SNR and CNR decreased due to post-processing limitations.

KEY POINTS

• IMS-EPI showed better image quality than SS-EPI. • IMS-EPI showed lower geometric distortion without affecting ADC compared with SS-EPI. • The SNR and CNR of IMS-EPI decreased due to post-processing limitations.

A 3D k-space Fourier encoding and reconstruction framework for simultaneous multi-slab acquisition

PURPOSE

To propose a novel 3D k-space Fourier encoding and reconstruction framework for simultaneous multi-slab (SMSlab) acquisition and demonstrate its efficacy in high-resolution imaging.

METHODS

First, it is illustrated in theory how the inter-slab gap interferes with the formation of the SMSlab 3D k-space. Then, joint RF and gradient encoding are applied to remove the inter-slab gap interference and form a SMSlab 3D k-space. In vivo experiments are performed to validate the proposed theory. Acceleration in the proposed SMSlab 3D k-space is also evaluated.

RESULTS

High-resolution (1.0 mm isotropic) images can be reconstructed using the proposed SMSlab 3D framework. Controlled aliasing in parallel imaging sampling and 2D GRAPPA reconstruction can also be applied in the SMSlab 3D k-space. Compared with conventional multi-slab acquisition, SMSlab exhibits better SNR maintainability (such as lower g-factors), especially at high acceleration factors.

CONCLUSION

It is demonstrated that the joint application of RF and gradient encoding enables SMSlab within a 3D Fourier encoding framework. Images with high isotropic resolution can be reconstructed, and further acceleration is also applicable. The proposed SMSlab 3D k-space can be valuable for both high-resolution and high-efficiency diffusion and functional MRI.

High-fidelity, high-isotropic-resolution diffusion imaging through gSlider acquisition with B 1 + and T1 corrections and integrated ΔB0 /Rx shim array

PURPOSE

B 1 + and T₁ corrections and dynamic multicoil shimming approaches were proposed to improve the fidelity of high-isotropic-resolution generalized slice-dithered enhanced resolution (gSlider) diffusion imaging.

METHODS

An extended reconstruction incorporating B 1 + inhomogeneity and T₁ recovery information was developed to mitigate slab-boundary artifacts in short-repetition time (TR) gSlider acquisitions. Slab-by-slab dynamic B₀ shimming using a multicoil integrated ΔB₀ /Rx shim array and high in-plane acceleration (R_inplane = 4) achieved with virtual-coil GRAPPA were also incorporated into a 1-mm isotropic resolution gSlider acquisition/reconstruction framework to achieve a significant reduction in geometric distortion compared to single-shot echo planar imaging (EPI).

RESULTS

The slab-boundary artifacts were alleviated by the proposed B 1 + and T₁ corrections compared to the standard gSlider reconstruction pipeline for short-TR acquisitions. Dynamic shimming provided >50% reduction in geometric distortion compared to conventional global second-order shimming. One-millimeter isotropic resolution diffusion data show that the typically problematic temporal and frontal lobes of the brain can be imaged with high geometric fidelity using dynamic shimming.

CONCLUSIONS

The proposed B 1 + and T₁ corrections and local-field control substantially improved the fidelity of high-isotropic-resolution diffusion imaging, with reduced slab-boundary artifacts and geometric distortion compared to conventional gSlider acquisition and reconstruction. This enabled high-fidelity whole-brain 1-mm isotropic diffusion imaging with 64 diffusion directions in 20 min using a 3T clinical scanner.

The quest for high spatial resolution diffusion-weighted imaging of the human brain in vivo

Diffusion-weighted imaging, a contrast unique to MRI, is used for assessment of tissue microstructure in vivo. However, this exquisite sensitivity to finer scales far above imaging resolution comes at the cost of vulnerability to errors caused by sources of motion other than diffusion motion. Addressing the issue of motion has traditionally limited diffusion-weighted imaging to a few acquisition techniques and, as a consequence, to poorer spatial resolution than other MRI applications. Advances in MRI imaging methodology have allowed diffusion-weighted MRI to push to ever higher spatial resolution. In this review we focus on the pulse sequences and associated techniques under development that have pushed the limits of image quality and spatial resolution in diffusion-weighted MRI.