Simultaneous Multi-slice EPI Research Articles

Dynamic off-resonance correction improves functional image analysis in fMRI of awake behaving non-human primates.

Use of functional MRI in awake non-human primate (NHPs) has recently increased. Scanning animals while awake makes data collection possible in the absence of anesthetic modulation and with an extended range of possible experimental designs. Robust awake NHP imaging however is challenging due to the strong artifacts caused by time-varying off-resonance changes introduced by the animal's body motion. In this study, we sought to thoroughly investigate the effect of a newly proposed dynamic off-resonance correction method on brain activation estimates using extended awake NHP data. We correct for dynamic B0 changes in reconstruction of highly accelerated simultaneous multi-slice EPI acquisitions by estimating and correcting for dynamic field perturbations. Functional MRI data were collected in four male rhesus monkeys performing a decision-making task in the scanner, and analyses of improvements in sensitivity and reliability were performed compared to conventional image reconstruction. Applying the correction resulted in reduced bias and improved temporal stability in the reconstructed time-series data. We found increased sensitivity to functional activation at the individual and group levels, as well as improved reliability of statistical parameter estimates. Our results show significant improvements in image fidelity using our proposed correction strategy, as well as greatly enhanced and more reliable activation estimates in GLM analyses.

Super-resolution QSM in little or no additional time for imaging (NATIve) using 2D EPI imaging in 3 orthogonal planes

Quantitative Susceptibility Mapping has the potential to provide additional insights into neurological diseases but is typically based on a quite long (5–10 min) 3D gradient-echo scan which is highly sensitive to motion. We propose an ultra-fast acquisition based on three orthogonal (sagittal, coronal and axial) 2D simultaneous multi-slice EPI scans with 1 mm in-plane resolution and 3 mm thick slices. Images in each orientation are corrected for susceptibility-related distortions and co-registered with an iterative non-linear Minimum Deformation Averaging (Volgenmodel) approach to generate a high SNR, super-resolution data set with an isotropic resolution of close to 1 mm. The net acquisition time is 3 times the volume acquisition time of EPI or about 12 s, but the three volumes could also replace “dummy scans” in fMRI, making it feasible to acquire QSM in little or No Additional Time for Imaging (NATIve). NATIve QSM values agreed well with reference 3D GRE QSM in the basal ganglia in healthy subjects. In patients with multiple sclerosis, there was also a good agreement between the susceptibility values within lesions and control ROIs and all lesions which could be seen on 3D GRE QSMs could also be visualized on NATIve QSMs. The approach is faster than conventional 3D GRE by a factor of 25–50 and faster than 3D EPI by a factor of 3–5. As a 2D technique, NATIve QSM was shown to be much more robust to motion than the 3D GRE and 3D EPI, opening up the possibility of studying neurological diseases involving iron accumulation and demyelination in patients who find it difficult to lie still for long enough to acquire QSM data with conventional methods.

Simultaneous multislice EPI prospective motion correction by real-time receiver phase correction and coil sensitivity map interpolation.

To improve the image reconstruction for prospective motion correction (PMC) of simultaneous multislice (SMS) EPI of the brain, an update of receiver phase and resampling of coil sensitivities are proposed and evaluated. A camera-based system was used to track head motion (3 translations and 3 rotations) and dynamically update the scanposition and orientation. We derived the change in receiver phase associated with a shifted field of view (FOV) and applied it in real-time to each k-space line of the EPI readout trains. Second, for the SMS reconstruction, we adapted resampled coil sensitivity profiles reflecting the movement of slices. Single-shot gradient-echo SMS-EPI scans were performed in phantoms and human subjects for validation. Brain SMS-EPI scans in the presence of motion with PMC and no phase correction for scan plane shift showed noticeable artifacts. These artifacts were visually and quantitatively attenuated when corrections were enabled. Correcting misaligned coil sensitivity maps improved the temporal SNR (tSNR) of time series by 24% (p = 0.0007) for scans with large movements (up to ˜35 mm and 30°). Correcting the receiver phase improved the tSNR of a scan with minimal head movement by 50% from 50 to 75 for a United Kingdom biobank protocol. Reconstruction-induced motion artifacts in single-shot SMS-EPI scans acquired with PMC can be removed by dynamically adjusting the receiver phase of each line across EPI readout trains and updating coil sensitivity profiles during reconstruction. The method may be a valuable tool for SMS-EPI scans in the presence of subject motion.

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

3Dpulse sequences enable high-resolution acquisition with a high SNRand ideal slice profiles, which, however, is particularly difficult for diffusion MRI (dMRI) due to the additional phase errors from diffusion encoding. 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 2Dsimultaneous multi-slice EPIwithin 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. 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. 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.

A split-label design for simultaneous measurements of perfusion in distant slices by pulsed arterial spin labeling.

PurposeMultislice arterial spin labeling (ASL) MRI acquisitions are currently challenging in skeletal muscle because of long transit times, translating into low‐perfusion SNR in distal slices when large spatial coverage is required. However, fiber type and oxidative capacity vary along the length of healthy muscles, calling for multislice acquisitions in clinical studies. We propose a new variant of flow alternating inversion recovery (FAIR) that generates sufficient ASL signal to monitor exercise‐induced perfusion changes in muscle in two distant slices.MethodsLabel around and between two 7‐cm distant slices was created by applying the presaturation/postsaturation and selective inversion modules selectively to each slice (split‐label multislice FAIR). Images were acquired using simultaneous multislice EPI. We validated our approach in the brain to take advantage of the high resting‐state perfusion, and applied it in the lower leg muscle during and after exercise, interleaved with a single‐slice FAIR as a reference.ResultsWe show that standard multislice FAIR leads to an underestimation of perfusion, while the proposed split‐label multislice approach shows good agreement with separate single‐slice FAIR acquisitions in brain, as well as in muscle following exercise.ConclusionSplit‐label FAIR allows measuring muscle perfusion in two distant slices simultaneously without losing sensitivity in the distal slice.

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.

Segmented K-space blipped-controlled aliasing in parallel imaging for high spatiotemporal resolution EPI.

A segmented k-space blipped-controlled aliasing in parallel imaging (skipped-CAIPI) sampling strategy for EPI is proposed, which allows for a flexible choice of EPI factor and phase encode bandwidth independent of the controlled aliasing in parallel imaging (CAIPI) sampling pattern. With previously proposed approaches, exactly two EPI trajectories were possible given a specific CAIPI pattern, either with slice gradient blips (blipped-CAIPI) or following a shot-selective CAIPI approach (higher resolution). Recently, interleaved multi-shot segmentation along shot-selective CAIPI trajectories has been applied for high-resolution anatomical imaging. For more flexibility and a broader range of applications, we propose segmentation along any blipped-CAIPI trajectory. Thus, all EPI factors and phase encode bandwidths available with traditional segmented EPI can be combined with controlled aliasing. Temporal SNR maps of moderate-to-high-resolution time series acquisitions at varying undersampling factors demonstrate beneficial sampling alternatives to blipped-CAIPI or shot-selective CAIPI. Rapid high-resolution scans furthermore demonstrate SNR-efficient and motion-robust structural imaging with almost arbitrary EPI factor and minimal noise penalty. Skipped-CAIPI sampling increases protocol flexibility for high spatiotemporal resolution EPI. In terms of SNR and efficiency, high-resolution functional or structural scans benefit vastly from a free choice of the CAIPI pattern. Even at moderate resolutions, the independence of sampling pattern, TE, and image matrix size is valuable for optimized functional protocol design. Although demonstrated with 3D-EPI, skipped-CAIPI is also applicable with simultaneous multislice EPI.

Comparison of SMS-EPI and 3D-EPI at 7T in an fMRI localizer study with matched spatiotemporal resolution and homogenized excitation profiles.

The simultaneous multi-slice EPI (SMS-EPI, a.k.a. MB-EPI) sequence has met immense popularity recently in functional neuroimaging. A still less common alternative is the use of 3D-EPI, which offers similar acceleration capabilities. The aim of this work was to compare the SMS-EPI and the 3D-EPI sequences in terms of sampling strategies for the detection of task-evoked activations at 7T using detection theory. To this end, the spatial and temporal resolutions of the sequences were matched (1.6 mm isotropic resolution, TR = 1200 ms) and their excitation profiles were homogenized by means of calibration-free parallel-transmission (Universal Pulses). We used a fast-event “localizer” paradigm of 5:20 min in order to probe sensorimotor functions (visual, auditory and motor tasks) as well as higher level functions (language comprehension, mental calculation), where results from a previous large-scale study at 3T (N = 81) served as ground-truth reference for the brain areas implicated in each cognitive function. In the current study, ten subjects were scanned while their activation maps were generated for each cognitive function with the GLM analysis. The SMS-EPI and 3D-EPI sequences were compared in terms of raw tSNR, t-score testing for the mean signal, activation strength and accuracy of the robust sensorimotor functions. To this end, the sensitivity and specificity of these contrasts were computed by comparing their activation maps to the reference brain areas obtained in the 3T study. Estimated flip angle distributions in the brain reported a normalized root mean square deviation from the target value below 10% for both sequences. The analysis of the t-score testing for the mean signal revealed temporal noise correlations, suggesting the use of this metric instead of the traditional tSNR for testing fMRI sequences. The SMS-EPI and 3D-EPI thereby yielded similar performance from a detection theory perspective.

PEC-GRAPPA reconstruction of simultaneous multislice EPI with slice-dependent 2D Nyquist ghost correction.

To provide simultaneous multislice (SMS) EPI reconstruction with k-space implementation and robust Nyquist ghost correction. 2D phase error correction SENSE (PEC-SENSE) was recently developed for Nyquist ghost correction in SMS EPI reconstruction for which virtual coil simultaneous autocalibration and k-space estimation (VC-SAKE) was used to remove slice-dependent Nyquist ghosts and intershot 2D phase variations in multi-shot EPI reference scan. However, masking coil sensitivity maps to exclude background region in PEC-SENSE and manually selecting slice-wise target ranks in VC-SAKE are cumbersome procedures in practice. To avoid masking, the concept of PEC-SENSE is extended to k-space implementation and termed as PEC-GRAPPA. Furthermore, a singular value shrinkage scheme is incorporated in VC-SAKE to circumvent the empirical slice-wise target rank selection. PEC-GRAPPA was evaluated and compared to PEC-SENSE with/without masking and 1D linear phase correction GRAPPA. PEC-GRAPPA robustly reconstructed SMS EPI images from 7T phantom and human brain data, effectively removing the phase error-induced artifacts. The resulting residual artifact level and temporal SNR were comparable to those by PEC-SENSE with careful tuning. PEC-GRAPPA outperformed PEC-SENSE without masking and 1D linear phase correction GRAPPA. Our proposed PEC-GRAPPA approach effectively removes the artifacts caused by Nyquist ghosts in SMS EPI without cumbersome tuning. This approach provides a robust and practical implementation of SMS EPI reconstruction in k-space with slice-dependent 2D Nyquist ghost correction.

A framework for motion correction of background suppressed arterial spin labeling perfusion images acquired with simultaneous multi-slice EPI.

PurposeWhen using simultaneous multi‐slice (SMS) EPI for background suppressed (BGS) arterial spin labeling (ASL), correction of through‐plane motion could introduce artefacts, because the slices with most effective BGS are adjacent to slices with the least BGS. In this study, a new framework is presented to correct for such artefacts.MethodsThe proposed framework consists of 3 steps: (1) homogenization of the static tissue signal over the different slices to eliminate most inter‐slice differences because of different levels of BGS, (2) application of motion correction, and (3) extraction of a perfusion‐weighted signal using a general linear model. The proposed framework was evaluated by simulations and a functional ASL study with intentional head motion.ResultsSimulation studies demonstrated that the strong signal differences between slices with the most and least effective BGS caused sub‐optimal estimation of motion parameters when through‐plane motion was present. Although use of the M0 image as the reference for registration allowed 82% improvement of motion estimation for through‐plane motion, it still led to residual subtraction errors caused by different static tissue signal between control and label because of different BGS levels. By using our proposed framework, those problems were minimized, and the accuracy of CBF estimation was improved. Moreover, the functional ASL study showed improved detection of visual and motor activation when applying the framework as compared to conventional motion correction, as well as when motion correction was completely omitted.ConclusionWhen combining BGS‐ASL with SMS‐EPI, particular attention is needed to avoid artefacts introduced by motion correction. With the proposed framework, these issues are minimized.

High resolution isotropic diffusion imaging in post-mortem neonates: a feasibility study

To investigate the potential of advanced diffusion weighted imaging (DWI) in post-mortem MRI (PMMR) at 3T. We acquired PMMR brain and body imaging in 12 neonates, mean gestational age 33.4 weeks (range 29-37 weeks) at 3T and 1.5T. Head and body diffusion imaging at 1.5T consisted of bipolar diffusion encoding and single-shot spin-echo echo-planar imaging (SE-EPI) for acquisition (echo time (TE) 96 ms; repetition time (TR) 2700 ms; voxel size 1.8 x 1.8 mm in-plane with slice thickness 5 mm; b-values of 500 and 1000 s/mm2 applied in three orthogonal directions; total acquisition time 2:12). A whole-body 3T diffusion imaging protocol using monopolar diffusion encoding and simultaneous multislice EPI acquisition with gradients applied in 12 uniformly distributed directions was obtained (TE 53.4 ms; TR 5600 ms; 1.8 mm isotropic; multiband factor 2; b-values of 250, 750, 1250 and 1750 s/mm2; acquisition time 2:09 for a single b-value). There was significant improvement in image quality in multiband, multislice diffusion PMMR protocol. On visual assessment of image quality, 1.5T DWI scored poorly (mean 2.4 SD ± 0.47), and all 3T b-values individually scored significantly higher (p < 0.001) apart from b = 250 s/mm2 which was not significantly different. Recent advances in diffusion sequences and hardware utilising higher field strengths and gradient performance allows whole-body diffusion PMMR imaging at high resolution with improved image quality compared to the current clinical approach. We have demonstrated feasibility of a multislice, multiband quantitative diffusion imaging sequence in the perinatal post-mortem setting. This will allow more detailed and quantitative clinical PMMR investigations using diffusion MRI in the future.

Robust SENSE reconstruction of simultaneous multislice EPI with low-rank enhanced coil sensitivity calibration and slice-dependent 2D Nyquist ghost correction.

To improve simultaneous multislice (SMS) EPI by robust Nyquist ghost correction in both coil sensitivity calibration and SMS reconstruction. To derive coil sensitivity and slice-dependent phase difference map between positive- and negative-echo images, single-band EPI reference data are fully sampled with EPI parameters matched to SMS acquisition. First, the reference data are organized into positive- and negative-echo virtual channels where missing data are estimated using low-rank-based simultaneous autocalibrating and k-space estimation (SAKE) at small matrix size. The resulting ghost-free positive- and negative-echo images are combined to generate coil sensitivity maps. Second, full-matrix positive- and negative-echo images are SENSE reconstructed from the reference data. Their phase difference or error map is then calculated. Last, SMS EPI is reconstructed using phase error correction SENSE (PEC-SENSE) that incorporates phase error map into coil sensitivity maps for negative-echo data. The proposed method was evaluated using both experimental data from 7T systems and simulations. Virtual coil SAKE eliminated Nyquist ghosts in the single-band EPI, yielding high-quality coil sensitivity maps and phase error maps. The subsequent PEC-SENSE robustly reconstructed SMS EPI under various conditions, including presence of in-plane acceleration, with lesser artifacts and higher temporal SNR than slice-dependent 1D linear correction method. The proposed procedure of virtual coil SAKE calibration and PEC-SENSE reconstruction substantially reduces all ghost-related artifacts originating either directly from SMS EPI data or indirectly from EPI-based coil sensitivity maps. It is computationally efficient, and generally applicable to all SMS EPI-based applications.

Improved Spatiotemporal Resolution of Dynamic Susceptibility Contrast Perfusion MRI in Brain Tumors Using Simultaneous Multi-Slice Echo-Planar Imaging.

DSC perfusion MR imaging in brain tumors requires a trade-off between spatial and temporal resolution, resulting in less spatial coverage to meet the temporal resolution requirements for accurate relative CBV estimation. DSC-MR imaging could potentially benefit from the advantages associated with simultaneous multi-slice imaging, including increased spatiotemporal resolution. In the current article, we demonstrate how simultaneous multi-slice EPI can be used to improve DSC-MR imaging spatiotemporal resolution in patients with glioblastoma.

Pushing the limits of ultra-high resolution human brain imaging with SMS-EPI demonstrated for columnar level fMRI

Encoding higher spatial resolution in simultaneous multi-slice (SMS) EPI is highly dependent on gradient performance, high density receiver coil arrays and pulse sequence optimization. We simulate gradient amplitude and slew rate determination of EPI imaging performance in terms of minimum TE, echo spacing (ES) and spatial resolution. We discuss the effects of image zooming in pulse sequences that have been used for sub-millimeter resolutions and the trade-offs in using partial Fourier and parallel imaging to reduce TE, PSF and ES. Using optimizations for SMS EPI pulse sequences with available gradient and receiver hardware, experimental results in ultra-high resolution (UHR) (0.45–0.5mm isotropic) SMS-EPI fMRI and mapping ocular dominance columns (ODC) in human brain at 0.5 mm isotropic resolution are demonstrated. We discuss promising future directions of UHR fMRI.

Simultaneous multi-slice (SMS) acquisition enhances the sensitivity of hemodynamic mapping using gas challenges.

Hemodynamic mapping using gas inhalation has received increasing interest in recent years. Cerebrovascular reactivity (CVR), which reflects the ability of the brain vasculature to dilate in response to a vasoactive stimulus, can be measured by CO2 inhalation with continuous acquisition of blood oxygen level-dependent (BOLD) magnetic resonance images. Cerebral blood volume (CBV) can be measured by O2 inhalation. These hemodynamic mapping methods are appealing because of their absence of gadolinium contrast agent, their ability to assess both baseline perfusion and vascular reserve, and their utility in calibrating the functional magnetic resonance imaging (fMRI) signal. However, like other functional and physiological indices, a major drawback of these measurements is their poor sensitivity and reliability. Simultaneous multi-slice echo planar imaging (SMS EPI) is a fast imaging technology that allows the excitation and acquisition of multiple two-dimensional slices simultaneously, and has been shown to enhance the sensitivity of several MRI applications. To our knowledge, the benefit of SMS in gas inhalation imaging has not been investigated. In this work, we compared the sensitivity of CO2 and O2 inhalation data collected using SMS factor 2 (SMS2) and SMS factor 3 (SMS3) with those collected using conventional EPI (SMS1). We showed that the sensitivity of SMS scans was significantly (p=0.01) higher than that of conventional EPI, although no difference was found between SMS2 and SMS3 (p=0.3). On a voxel-wise level, approximately 20-30% of voxels in the brain showed a significant enhancement in sensitivity when using SMS compared with conventional EPI, with other voxels showing an increase, but not reaching statistical significance. When using SMS, the scan duration can be reduced by half, whilst maintaining the sensitivity of conventional EPI. The availability of a sensitive acquisition technique can further enhance the potential of gas inhalation MRI in clinical applications.

Improved artifact correction for combined electroencephalography/functional MRI by means of synchronization and use of vectorcardiogram recordings

To demonstrate that two methodological developments (synchronization of the MR scanner and electroencephalography [EEG] clocks and use of the scanner's vectorcardiogram [VCG]) improve the quality of EEG data recorded in combined EEG/functional MRI experiments in vivo. EEG data were recorded using a 32-channel system, during simultaneous multislice EPI acquisition carried out on a 3 Tesla scanner. Recordings were made on three subjects in the resting state and on five subjects using a block paradigm involving visual stimulation with a 10-Hz flashing checkerboard. Gradient artifacts were significantly reduced in the EEG data recorded in vivo when synchronization and a TR equal to a multiple of the EEG clock period were used. This was evident from the greater attenuation of the signal at multiples of the slice acquisition frequency. Pulse artifact correction based on R-peak markers derived from the VCG was shown to offer a robust alternative to the conventionally used ECG-based method. Driven EEG responses at frequencies of up to 60 Hz due to the visual stimulus could be more readily detected in data recorded with EEG and MR scanner clock synchronization. Synchronization of the scanner and EEG clocks, along with VCG-based R-peak detection is advantageous in removing gradient and pulse artifacts in combined EEG/fMRI recordings. This approach is shown to allow the robust detection of high frequency driven activity in the EEG data.