Distortion correction in EPI at ultra-high-field MRI using PSF mapping with optimal combination of shift detection dimension

Despite its wide use, echo‐planar imaging (EPI) suffers from geometric distortions due to off‐resonance effects, i.e., strong magnetic field inhomogeneity and susceptibility. This article reports a novel method for correcting the distortions observed in EPI acquired at ultra‐high‐field such as 7 T. Point spread function (PSF) mapping methods have been proposed for correcting the distortions in EPI. The PSF shift map can be derived either along the nondistorted or the distorted coordinates. Along the nondistorted coordinates more information about compressed areas is present but it is prone to PSF‐ghosting artifacts induced by large k‐space shift in PSF encoding direction. In contrast, shift maps along the distorted coordinates contain more information in stretched areas and are more robust against PSF‐ghosting. In ultra‐high‐field MRI, an EPI contains both compressed and stretched regions depending on the B₀ field inhomogeneity and local susceptibility. In this study, we present a new geometric distortion correction scheme, which selectively applies the shift map with more information content. We propose a PSF‐ghost elimination method to generate an artifact‐free pixel shift map along nondistorted coordinates. The proposed method can correct the effects of the local magnetic field inhomogeneity induced by the susceptibility effects along with the PSF‐ghost artifact cancellation. We have experimentally demonstrated the advantages of the proposed method in EPI data acquisitions in phantom and human brain using 7‐T MRI. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.     

Removal of EPI Nyquist ghost artifacts with two-dimensional phase correction.

Odd-even echo inconsistencies result in Nyquist ghost artifacts in the reconstructed EPI images. The ghost artifacts reduce the image signal-to-noise ratio and make it difficult to correctly interpret the EPI data. In this article a new 2D phase mapping protocol and a postprocessing algorithm are presented for an effective Nyquist ghost artifacts removal. After an appropriate k-space data regrouping, a 2D map accurately encoding low- and high-order phase errors is derived from two phase-encoded reference scans, which were originally proposed by Hu and Le (Magn Reson Med 36:166-171;1996) for their 1D nonlinear correction method. The measured phase map can be used in the postprocessing algorithm developed to remove ghost artifacts in subsequent EPI experiments. Experimental results from phantom, animal, and human studies suggest that the new technique is more effective than previously reported methods and has a better tolerance to signal intensity differences between reference and actual EPI scans. The proposed method may potentially be applied to repeated EPI measurements without subject movements, such as functional MRI and diffusion coefficient mapping.     

Two‐dimensional phase cycled reconstruction for inherent correction of echo‐planar imaging nyquist artifacts

The inconsistency of k‐space trajectories results in Nyquist artifacts in echo‐planar imaging (EPI). Traditional techniques often only correct for phase errors along the frequency‐encoding direction (one‐dimensional correction), which may leave significant residual artifacts, particularly for oblique‐plane EPI or in the presence of cross‐term eddy currents. As compared with one‐dimensional correction, two‐dimensional (2D) phase correction can be much more effective in suppressing Nyquist artifacts. However, most existing 2D correction methods require reference scans and may not be generally applicable to different imaging protocols. Furthermore, EPI reconstruction with these 2D phase correction methods is susceptible to error amplification due to subject motion. To address these limitations, we report an inherent and general 2D phase correction technique for EPI Nyquist removal. First, a series of images are generated from the original dataset, by cycling through different possible values of phase errors using a 2D reconstruction framework. Second, the image with the lowest artifact level is identified from images generated in the first step using criteria based on background energy in sorted and sigmoid‐weighted signals. In this report, we demonstrate the effectiveness of our new method in removing Nyquist ghosts in single‐shot, segmented and parallel EPI without acquiring additional reference scans and the subsequent error amplifications. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.     

Real-time autoshimming for echo planar timecourse imaging.

Head motion within an applied magnetic field alters the effective shim within the brain, causing geometric distortions in echo planar imaging (EPI). Even if subtle, change in shim can lead to artifactual signal changes in timecourse EPI acquisitions, which are typically performed for functional MRI (fMRI) or diffusion tensor imaging. Magnetic field maps acquired before and after head motions of clinically realistic magnitude indicate that motion-induced changes in magnetic field may cause translations exceeding 3 mm in the phase-encoding direction of the EPI images. The field maps also demonstrate a trend toward linear variations in shim changes as a function of position within the head, suggesting that a real-time, first-order correction may compensate for motion-induced changes in magnetic field. This article presents a navigator pulse sequence and processing method, termed a "shim NAV," for real-time detection of linear shim changes, and a shim-compensated EPI pulse sequence for dynamic correction of linear shim changes. In vivo and phantom experiments demonstrate the detection accuracy of shim NAVs in the presence of applied gradient shims. Phantom experiments demonstrate reduction of geometric distortion and image artifact using shim-compensated EPI in the presence of applied gradient shims. In vivo experiments with intentional interimage subject motion demonstrate improved alignment of timecourse EPI images when using the shim NAV-detected values to update the shim-compensated EPI acquisition in real time.     

EPI distortion correction from a simultaneously acquired distortion map using TRAIL

PURPOSE: To develop a method for shot-by-shot distortion correction of single-shot echo-planar imaging (EPI) that is capable of correcting each image individually using a distortion measurement performed during acquisition of the image itself. MATERIALS AND METHODS: The recently-introduced method known as two reduced acquisitions interleaved (TRAIL) was extended to measure the distribution of the main magnetic field B0 with each shot. This corresponded to a map of distortion, and allowed distortion to be corrected in the acquired images. RESULTS: Distortion-corrected images were demonstrated in the human brain. The distortion field could be directly visualized using the "stripe" distribution imposed by the TRAIL pulse sequence. This confirmed the success of the correction. Over a time-course measurement of 10 images, variance was reduced by using shot-by-shot distortion correction compared to correction with a constant field map. CONCLUSION: Shot-by-shot distortion correction may be performed for EPI images acquired using an extension of the TRAIL technique, ensuring that the correction reflects the actual distortion pattern and not merely a previously measured, but possibly no longer valid, distortion field. This avoids errors due to changes in the distortion field or misregistration of a previously measured distortion map resulting from subject motion.     

Phase labeling using sensitivity encoding (PLUS): Data acquisition and image reconstruction for geometric distortion correction in EPI

Geometric distortion caused by magnetic field inhomogeneity is generally an inevitable tradeoff for fast MRI acquisitions using echo‐planar imaging. Most of the existing distortion‐correction techniques require separate scans for field maps in order to correct the distortion contained in a measurement. A drawback of these current techniques is that the field map scans and the measurement can capture different patient positions, which invalidates the stationary condition. A new method was developed in this work to correct geometric distortion by using local phase shifts derived directly from the measurement itself, without the need of extra field map scans. This self‐sufficient method takes advantage of parallel imaging and k‐space trajectory modification to produce multiple images from a single acquisition. The measurement is also used to derive sensitivity maps for parallel imaging reconstruction. The derived phase shifts are retrospectively applied to the measurement for correction of geometric distortion in the measurement itself. The proposed method was successfully demonstrated using experimental data from a phantom and a human brain. Magn Reson Med, 2009. © 2008 Wiley‐Liss, Inc.     

Correction of concomitant magnetic field-induced image artifacts in nonaxial echo-planar imaging.

Echo-planar images acquired in nonaxial planes are often distorted. Such image distortion has limited the applications of the echo-planar imaging (EPI) technique. In this article, it is demonstrated that a considerable amount of the distortion is caused by the higher-order magnetic field concomitant with the linear magnetic field gradient, or the concomitant magnetic field. The image distortion caused by the concomitant magnetic field is more prominent when a higher gradient amplitude is used for readout. It is also shown that the concomitant magnetic field can cause ghosting and blurring. A theoretical analysis is performed for the concomitant field effect in nonaxial EPI images. A point-by-point (or line-by-line) phase correction algorithm is developed to correct the image distortion, ghosting, and blurring. A postreconstruction processing algorithm is also developed to correct image distortion with much higher computational efficiency. Experimental results show that both correction methods effectively reduce the image distortion in coronal or sagittal images.     

High spatial resolution EPI using an odd number of interleaves.

Ghost artifacts in echoplanar imaging (EPI) arise from phase errors caused by differences in eddy currents and gradient ramping during left-to-right traversal of kx(forward echo) versus right-to-left traversal of kx (reverse echo). Reference scans do not always reduce the artifact and may make image quality worse. To eliminate the need for reference scans, a ghost artifact reduction technique based on image phase correction was developed, in which phase errors are directly estimated from images reconstructed separately using only the forward or only the reverse echos. In practice, this technique is applicable only to single-shot EPI that produces only one ghost (shifted 1/2 the field of view from the parent image), because the technique requires that the ghosts do not completely overlap the parent image. For higher spatial resolution, typically an even number of separate k-space traversals (interleaves) are combined to produce one large data set. In this paper, we show that data obtained from an even number of interleaves cannot be combined to produce only one ghost, and image phase correction cannot be applied. We then show that data obtained from an odd number of interleaves can be combined to produce only one ghost, and image phase correction can be applied to reduce ghost intensity significantly. This "odd-number interleaf EPI" provides spatial and temporal resolution tradeoffs that are complementary to, or can replace, those of even-number interleaf EPI. Odd-number interleaf EPI may be particularly useful for MR systems in which reference scans have been unreliable.     

Correction of off resonance-related distortion in echo-planar imaging using EPI-based field maps

We present, here, a simple method for measurement and correction of off-resonance related geometric distortion in echo-planar imaging (EP1). This method uses high signal-to-noise ratio (SNR) EPI-based field maps, rapidly acquired using a series of gradient recalled images collected across a range of TE values. This field map is distorted in the same manner as the EPI images to be unwarped, providing a direct look-up table for the correct location of each pixel of data. This method adds very little scan time and is robust and easy to implement.     

Minimization of Nyquist ghosting for echo‐planar imaging at ultra‐high fields based on a “negative readout gradient” strategy

Purpose:

To improve the traditional Nyquist ghost correction approach in echo planar imaging (EPI) at high fields, via schemes based on the reversal of the EPI readout gradient polarity for every other volume throughout a functional magnetic resonance imaging (fMRI) acquisition train.

Materials and Methods:

An EPI sequence in which the readout gradient was inverted every other volume was implemented on two ultrahigh‐field systems. Phantom images and fMRI data were acquired to evaluate ghost intensities and the presence of false‐positive blood oxygenation level‐dependent (BOLD) signal with and without ghost correction. Three different algorithms for ghost correction of alternating readout EPI were compared.

Results:

Irrespective of the chosen processing approach, ghosting was significantly reduced (up to 70% lower intensity) in both rat brain images acquired on a 9.4T animal scanner and human brain images acquired at 7T, resulting in a reduction of sources of false‐positive activation in fMRI data.

Conclusion:

It is concluded that at high B₀ fields, substantial gains in Nyquist ghost correction of echo planar time series are possible by alternating the readout gradient every other volume. J. Magn. Reson. Imaging 2009;30:1171–1178. © 2009 Wiley‐Liss, Inc.     

Two‐dimensional phase correction method for single and multi‐shot echo planar imaging

Ghost artifacts are a serious issue in single and multi‐shot echo planar imaging. Because of these coherent artifacts, it is essential to consistently suppress the ghosts. In this article, we present a phase correction algorithm that achieves excellent ghost suppression for single and multi‐shot echo planar imaging. The phase correction is performed along both the x (read) direction and y (phase) direction. To this end, we apply a double field of view prescan and compute the phase required for ghost suppression. This phase is fitted to a 2D polynomial. The fitted phase is used to correct the echo planar imaging images. The correction algorithm can be used with any readout gradient polarities and any number of shots. A flow chart of the correction method is provided to better clarify the full process. Finally, phantom and volunteer images demonstrate the improvement of artifact suppression obtained with this algorithm over conventional phase correction methods. Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.     

High‐resolution fMRI with higher‐order generalized series imaging and parallel imaging techniques (HGS‐parallel)

Purpose

To develop a novel approach for high‐resolution functional MRI (fMRI) using the conventional gradient‐echo sequence.

Materials and Methods

Echo‐planar imaging (EPI) techniques have generally been used for fMRI studies due to their fast imaging time. However, it is difficult for studying brain function at the submillimeter level using this sequence. In addition, EPI techniques have some drawbacks, such as Nyquist ghosts and geometric distortions in the reconstructed images, and subsequently require additional postprocessing to reduce these artifacts. One way of solving these problems is to acquire fMRI data by means of a conventional gradient‐echo imaging sequence instead of EPI. To provide a fast imaging time, the proposed method combines higher‐order generalized series (HGS) imaging with a parallel imaging technique which is called the HGS‐parallel technique.

Results

The proposed HGS‐parallel technique achieves a 12.8‐fold acceleration in imaging time without the cost of spatial resolution. The proposed method was verified through the application of fMRI studies on normal subjects.

Conclusion

This study suggests that the proposed method can be used for high‐resolution fMRI studies without the geometric distortion and the Nyquist ghost artifacts compared to EPI. J. Magn. Reson. Imaging 2009;29:924–936. © 2009 Wiley‐Liss, Inc.     

Optimized distortion correction technique for echo planar imaging.

A new phase-shifted EPI pulse sequence is described that encodes EPI phase errors due to all off-resonance factors, including B(o) field inhomogeneity, eddy current effects, and gradient waveform imperfections. Combined with the previously proposed multichannel modulation postprocessing algorithm (Chen and Wyrwicz, MRM 1999;41:1206-1213), the encoded phase error information can be used to effectively remove geometric distortions in subsequent EPI scans. The proposed EPI distortion correction technique has been shown to be effective in removing distortions due to gradient waveform imperfections and phase gradient-induced eddy current effects. In addition, this new method retains advantages of the earlier method, such as simultaneous correction of different off-resonance factors without use of a complicated phase unwrapping procedure. The effectiveness of this technique is illustrated with EPI studies on phantoms and animal subjects. Implementation to different versions of EPI sequences is also described. Magn Reson Med 45:525-528, 2001.     

Diffusion tensor imaging (DTI) with retrospective motion correction for large-scale pediatric imaging

Purpose:

To develop and implement a clinical DTI technique suitable for the pediatric setting that retrospectively corrects for large motion without the need for rescanning and/or reacquisition strategies, and to deliver high‐quality DTI images (both in the presence and absence of large motion) using procedures that reduce image noise and artifacts.

Materials and Methods:

We implemented an in‐house built generalized autocalibrating partially parallel acquisitions (GRAPPA)‐accelerated diffusion tensor (DT) echo‐planar imaging (EPI) sequence at 1.5T and 3T on 1600 patients between 1 month and 18 years old. To reconstruct the data, we developed a fully automated tailored reconstruction software that selects the best GRAPPA and ghost calibration weights; does 3D rigid‐body realignment with importance weighting; and employs phase correction and complex averaging to lower Rician noise and reduce phase artifacts. For select cases we investigated the use of an additional volume rejection criterion and b‐matrix correction for large motion.

Results:

The DTI image reconstruction procedures developed here were extremely robust in correcting for motion, failing on only three subjects, while providing the radiologists high‐quality data for routine evaluation.

Conclusion:

This work suggests that, apart from the rare instance of continuous motion throughout the scan, high‐quality DTI brain data can be acquired using our proposed integrated sequence and reconstruction that uses a retrospective approach to motion correction. In addition, we demonstrate a substantial improvement in overall image quality by combining phase correction with complex averaging, which reduces the Rician noise that biases noisy data. J. Magn. Reson. Imaging 2012;36:961–971. © 2012 Wiley Periodicals, Inc.     

Off-resonance artifacts correction with convolution in k-space (ORACLE)

Off-resonance artifacts hinder the wider applicability of echo-planar imaging and non-Cartesian MRI methods such as radial and spiral. In this work, a general and rapid method is proposed for off-resonance artifacts correction based on data convolution in k-space. The acquired k-space is divided into multiple segments based on their acquisition times. Off-resonance-induced artifact within each segment is removed by applying a convolution kernel, which is the Fourier transform of an off-resonance correcting spatial phase modulation term. The field map is determined from the inverse Fourier transform of a basis kernel, which is calibrated from data fitting in k-space. The technique was demonstrated in phantom and in vivo studies for radial, spiral and echo-planar imaging datasets. For radial acquisitions, the proposed method allows the self-calibration of the field map from the imaging data, when an alternating view-angle ordering scheme is used. An additional advantage for off-resonance artifacts correction based on data convolution in k-space is the reusability of convolution kernels to images acquired with the same sequence but different contrasts.     

Point spread function mapping with parallel imaging techniques and high acceleration factors: fast, robust, and flexible method for echo-planar imaging distortion correction.

Echo-planar imaging (EPI) is an ultrafast magnetic resonance (MR) imaging technique prone to geometric distortions. Various correction techniques have been developed to remedy these distortions. Here improvements of the point spread function (PSF) mapping approach are presented, which enable reliable and fully automated distortion correction of echo-planar images at high field strengths. The novel method is fully compatible with EPI acquisitions using parallel imaging. The applicability of parallel imaging to further accelerate PSF acquisition is shown. The possibility of collecting PSF data sets with total acceleration factors higher than the number of coil elements is demonstrated. Additionally, a new approach to visualize and interpret distortions in the context of various imaging and reconstruction methods based on the PSF is proposed. The reliable performance of the PSF mapping technique is demonstrated on phantom and volunteer scans at field strengths of up to 4 T.     

High‐resolution human diffusion tensor imaging using 2‐D navigated multishot SENSE EPI at 7 T

The combination of parallel imaging with partial Fourier acquisition has greatly improved the performance of diffusion‐weighted single‐shot EPI and is the preferred method for acquisitions at low to medium magnetic field strength such as 1.5 or 3 T. Increased off‐resonance effects and reduced transverse relaxation times at 7 T, however, generate more significant artifacts than at lower magnetic field strength and limit data acquisition. Additional acceleration of k‐space traversal using a multishot approach, which acquires a subset of k‐space data after each excitation, reduces these artifacts relative to conventional single‐shot acquisitions. However, corrections for motion‐induced phase errors are not straightforward in accelerated, diffusion‐weighted multishot EPI because of phase aliasing. In this study, we introduce a simple acquisition and corresponding reconstruction method for diffusion‐weighted multishot EPI with parallel imaging suitable for use at high field. The reconstruction uses a simple modification of the standard sensitivity‐encoding (SENSE) algorithm to account for shot‐to‐shot phase errors; the method is called image reconstruction using image‐space sampling function (IRIS). Using this approach, reconstruction from highly aliased in vivo image data using 2‐D navigator phase information is demonstrated for human diffusion‐weighted imaging studies at 7 T. The final reconstructed images show submillimeter in‐plane resolution with no ghosts and much reduced blurring and off‐resonance artifacts. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.     

Correction of spatial distortion in EPI due to inhomogeneous static magnetic fields using the reversed gradient method

PURPOSE: To derive and implement a method for correcting spatial distortion caused by in vivo inhomogeneous static magnetic fields in echo-planar imaging (EPI). MATERIALS AND METHODS: The reversed gradient method, which was initially devised to correct distortion in images generated by spin-warp MRI, was adapted to correct distortion in EP images. This method provides point-by-point correction of distortion throughout the image. EP images, acquired with a 3 T MRI system, of a phantom and a volunteer's head were used to test the correction method. RESULTS: Good correction was observed in all cases. Spatial distortion in the uncorrected images ranged up to 4 pixels (12 mm) and was corrected successfully. CONCLUSION: The correction was improved by the application of a nonlinear interpolation scheme. The correction requires that two EP images be acquired at each slice position. This increases the acquisition time, but an improved signal-to-noise ratio (SNR) is seen in the corrected image. The local SNR gain decreases with increasing distortion. In many EPI acquisition schemes, multiple images are averaged at each slice position to increase the SNR; in such cases the reversed gradient correction method can be applied with no increase in acquisition duration.     

Ghost phase cancellation with phase-encoding gradient modulation

Motion artifacts are a dominant cause of magnetic resonance image quality degradation. Periodic or nearly periodic motion results in image replicates of the moving structures in spin-warp Fourier imaging. The replicates, or ghosts, propagate in the image in the phase encoding, or y, direction. These ghosted images can be considered to consist of the time-averaged spin density I₀and a ghost mask g. A set of J ghosted images I_j may be acquired in which the ghost mask is intentionally phase shifted by varying amounts relative to I₀ with interleaved acquisitions that have shifted phaseencoding orders or by acquiring multiple images during a single readout period in the presence of an oscillating phase-encoding gradient. The resulting complex images I_j have the same time-averaged spin density I₀ but have ghost contributions g_j that, on a pixel-by-pixel basis, trace part of a circle around I₀. The source images I_j can then be used to estimate I₀. Simulations and experiments with the phase-encoding gradient modulation method show good general ghost suppression for a variety of quasi-periodic motion sources including both respiratory-type artifacts and flow artifacts. The primary limitation of the method is the need for rapid gradient switching.     

View angle tilting echo planar imaging for distortion correction

Geometric distortion caused by field inhomogeneity along the phase‐encode direction is one of the most prominent artifacts due to a relatively low effective bandwidth along that direction in magnetic resonance echo planar imaging. This work describes a method for correcting in‐plane image distortion along the phase‐encode direction using a view angle tilting imaging technique in spin‐echo echo planar imaging. Spin‐echo echo planar imaging with view angle tilting uses the addition of gradient blips along the slice‐select direction, concurrently applied with the phase‐encode gradient blips, producing an additional phase. This phase effectively offsets an unwanted phase accumulation caused by field inhomogeneity, resulting in the removal of image distortion along the phase‐encode direction. The proposed method is simple and straightforward both in implementation and application with no scan time penalty. Therefore, it is readily applicable on commercial scanners without having any customized postprocessing. The efficacy of the spin‐echo echo planar imaging with view angle tilting technique in the correction of image distortion is demonstrated in phantom and in vivo brain imaging. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.