Improved image reconstruction for partial Fourier gradient-echo echo-planar imaging (EPI)

Partial Fourier in the presence of respiratory motion in prostate diffusion-weighted echo planar imaging

PURPOSE

To investigate the effect of respiratory motion in terms of signal loss in prostate diffusion-weighted imaging (DWI), and to evaluate the usage of partial Fourier in a free-breathing protocol in a clinically relevant b-value range using both single-shot and multi-shot acquisitions.

METHODS

A controlled breathing DWI acquisition was first employed at 3 T to measure signal loss from deep breathing patterns. Single-shot and multi-shot (2-shot) acquisitions without partial Fourier (no pF) and with partial Fourier (pF) factors of 0.75 and 0.65 were employed in a free-breathing protocol. The apparent SNR and ADC values were evaluated in 10 healthy subjects to measure if low pF factors caused low apparent SNR or overestimated ADC.

RESULTS

Controlled breathing experiments showed a difference in signal coefficient of variation between shallow and deep breathing. In free-breathing single-shot acquisitions, the pF 0.65 scan showed a significantly (p < 0.05) higher apparent SNR than pF 0.75 and no pF in the peripheral zone (PZ) of the prostate. In the multi-shot acquisitions in the PZ, pF 0.75 had a significantly higher apparent SNR than 0.65 pF and no pF. The single-shot pF 0.65 scan had a significantly lower ADC than single-shot no pF.

CONCLUSION

Deep breathing patterns can cause intravoxel dephasing in prostate DWI. For single-shot acquisitions at a b-value of 800 s/mm2, any potential risks of motion-related artefacts at low pF factors (pF 0.65) were outweighed by the increase in signal from a lower TE, as shown by the increase in apparent SNR. In multi-shot acquisitions however, the minimum pF factor should be larger, as shown by the lower apparent SNR at low pF factors.

Distortion correction using topup algorithm by single k-space (TASK) for echo planar imaging

Distortion of echo planar imaging (EPI) can be corrected using B0 field maps, which can be estimated with the topup algorithm that requires two EPI images with opposite distortions. In this study, we propose a new algorithm, termed topup algorithm by single K-space (TASK), to generate two input images from a single k-space for the topup algorithm to correct EPI distortions. The centric EPI contains the opposite phase-encoding polarities in one k-space, which can be divided into two halves with opposite distortions. Therefore, two inputs could be extracted by dividing the k-space into halves and processing them using the proposed procedure including an iterative procedure of automatic brain masking and uniformity correction. The efficiency of TASK was evaluated using 3D EPI. Quantitative evaluations showed that TASK corrected EPI distortion at a similar level to the traditional methods. The estimated field maps from the conventional topup and TASK showed a high correlation ([Formula: see text]). An ablation study showed the validity of every suggested step. Furthermore, it was confirmed that TASK was effective for distortion correction of two-shot centric EPI as well, demonstrating its wider applicability. In conclusion, TASK can correct EPI distortions by its own single k-space information with no additional scan.

Improved Resting-State Functional MRI Using Multi-Echo Echo-Planar Imaging on a Compact 3T MRI Scanner with High-Performance Gradients

In blood-oxygen-level-dependent (BOLD)-based resting-state functional (RS-fMRI) studies, usage of multi-echo echo-planar-imaging (ME-EPI) is limited due to unacceptable late echo times when high spatial resolution is used. Equipped with high-performance gradients, the compact 3T MRI system (C3T) enables a three-echo whole-brain ME-EPI protocol with smaller than 2.5 mm isotropic voxel and shorter than 1 s repetition time, as required in landmark fMRI studies. The performance of the ME-EPI was comprehensively evaluated with signal variance reduction and region-of-interest-, seed- and independent-component-analysis-based functional connectivity analyses and compared with a counterpart of single-echo EPI with the shortest TR possible. Through the multi-echo combination, the thermal noise level is reduced. Functional connectivity, as well as signal intensity, are recovered in the medial orbital sulcus and anterior transverse collateral sulcus in ME-EPI. It is demonstrated that ME-EPI provides superior sensitivity and accuracy for detecting functional connectivity and/or brain networks in comparison with single-echo EPI. In conclusion, the high-performance gradient enabled high-spatial-temporal resolution ME-EPI would be the method of choice for RS-fMRI study on the C3T.

Minimizing susceptibility-induced BOLD sensitivity loss in multi-band accelerated fMRI using point spread function mapping and gradient reversal

Objective. Interleaved reverse-gradient fMRI (RG-fMRI) with a point-spread-function (PSF) mapping-based distortion correction scheme has the potential to minimize signal loss in echo-planar-imaging (EPI). In this work, the RG-fMRI is further improved by imaging protocol optimization and application of reverse Fourier acquisition.Approach. Multi-band imaging was adapted for RG-fMRI to improve the temporal and spatial resolution. To better understand signal dropouts in forward and reverse EPIs, a simple theoretical relationship between echo shift and geometric distortion was derived and validated by the reliable measurements using PSF mapping method. After examining practical imaging protocols for RG-fMRI in three subjects on both a conventional whole-body and a high-performance compact 3 T, the results were compared and the feasibility to further improve the RG-fMRI scheme were explored. High-resolution breath-holding RG-fMRI was conducted with nine subjects on the compact 3 T and the fMRI reliability improvement in high susceptibility brain regions was demonstrated. Finally, reverse Fourier acquisition was applied to RG-fMRI, and its benefit was assessed by a simulation study based on the breath-holding RG-fMRI data.Main results. The temporal and spatial resolution of the multi-band RG-fMRI became feasible for whole-brain fMRI. Echo shift measurements from PSF mapping well estimated signal dropout effects in the EPI pair and were useful to further improve the RG-fMRI scheme. Breath-holding RG-fMRI demonstrated improved fMRI reliability in high susceptibility brain regions. Reverse partial Fourier acquisition omitting the late echoes could further improve the temporal or spatial resolution for RG-fMRI without noticeable signal degradation and spatial resolution loss.Significance. With the improved imaging scheme, RG-fMRI could reliably investigate the functional mechanisms of the human brain in the temporal and frontal areas suffering from susceptibility-induced functional sensitivity loss.

Partial Fourier reconstruction of complex MR images using complex-valued convolutional neural networks

PURPOSE

To provide a complex-valued deep learning approach for partial Fourier (PF) reconstruction of complex MR images.

METHODS

Conventional PF reconstruction methods, such as projection onto convex sets (POCS), uses low-resolution image phase information from the central symmetrically sampled k-space for image reconstruction. However, this smooth phase constraint undermines the phase estimation accuracy in presence of rapid local phase variations, causing image artifacts and limiting the extent of PF reconstruction. Using both magnitude and phase characteristics in big complex image datasets, we propose a complex-valued deep learning approach with an unrolled network architecture for PF reconstruction that iteratively reconstructs PF sampled data and enforces data consistency. We evaluate our approach for reconstructing both spin-echo and gradient-echo data.

RESULTS

The proposed method outperformed the iterative POCS PF reconstruction method. It produced better artifact suppression and recovery of both image magnitude and phase details in presence of local phase changes. No noise amplification was observed even for highly PF reconstruction. Moreover, the network trained on axial brain data could reconstruct sagittal and coronal brain and knee data. This method could be extended to 2D PF reconstruction and joint multi-slice PF reconstruction.

CONCLUSION

Our proposed method can effectively reconstruct MR data even at low PF fractions, yielding high-fidelity magnitude and phase images. It presents a valuable alternative to conventional PF reconstruction, especially for phase-sensitive 2D or 3D MRI applications.

Single-shot pseudo-centric EPI for magnetization-prepared imaging

PURPOSE

To implement a single-shot centric-reordered EPI (1sh-CenEPI), which reduces TE significantly, thus enabling to improve SNR for magnetization-prepared imaging.

METHODS

We proposed a 1sh-CenEPI in which grouped oscillating readout gradients, phase-encoding blips within each group, and big phase-encoding jumps between two consecutive groups are incorporated to encode whole k-space from the center to the edges in a single shot. The concept was tested on phantoms and human brains at 3 T. In addition, the proposed reordering scheme was applied to pseudo-continuous arterial spin labeling for evaluating the efficiency of the centric reordering in magnetization-prepared imaging.

RESULTS

The proposed 1sh-CenEPI reduced TE from 50 ms to 1.4 ms for gradient-echo EPI, and from 100 ms to 7 ms for spin-echo EPI, while the elongation of readout duration was below 10% of the whole readout duration in most cases. The 1sh-CenEPI images exhibited no distinct geometric distortion both in phantom and human brain, comparable to the conventional two-shot center-out EPI. In pseudo-continuous arterial spin labeling results, 3-fold temporal SNR increase and 2-fold spatial SNR increase in the perfusion-weighted images were achieved with 1sh-CenEPI compared with the conventional linear ordering, whereas the cerebral blood flow values were consistent with previous studies.

CONCLUSION

The proposed 1sh-CenEPI significantly reduced TE while maintaining similar readout window and providing images comparable to the conventional linear and multishot center-out EPI images. It can be a qualified candidate as a new readout for various magnetization-prepared imaging techniques.

The benefit of high-performance gradients on echo planar imaging for BOLD-based resting-state functional MRI

Improved gradient performance in an MRI system reduces distortion in echo planar imaging (EPI), which has been a key imaging method for functional studies. A lightweight, low-cryogen compact 3T MRI scanner (C3T) is capable of achieving 80 mT m^-1 gradient amplitude with 700 T m^-1 s^-1 slew rate, in comparison with a conventional whole-body 3T MRI scanner (WB3T, 50 mT m^-1 with 200 T m^-1 s^-1). We investigated benefits of the high-performance gradients in a high-spatial-resolution (1.5 mm isotropic) functional MRI study. Reduced echo spacing in the EPI pulse sequence inherently leads to less severe geometric distortion, which provided higher accuracy than with WB3T for registration between EPI and anatomical images. The cortical coverage of C3T datasets was improved by more accurate signal depiction (i.e. less dropout or pile-up). Resting-state functional analysis results showed that greater magnitude and extent in functional connectivity (FC) for the C3T than the WB3T when the selected seed region is susceptible to distortions, while the FC matrix for well-known brain networks showed little difference between the two scanners. This shows that the improved quality in EPI is particularly valuable for studying certain brain regions typically obscured by severe distortion.

Deconvolution-based distortion correction of EPI using analytic single-voxel point-spread functions

PURPOSE

To develop a postprocessing algorithm that corrects geometric distortions due to spatial variations of the static magnetic field amplitude, B₀ , and effects from relaxation during signal acquisition in EPI.

THEORY AND METHODS

An analytic, complex point-spread function is deduced for k-space trajectories of EPI variants and applied to corresponding acquisitions in a resolution phantom and in human volunteers at 3 T. With the analytic point-spread function and experimental maps of B₀ (and, optionally, the effective transverse relaxation time, T 2 * ) as input, a point-spread function matrix operator is devised for distortion correction by a Thikonov-regularized deconvolution in image space. The point-spread function operator provides additional information for an appropriate correction of the signal intensity distribution. A previous image combination algorithm for acquisitions with opposite phase blip polarities is adapted to the proposed method to recover destructively interfering signal contributions.

RESULTS

Applications of the proposed deconvolution-based distortion correction ("DecoDisCo") algorithm demonstrate excellent distortion corrections and superior performance regarding the recovery of an undistorted intensity distribution in comparison to a multifrequency reconstruction. Examples include full and partial Fourier standard EPI scans as well as double-shot center-out trajectories. Compared with other distortion-correction approaches, DecoDisCo permits additional deblurring to obtain sharper images in cases of significant T 2 * effects.

CONCLUSION

Robust distortion corrections in EPI acquisitions are feasible with high quality by regularized deconvolution with an analytic point-spread function. The general algorithm, which is publicly released on GitHub, can be straightforwardly adapted for specific EPI variants or other acquisition schemes.

Improved PRF-based MR thermometry using k-space energy spectrum analysis

PURPOSE

Proton resonance frequency (PRF) thermometry encodes information in the phase of MRI signals. A multiplicative factor converts phase changes into temperature changes, and this factor includes the TE. However, phase variations caused by B₀ and/or B₁ inhomogeneities can effectively change TE in ways that vary from pixel to pixel. This work presents how spatial phase variations affect temperature maps and how to correct for corresponding errors.

METHODS

A method called "k-space energy spectrum analysis" was used to map regions in the object domain to regions in the k-space domain. Focused ultrasound heating experiments were performed in tissue-mimicking gel phantoms under two scenarios: with and without proper shimming. The second scenario, with deliberately de-adjusted shimming, was meant to emulate B₀ inhomogeneities in a controlled manner. The TE errors were mapped and compensated for using k-space energy spectrum analysis, and corrected results were compared with reference results. Furthermore, a volunteer was recruited to help evaluate the magnitude of the errors being corrected.

RESULTS

The in vivo abdominal results showed that the TE and heating errors being corrected can readily exceed 10%. In phantom results, a linear regression between reference and corrected temperatures results provided a slope of 0.971 and R² of 0.9964. Analysis based on the Bland-Altman method provided a bias of -0.0977°C and 95% limits of agreement that were 0.75°C apart.

CONCLUSION

Spatially varying TE errors, such as caused by B₀ and/or B₁ inhomogeneities, can be detected and corrected using the k-space energy spectrum analysis method, for increased accuracy in proton resonance frequency thermometry.

Enhanced hyperpolarized chemical shift imaging based on a priori segmented information

PURPOSE

The purpose of the study was to develop an approach for improving the resolution and sensitivity of hyperpolarized ¹³ C MRSI based on a priori anatomical information derived from featured, water-based ¹ H images.

METHODS

A reconstruction algorithm exploiting ¹ H MRI for the redefinition of the ¹³ C MRSI anatomies was developed, based on a modification of the spectroscopy with linear algebraic modeling (SLAM) principle. To enhance ¹³ C spatial resolution and reduce spillover effects without compromising SNR, this model was extended by endowing it with a search allowing smooth variations in the ¹³ C MR intensity within the targeted regions of interest.

RESULTS

Experiments were performed in vitro on enzymatic solutions and in vivo on rodents, based on the administration of ¹³ C-enriched hyperpolarized pyruvate and urea. The spectral images reconstructed for these substrates and from metabolic products based on predefined ¹ H anatomical compartments using the new algorithm, compared favorably with those arising from conventional Fourier-based analyses of the same data. The new approach also delivered reliable kinetic ¹³ C results, for the kind of processes and timescales usually targeted by hyperpolarized MRSI.

CONCLUSION

A simple, flexible strategy is introduced to boost the sensitivity and resolution provided by hyperpolarized ¹³ C MRSI, based on readily available ¹ H MR information.

Efficacy of the projection onto convex sets (POCS) algorithm at Gd-EOB-DTPA-enhanced hepatobiliary-phase hepatic MRI

PURPOSE

To investigate the efficacy of the projection onto convex sets (POCS) algorithm at Gd-EOB-DTPA-enhanced hepatobiliary-phase MRI.

METHODS

In phantom study, we scanned a phantom and obtained images by conventional means (P1 images), by partial-Fourier image reconstruction (PF, P2 images) and by PF with the POCS algorithm (P3 images). Then we acquired and compared subtraction images (P2-P1 images and P3-P1 images). In clinical study, 55 consecutive patients underwent Gd-EOB-DTPA (EOB)-enhanced 3D hepatobiliary-phase MRI on a 1.5T scanner. Images were obtained using conventional method (C1 images), PF (C2 images), and PF with POCS (C3 images). The acquisition time was 17-, 14-, and 14 s for protocols C1, C2 and C3, respectively. Two radiologists assigned grades for hepatic vessel sharpness and we compared the visual grading among the 3 protocols. And one radiologist compared signal-to-noise-ratio (SNR) of the hepatic parenchyma.

RESULTS

In phantom study, there was no difference in signal intensity on a peripheral phantom column on P3-P1 images. In clinical study, there was no significant difference between C1 and C3 images (2.62 ± 0.49 vs. 2.58 ± 0.49, p = 0.70) in the score assigned for vessel sharpness nor in SNR (13.3 ± 2.67 vs. 13.1 ± 2.51, p = 0.18).

CONCLUSION

The POCS algorithm makes it possible to reduce the scan time of hepatobiliary phase (from 17 to 14 s) without reducing SNR and without increasing artifacts.

Correction for Eddy Current-Induced Echo-Shifting Effect in Partial-Fourier Diffusion Tensor Imaging

In most diffusion tensor imaging (DTI) studies, images are acquired with either a partial-Fourier or a parallel partial-Fourier echo-planar imaging (EPI) sequence, in order to shorten the echo time and increase the signal-to-noise ratio (SNR). However, eddy currents induced by the diffusion-sensitizing gradients can often lead to a shift of the echo in k-space, resulting in three distinct types of artifacts in partial-Fourier DTI. Here, we present an improved DTI acquisition and reconstruction scheme, capable of generating high-quality and high-SNR DTI data without eddy current-induced artifacts. This new scheme consists of three components, respectively, addressing the three distinct types of artifacts. First, a k-space energy-anchored DTI sequence is designed to recover eddy current-induced signal loss (i.e., Type 1 artifact). Second, a multischeme partial-Fourier reconstruction is used to eliminate artificial signal elevation (i.e., Type 2 artifact) associated with the conventional partial-Fourier reconstruction. Third, a signal intensity correction is applied to remove artificial signal modulations due to eddy current-induced erroneous T₂^∗-weighting (i.e., Type 3 artifact). These systematic improvements will greatly increase the consistency and accuracy of DTI measurements, expanding the utility of DTI in translational applications where quantitative robustness is much needed.

Motion robust GRAPPA for echo-planar imaging

PURPOSE

A readout-segmented method for acquiring robust GRAPPA calibration data for echo-planar imaging (EPI) was proposed and compared with two previous methods, including the gold standard interleaved approach and a single shot method with halved phase encode resolution.

THEORY AND METHODS

The readout-segmented and single shot techniques acquire adjacent phase encode lines in the same shot to obtain the calibration data, rather than interleaving of lines between shots, to decrease sensitivity to motion. Additionally, it uses multiple segments with shortened frequency encode extent to match the phase encode bandwidth to the undersampled data, which decreases sensitivity to B0 inhomogeneity. The three methods were tested using simulations and EPI scans of the brain in healthy volunteers.

RESULTS

The interleaved approach exhibited high sensitivity to motion, while residual undersampling artifacts remained in the single shot method due to mismatch of B0 inhomogeneity between the calibration and undersampled data. The readout segmented method exhibited no such errors, having 30% lower ghosting intensity than the single shot method and 90% lower ghosting intensity than the interleaved approach in moving subjects.

CONCLUSION

Artifacts from B0 inhomogeneity and motion during calibration scans for EPI GRAPPA can be mitigated with a readout segmented calibration scan.

Interleaved EPI based fMRI improved by multiplexed sensitivity encoding (MUSE) and simultaneous multi-band imaging

Functional magnetic resonance imaging (fMRI) is a non-invasive and powerful imaging tool for detecting brain activities. The majority of fMRI studies are performed with single-shot echo-planar imaging (EPI) due to its high temporal resolution. Recent studies have demonstrated that, by increasing the spatial-resolution of fMRI, previously unidentified neuronal networks can be measured. However, it is challenging to improve the spatial resolution of conventional single-shot EPI based fMRI. Although multi-shot interleaved EPI is superior to single-shot EPI in terms of the improved spatial-resolution, reduced geometric distortions, and sharper point spread function (PSF), interleaved EPI based fMRI has two main limitations: 1) the imaging throughput is lower in interleaved EPI; 2) the magnitude and phase signal variations among EPI segments (due to physiological noise, subject motion, and B0 drift) are translated to significant in-plane aliasing artifact across the field of view (FOV). Here we report a method that integrates multiple approaches to address the technical limitations of interleaved EPI-based fMRI. Firstly, the multiplexed sensitivity-encoding (MUSE) post-processing algorithm is used to suppress in-plane aliasing artifacts resulting from time-domain signal instabilities during dynamic scans. Secondly, a simultaneous multi-band interleaved EPI pulse sequence, with a controlled aliasing scheme incorporated, is implemented to increase the imaging throughput. Thirdly, the MUSE algorithm is then generalized to accommodate fMRI data obtained with our multi-band interleaved EPI pulse sequence, suppressing both in-plane and through-plane aliasing artifacts. The blood-oxygenation-level-dependent (BOLD) signal detectability and the scan throughput can be significantly improved for interleaved EPI-based fMRI. Our human fMRI data obtained from 3 Tesla systems demonstrate the effectiveness of the developed methods. It is expected that future fMRI studies requiring high spatial-resolvability and fidelity will largely benefit from the reported techniques.

Interleaved diffusion-weighted improved by adaptive partial-Fourier and multiband multiplexed sensitivity-encoding reconstruction

PURPOSE

We report a series of techniques to reliably eliminate artifacts in interleaved echo-planar imaging (EPI) based diffusion-weighted imaging (DWI).

METHODS

First, we integrate the previously reported multiplexed sensitivity encoding (MUSE) algorithm with a new adaptive Homodyne partial-Fourier reconstruction algorithm, so that images reconstructed from interleaved partial-Fourier DWI data are free from artifacts even in the presence of either (a) motion-induced k-space energy peak displacement, or (b) susceptibility field gradient induced fast phase changes. Second, we generalize the previously reported single-band MUSE framework to multiband MUSE, so that both through-plane and in-plane aliasing artifacts in multiband multishot interleaved DWI data can be effectively eliminated.

RESULTS

The new adaptive Homodyne-MUSE reconstruction algorithm reliably produces high-quality and high-resolution DWI, eliminating residual artifacts in images reconstructed with previously reported methods. Furthermore, the generalized MUSE algorithm is compatible with multiband and high-throughput DWI.

CONCLUSION

The integration of the multiband and adaptive Homodyne-MUSE algorithms significantly improves the spatial-resolution, image quality, and scan throughput of interleaved DWI. We expect that the reported reconstruction framework will play an important role in enabling high-resolution DWI for both neuroscience research and clinical uses.

MRI reconstruction from 2D truncated k-space

PURPOSE

To shorten acquisition time by means of both partial scanning and partial echo acquisition and to reconstruct images from such 2D partial k-space acquisitions.

MATERIALS AND METHODS

We propose an approach to reconstructing magnetic resonance images from 2D truncated k-space in which the k-space is truncated in both phase- and frequency-encoding directions. Unlike conventional reconstruction techniques, the proposed approach is based on a newly developed 2D singularity function analysis (SFA) model and a sparse representation of an image whose parameters can be estimated from the 2D partial k-space data. Such a sparse representation leads to an accurate recovery of the missing k-space data and, hence, an accurate reconstruction of the image.

RESULTS

The proposed approach can reconstruct an image from as little as 20%-30% of the k-space data and the quality of the reconstructed image is comparable to the reference image that is reconstructed from the complete k-space data.

CONCLUSION

Despite the high asymmetry of a 2D truncated k-space, the proposed approach allows for accurate reconstruction without the need of phase correction and, thus, overcomes the assumption of slow phase variations that is usually required by the existing reconstruction methods. It provides a new way of fast imaging for applications that require a significant reduction of the acquisition time.

Cardinal series to restore NMR-signals dominated by strong inhomogeneous broadening

We have devised two numerical methods of restoring incomplete band-limited NMR-signals to integrity by either interpolating or extrapolating them. Both methods are based on use of the finite cardinal series, whose filtering properties were discussed previously, to model signals. They require no prior knowledge about the system under study, but only that the available parts of the signal were oversampled enough. The methods were tested on two types of computer-simulated signal. It proved superior to the linear prediction methods and Lagrange interpolation when applied to signals measured in highly inhomogeneous magnetic fields. The extrapolation method was then applied to restore experimentally-measured refocused FID-signals of a porous medium. The missing parts of the signal of up to several times the size of its Nyquist period could be recovered by either method.

Recovery of signal loss due to an in-plane susceptibility gradient in the gradient echo EPI through acquisition of extended phase-encoding lines

In gradient echo imaging the in-plane susceptibility gradient causes an echo shift which results in signal loss. The loss of signal becomes more severe in gradient echo EPI, due to the low amplitude of the gradient which is applied in the phase-encoding direction during a long echo train. As the readout gradient amplitude is set to be very high in gradient echo EPI, the echo shift in the readout direction is negligible compared to that in the phase-encoding direction. Traditionally, a z-shimming technique has been applied to the phase-encoding direction of gradient echo EPI to restore the lost signal. This technique, however, requires a significant increase of scan time, as is also the case with the through-plane z-shimming technique. A new approach that allows one to restore the lost signal is to acquire additional phase-encoding lines beyond the regular phase-encoding range. The extension of the phase-encoding lines prior to the regular phase-encoding range exploits the delay time for optimum echo time of the BOLD sensitivity. Therefore, scan time is increased only for the extended phase-encoding lines posterior to the regular phase-encoding range. This technique has been confirmed experimentally by imaging human subject's heads at 3T.