Phase-encoding Direction Research Articles

3D distortion-free, reduced FOV diffusion-prepared gradient echo at 3 T.

To develop a 3D distortion-free reduced-FOV diffusion-prepared gradient-echo sequence and demonstrate its application in vivo for diffusion imaging of the spinal cord in healthy volunteers. A 3D multi-shot reduced-FOV diffusion-prepared gradient-echo acquisition is achieved using a slice-selective tip-down pulse in the phase-encoding direction in the diffusion preparation, combined with magnitude stabilizers, centric k-space encoding, and 2D phase navigators to correct for intershot phase errors. The accuracy of the ADC values obtained using the proposed approach was evaluated in a diffusion phantom and compared to the tabulated reference ADC values and to the ADC values obtained using a standard spin echo diffusion-weighted single-shot EPI sequence (DW-SS-EPI). Five healthy volunteers were scanned at 3 T using the proposed sequence, DW-SS-EPI, and a clinical diffusion-weighted multi-shot readout-segmented EPI sequence (RESOLVE) for cervical spinal cord imaging. Image quality, perceived SNR, and image distortion were assessed by two expert radiologists. ADC maps were calculated, and ADC values obtained with the proposed sequence were compared to those obtained using DW-SS-EPI and RESOLVE. Consistent ADC estimates were measured in the diffusion phantom with the proposed sequence and the conventional DW-SS-EPI sequence, and the ADC values were in close agreement with the reference values provided by the manufacturer of the phantom. In vivo, the proposed sequence demonstrated improved image quality, improved perceived SNR, and reduced perceived distortion compared to DW-SS-EPI, whereas all measures were comparable against RESOLVE. There were no significant differences in ADC values estimated in vivo for each of the sequences. 3D distortion-free diffusion-prepared imaging can be achieved using the proposed sequence.

Value of Spinal Cord Diffusion Imaging and Tractography in Providing Predictive Factors for Tumor Resection in Patients with Intramedullary Tumors: A Pilot Study.

This pilot study aimed to investigate the interest of high angular resolution diffusion imaging (HARDI) and tractography of the spinal cord (SC) in the management of patients with intramedullary tumors by providing predictive elements for tumor resection. Eight patients were included in a prospective study. HARDI images of the SC were acquired using a 3T MRI scanner with a reduced field of view. Opposed phase-encoding directions allowed distortion corrections. SC fiber tracking was performed using a deterministic approach, with extraction of tensor metrics. Then, regions of interest were drawn to track the spinal pathways of interest. HARDI and tractography added value by providing characteristics about the microstructural organization of the spinal white fibers. In patients with SC tumors, tensor metrics demonstrated significant changes in microstructural architecture, axonal density, and myelinated fibers (all, p < 0.0001) of the spinal white matter. Tractography aided in the differentiation of tumor histological types (SC-invaded vs. pushed back by the tumor), and differentiation of the spinal tracts enabled the determination of precise anatomical relationships between the tumor and the SC, defining the tumor resectability. This study underlines the value of using HARDI and tractography in patients with intramedullary tumors, to show alterations in SC microarchitecture and to differentiate spinal tracts to establish predictive factors for tumor resectability.

Limitations of 2-dimensional line-scan MRI for directly measuring neural activity

Abstract A 2D-line-scan MRI sequence has been reported to directly measure neural responses to stimuli (the “DIANA response”). Attempts to replicate the DIANA response have failed, even with higher field strength and more repetitions. Part of this discrepancy is likely due to a limited understanding of how physiological noise manifests in 2D-line-scan acquisition sequences. Specifically, it is unclear what the consequences are of breaking the assumption that the imaging substrate remains constant between each line acquisition. To answer this question, we collected 2D-line-scan data at 3T from human subjects viewing a blank screen. We found temporal fluctuations in the reconstructed time series that could easily be confused with neural responses to stimuli. These fluctuations were present both in the head and in the surrounding empty volume along the span of the phase-encoding direction from the head. The timing of these fluctuations varied systematically and smoothly along the phase-encoding direction. These artifacts are similar to well-known phase-encode artifacts in EPI and GRE images, but are exacerbated due to longer acquisition times in the 2D-line-scan sequence (seconds vs milliseconds). We explain these artifacts with a model that accounts for the acquisition sequence and incorporates time-varying contrast fluctuations and movement in the imaging substrate. Using the model, we quantify the amount of cortical- and scan-averaging one might need to reliably distinguish a DIANA response from noise.

Fast and silent MRI using nonlinear gradient fields at the ultrasonic gradient switching frequency of 20 kHz with a Point Spread Function framework reconstruction.

To demonstrate the feasibility of using a nonlinear gradient field for spatial encoding at the ultrasonic switching frequency of 20 kHz and present a framework to reconstruct data acquired in this way. Nonlinear encoding at 20 kHz was realized by using a single-axis silent gradient insert for imaging in the periphery, that, is the nonlinear region, of the gradient field. The gradient insert induces a rapidly oscillating gradient field in the phase-encode direction, which enables nonlinear encoding when combined with a Cartesian readout from the linear whole-body gradients. Data from a 2D gradient echo sequence were reconstructed using a point spread function (PSF) framework. Accelerated scans were also simulated via retrospective undersampling (R = 1 to R = 8) to determine the effectiveness of the PSF-framework for accelerated imaging. Using a nonlinear gradient field switched at 20 kHz and the PSF-framework resulted in images of comparable quality to images from conventional Cartesian linear encoding. At increased acceleration factors (R ≤ 8), the PSF-framework outperformed linear SENSE reconstructions by improved controlling of aliasing artifacts. Using the PSF-framework, images of comparable quality to conventional SENSE reconstructions are possible via combining traditional linear and ultrasonic oscillating nonlinear encoding fields. Using nonlinear gradient fields relaxes the demand for strictly linear gradient fields, enabling much higher slew rates with a reduced risk of peripheral nerve stimulation or cardiac stimulation, which could aid in extension to ultrasonic whole-body MRI. The lack of aliasing artifacts also highlights the potential of accelerated imaging using the PSF-framework.

Fast 3D fMRI acquisition with high spatial resolutions over a reduced FOV.

To develop and demonstrate a fast 3D fMRI acquisition technique with high spatial resolution over a reduced FOV, named k-t 3D reduced FOV imaging (3D-rFOVI). Based on 3D gradient-echo EPI, k-t 3D-rFOVI used a 2D RF pulse to reduce the FOV in the in-plane phase-encoding direction, boosting spatial resolution without increasing echo train length. For image acceleration, full sampling was applied in the central k-space region along the through-slab direction (kz) for all time frames, while randomized undersampling was used in outer kz regions at different time frames. Images were acquired at 3T and reconstructed using a method based on partial separability. fMRI detection sensitivity of k-t 3D-rFOVI was quantitively analyzed with simulation data. Human visual fMRI experiments were performed to evaluate k-t 3D-rFOVI and compare it with a commercial multiband EPI sequence. The simulation data showed that k-t 3D-rFOVI can detect 100% of fMRI activations with an acceleration factor (R) of 2 and ˜80% with R = 6. In the human fMRI data acquired with 1.5-mm spatial resolution and 800-ms volume TR (TRvol), k-t 3D-rFOVI with R = 4 detected 46% more activated voxels in the visual cortex than the multiband EPI. Additional fMRI experiments showed that k-t 3D-rFOVI can achieve TRvol of 480 ms with R = 6, while reliably detecting visual activation. k-t 3D-rFOVI can simultaneously achieve a high spatial resolution (1.5-mm isotropically) and short TRvol (480-ms) at 3T. It offers a robust acquisition technique for fast fMRI studies over a focused brain volume.

Solving the Pervasive Problem of Protocol Non-Compliance in MRI using an Open-Source tool mrQA

Pooling data across diverse sources acquired by multisite consortia requires compliance with a predefined reference protocol i.e., ensuring different sites and scanners for a given project have used identical or compatible MR physics parameter values. Traditionally, this has been an arduous and manual process due to difficulties in working with the complicated DICOM standard and lack of resources allocated towards protocol compliance. Moreover, issues of protocol compliance is often overlooked for lack of realization that parameter values are routinely improvised/modified locally at various sites. The inconsistencies in acquisition protocols can reduce SNR, statistical power, and in the worst case, may invalidate the results altogether. An open-source tool, mrQA was developed to automatically assess protocol compliance on standard dataset formats such as DICOM and BIDS, and to study the patterns of non-compliance in over 20 open neuroimaging datasets, including the large ABCD study. The results demonstrate that the lack of compliance is rather pervasive. The frequent sources of non-compliance include but are not limited to deviations in Repetition Time, Echo Time, Flip Angle, and Phase Encoding Direction. It was also observed that GE and Philips scanners exhibited higher rates of non-compliance relative to the Siemens scanners in the ABCD dataset. Continuous monitoring for protocol compliance is strongly recommended before any pre/post-processing, ideally right after the acquisition, to avoid the silent propagation of severe/subtle issues. Although, this study focuses on neuroimaging datasets, the proposed tool mrQA can work with any DICOM-based datasets.

Enhancing quality and speed in database-free neural network reconstructions of undersampled MRI with SCAMPI.

We present SCAMPI (Sparsity Constrained Application of deep Magnetic resonance Priors for Image reconstruction), an untrained deep Neural Network for MRI reconstruction without previous training on datasets. It expands the Deep Image Prior approach with a multidomain, sparsity-enforcing loss function to achieve higher image quality at a faster convergence speed than previously reported methods. Two-dimensional MRI data from the FastMRI dataset with Cartesian undersampling in phase-encoding direction were reconstructed for different acceleration rates for single coil and multicoil data. The performance of our architecture was compared to state-of-the-art Compressed Sensing methods and ConvDecoder, another untrained Neural Network for two-dimensional MRI reconstruction. SCAMPI outperforms these by better reducing undersampling artifacts and yielding lower error metrics in multicoil imaging. In comparison to ConvDecoder, the U-Net architecture combined with an elaborated loss-function allows for much faster convergence at higher image quality. SCAMPI can reconstruct multicoil data without explicit knowledge of coil sensitivity profiles. Moreover, it is a novel tool for reconstructing undersampled single coil k-space data. Our approach avoids overfitting to dataset features, that can occur in Neural Networks trained on databases, because the network parameters are tuned only on the reconstruction data. It allows better results and faster reconstruction than the baseline untrained Neural Network approach.

Validation of echo planar imaging based diffusion-weighted magnetic resonance imaging on a 0.35 T MR-Linac

Background and PurposeThe feasibility of acquiring diffusion-weighted imaging (DWI) images on an MR-Linac for quantitative response assessment during radiotherapy was explored. DWI data obtained with a Spin Echo Echo Planar Imaging sequence adapted for a 0.35 T MR-Linac were examined and compared with DWI data from a conventional 3 T scanner. Materials and MethodsApparent diffusion coefficient (ADC) measurements and a distortion correction technique were investigated using DWI-calibrated phantoms and in the brains of seven volunteers. All DWI utilized two phase-encoding directions for distortion correction and off-resonance field estimation. ADC maps in the brain were analyzed for automatically segmented normal tissues. ResultsPhantom ADC measurements on the MR-Linac were within a 3 % margin of those recorded by the 3 T scanner. The maximum distortion observed in the phantom was 2.0 mm prior to correction and 1.1 mm post-correction on the MR-Linac, compared to 6.0 mm before correction and 3.6 mm after correction at 3 T. In vivo, the average ADC values for gray and white matter exhibited variations of 14 % and 4 %, respectively, for different selections of b-values on the MR-Linac. Distortions in brain images before correction, estimated through the off-resonance field, reached 2.7 mm on the MR-Linac and 12 mm at 3 T. ConclusionAccurate ADC measurements are achievable on a 0.35 T MR-Linac, both in phantom and in vivo. The selection of b-values significantly influences ADC values in vivo. DWI on the MR-Linac demonstrated lower distortion levels, with a maximum distortion reduced to 1.1 mm after correction.

Thin-slice reverse encoding distortion correction DWI facilitates visualization of non-functioning pituitary neuroendocrine tumor (PitNET)/pituitary adenoma and surrounding normal structures

BackgroundTo evaluate the clinical usefulness of thin-slice echo-planar imaging (EPI)-based diffusion-weighted imaging (DWI) with an on-console distortion correction technique, termed reverse encoding distortion correction DWI (RDC-DWI), in patients with non-functioning pituitary neuroendocrine tumor (PitNET)/pituitary adenoma.MethodsPatients with non-functioning PitNET/pituitary adenoma who underwent 3-T RDC-DWI between December 2021 and September 2022 were retrospectively enrolled. Image quality was compared among RDC-DWI, DWI with correction for distortion induced by B0 inhomogeneity alone (B0-corrected-DWI), and original EPI-based DWI with anterior-posterior phase-encoding direction (AP-DWI). Susceptibility artifact, anatomical visualization of cranial nerves, overall tumor visualization, and visualization of cavernous sinus invasion were assessed qualitatively. Quantitative assessment of geometric distortion was performed by evaluation of anterior and posterior displacement between each DWI and the corresponding three-dimensional T2-weighted imaging. Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and apparent diffusion coefficient values were measured.ResultsSixty-four patients (age 70.8 ± 9.9 years [mean ± standard deviation]; 33 females) with non-functioning PitNET/pituitary adenoma were evaluated. In terms of susceptibility artifacts in the frontal and temporal lobes, visualization of left trigeminal nerve, overall tumor visualization, and anterior displacement, RDC-DWI performed the best and B0-corrected-DWI performed better than AP-DWI. The right oculomotor and right trigeminal nerves were better visualized by RDC-DWI than by B0-corrected-DWI and AP-DWI. Visualization of cavernous sinus invasion and posterior displacement were better by RDC-DWI and B0-corrected-DWI than by AP-DWI. SNR and CNR were the highest for RDC-DWI.ConclusionsRDC-DWI achieved excellent image quality regarding susceptibility artifact, geometric distortion, and tumor visualization in patients with non-functioning PitNET/pituitary adenoma.Relevance statementRDC-DWI facilitates excellent visualization of the pituitary region and surrounding normal structures, and its on-console distortion correction technique is convenient. RDC-DWI can clearly depict cavernous sinus invasion of PitNET/pituitary adenoma even without contrast medium.Key points• RDC-DWI is an EPI-based DWI technique with a novel on-console distortion correction technique.• RDC-DWI corrects distortion due to B0 field inhomogeneity and eddy current.• We evaluated the usefulness of thin-slice RDC-DWI in non-functioning PitNET/pituitary adenoma.• RDC-DWI exhibited excellent visualization in the pituitary region and surrounding structures.• In addition, the on-console distortion correction of RDC-DWI is clinically convenient.Graphical

Effect of Phase Encoding Direction on Image Quality in Single-Shot EPI Diffusion-Weighted Imaging of the Breast.

In breast diffusion-weighted imaging (DWI), distortion and physiologic artifacts affect clinical interpretation. Image quality can be optimized by addressing the effect of phase encoding (PE) direction on these artifacts. To compare distortion artifacts in breast DWI acquired with different PE directions and polarities, and to discuss their clinical implications. Prospective. Eleven healthy volunteers (median age: 47 years old; range: 22-74 years old) and a breast phantom. Single-shot echo planar DWI and three-dimensional fast gradient echo sequences at 3 T. All DWI data were acquired with left-right, right-left, posterior-anterior, and anterior-posterior PE directions. In phantom data, displacement magnitude was evaluated by comparing the location of landmarks in anatomical and DWI images. Three breast radiologists (5, 17, and 23 years of experience) assessed the presence or absence of physiologic artifacts in volunteers' DWI datasets and indicated their PE-direction preference. Analysis of variance with post-hoc tests were used to assess differences in displacement magnitude across DWI datasets and observers. A binomial test and a chi-squared test were used to evaluateif each in vivo DWI dataset had an equal probability (25%) of being preferred by radiologists. Inter-reader agreement was evaluated using Gwet's AC1 agreement coefficient. A P-value <0.05 was considered statistically significant. In the phantom study, median displacement was the significantly largest in posterior-anterior data. While the displacement in the anterior-posterior and left-right data were equivalent (P = 0.545). In the in vivo data, there were no physiological artifacts observed in any dataset, regardless of PE direction. In the reader study, there was a significant preference for the posterior-anterior datasets which were selected 94% of the time. There was good agreement between readers (0.936). This study showed the impact of PE direction on distortion artifacts in breast DWI. In healthy volunteers, the posterior-to-anterior PE direction was preferred by readers. 2 TECHNICAL EFFICACY: Stage 1.

Physics-informed deep learning for T2-deblurred superresolution turbo spin echo MRI.

Deep learning superresolution (SR) is a promising approach to reduce MRI scan time without requiring custom sequences or iterative reconstruction. Previous deep learning SR approaches have generated low-resolution training images by simple k-space truncation, but this does not properly model in-plane turbo spin echo (TSE) MRI resolution degradation, which has variable T2 relaxation effects in different k-space regions. To fill this gap, we developed a T2 -deblurred deep learning SR method for the SR of 3D-TSE images. A SR generative adversarial network was trained using physically realistic resolution degradation (asymmetric T2 weighting of raw high-resolution k-space data). For comparison, we trained the same network structure on previous degradation models without TSE physics modeling. We tested all models for both retrospective and prospective SR with 3 × 3 acceleration factor (in the two phase-encoding directions) of genetically engineered mouse embryo model TSE-MR images. The proposed method can produce high-quality 3 × 3 SR images for a typical 500-slice volume with 6-7 mouse embryos. Because 3 × 3 SR was performed, the image acquisition time can be reduced from 15 h to 1.7 h. Compared to previous SR methods without TSE modeling, the proposed method achieved the best quantitative imaging metrics for both retrospective and prospective evaluations and achieved the best imaging-quality expert scores for prospective evaluation. The proposed T2 -deblurring method improved accuracy and image quality of deep learning-based SR of TSE MRI. This method has the potential to accelerate TSE image acquisition by a factor of up to 9.

Simultaneous T2 -weighted real-time MRI of two orthogonalslices.

MR guidance is used during therapy to detect and compensate for lesion motion. T2 -weighted MRI often has a superior lesion contrast in comparison to T1 -weighted real-time imaging. The purpose of this work was to design a fast T2 -weighted sequence capable of simultaneously acquiring two orthogonal slices, enabling real-time tracking of lesions. To generate a T2 contrast in two orthogonal slices simultaneously, a sequence (Ortho-SFFP-Echo) was designed that samples the T2 -weighted spin echo (S- ) signal in a TR-interleaved acquisition of two slices. Slice selection and phase-encoding directions are swapped between the slices, leading to a unique set of spin-echo signal conditions. To minimize motion-related signal dephasing, additional flow-compensation strategies are implemented. In both the abdominal breathing phantom and in vivo experiments, a time series was acquired using Ortho-SSFP-Echo. The centroid of the target was tracked in postprocessing steps. In the phantom, the lesion could be identified and delineated in the dynamic images. In the volunteer experiments, the kidney was visualized with a T2 contrast at a temporal resolution of 0.45 s under free-breathing conditions. A respiratory belt demonstrated a strong correlation with the time course of the kidney centroid in the head-foot direction. A hypointense saturation band at the slice overlap did not inhibit lesion tracking in the semi-automatic postprocessing steps. The Ortho-SFFP-Echo sequence delivers real-time images with a T2 -weighted contrast in two orthogonal slices. The sequence allows for simultaneous acquisition, which could be beneficial for real-time motion tracking in radiotherapy or interventional MRI.

Effects of phase encoding direction on test-retest reliability of human functional connectome

The majority of human connectome studies in the literature based on functional magnetic resonance imaging (fMRI) data use either an anterior-to-posterior (AP) or a posterior-to-anterior (PA) phase encoding direction (PED). However, whether and how PED would affect test-retest reliability of functional connectome is unclear. Here, in a sample of healthy subjects with two sessions of fMRI scans separated by 12 weeks (two runs per session, one with AP, the other with PA), we tested the influence of PED on global, nodal, and edge connectivity in the constructed brain networks. All data underwent the state-of-the-art Human Connectome Project (HCP) pipeline to correct for phase-encoding-related distortions before entering analysis. We found that at the global level, the PA scans showed significantly higher intraclass correlation coefficients (ICCs) for global connectivity compared with AP scans, which was particularly prominent when using the Seitzman-300 atlas (versus the CAB-NP-718 atlas). At the nodal level, regions most strongly affected by PED were consistently mapped to the cingulate cortex, temporal lobe, sensorimotor areas, and visual areas, with significantly higher ICCs during PA scans compared with AP scans, regardless of atlas. Better ICCs were also observed during PA scans at the edge level, in particular when global signal regression (GSR) was not performed. Further, we demonstrated that the observed reliability differences between PEDs may relate to a similar effect on the reliability of temporal signal-to-noise ratio (tSNR) in the same regions (that PA scans were associated with higher reliability of tSNR than AP scans). Averaging the connectivity outcome from the AP and PA scans could increase median ICCs, especially at the nodal and edge levels. Similar results at the global and nodal levels were replicated in an independent, public dataset from the HCP-Early Psychosis (HCP-EP) study with a similar design but a much shorter scan session interval. Our findings suggest that PED has significant effects on the reliability of connectomic estimates in fMRI studies. We urge that these effects need to be carefully considered in future neuroimaging designs, especially in longitudinal studies such as those related to neurodevelopment or clinical intervention.

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

PurposeTo 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. MethodsWe 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. ResultsBoth 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. ConclusionsThe 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.

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

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

Automated Mapping of Residual Distortion Severity in Diffusion MRI.

Susceptibility-induced distortion is a common artifact in diffusion MRI (dMRI), which deforms the dMRI locally and poses significant challenges in connectivity analysis. While various methods were proposed to correct the distortion, residual distortions often persist at varying degrees across brain regions and subjects. Generating a voxel-level residual distortion severity map can thus be a valuable tool to better inform downstream connectivity analysis. To fill this current gap in dMRI analysis, we propose a supervised deep-learning network to predict a severity map of residual distortion. The training process is supervised using the structural similarity index measure (SSIM) of the fiber orientation distribution (FOD) in two opposite phase encoding (PE) directions. Only b0 images and related outputs from the distortion correction methods are needed as inputs in the testing process. The proposed method is applicable in large-scale datasets such as the UK Biobank, Adolescent Brain Cognitive Development (ABCD), and other emerging studies that only have complete dMRI data in one PE direction but acquires b0 images in both PEs. In our experiments, we trained the proposed model using the Lifespan Human Connectome Project Aging (HCP-Aging) dataset and apply the trained model to data from UK Biobank. Our results show low training, validation, and test errors, and the severity map correlates excellently with an FOD integrity measure in both HCP-Aging and UK Biobank data. The proposed method is also highly efficient and can generate the severity map in around 1 second for each subject.

A 2D-GRAPPA Algorithm with a Boomerang Kernel for 3D MRI Data Accelerated along Two Phase-Encoding Directions

For the reconstruction of 3D MRI data that are accelerated along the two phase-encoding directions, the 2D-generalized autocalibrating partially parallel acquisitions (GRAPPA) algorithm can be used to estimate the missing data in the k-space. We propose a new boomerang-shaped kernel based on theoretic and systemic analyses of the shape and dimensions of the kernel. The reconstruction efficiency of the 2D-GRAPPA algorithm with the proposed boomerang-shaped kernel (i.e., boomerang kernel (BK)-2D-GRAPPA) was compared with other 2D-GRAPPA algorithms that utilize different types of kernels (i.e., EX-2D-GRAPPA and SK-2D-GRAPPA) based on computer simulation, phantom and in vivo experiments. The proposed method was validated for different sets of ACS lines with acceleration factors from four to eight and various sizes of the kernels. A quantitative analysis was also performed by comparing the normalized root mean squared error (nRMSE) in the images and the undersampled edges. Computer simulation, in vivo and phantom experiments, and the quantitative analysis, showed that the proposed method could reduce aliasing artifacts without reducing the SNRs of the reconstructed images.

Improving accelerated MRI by deep learning withsparsified complex data.

To obtain high-quality accelerated MR images with complex-valued reconstruction from undersampled k-space data. The MRI scans from human subjects were retrospectively undersampled with a regular pattern using skipped phase encoding, leading to ghosts in zero-filling reconstruction. A complex difference transform along the phase-encoding direction was applied in image domain to yield sparsified complex-valued edge maps. These sparse edge maps were used to train a complex-valued U-type convolutional neural network (SCU-Net) for deghosting. A k-space inverse filtering was performed on the predicted deghosted complex edge maps from SCU-Net to obtain final complex images. The SCU-Net was compared with other algorithms including zero-filling, GRAPPA, RAKI, finite difference complex U-type convolutional neural network (FDCU-Net), and CU-Net, both qualitatively and quantitatively, using such metrics as structural similarity index, peak SNR, and normalized mean square error. The SCU-Net was found to be effective in deghosting aliased edge maps even at high acceleration factors. High-quality complex images were obtained by performing an inverse filtering on deghosted edge maps. The SCU-Net compared favorably with other algorithms. Using sparsified complex data, SCU-Net offers higher reconstruction quality for regularly undersampled k-space data. The proposed method is especially useful for phase-sensitive MRI applications.

Simultaneous Optimization of MP2RAGE T1 -weighted (UNI) and FLuid And White matter Suppression (FLAWS) brain images at 7T using Extended Phase Graph (EPG) Simulations.

The MP2RAGE sequence is typically optimized for either T1 -weighted uniform image (UNI) or gray matter-dominant fluid and white matter suppression (FLAWS) contrast images. Here, the purpose was to optimize an MP2RAGE protocol at 7 Tesla to provide UNI and FLAWS images simultaneously in a clinically applicable acquisition time at <0.7 mm isotropic resolution. Using the extended phase graph formalism, the signal evolution of the MP2RAGE sequence was simulated incorporating T2 relaxation, diffusion, RF spoiling, and B1 + variability. Flip angles and TI were optimized at different TRs (TRMP2RAGE ) to produce an optimal contrast-to-noise ratio for UNI and FLAWS images. Simulation results were validated by comparison to MP2RAGE brain scans of 5 healthy subjects, and a final protocol at TRMP2RAGE = 4000 ms was applied in 19 subjects aged 8-62 years with and without epilepsy. FLAWS contrast images could be obtained while maintaining >85% of the optimal UNI contrast-to-noise ratio. Using TI1 /TI2 /TRMP2RAGE of 650/2280/4000 ms, 6/8 partial Fourier in the inner phase-encoding direction, and GRAPPA factor=4 in the other, images with 0.65 mm isotropic resolution were produced in <7.5 min. The contrast-to-noise ratio was around 20% smaller at TRMP2RAGE = 4000 ms compared to that at TRMP2RAGE = 5000 ms; however, the 20% shorter duration makes TRMP2RAGE = 4000 ms a good candidate for clinical applications example, pediatrics. FLAWS and UNI images could be obtained in a single scan with 0.65 mm isotropic resolution, providing a set of high-contrast images and full brain coverage in a clinically applicable scan time. Images with excellent anatomical detail were demonstrated over a wide age range using the optimized parameter set.

Joint K-space and Image-space Parallel Imaging (KIPI) for accelerated chemical exchange saturation transfer acquisition.

To develop an auto-calibrated technique by joint K-space and Image-space Parallel Imaging (KIPI) for accelerated CEST acquisition. The KIPI method selects a calibration frame with a low acceleration factor (AF) and auto-calibration signals (ACS) acquired, from which the coil sensitivity profiles and artifact correction maps are calculated after restoring the k-space by GRAPPA. Then the other frames with high AF and without ACS can be reconstructed by SENSE and artifact suppression. The signal leakage due to the T2 -decay filtering in k-space compromises the SENSE reconstruction, which can be corrected by the artifact suppression algorithm of KIPI. The 2D and 3D imaging experiments were done on the phantom, healthy volunteer, and brain tumor patient with a 3T scanner. The proposed KIPI method was evaluated by retrospectively undersampled data with variable AFs and compared against existing parallel imaging methods (SENSE/auto, GRAPPA, and ESPIRiT). KIPI enabled CEST frames with random AFs to achieve similar image quality, eliminated the strong aliasing artifacts, and generated significantly smaller errors than the other methods (p < 0.01). The KIPI method permitted an AF up to 12-fold in both phase-encoding and slice-encoding directions for 3D CEST source images, achieving an overall 8.2-fold speedup in scan time. KIPI is a novel auto-calibrated parallel imaging method that enables variable AFs for different CEST frames, achieves a significant reduction in scan time, and does not compromise the accuracy of CEST maps.