NOTE Robust EPI Nyquist Ghost Removal by Incorporating Phase Error Correction With Sensitivity Encoding (PEC-SENSE) Victor B. Xie, 1,2y Mengye Lyu, 1,2y Yilong Liu, 1,2 Yanqiu Feng, 1,2,3 and Ed X. Wu 1,2 * Purpose: The existing approach of Nyquist ghost correction by parallel imaging in echo planar imaging (EPI) can suffer from image noise amplification. We propose a method that estimates a phase error map from multi-channel data itself and incorpo- rates it into the sensitivity encoding (SENSE) reconstruction for Nyquist ghost correction without compromising the image SNR. Methods: This method first reconstructs two ghost-free images from positive and negative echoes using SENSE, respectively, from which the phase error map is computed. This map is then incorporated into the coil sensitivity maps for the negative echo image during the joint SENSE reconstruc- tion of all k-space data to obtain the final ghost-free image. Phantom and in vivo EPI experiments at 7 T and 3 T were per- formed to evaluate the proposed method. Results: Nyquist ghost was effectively removed in all images even under oblique imaging and poor eddy current conditions. Resulting image signal-to-noise ratio (SNR) was comparable to that by the traditional linear phase error correction method and higher than that by a previous SENSE-based parallel imaging correction approach. Conclusion: The proposed correction method can robustly eliminate Nyquist ghost while preserving the image SNR. This approach requires no additional calibration data beyond stan- dard coil sensitivity maps and can be readily applied to all EPI applications. Magn Reson Med 000:000–000, 2017. V C 2017 International Society for Magnetic Resonance in Medicine. Key words: MRI; EPI; Nyquist ghost; parallel imaging; SENSE INTRODUCTION Echo planar imaging (EPI) is widely applied in various MRI applications because of its fast imaging capability. However, because EPI acquires k-space data in both readout polarities, gradient time delay, eddy current, field inhomogeneities, and other hardware imperfections misalign k-space trajectory in opposite readout polarities, producing a Nyquist ghost in the reconstructed images. A number of methods have been proposed to correct the Nyquist ghost, most of which correct the k-space misalignment along the readout direction (1–3). These methods estimate k-space misalignment from non- phase-encoded or phase-encoded scans or data itself and, subsequently, correct the phase difference along the readout direction in the image domain. These meth- ods can remove most of the Nyquist ghost. However, all these methods are problematic when high-order 2D phase errors are present attributed to eddy current or magnetic susceptibility effect, especially in oblique imaging where different physical gradients may have different eddy current and time delay (4). The 2D phase error correction methods estimate the phase error map from calibration scans (5,6), and phase inconsistency between positive and negative echo images is subse- quently removed in the image space. These methods can robustly correct the Nyquist ghost, but require extra EPI calibration scans. The use of phased array coils has enabled several new methods for Nyquist ghost correction based on parallel imaging (7–11). In these methods, single-shot EPI k- space data are separated into positive and negative echo groups based on their readout polarity. Each group can be treated as a data set that is undersampled by twice the acceleration factor and thus can be reconstructed into a ghost-free image using parallel imaging reconstruc- tion methods. However, all these methods can suffer from signal-to-noise ratio (SNR) reduction attributed to noise amplification during parallel imaging reconstruc- tion. A recently proposed method, termed dual-polarity generalized autocalibrating partial parallel acquisition (GRAPPA) (DPG) (12), trains multiple GRAPPA kernels from temporally encoded calibration scans and then uti- lizes these kernels to synthesize missing k-space data and correct inherent EPI phase errors simultaneously. This method can robustly remove an EPI ghost induced by high-order phase errors and improve image quality, but it requires EPI calibration scans. In this study, we propose a sensitivity encoding (SENSE)-based (13) Nyquist ghost correction method to robustly correct the Nyquist ghost by estimating a phase error map and incorporating its correction during the final SENSE image reconstruction. This phase error cor- rection approach, termed PEC-SENSE, first reconstructs two ghost-free images from positive and negative echoes, 1 Laboratory of Biomedical Imaging and Signal Processing, The University of Hong Kong, Pokfulam, Hong Kong SAR, China. 2 Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China. 3 School of Biomedical Engineering, Southern Medical University, Guang- zhou, China. Grant sponsor: Hong Kong Research Grant Council; Grant numbers: GRF HKU17103015, GRF HKU17115116, and CRF C7048-16G. *Correspondence to: Ed X. Wu, Ph.D., Department of Electrical and Elec- tronic Engineering, The University of Hong Kong, LB 1037, 10/F, Laboratory Block, Faculty of Medicine Building, The University of Hong Kong, 21 Sas- soon Road, Pokfulam, Hong Kong SAR, China. E-mail: ewu@eee.hku.hk Part of this work has been orally presented at the Annual Meeting of Inter- national Society for Magnetic Resonance in Medicine (ISMRM), Singapore, 7–13 May 2016. y These authors contributed equally to this work. Received 25 July 2016; revised 21 March 2017; accepted 21 March 2017 DOI 10.1002/mrm.26710 Published online 00 Month 2017 in Wiley Online Library (wileyonlinelibrary. com). Magnetic Resonance in Medicine 00:00–00 (2017) V C 2017 International Society for Magnetic Resonance in Medicine 1