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Huo Z, Wen K, Luo Y, Neji R, Kunze KP, Ferreira PF, Pennell DJ, Scott AD, Nielles-Vallespin S. Referenceless Nyquist ghost correction outperforms standard navigator-based method and improves efficiency of in vivo diffusion tensor cardiovascular magnetic resonance. Magn Reson Med 2024; 91:2403-2416. [PMID: 38263908 DOI: 10.1002/mrm.30012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/20/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024]
Abstract
PURPOSE The study aims to assess the potential of referenceless methods of EPI ghost correction to accelerate the acquisition of in vivo diffusion tensor cardiovascular magnetic resonance (DT-CMR) data using both computational simulations and data from in vivo experiments. METHODS Three referenceless EPI ghost correction methods were evaluated on mid-ventricular short axis DT-CMR spin echo and STEAM datasets from 20 healthy subjects at 3T. The reduced field of view excitation technique was used to automatically quantify the Nyquist ghosts, and DT-CMR images were fit to a linear ghost model for correction. RESULTS Numerical simulation showed the singular value decomposition (SVD) method is the least sensitive to noise, followed by Ghost/Object method and entropy-based method. In vivo experiments showed significant ghost reduction for all correction methods, with referenceless methods outperforming navigator methods for both spin echo and STEAM sequences at b = 32, 150, 450, and 600 smm - 2 $$ {\mathrm{smm}}^{-2} $$ . It is worth noting that as the strength of the diffusion encoding increases, the performance gap between the referenceless method and the navigator-based method diminishes. CONCLUSION Referenceless ghost correction effectively reduces Nyquist ghost in DT-CMR data, showing promise for enhancing the accuracy and efficiency of measurements in clinical practice without the need for any additional reference scans.
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Affiliation(s)
- Zimu Huo
- CMR Unit, Royal Brompton Hosptial, Guy's and St Thomas' NHS Foundation Trust, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Ke Wen
- CMR Unit, Royal Brompton Hosptial, Guy's and St Thomas' NHS Foundation Trust, London, UK
- NHLI, Imperial College London, London, UK
| | - Yaqing Luo
- CMR Unit, Royal Brompton Hosptial, Guy's and St Thomas' NHS Foundation Trust, London, UK
- NHLI, Imperial College London, London, UK
| | - Radhouene Neji
- MR Research Collaborations, Siemens Healthcare Limited, Camberley, UK
| | - Karl P Kunze
- MR Research Collaborations, Siemens Healthcare Limited, Camberley, UK
| | - Pedro F Ferreira
- CMR Unit, Royal Brompton Hosptial, Guy's and St Thomas' NHS Foundation Trust, London, UK
- NHLI, Imperial College London, London, UK
| | - Dudley J Pennell
- CMR Unit, Royal Brompton Hosptial, Guy's and St Thomas' NHS Foundation Trust, London, UK
- NHLI, Imperial College London, London, UK
| | - Andrew D Scott
- CMR Unit, Royal Brompton Hosptial, Guy's and St Thomas' NHS Foundation Trust, London, UK
- NHLI, Imperial College London, London, UK
| | - Sonia Nielles-Vallespin
- CMR Unit, Royal Brompton Hosptial, Guy's and St Thomas' NHS Foundation Trust, London, UK
- NHLI, Imperial College London, London, UK
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Jin D, Li X, Qian Y, Qiao Y, Liu L, Tian J, Wang L, Ma Y, Qin Y, Zhu Y. Modified respiratory-triggered SPACE sequences for magnetic resonance cholangiopancreatography. Eur J Radiol Open 2024; 12:100564. [PMID: 38681662 PMCID: PMC11046076 DOI: 10.1016/j.ejro.2024.100564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/01/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024] Open
Abstract
Background Respiratory-triggered (RT) and breath-hold are the most common acquisition modalities for magnetic resonance cholangiopancreatography (MRCP). The present study compared the three different acquisition modalities for optimizing the use of MRCP in patients with diseases of the pancreatic and biliary systems. Materials and methods Three MRCP acquisition modalities were used in this study: conventional respiratory-triggered sampling perfection with application-optimized contrasts using different flip evolutions (RT-SPACE), modified RT-SPACE, and breath-hold (BH)-SPACE. Fifty-eight patients with clinically suspected pancreatic and biliary system disease were included. All image data were acquired on a 1.5 T MR. Scan time and image quality were compared between the three acquisition modalities. Friedman test, which was followed by post-hoc analysis, was performed among triple-scan protocol. Results There was a significant difference in the mean acquisition time among conventional RT-SPACE, modified RT-SPACE, and BH-SPACE (167.41±32.11 seconds vs 50.84±73.78 seconds vs 18.00 seconds, P <0.001). Signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were also significantly different among the three groups (P <0.001). The SNR and CNR were higher in the RT-SPACE group than in the BH-SPACE group (P <0.05). However, there were no statistically significant differences (P >0.05) among the 3 groups regarding quality of overall image, image clarity, background inhibition, and visualization of the pancreatic and biliary system. Conclusions MRCP acquisition with the modified RT-SPACE sequence greatly shortens the acquisition time with comparable quality images. The MRCP acquisition modality could be designed based on the patient's situation to improve the examination pass rate and obtain excellent images for diagnosis.
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Affiliation(s)
| | | | - Yifan Qian
- Department of Radiology, Xi’an Daxing Hospital, Xi’an, China
| | - Yanqiang Qiao
- Department of Radiology, Xi’an Daxing Hospital, Xi’an, China
| | - Liyao Liu
- Department of Radiology, Xi’an Daxing Hospital, Xi’an, China
| | - Juan Tian
- Department of Radiology, Xi’an Daxing Hospital, Xi’an, China
| | - Lei Wang
- Department of Radiology, Xi’an Daxing Hospital, Xi’an, China
| | - Yongli Ma
- Department of Radiology, Xi’an Daxing Hospital, Xi’an, China
| | - Yue Qin
- Department of Radiology, Xi’an Daxing Hospital, Xi’an, China
| | - Yinhu Zhu
- Department of Radiology, Xi’an Daxing Hospital, Xi’an, China
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Feinberg DA, Beckett AJS, Vu AT, Stockmann J, Huber L, Ma S, Ahn S, Setsompop K, Cao X, Park S, Liu C, Wald LL, Polimeni JR, Mareyam A, Gruber B, Stirnberg R, Liao C, Yacoub E, Davids M, Bell P, Rummert E, Koehler M, Potthast A, Gonzalez-Insua I, Stocker S, Gunamony S, Dietz P. Next-generation MRI scanner designed for ultra-high-resolution human brain imaging at 7 Tesla. Nat Methods 2023; 20:2048-2057. [PMID: 38012321 PMCID: PMC10703687 DOI: 10.1038/s41592-023-02068-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 10/09/2023] [Indexed: 11/29/2023]
Abstract
To increase granularity in human neuroimaging science, we designed and built a next-generation 7 Tesla magnetic resonance imaging scanner to reach ultra-high resolution by implementing several advances in hardware. To improve spatial encoding and increase the image signal-to-noise ratio, we developed a head-only asymmetric gradient coil (200 mT m-1, 900 T m-1s-1) with an additional third layer of windings. We integrated a 128-channel receiver system with 64- and 96-channel receiver coil arrays to boost signal in the cerebral cortex while reducing g-factor noise to enable higher accelerations. A 16-channel transmit system reduced power deposition and improved image uniformity. The scanner routinely performs functional imaging studies at 0.35-0.45 mm isotropic spatial resolution to reveal cortical layer functional activity, achieves high angular resolution in diffusion imaging and reduces acquisition time for both functional and structural imaging.
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Affiliation(s)
- David A Feinberg
- Erwin Hahn 7T MRI Laboratory, Henry H. Wheeler Brain Imaging Center, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
- Advanced MRI Technologies, Sebastopol, CA, USA.
| | - Alexander J S Beckett
- Erwin Hahn 7T MRI Laboratory, Henry H. Wheeler Brain Imaging Center, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
- Advanced MRI Technologies, Sebastopol, CA, USA
| | - An T Vu
- Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
- San Francisco Veteran Affairs Health Care System, San Francisco, CA, USA
| | - Jason Stockmann
- A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Laurentius Huber
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | | | | | - Kawin Setsompop
- Radiological Sciences Laboratory, Stanford University, Stanford, CA, USA
| | - Xiaozhi Cao
- Radiological Sciences Laboratory, Stanford University, Stanford, CA, USA
| | - Suhyung Park
- Erwin Hahn 7T MRI Laboratory, Henry H. Wheeler Brain Imaging Center, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Computer Engineering, Chonnam National University, Gwangju, Republic of Korea
- Department of ICT Convergence System Engineering, Chonnam National University, Gwangju, Republic of Korea
| | - Chunlei Liu
- Erwin Hahn 7T MRI Laboratory, Henry H. Wheeler Brain Imaging Center, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Lawrence L Wald
- A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Jonathan R Polimeni
- A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Azma Mareyam
- A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Bernhard Gruber
- A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
- BARNLabs, Muenzkirchen, Austria
| | | | - Congyu Liao
- Radiological Sciences Laboratory, Stanford University, Stanford, CA, USA
| | - Essa Yacoub
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - Mathias Davids
- A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
- Computer Assisted Clinical Medicine, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Paul Bell
- Siemens Medical Solutions, Malvern, PA, USA
| | | | | | | | | | | | - Shajan Gunamony
- Imaging Centre of Excellence, University of Glasgow, Glasgow, UK
- MR CoilTech Limited, Glasgow, UK
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Weygand J, Armstrong T, Bryant JM, Andreozzi JM, Oraiqat IM, Nichols S, Liveringhouse CL, Latifi K, Yamoah K, Costello JR, Frakes JM, Moros EG, El Naqa IM, Naghavi AO, Rosenberg SA, Redler G. Accurate, repeatable, and geometrically precise diffusion-weighted imaging on a 0.35 T magnetic resonance imaging-guided linear accelerator. Phys Imaging Radiat Oncol 2023; 28:100505. [PMID: 38045642 PMCID: PMC10692914 DOI: 10.1016/j.phro.2023.100505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023] Open
Abstract
Background and purpose Diffusion weighted imaging (DWI) allows for the interrogation of tissue cellularity, which is a surrogate for cellular proliferation. Previous attempts to incorporate DWI into the workflow of a 0.35 T MR-linac (MRL) have lacked quantitative accuracy. In this study, accuracy, repeatability, and geometric precision of apparent diffusion coefficient (ADC) maps produced using an echo planar imaging (EPI)-based DWI protocol on the MRL system is illustrated, and in vivo potential for longitudinal patient imaging is demonstrated. Materials and methods Accuracy and repeatability were assessed by measuring ADC values in a diffusion phantom at three timepoints and comparing to reference ADC values. System-dependent geometric distortion was quantified by measuring the distance between 93 pairs of phantom features on ADC maps acquired on a 0.35 T MRL and a 3.0 T diagnostic scanner and comparing to spatially precise CT images. Additionally, for five sarcoma patients receiving radiotherapy on the MRL, same-day in vivo ADC maps were acquired on both systems, one of which at multiple timepoints. Results Phantom ADC quantification was accurate on the 0.35 T MRL with significant discrepancies only seen at high ADC. Average geometric distortions were 0.35 (±0.02) mm and 0.85 (±0.02) mm in the central slice and 0.66 (±0.04) mm and 2.14 (±0.07) mm at 5.4 cm off-center for the MRL and diagnostic system, respectively. In the sarcoma patients, a mean pretreatment ADC of 910x10-6 (±100x10-6) mm2/s was measured on the MRL. Conclusions The acquisition of accurate, repeatable, and geometrically precise ADC maps is possible at 0.35 T with an EPI approach.
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Affiliation(s)
- Joseph Weygand
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | | | | | | | - Steven Nichols
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Kujtim Latifi
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Kosj Yamoah
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Jessica M. Frakes
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Eduardo G. Moros
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Issam M. El Naqa
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
- Department of Machine Learning, Moffitt Cancer Center, Tampa, FL, USA
| | - Arash O. Naghavi
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Gage Redler
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
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Pan Z, Ma X, Dai E, Auerbach EJ, Guo H, Uğurbil K, Wu X. Reconstruction for 7T high-resolution whole-brain diffusion MRI using two-stage N/2 ghost correction and L1-SPIRiT without single-band reference. Magn Reson Med 2023; 89:1915-1930. [PMID: 36594439 PMCID: PMC9992311 DOI: 10.1002/mrm.29573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/28/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023]
Abstract
PURPOSE To combine a new two-stage N/2 ghost correction and an adapted L1-SPIRiT method for reconstruction of 7T highly accelerated whole-brain diffusion MRI (dMRI) using only autocalibration scans (ACS) without the need of additional single-band reference (SBref) scans. METHODS The proposed ghost correction consisted of a 3-line reference approach in stage 1 and the reference-free entropy method in stage 2. The adapted L1-SPIRiT method was formulated within the 3D k-space framework. Its efficacy was examined by acquiring two dMRI data sets at 1.05-mm isotropic resolutions with a total acceleration of 6 or 9 (i.e., 2-fold or 3-fold slice and 3-fold in-plane acceleration). Diffusion analysis was performed to derive DTI metrics and estimate fiber orientation distribution functions (fODFs). The results were compared with those of 3D k-space GRAPPA using only ACS, all in reference to 3D k-space GRAPPA using both ACS and SBref (serving as a reference). RESULTS The proposed ghost correction eliminated artifacts more robustly than conventional approaches. Our adapted L1-SPIRiT method outperformed 3D k-space GRAPPA when using only ACS, improving image quality to what was achievable with 3D k-space GRAPPA using both ACS and SBref scans. The improvement in image quality further resulted in an improvement in estimation performances for DTI and fODFs. CONCLUSION The combination of our new ghost correction and adapted L1-SPIRiT method can reliably reconstruct 7T highly accelerated whole-brain dMRI without the need of SBref scans, increasing acquisition efficiency and reducing motion sensitivity.
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Affiliation(s)
- Ziyi Pan
- Center for Biomedical Imaging Research, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Xiaodong Ma
- Center for Magnetic Resonance Research, Radiology, Medical School, University of Minnesota, Minneapolis, MN, United States
| | - Erpeng Dai
- Department of Radiology, Stanford University, Stanford, CA, United States
| | - Edward J. Auerbach
- Center for Magnetic Resonance Research, Radiology, Medical School, University of Minnesota, Minneapolis, MN, United States
| | - Hua Guo
- Center for Biomedical Imaging Research, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Kâmil Uğurbil
- Center for Magnetic Resonance Research, Radiology, Medical School, University of Minnesota, Minneapolis, MN, United States
| | - Xiaoping Wu
- Center for Magnetic Resonance Research, Radiology, Medical School, University of Minnesota, Minneapolis, MN, United States
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Ramos-Llordén G, Park D, Kirsch JE, Scholz A, Keil B, Maffei C, Lee HH, Bilgiç B, Edlow BL, Mekkaoui C, Yendiki A, Witzel T, Huang SY. Eddy current-induced artifacts correction in high gradient strength diffusion MRI with dynamic field monitoring: demonstration in ex vivo human brain imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528684. [PMID: 36824894 PMCID: PMC9948962 DOI: 10.1101/2023.02.15.528684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Purpose To demonstrate the advantages of spatiotemporal magnetic field monitoring to correct eddy current-induced artifacts (ghosting and geometric distortions) in high gradient strength diffusion MRI (dMRI). Methods A dynamic field camera with 16 NMR field probes was used to characterize eddy current fields induced from diffusion gradients for different gradients strengths (up to 300 mT/m), diffusion directions, and shots in a 3D multi-shot EPI sequence on a 3T Connectom scanner. The efficacy of dynamic field monitoring-based image reconstruction was demonstrated on high-resolution whole brain ex vivo dMRI. A 3D multi-shot image reconstruction framework was informed with the actual nonlinear phase evolution measured with the dynamic field camera, thereby accounting for high-order eddy currents fields on top of the image encoding gradients in the image formation model. Results Eddy current fields from diffusion gradients at high gradient strength in a 3T Connectom scanner are highly nonlinear in space and time, inducing high-order spatial phase modulations between odd/even echoes and shots that are not static during the readout. Superior reduction of ghosting and geometric distortion was achieved with dynamic field monitoring compared to ghosting approaches such as navigator- and structured low-rank-based methods or MUSE, followed by image-based distortion correction with eddy. Improved dMRI analysis is demonstrated with diffusion tensor imaging and high-angular resolution diffusion imaging. Conclusion Strong eddy current artifacts characteristic of high gradient strength dMRI can be well corrected with dynamic field monitoring-based image reconstruction, unlike the two-step approach consisting of ghosting correction followed by geometric distortion reduction with eddy.
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Ramos-Llordén G, Lobos RA, Kim TH, Tian Q, Witzel T, Lee HH, Scholz A, Keil B, Yendiki A, Bilgiç B, Haldar JP, Huang SY. High-fidelity, high-spatial-resolution diffusion magnetic resonance imaging of ex vivo whole human brain at ultra-high gradient strength with structured low-rank echo-planar imaging ghost correction. NMR IN BIOMEDICINE 2023; 36:e4831. [PMID: 36106429 PMCID: PMC9883835 DOI: 10.1002/nbm.4831] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 08/20/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Diffusion magnetic resonance imaging (dMRI) of whole ex vivo human brain specimens enables three-dimensional (3D) mapping of structural connectivity at the mesoscopic scale, providing detailed evaluation of fiber architecture and tissue microstructure at a spatial resolution that is difficult to access in vivo. To account for the short T2 and low diffusivity of fixed tissue, ex vivo dMRI is often acquired using strong diffusion-sensitizing gradients and multishot/segmented 3D echo-planar imaging (EPI) sequences to achieve high spatial resolution. However, the combination of strong diffusion-sensitizing gradients and multishot/segmented EPI readout can result in pronounced ghosting artifacts incurred by nonlinear spatiotemporal variations in the magnetic field produced by eddy currents. Such ghosting artifacts cannot be corrected with conventional correction solutions and pose a significant roadblock to leveraging human MRI scanners with ultrahigh gradients for ex vivo whole-brain dMRI. Here, we show that ghosting-correction approaches that correct for either polarity-related ghosting or shot-to-shot variations in a separate manner are suboptimal for 3D multishot diffusion-weighted EPI experiments in fixed human brain specimens using strong diffusion-sensitizing gradients on the 3-T Connectom MRI scanner, resulting in orientationally biased dMRI estimates. We apply a recently developed advanced k-space reconstruction method based on structured low-rank matrix (SLM) modeling that handles both polarity-related ghosting and shot-to-shot variation simultaneously, to mitigate artifacts in high-angular resolution multishot dMRI data acquired in several fixed human brain specimens at 0.7-0.8-mm isotropic spatial resolution using b-values up to 10,000 s/mm2 and gradient strengths up to 280 mT/m. We demonstrate the improved mapping of diffusion tensor imaging and fiber orientation distribution functions in key neuroanatomical areas distributed across the whole brain using SLM-based EPI ghost correction compared with alternative techniques.
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Affiliation(s)
- Gabriel Ramos-Llordén
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Rodrigo A. Lobos
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, California, USA
| | - Tae Hyung Kim
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
- Computer Engineering, Hongik University, Seoul, Republic of Korea
| | - Qiyuan Tian
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Hong-Hsi Lee
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Alina Scholz
- Institute of Medical Physics and Radiation Protection, Mittelhessen University of Applied Sciences, Giessen, Germany
| | - Boris Keil
- Institute of Medical Physics and Radiation Protection, Mittelhessen University of Applied Sciences, Giessen, Germany
- Department of Diagnostic and Interventional Radiology, University Hospital Marburg, Philipps University of Marburg, Marburg, Germany
| | - Anastasia Yendiki
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Berkin Bilgiç
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Justin P. Haldar
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, California, USA
| | - Susie Y. Huang
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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8
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Ozenne V, Bour P, Denis de Senneville B, Quesson B. 3D motion strategy for online volumetric thermometry using simultaneous multi-slice EPI at 1.5T: an evaluation study. Int J Hyperthermia 2023; 40:2194595. [PMID: 37080550 DOI: 10.1080/02656736.2023.2194595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
PURPOSE In presence of respiratory motion, temperature mapping is altered by in-plane and through-plane displacements between successive acquisitions together with periodic phase variations. Fast 2D Echo Planar Imaging (EPI) sequence can accommodate intra-scan motion, but limited volume coverage and inter-scan motion remain a challenge during free-breathing acquisition since position offsets can arise between the different slices. METHOD To address this limitation, we evaluated a 2D simultaneous multi-slice EPI sequence with multiband (MB) acceleration during radiofrequency ablation on a mobile gel and in the liver of a volunteer (no heating). The sequence was evaluated in terms of resulting inter-scan motion, temperature uncertainty and elevation, potential false-positive heating and repeatability. Lastly, to account for potential through-plane motion, a 3D motion compensation pipeline was implemented and evaluated. RESULTS In-plane motion was compensated whatever the MB factor and temperature distribution was found in agreement during both the heating and cooling periods. No obvious false-positive temperature was observed under the conditions being investigated. Repeatability of measurements results in a 95% uncertainty below 2 °C for MB1 and MB2. Uncertainty up to 4.5 °C was reported with MB3 together with the presence of aliasing artifacts. Lastly, fast simultaneous multi-slice EPI combined with 3D motion compensation reduce residual out-of-plane motion. CONCLUSION Volumetric temperature imaging (12 slices/700 ms) could be performed with 2 °C accuracy or less, and offer tradeoffs in acquisition time or volume coverage. Such a strategy is expected to increase procedure safety by monitoring large volumes more rapidly for MR-guided thermotherapy on mobile organs.
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Affiliation(s)
- Valéry Ozenne
- IHU Liryc, Electrophysiology and Heart Modeling Institute, Fondation Bordeaux Université, Pessac-Bordeaux, France
- University of Bordeaux, Centre de recherche Cardio-Thoracique de Bordeaux, Bordeaux, France
- INSERM, Centre de recherche Cardio-Thoracique de Bordeaux, Bordeaux, France
| | - Pierre Bour
- IHU Liryc, Electrophysiology and Heart Modeling Institute, Fondation Bordeaux Université, Pessac-Bordeaux, France
- University of Bordeaux, Centre de recherche Cardio-Thoracique de Bordeaux, Bordeaux, France
- INSERM, Centre de recherche Cardio-Thoracique de Bordeaux, Bordeaux, France
| | | | - Bruno Quesson
- IHU Liryc, Electrophysiology and Heart Modeling Institute, Fondation Bordeaux Université, Pessac-Bordeaux, France
- University of Bordeaux, Centre de recherche Cardio-Thoracique de Bordeaux, Bordeaux, France
- INSERM, Centre de recherche Cardio-Thoracique de Bordeaux, Bordeaux, France
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Powell E, Schneider T, Battiston M, Grussu F, Toosy A, Clayden JD, Wheeler‐Kingshott CAMG. SENSE EPI reconstruction with 2D phase error correction and channel-wise noise removal. Magn Reson Med 2022; 88:2157-2166. [PMID: 35877787 PMCID: PMC9545987 DOI: 10.1002/mrm.29349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 11/23/2022]
Abstract
PURPOSE To develop a robust reconstruction pipeline for EPI data that enables 2D Nyquist phase error correction using sensitivity encoding without incurring major noise artifacts in low SNR data. METHODS SENSE with 2D phase error correction (PEC-SENSE) was combined with channel-wise noise removal using Marcenko-Pastur principal component analysis (MPPCA) to simultaneously eliminate Nyquist ghost artifacts in EPI data and mitigate the noise amplification associated with phase correction using parallel imaging. The proposed pipeline (coined SPECTRE) was validated in phantom DW-EPI data using the accuracy and precision of diffusion metrics; ground truth values were obtained from data acquired with a spin echo readout. Results from the SPECTRE pipeline were compared against PEC-SENSE reconstructions with three alternate denoising strategies: (i) no denoising; (ii) denoising of magnitude data after image formation; (iii) denoising of complex data after image formation. SPECTRE was then tested using highb $$ b $$ -value (i.e., low SNR) diffusion data (up tob = 3000 $$ b=3000 $$ s/mm2 $$ {}^2 $$ ) in four healthy subjects. RESULTS Noise amplification associated with phase error correction incurred a 23% bias in phantom mean diffusivity (MD) measurements. Phantom MD estimates using the SPECTRE pipeline were within 8% of the ground truth value. In healthy volunteers, the SPECTRE pipeline visibly corrected Nyquist ghost artifacts and reduced associated noise amplification in highb $$ b $$ -value data. CONCLUSION The proposed reconstruction pipeline is effective in correcting low SNR data, and improves the accuracy and precision of derived diffusion metrics.
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Affiliation(s)
- Elizabeth Powell
- Queen Square MS Centre, UCL Institute of NeurologyUniversity College LondonLondonUK
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical EngineeringUniversity College LondonLondonUK
| | | | - Marco Battiston
- Queen Square MS Centre, UCL Institute of NeurologyUniversity College LondonLondonUK
| | - Francesco Grussu
- Queen Square MS Centre, UCL Institute of NeurologyUniversity College LondonLondonUK
- Radiomics GroupVall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital CampusBarcelonaSpain
| | - Ahmed Toosy
- Queen Square MS Centre, UCL Institute of NeurologyUniversity College LondonLondonUK
| | - Jonathan D. Clayden
- Developmental Imaging and Biophysics Section, Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Claudia A. M. Gandini Wheeler‐Kingshott
- Queen Square MS Centre, UCL Institute of NeurologyUniversity College LondonLondonUK
- Department of Brain and Behavioural SciencesUniversity of PaviaPaviaItaly
- Brain MRI 3T CenterIRCCS Mondino FoundationPaviaItaly
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10
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Cho J, Liao C, Tian Q, Zhang Z, Xu J, Lo WC, Poser BA, Stenger VA, Stockmann J, Setsompop K, Bilgic B. Highly accelerated EPI with wave encoding and multi-shot simultaneous multislice imaging. Magn Reson Med 2022; 88:1180-1197. [PMID: 35678236 DOI: 10.1002/mrm.29291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 11/09/2022]
Abstract
PURPOSE To introduce wave-encoded acquisition and reconstruction techniques for highly accelerated EPI with reduced g-factor penalty and image artifacts. THEORY AND METHODS Wave-EPI involves application of sinusoidal gradients during the EPI readout, which spreads the aliasing in all spatial directions, thereby taking better advantage of 3D coil sensitivity profiles. The amount of voxel spreading that can be achieved by the wave gradients during the short EPI readout period is constrained by the slew rate of the gradient coils and peripheral nerve stimulation monitor. We propose to use a "half-cycle" sinusoidal gradient to increase the amount of voxel spreading that can be achieved while respecting the slew and stimulation constraints. Extending wave-EPI to multi-shot acquisition minimizes geometric distortion and voxel blurring at high in-plane resolutions, while structured low-rank regularization mitigates shot-to-shot phase variations. To address gradient imperfections, we propose to use different point spread functions for the k-space lines with positive and negative polarities, which are calibrated with a FLEET-based reference scan. RESULTS Wave-EPI enabled whole-brain single-shot gradient-echo (GE) and multi-shot spin-echo (SE) EPI acquisitions at high acceleration factors at 3T and was combined with g-Slider encoding to boost the SNR level in 1 mm isotropic diffusion imaging. Relative to blipped-CAIPI, wave-EPI reduced average and maximum g-factors by up to 1.21- and 1.37-fold at Rin × Rsms = 3 × 3, respectively. CONCLUSION Wave-EPI allows highly accelerated single- and multi-shot EPI with reduced g-factor and artifacts and may facilitate clinical and neuroscientific applications of EPI by improving the spatial and temporal resolution in functional and diffusion imaging.
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Affiliation(s)
- Jaejin Cho
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Congyu Liao
- Radiological Sciences Laboratory, Department of Radiology, Stanford University, Stanford, California, USA.,Department of Electrical Engineering, Stanford University, Stanford, California, USA
| | - Qiyuan Tian
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Zijing Zhang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Jinmin Xu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Wei-Ching Lo
- Siemens Medical Solutions, Boston, Massachusetts, USA
| | - Benedikt A Poser
- Maastricht Brain Imaging Center, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - V Andrew Stenger
- MR Research Program, Department of Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, Hawaii, USA
| | - Jason Stockmann
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kawin Setsompop
- Radiological Sciences Laboratory, Department of Radiology, Stanford University, Stanford, California, USA.,Department of Electrical Engineering, Stanford University, Stanford, California, USA
| | - Berkin Bilgic
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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11
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Wang L, Wang C, Wang F, Chu YH, Yang Z, Wang H. EPI phase error correction with deep learning (PEC-DL) at 7 T. Magn Reson Med 2022; 88:1775-1784. [PMID: 35696532 DOI: 10.1002/mrm.29317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022]
Abstract
PURPOSE The phase mismatch between odd and even echoes in EPI causes Nyquist ghost artifacts. Existing ghost correction methods often suffer from severe residual artifacts and are ineffective with k-space undersampling data. This study proposed a deep learning-based method (PEC-DL) to correct phase errors for DWI at 7 Tesla. METHODS The acquired k-space data were divided into 2 independent undersampled datasets according to their readout polarities. Then the proposed PEC-DL network reconstructed 2 ghost-free images using the undersampled data without calibration and navigator data. The network was trained with fully sampled images and applied to two- and fourfold accelerated data. Healthy volunteers and patients with Moyamoya disease were recruited to validate the efficacy of the PEC-DL method. RESULTS The PEC-DL method was capable to mitigate the ghost artifacts in DWI in healthy volunteers as well as patients with Moyamoya disease. The fourfold accelerated results showed much less distortion in the lesions of the Moyamoya patient using high b-value DWI and the corresponding ADC maps. The ghost-to-signal ratios were significantly lower in PEC-DL images compared to conventional linear phase corrections, mini-entropy, and PEC-GRAPPA algorithms. CONCLUSION The proposed method can effectively eliminate ghost artifacts for full sampled and up to fourfold accelerated EPI data without calibration and navigator data.
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Affiliation(s)
- Lili Wang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, People's Republic of China
| | - Chengyan Wang
- Human Phenome Institute, Fudan University, Shanghai, People's Republic of China
| | - Fanwen Wang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, People's Republic of China
| | - Ying-Hua Chu
- MR Collaboration, Siemens Healthcare Ltd., Shanghai, People's Republic of China
| | - Zidong Yang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, People's Republic of China
| | - He Wang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, People's Republic of China.,MR Collaboration, Siemens Healthcare Ltd., Shanghai, People's Republic of China
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12
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What's New and What's Next in Diffusion MRI Preprocessing. Neuroimage 2021; 249:118830. [PMID: 34965454 PMCID: PMC9379864 DOI: 10.1016/j.neuroimage.2021.118830] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/26/2021] [Accepted: 12/15/2021] [Indexed: 02/07/2023] Open
Abstract
Diffusion MRI (dMRI) provides invaluable information for the study of tissue microstructure and brain connectivity, but suffers from a range of imaging artifacts that greatly challenge the analysis of results and their interpretability if not appropriately accounted for. This review will cover dMRI artifacts and preprocessing steps, some of which have not typically been considered in existing pipelines or reviews, or have only gained attention in recent years: brain/skull extraction, B-matrix incompatibilities w.r.t the imaging data, signal drift, Gibbs ringing, noise distribution bias, denoising, between- and within-volumes motion, eddy currents, outliers, susceptibility distortions, EPI Nyquist ghosts, gradient deviations, B1 bias fields, and spatial normalization. The focus will be on “what’s new” since the notable advances prior to and brought by the Human Connectome Project (HCP), as presented in the predecessing issue on “Mapping the Connectome” in 2013. In addition to the development of novel strategies for dMRI preprocessing, exciting progress has been made in the availability of open source tools and reproducible pipelines, databases and simulation tools for the evaluation of preprocessing steps, and automated quality control frameworks, amongst others. Finally, this review will consider practical considerations and our view on “what’s next” in dMRI preprocessing.
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13
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Wang F, Dong Z, Tian Q, Liao C, Fan Q, Hoge WS, Keil B, Polimeni JR, Wald LL, Huang SY, Setsompop K. In vivo human whole-brain Connectom diffusion MRI dataset at 760 µm isotropic resolution. Sci Data 2021; 8:122. [PMID: 33927203 PMCID: PMC8084962 DOI: 10.1038/s41597-021-00904-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/26/2021] [Indexed: 01/18/2023] Open
Abstract
We present a whole-brain in vivo diffusion MRI (dMRI) dataset acquired at 760 μm isotropic resolution and sampled at 1260 q-space points across 9 two-hour sessions on a single healthy participant. The creation of this benchmark dataset is possible through the synergistic use of advanced acquisition hardware and software including the high-gradient-strength Connectom scanner, a custom-built 64-channel phased-array coil, a personalized motion-robust head stabilizer, a recently developed SNR-efficient dMRI acquisition method, and parallel imaging reconstruction with advanced ghost reduction algorithm. With its unprecedented resolution, SNR and image quality, we envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance the understanding of human brain structures and connectivity. This comprehensive dataset can also be used as a test bed for new modeling, sub-sampling strategies, denoising and processing algorithms, potentially providing a common testing platform for further development of in vivo high resolution dMRI techniques. Whole brain anatomical T1-weighted and T2-weighted images at submillimeter scale along with field maps are also made available.
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Affiliation(s)
- Fuyixue Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, USA.
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA.
| | - Zijing Dong
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Qiyuan Tian
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, USA
| | - Congyu Liao
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, USA
| | - Qiuyun Fan
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, USA
| | - W Scott Hoge
- Department of Radiology, Brigham and Women's Hospital, Boston, MA, USA
| | - Boris Keil
- Department of Life Science Engineering, Institute of Medical Physics and Radiation Protection, Giessen, Germany
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Lawrence L Wald
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Susie Y Huang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Kawin Setsompop
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
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14
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Viessmann O, Polimeni JR. High-resolution fMRI at 7 Tesla: challenges, promises and recent developments for individual-focused fMRI studies. Curr Opin Behav Sci 2021; 40:96-104. [PMID: 33816717 DOI: 10.1016/j.cobeha.2021.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Limited detection power has been a bottleneck for subject-specific functional MRI (fMRI) studies, however the higher signal-to-noise ratio afforded by ultra-high magnetic fields (≥ 7 Tesla) provides levels of sensitivity and resolution needed to study individual subjects. What may be surprising is that higher imaging resolution may provide both higher specificity and sensitivity due to reductions in partial volume effects and reduced physiological noise. However, challenges remain to ensure high data quality and to reduce variability in ultra-high field fMRI. We discuss session-specific biases including those caused by factors related to instrumentation, anatomy, and physiology-which can translate into variability across sessions-and how to minimize these to help ultra-high field fMRI reach its full potential for individual-focused studies.
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Affiliation(s)
- Olivia Viessmann
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Radiology, Harvard Medical School, Boston, MA, USA.,Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
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15
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Lobos RA, Hoge WS, Javed A, Liao C, Setsompop K, Nayak KS, Haldar JP. Robust autocalibrated structured low-rank EPI ghost correction. Magn Reson Med 2020; 85:3403-3419. [PMID: 33332652 DOI: 10.1002/mrm.28638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE We propose and evaluate a new structured low-rank method for echo-planar imaging (EPI) ghost correction called Robust Autocalibrated LORAKS (RAC-LORAKS). The method can be used to suppress EPI ghosts arising from the differences between different readout gradient polarities and/or the differences between different shots. It does not require conventional EPI navigator signals, and is robust to imperfect autocalibration data. METHODS Autocalibrated LORAKS is a previous structured low-rank method for EPI ghost correction that uses GRAPPA-type autocalibration data to enable high-quality ghost correction. This method works well when the autocalibration data are pristine, but performance degrades substantially when the autocalibration information is imperfect. RAC-LORAKS generalizes Autocalibrated LORAKS in two ways. First, it does not completely trust the information from autocalibration data, and instead considers the autocalibration and EPI data simultaneously when estimating low-rank matrix structure. Second, it uses complementary information from the autocalibration data to improve EPI reconstruction in a multi-contrast joint reconstruction framework. RAC-LORAKS is evaluated using simulations and in vivo data, including comparisons to state-of-the-art methods. RESULTS RAC-LORAKS is demonstrated to have good ghost elimination performance compared to state-of-the-art methods in several complicated EPI acquisition scenarios (including gradient-echo brain imaging, diffusion-encoded brain imaging, and cardiac imaging). CONCLUSIONS RAC-LORAKS provides effective suppression of EPI ghosts and is robust to imperfect autocalibration data.
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Affiliation(s)
- Rodrigo A Lobos
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA.,Signal and Image Processing Institute, University of Southern California, Los Angeles, CA, USA
| | - W Scott Hoge
- Department of Radiology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Ahsan Javed
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA.,Signal and Image Processing Institute, University of Southern California, Los Angeles, CA, USA
| | - Congyu Liao
- Department of Radiology, Harvard Medical School, Boston, MA, USA.,Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
| | - Kawin Setsompop
- Department of Radiology, Harvard Medical School, Boston, MA, USA.,Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
| | - Krishna S Nayak
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA.,Signal and Image Processing Institute, University of Southern California, Los Angeles, CA, USA.,Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Justin P Haldar
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA.,Signal and Image Processing Institute, University of Southern California, Los Angeles, CA, USA.,Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
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16
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Wallace TE, Polimeni JR, Stockmann JP, Hoge WS, Kober T, Warfield SK, Afacan O. Dynamic distortion correction for functional MRI using FID navigators. Magn Reson Med 2020; 85:1294-1307. [PMID: 32970869 DOI: 10.1002/mrm.28505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/06/2020] [Accepted: 08/14/2020] [Indexed: 11/08/2022]
Abstract
PURPOSE To develop a method for slice-wise dynamic distortion correction for EPI using rapid spatiotemporal B0 field measurements from FID navigators (FIDnavs) and to evaluate the efficacy of this new approach relative to an established data-driven technique. METHODS A low-resolution reference image was used to create a forward model of FIDnav signal changes to enable estimation of spatiotemporal B0 inhomogeneity variations up to second order from measured FIDnavs. Five volunteers were scanned at 3 T using a 64-channel coil with FID-navigated EPI. The accuracy of voxel shift measurements and geometric distortion correction was assessed for experimentally induced magnetic field perturbations. The temporal SNR was evaluated in EPI time-series acquired at rest and with a continuous nose-touching action, before and after image realignment. RESULTS Field inhomogeneity coefficients and voxel shift maps measured using FIDnavs were in excellent agreement with multi-echo EPI measurements. The FID-navigated distortion correction accurately corrected image geometry in the presence of induced magnetic field perturbations, outperforming the data-driven approach in regions with large field offsets. In functional MRI scans with nose touching, FIDnav-based correction yielded temporal SNR gains of 30% in gray matter. Following image realignment, which accounted for global image shifts, temporal SNR gains of 3% were achieved. CONCLUSIONS Our proposed application of FIDnavs enables slice-wise dynamic distortion correction with high temporal efficiency. We achieved improved signal stability by leveraging the encoding information from multichannel coils. This approach can be easily adapted to other EPI-based sequences to improve temporal SNR for a variety of clinical and research applications.
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Affiliation(s)
- Tess E Wallace
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan R Polimeni
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jason P Stockmann
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - W Scott Hoge
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Tobias Kober
- Advanced Clinical Imaging Technology, Siemens Healthcare AG, Lausanne, Switzerland.,Department of Radiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.,LTS5, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Simon K Warfield
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Onur Afacan
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
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17
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Stirnberg R, Stöcker T. Segmented K-space blipped-controlled aliasing in parallel imaging for high spatiotemporal resolution EPI. Magn Reson Med 2020; 85:1540-1551. [PMID: 32936488 DOI: 10.1002/mrm.28486] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE 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. THEORY AND METHODS 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. RESULTS 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. CONCLUSION 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.
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Affiliation(s)
| | - Tony Stöcker
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Physics and Astronomy, University of Bonn, Bonn, Germany
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18
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Berman AJL, Grissom WA, Witzel T, Nasr S, Park DJ, Setsompop K, Polimeni JR. Ultra-high spatial resolution BOLD fMRI in humans using combined segmented-accelerated VFA-FLEET with a recursive RF pulse design. Magn Reson Med 2020; 85:120-139. [PMID: 32705723 DOI: 10.1002/mrm.28415] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 11/08/2022]
Abstract
PURPOSE To alleviate the spatial encoding limitations of single-shot echo-planar imaging (EPI) by developing multi-shot segmented EPI for ultra-high-resolution functional MRI (fMRI) with reduced ghosting artifacts from subject motion and respiration. THEORY AND METHODS Segmented EPI can reduce readout duration and reduce acceleration factors, however, the time elapsed between segment acquisitions (on the order of seconds) can result in intermittent ghosting, limiting its use for fMRI. Here, "FLEET" segment ordering, where segments are looped over before slices, was combined with a variable flip angle progression (VFA-FLEET) to improve inter-segment fidelity and maximize signal for fMRI. Scaling a sinc pulse's flip angle for each segment (VFA-FLEET-Sinc) produced inconsistent slice profiles and ghosting, therefore, a recursive Shinnar-Le Roux (SLR) radiofrequency (RF) pulse design was developed (VFA-FLEET-SLR) to generate unique pulses for every segment that together produce consistent slice profiles and signals. RESULTS The temporal stability of VFA-FLEET-SLR was compared against conventional-segmented EPI and VFA-FLEET-Sinc at 3T and 7T. VFA-FLEET-SLR showed reductions in both intermittent and stable ghosting compared to conventional-segmented and VFA-FLEET-Sinc, resulting in improved image quality with a minor trade-off in temporal SNR. Combining VFA-FLEET-SLR with acceleration, we achieved a 0.6-mm isotropic acquisition at 7T, without zoomed imaging or partial Fourier, demonstrating reliable detection of blood oxygenation level-dependent (BOLD) responses to a visual stimulus. To counteract the increased repetition time from segmentation, simultaneous multi-slice VFA-FLEET-SLR was demonstrated using RF-encoded controlled aliasing. CONCLUSIONS VFA-FLEET with a recursive RF pulse design supports acquisitions with low levels of artifact and spatial blur, enabling fMRI at previously inaccessible spatial resolutions with a "full-brain" field of view.
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Affiliation(s)
- Avery J L Berman
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - William A Grissom
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Thomas Witzel
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shahin Nasr
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel J Park
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Kawin Setsompop
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Afacan O, Hoge WS, Wallace TE, Gholipour A, Kurugol S, Warfield SK. Simultaneous Motion and Distortion Correction Using Dual-Echo Diffusion-Weighted MRI. J Neuroimaging 2020; 30:276-285. [PMID: 32374453 DOI: 10.1111/jon.12708] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/02/2020] [Accepted: 03/19/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND AND PURPOSE Geometric distortions resulting from large pose changes reduce the accuracy of motion measurements and interfere with the ability to generate artifact-free information. Our goal is to develop an algorithm and pulse sequence to enable motion-compensated, geometric distortion compensated diffusion-weighted MRI, and to evaluate its efficacy in correcting for the field inhomogeneity and position changes, induced by large and frequent head motions. METHODS Dual echo planar imaging (EPI) with a blip-reversed phase encoding distortion correction technique was evaluated in five volunteers in two separate experiments and compared with static field map distortion correction. In the first experiment, dual-echo EPI images were acquired in two head positions designed to induce a large field inhomogeneity change. A field map and a distortion-free structural image were acquired at each position to assess the ability of dual-echo EPI to generate reliable field maps and enable geometric distortion correction in both positions. In the second experiment, volunteers were asked to move to multiple random positions during a diffusion scan. Images were reconstructed using the dual-echo correction and a slice-to-volume registration (SVR) registration algorithm. The accuracy of SVR motion estimates was compared to externally measured ground truth motion parameters. RESULTS Our results show that dual-echo EPI can produce slice-level field maps with comparable quality to field maps generated by the reference gold standard method. We also show that slice-level distortion correction improves the accuracy of SVR algorithms as slices acquired at different orientations have different levels of distortion, which can create errors in the registration process. CONCLUSIONS Dual-echo acquisitions with blip-reversed phase encoding can be used to generate slice-level distortion-free images, which is critical for motion-robust slice to volume registration. The distortion corrected images not only result in better motion estimates, but they also enable a more accurate final diffusion image reconstruction.
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Affiliation(s)
- Onur Afacan
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - W Scott Hoge
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Radiology, Brigham and Women's Hospital, Boston, MA
| | - Tess E Wallace
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ali Gholipour
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Sila Kurugol
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Simon K Warfield
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA
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20
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Bilgic B, Chatnuntawech I, Manhard MK, Tian Q, Liao C, Iyer SS, Cauley SF, Huang SY, Polimeni JR, Wald LL, Setsompop K. Highly accelerated multishot echo planar imaging through synergistic machine learning and joint reconstruction. Magn Reson Med 2019; 82:1343-1358. [PMID: 31106902 PMCID: PMC6626584 DOI: 10.1002/mrm.27813] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 04/22/2019] [Accepted: 04/22/2019] [Indexed: 12/13/2022]
Abstract
PURPOSE To introduce a combined machine learning (ML)- and physics-based image reconstruction framework that enables navigator-free, highly accelerated multishot echo planar imaging (msEPI) and demonstrate its application in high-resolution structural and diffusion imaging. METHODS Single-shot EPI is an efficient encoding technique, but does not lend itself well to high-resolution imaging because of severe distortion artifacts and blurring. Although msEPI can mitigate these artifacts, high-quality msEPI has been elusive because of phase mismatch arising from shot-to-shot variations which preclude the combination of the multiple-shot data into a single image. We utilize deep learning to obtain an interim image with minimal artifacts, which permits estimation of image phase variations attributed to shot-to-shot changes. These variations are then included in a joint virtual coil sensitivity encoding (JVC-SENSE) reconstruction to utilize data from all shots and improve upon the ML solution. RESULTS Our combined ML + physics approach enabled Rinplane × multiband (MB) = 8- × 2-fold acceleration using 2 EPI shots for multiecho imaging, so that whole-brain T2 and T2 * parameter maps could be derived from an 8.3-second acquisition at 1 × 1 × 3-mm3 resolution. This has also allowed high-resolution diffusion imaging with high geometrical fidelity using 5 shots at Rinplane × MB = 9- × 2-fold acceleration. To make these possible, we extended the state-of-the-art MUSSELS reconstruction technique to simultaneous multislice encoding and used it as an input to our ML network. CONCLUSION Combination of ML and JVC-SENSE enabled navigator-free msEPI at higher accelerations than previously possible while using fewer shots, with reduced vulnerability to poor generalizability and poor acceptance of end-to-end ML approaches.
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Affiliation(s)
- Berkin Bilgic
- Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Itthi Chatnuntawech
- National Nanotechnology Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Mary Kate Manhard
- Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Qiyuan Tian
- Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Congyu Liao
- Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Siddharth S. Iyer
- Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stephen F. Cauley
- Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Susie Y. Huang
- Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Jonathan R. Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Lawrence L. Wald
- Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Kawin Setsompop
- Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
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21
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Lee J, Han Y, Ryu JK, Park JY, Ye JC. k-Space deep learning for reference-free EPI ghost correction. Magn Reson Med 2019; 82:2299-2313. [PMID: 31321809 DOI: 10.1002/mrm.27896] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/08/2019] [Accepted: 06/14/2019] [Indexed: 11/12/2022]
Abstract
PURPOSE Nyquist ghost artifacts in echo planar imaging (EPI) are originated from phase mismatch between the even and odd echoes. However, conventional correction methods using reference scans often produce erroneous results especially in high-field MRI due to the nonlinear and time-varying local magnetic field changes. Recently, it was shown that the problem of ghost correction can be reformulated as k-space interpolation problem that can be solved using structured low-rank Hankel matrix approaches. Another recent work showed that data driven Hankel matrix decomposition can be reformulated to exhibit similar structures as deep convolutional neural network. By synergistically combining these findings, we propose a k-space deep learning approach that immediately corrects the phase mismatch without a reference scan in both accelerated and non-accelerated EPI acquisitions. THEORY AND METHODS To take advantage of the even and odd-phase directional redundancy, the k-space data are divided into 2 channels configured with even and odd phase encodings. The redundancies between coils are also exploited by stacking the multi-coil k-space data into additional input channels. Then, our k-space ghost correction network is trained to learn the interpolation kernel to estimate the missing virtual k-space data. For the accelerated EPI data, the same neural network is trained to directly estimate the interpolation kernels for missing k-space data from both ghost and subsampling. RESULTS Reconstruction results using 3T and 7T in vivo data showed that the proposed method outperformed the image quality compared to the existing methods, and the computing time is much faster. CONCLUSIONS The proposed k-space deep learning for EPI ghost correction is highly robust and fast, and can be combined with acceleration, so that it can be used as a promising correction tool for high-field MRI without changing the current acquisition protocol.
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Affiliation(s)
- Juyoung Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Yoseob Han
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Jae-Kyun Ryu
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, South Korea.,Department of Biomedical Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Jang-Yeon Park
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, South Korea.,Department of Biomedical Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Jong Chul Ye
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
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22
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McKay JA, Moeller S, Zhang L, Auerbach EJ, Nelson MT, Bolan PJ. Nyquist ghost correction of breast diffusion weighted imaging using referenceless methods. Magn Reson Med 2018; 81:2624-2631. [PMID: 30387902 DOI: 10.1002/mrm.27563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/27/2018] [Accepted: 09/16/2018] [Indexed: 01/20/2023]
Abstract
PURPOSE Correction of Nyquist ghosts for single-shot spin-echo EPI using the standard 3-line navigator often fails in breast DWI because of incomplete fat suppression, respiration, and greater B0 inhomogeneity. The purpose of this work is to compare the performance of the 3-line navigator with 4 data-driven methods termed "referenceless methods," including 2 previously proposed in literature, 1 introduced in this work, and finally a combination of all 3, in breast DWI. METHODS Breast DWI was acquired for 41 patients with SS SE-EPI. Raw data was corrected offline with the standard 3-line navigator and 4 referenceless methods, which modeled the ghost as a linear phase error and minimized 3 unique cost functions as well as the median solution of all 3. Ghost levels were evaluated based on the signal intensity in the background region, defined by a mask auto-generated from a T1 -weighted anatomical image. Ghost intensity measurements were fit to a linear mixed model including ghost correction method and b-value as covariates. RESULTS All 4 referenceless methods outperformed the standard 3-line navigator with statistical significance at all 4 b-values tested (b = 0, 100, 600, and 800 s/mm2 ). CONCLUSIONS Referenceless methods provide a robust way to reduce Nyquist ghosts in breast DWI without the need for any additional calibration scan.
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Affiliation(s)
- Jessica A McKay
- Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota.,Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota
| | - Steen Moeller
- Department of Radiology, University of Minnesota, Minneapolis, Minnesota.,Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota
| | - Lei Zhang
- Clinical and Translational Science Institute, University of Minnesota, Minneapolis, Minnesota
| | - Edward J Auerbach
- Department of Radiology, University of Minnesota, Minneapolis, Minnesota.,Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota
| | - Michael T Nelson
- Department of Radiology, University of Minnesota, Minneapolis, Minnesota
| | - Patrick J Bolan
- Department of Radiology, University of Minnesota, Minneapolis, Minnesota.,Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota
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23
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Lobos RA, Kim TH, Hoge WS, Haldar JP. Navigator-Free EPI Ghost Correction With Structured Low-Rank Matrix Models: New Theory and Methods. IEEE TRANSACTIONS ON MEDICAL IMAGING 2018; 37:2390-2402. [PMID: 29993978 PMCID: PMC6309699 DOI: 10.1109/tmi.2018.2822053] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Structured low-rank matrix models have previously been introduced to enable calibrationless MR image reconstruction from sub-Nyquist data, and such ideas have recently been extended to enable navigator-free echo-planar imaging (EPI) ghost correction. This paper presents a novel theoretical analysis which shows that, because of uniform subsampling, the structured low-rank matrix optimization problems for EPI data will always have either undesirable or non-unique solutions in the absence of additional constraints. This theory leads us to recommend and investigate problem formulations for navigator-free EPI that incorporate side information from either image-domain or k-space domain parallel imaging methods. The importance of using nonconvex low-rank matrix regularization is also identified. We demonstrate using phantom and in vivo data that the proposed methods are able to eliminate ghost artifacts for several navigator-free EPI acquisition schemes, obtaining better performance in comparison with the state-of-the-art methods across a range of different scenarios. Results are shown for both single-channel acquisition and highly accelerated multi-channel acquisition.
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24
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Liu Y, Lyu M, Barth M, Yi Z, Leong ATL, Chen F, Feng Y, Wu EX. PEC-GRAPPA reconstruction of simultaneous multislice EPI with slice-dependent 2D Nyquist ghost correction. Magn Reson Med 2018; 81:1924-1934. [PMID: 30368895 DOI: 10.1002/mrm.27546] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/17/2018] [Accepted: 09/01/2018] [Indexed: 12/15/2022]
Abstract
PURPOSE To provide simultaneous multislice (SMS) EPI reconstruction with k-space implementation and robust Nyquist ghost correction. METHODS 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. RESULTS 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. CONCLUSION 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.
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Affiliation(s)
- Yilong Liu
- Laboratory of Biomedical Imaging and Signal Processing, the University of Hong Kong, Hong Kong SAR, People's Republic of China.,Department of Electrical and Electronic Engineering, the University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Mengye Lyu
- Laboratory of Biomedical Imaging and Signal Processing, the University of Hong Kong, Hong Kong SAR, People's Republic of China.,Department of Electrical and Electronic Engineering, the University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Markus Barth
- Centre for Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Zheyuan Yi
- Laboratory of Biomedical Imaging and Signal Processing, the University of Hong Kong, Hong Kong SAR, People's Republic of China.,Department of Electrical and Electronic Engineering, the University of Hong Kong, Hong Kong SAR, People's Republic of China.,Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Alex T L Leong
- Laboratory of Biomedical Imaging and Signal Processing, the University of Hong Kong, Hong Kong SAR, People's Republic of China.,Department of Electrical and Electronic Engineering, the University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Fei Chen
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Yanqiu Feng
- School of Biomedical Engineering, Southern Medical University, Guangzhou, People's Republic of China
| | - Ed X Wu
- Laboratory of Biomedical Imaging and Signal Processing, the University of Hong Kong, Hong Kong SAR, People's Republic of China.,Department of Electrical and Electronic Engineering, the University of Hong Kong, Hong Kong SAR, People's Republic of China
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25
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Cho J, Park H. Technical Note: Interleaved bipolar acquisition and low‐rank reconstruction for water–fat separation in
MRI. Med Phys 2018; 45:3229-3237. [DOI: 10.1002/mp.12981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/07/2018] [Accepted: 05/07/2018] [Indexed: 11/06/2022] Open
Affiliation(s)
- JaeJin Cho
- Department of Electrical Engineering Korea Advanced Institute of Science and Technology (KAIST) Daejeon South Korea
| | - HyunWook Park
- Department of Electrical Engineering Korea Advanced Institute of Science and Technology (KAIST) Daejeon South Korea
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26
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Lobos RA, Javed A, Nayak KS, Hoge WS, Haldar JP. ROBUST AUTOCALIBRATED LORAKS FOR EPI GHOST CORRECTION. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2018; 2018:663-666. [PMID: 30984344 DOI: 10.1109/isbi.2018.8363661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Nyquist ghosts are a longstanding problem in a variety of fast MRI experiments that use echo-planar imaging (EPI). Recently, several structured low-rank matrix modeling approaches have been proposed that achieve state-of-the-art ghost-elimination, although the performance of these approaches is still inadequate in several important scenarios. We present a new structured low-rank matrix recovery ghost correction method that we call Robust Autocalibrated LORAKS (RAC-LORAKS). RAC-LORAKS incorporates constraints from autocalibration data to avoid ill-posedness, but allows adaptation of these constraints to gain robustness against possible autocalibration imperfections. RAC-LORAKS is tested in two challenging scenarios: highly-undersampled multi-channel EPI of the brain, and cardiac EPI with a double-oblique slice orientation. Results show that RAC-LORAKS can provide substantial improvements over existing ghost correction methods, and potentially enables new imaging applications that were previously confounded by ghost artifacts.
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Affiliation(s)
- Rodrigo A Lobos
- Signal and Image Processing Institute, University of Southern California, Los Angeles, CA 90089
| | - Ahsan Javed
- Signal and Image Processing Institute, University of Southern California, Los Angeles, CA 90089
| | - Krishna S Nayak
- Signal and Image Processing Institute, University of Southern California, Los Angeles, CA 90089
| | - W Scott Hoge
- Radiology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Justin P Haldar
- Signal and Image Processing Institute, University of Southern California, Los Angeles, CA 90089
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27
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Yarach U, Tung YH, Setsompop K, In MH, Chatnuntawech I, Yakupov R, Godenschweger F, Speck O. Dynamic 2D self-phase-map Nyquist ghost correction for simultaneous multi-slice echo planar imaging. Magn Reson Med 2018; 80:1577-1587. [PMID: 29427393 DOI: 10.1002/mrm.27123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 01/08/2018] [Accepted: 01/17/2018] [Indexed: 11/10/2022]
Abstract
PURPOSE To develop a reconstruction pipeline that intrinsically accounts for both simultaneous multislice echo planar imaging (SMS-EPI) reconstruction and dynamic slice-specific Nyquist ghosting correction in time-series data. METHODS After 1D slice-group average phase correction, the separate polarity (i.e., even and odd echoes) SMS-EPI data were unaliased by slice GeneRalized Autocalibrating Partial Parallel Acquisition. Both the slice-unaliased even and odd echoes were jointly reconstructed using a model-based framework, extended for SMS-EPI reconstruction that estimates a 2D self-phase map, corrects dynamic slice-specific phase errors, and combines data from all coils and echoes to obtain the final images. RESULTS The percentage ghost-to-signal ratios (%GSRs) and its temporal variations for MB3Ry 2 with a field of view/4 shift in a human brain obtained by the proposed dynamic 2D and standard 1D phase corrections were 1.37 ± 0.11 and 2.66 ± 0.16, respectively. Even with a large regularization parameter λ applied in the proposed reconstruction, the smoothing effect in fMRI activation maps was comparable to a very small Gaussian kernel size 1 × 1 × 1 mm3 . CONCLUSION The proposed reconstruction pipeline reduced slice-specific phase errors in SMS-EPI, resulting in reduction of GSR. It is applicable for functional MRI studies because the smoothing effect caused by the regularization parameter selection can be minimal in a blood-oxygen-level-dependent activation map.
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Affiliation(s)
- Uten Yarach
- Department of Radiologic Technology, Chiang Mai University, Chiang Mai, Thailand
| | - Yi-Hang Tung
- Department of Biomedical Magnetic Resonance, Otto-von-Guericke University Magdeburg, Germany
| | - Kawin Setsompop
- A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Myung-Ho In
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Itthi Chatnuntawech
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Renat Yakupov
- Department of Biomedical Magnetic Resonance, Otto-von-Guericke University Magdeburg, Germany
| | - Frank Godenschweger
- Department of Biomedical Magnetic Resonance, Otto-von-Guericke University Magdeburg, Germany
| | - Oliver Speck
- Department of Biomedical Magnetic Resonance, Otto-von-Guericke University Magdeburg, Germany.,Leibniz Institute for Neurobiology, Magdeburg, Germany.,German Centre for Neurodegenerative Diseases (DZNE), Site Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany
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28
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Lyu M, Barth M, Xie VB, Liu Y, Ma X, Feng Y, Wu EX. Robust SENSE reconstruction of simultaneous multislice EPI with low‐rank enhanced coil sensitivity calibration and slice‐dependent 2D Nyquist ghost correction. Magn Reson Med 2018; 80:1376-1390. [DOI: 10.1002/mrm.27120] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 12/13/2017] [Accepted: 01/11/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Mengye Lyu
- Laboratory of Biomedical Imaging and Signal Processing, the University of Hong KongHong Kong SAR People's Republic of China
- Department of Electrical and Electronic Engineeringthe University of Hong KongHong Kong SAR People's Republic of China
| | - Markus Barth
- Centre for Advanced Imaging, University of QueenslandBrisbane Queensland Australia
| | - Victor B. Xie
- Laboratory of Biomedical Imaging and Signal Processing, the University of Hong KongHong Kong SAR People's Republic of China
- Department of Electrical and Electronic Engineeringthe University of Hong KongHong Kong SAR People's Republic of China
- Toshiba Medical Systems (China)Beijing People's Republic of China
| | - Yilong Liu
- Laboratory of Biomedical Imaging and Signal Processing, the University of Hong KongHong Kong SAR People's Republic of China
- Department of Electrical and Electronic Engineeringthe University of Hong KongHong Kong SAR People's Republic of China
| | - Xin Ma
- Laboratory of Biomedical Imaging and Signal Processing, the University of Hong KongHong Kong SAR People's Republic of China
- Department of Electrical and Electronic Engineeringthe University of Hong KongHong Kong SAR People's Republic of China
| | - Yanqiu Feng
- Laboratory of Biomedical Imaging and Signal Processing, the University of Hong KongHong Kong SAR People's Republic of China
- School of Biomedical EngineeringSouthern Medical UniversityGuangzhou Guangdong People's Republic of China
| | - Ed X. Wu
- Laboratory of Biomedical Imaging and Signal Processing, the University of Hong KongHong Kong SAR People's Republic of China
- Department of Electrical and Electronic Engineeringthe University of Hong KongHong Kong SAR People's Republic of China
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29
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Hoge WS, Setsompop K, Polimeni JR. Dual-polarity slice-GRAPPA for concurrent ghost correction and slice separation in simultaneous multi-slice EPI. Magn Reson Med 2018; 80:1364-1375. [PMID: 29424460 DOI: 10.1002/mrm.27113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 01/04/2018] [Accepted: 01/08/2018] [Indexed: 12/15/2022]
Abstract
PURPOSE A ghost correction strategy for Simultaneous Multi-Slice (SMS) EPI methods that provides improved ghosting artifact reduction compared to conventional methods is presented. Conventional Nyquist ghost correction methods for SMS-EPI rely on navigator data that contain phase errors from all slices in the simultaneously acquired slice-group. These navigator data may contain spatially nonlinear phase differences near regions of B0 inhomogeneity, which violates the linear model employed by most EPI ghost correction algorithms, resulting in poor reconstructions. METHODS Dual-Polarity GRAPPA (DPG) was previously shown to accurately model and correct both spatially nonlinear and 2D phase errors in conventional single-slice EPI data. Here, an extension we call Dual-Polarity slice-GRAPPA (DPsG) is adapted to the slice-GRAPPA method and applied to SMS-EPI data for slice separation and ghost correction concurrently-eliminating the need for a separate ghost correction step while also providing improved slice-specific EPI phase error correction. RESULTS Images from in vivo SMS-EPI data reconstructed using DPsG in place of conventional Nyquist ghost correction and slice-GRAPPA are presented. DPsG is shown to reduce ghosting artifacts and provide improved temporal SNR compared to the conventional reconstruction. CONCLUSION The proposed use of DPsG for SMS-EPI reconstruction can provide images with lower artifact levels, higher image fidelity, and improved time-series stability compared to conventional reconstruction methods.
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Affiliation(s)
- W Scott Hoge
- Department of Radiology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kawin Setsompop
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, Massachusetts.,Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, Massachusetts.,Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts
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30
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Yarach U, In M, Chatnuntawech I, Bilgic B, Godenschweger F, Mattern H, Sciarra A, Speck O. Model-based iterative reconstruction for single-shot EPI at 7T. Magn Reson Med 2017; 78:2250-2264. [PMID: 28185433 PMCID: PMC5552473 DOI: 10.1002/mrm.26633] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 01/07/2017] [Accepted: 01/11/2017] [Indexed: 12/30/2022]
Abstract
PURPOSE To describe a model-based reconstruction strategy for single-shot echo planar imaging (EPI) that intrinsically accounts for k-space nonuniformity, Nyquist ghosting, and geometric distortions during rather than before or after image reconstruction. METHODS Ramp sampling and inhomogeneous B0 field-induced distortion cause the EPI samples to lie on a non-Cartesian grid, thus requiring the nonuniform fast Fourier transform. Additionally, a 2D Nyquist ghost phase correction without the need for extra navigator acquisition is included in the proposed reconstruction. Coil compression is also incorporated to reduce the computational load. The proposed method is applied to phantom and human brain MRI data. RESULTS The results demonstrate that Nyquist ghosting and geometric distortions are reduced by the proposed reconstruction. The proposed 2D phase correction is superior to a conventional 1D correction. The reductions of both artifacts lead to improved temporal signal-to-noise ratio (tSNR). The virtual coil results suggest that the processing time can be reduced by up to 75%, with a mean tSNR loss of only 3.2% when using 8-virtual instead of 32-physical coils for twofold undersampled data. CONCLUSION The proposed reconstruction improves the quality (ghosting, geometry, and tSNR) of EPI without requiring calibration data for Nyquist ghost correction. Magn Reson Med 78:2250-2264, 2017. © 2017 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- U. Yarach
- Department of Biomedical Magnetic Resonance, Otto-von-Guericke University Magdeburg, Germany
- Department of Radiological Technology, Chiang Mai University, Chiangmai, Thailand
| | - M.H. In
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - I. Chatnuntawech
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - B. Bilgic
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
- A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - F. Godenschweger
- Department of Biomedical Magnetic Resonance, Otto-von-Guericke University Magdeburg, Germany
| | - H. Mattern
- Department of Biomedical Magnetic Resonance, Otto-von-Guericke University Magdeburg, Germany
| | - A. Sciarra
- Department of Biomedical Magnetic Resonance, Otto-von-Guericke University Magdeburg, Germany
| | - O. Speck
- Department of Biomedical Magnetic Resonance, Otto-von-Guericke University Magdeburg, Germany
- Leibniz Institute for Neurobiology, Magdeburg, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Site Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
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Hamilton J, Franson D, Seiberlich N. Recent advances in parallel imaging for MRI. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 101:71-95. [PMID: 28844222 PMCID: PMC5927614 DOI: 10.1016/j.pnmrs.2017.04.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/09/2017] [Accepted: 04/17/2017] [Indexed: 05/22/2023]
Abstract
Magnetic Resonance Imaging (MRI) is an essential technology in modern medicine. However, one of its main drawbacks is the long scan time needed to localize the MR signal in space to generate an image. This review article summarizes some basic principles and recent developments in parallel imaging, a class of image reconstruction techniques for shortening scan time. First, the fundamentals of MRI data acquisition are covered, including the concepts of k-space, undersampling, and aliasing. It is demonstrated that scan time can be reduced by sampling a smaller number of phase encoding lines in k-space; however, without further processing, the resulting images will be degraded by aliasing artifacts. Nearly all modern clinical scanners acquire data from multiple independent receiver coil arrays. Parallel imaging methods exploit properties of these coil arrays to separate aliased pixels in the image domain or to estimate missing k-space data using knowledge of nearby acquired k-space points. Three parallel imaging methods-SENSE, GRAPPA, and SPIRiT-are described in detail, since they are employed clinically and form the foundation for more advanced methods. These techniques can be extended to non-Cartesian sampling patterns, where the collected k-space points do not fall on a rectangular grid. Non-Cartesian acquisitions have several beneficial properties, the most important being the appearance of incoherent aliasing artifacts. Recent advances in simultaneous multi-slice imaging are presented next, which use parallel imaging to disentangle images of several slices that have been acquired at once. Parallel imaging can also be employed to accelerate 3D MRI, in which a contiguous volume is scanned rather than sequential slices. Another class of phase-constrained parallel imaging methods takes advantage of both image magnitude and phase to achieve better reconstruction performance. Finally, some applications are presented of parallel imaging being used to accelerate MR Spectroscopic Imaging.
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Affiliation(s)
- Jesse Hamilton
- Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
| | - Dominique Franson
- Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
| | - Nicole Seiberlich
- Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA; Radiology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
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Xie VB, Lyu M, Liu Y, Feng Y, Wu EX. Robust EPI Nyquist ghost removal by incorporating phase error correction with sensitivity encoding (PEC-SENSE). Magn Reson Med 2017; 79:943-951. [PMID: 28590562 DOI: 10.1002/mrm.26710] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 03/21/2017] [Accepted: 03/21/2017] [Indexed: 11/11/2022]
Abstract
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 incorporates 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 reconstruction 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 performed 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 standard coil sensitivity maps and can be readily applied to all EPI applications. Magn Reson Med 79:943-951, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Victor B Xie
- Laboratory of Biomedical Imaging and Signal Processing, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.,Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Mengye Lyu
- Laboratory of Biomedical Imaging and Signal Processing, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.,Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yilong Liu
- Laboratory of Biomedical Imaging and Signal Processing, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.,Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yanqiu Feng
- Laboratory of Biomedical Imaging and Signal Processing, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.,Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.,School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Ed X Wu
- Laboratory of Biomedical Imaging and Signal Processing, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.,Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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Stäb D, Bollmann S, Langkammer C, Bredies K, Barth M. Accelerated mapping of magnetic susceptibility using 3D planes-on-a-paddlewheel (POP) EPI at ultra-high field strength. NMR IN BIOMEDICINE 2017; 30:e3620. [PMID: 27763692 DOI: 10.1002/nbm.3620] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 07/04/2016] [Accepted: 08/17/2016] [Indexed: 06/06/2023]
Abstract
With the advent of ultra-high field MRI scanners in clinical research, susceptibility based MRI has recently gained increasing interest because of its potential to assess subtle tissue changes underlying neurological pathologies/disorders. Conventional, but rather slow, three-dimensional (3D) spoiled gradient-echo (GRE) sequences are typically employed to assess the susceptibility of tissue. 3D echo-planar imaging (EPI) represents a fast alternative but generally comes with echo-time restrictions, geometrical distortions and signal dropouts that can become severe at ultra-high fields. In this work we assess quantitative susceptibility mapping (QSM) at 7 T using non-Cartesian 3D EPI with a planes-on-a-paddlewheel (POP) trajectory, which is created by rotating a standard EPI readout train around its own phase encoding axis. We show that the threefold accelerated non-Cartesian 3D POP EPI sequence enables very fast, whole brain susceptibility mapping at an isotropic resolution of 1 mm and that the high image quality has sufficient signal-to-noise ratio in the phase data for reliable QSM processing. The susceptibility maps obtained were comparable with regard to QSM values and geometric distortions to those calculated from a conventional 4 min 3D GRE scan using the same QSM processing pipeline. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Daniel Stäb
- The Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland, Australia
- Department of Diagnostic and Interventional Radiology, University of Würzburg, Würzburg, Germany
| | - Steffen Bollmann
- The Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Kristian Bredies
- Institute for Mathematics and Scientific Computing, University of Graz, Graz, Austria
| | - Markus Barth
- The Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland, Australia
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Soares JM, Magalhães R, Moreira PS, Sousa A, Ganz E, Sampaio A, Alves V, Marques P, Sousa N. A Hitchhiker's Guide to Functional Magnetic Resonance Imaging. Front Neurosci 2016; 10:515. [PMID: 27891073 PMCID: PMC5102908 DOI: 10.3389/fnins.2016.00515] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/25/2016] [Indexed: 12/12/2022] Open
Abstract
Functional Magnetic Resonance Imaging (fMRI) studies have become increasingly popular both with clinicians and researchers as they are capable of providing unique insights into brain functions. However, multiple technical considerations (ranging from specifics of paradigm design to imaging artifacts, complex protocol definition, and multitude of processing and methods of analysis, as well as intrinsic methodological limitations) must be considered and addressed in order to optimize fMRI analysis and to arrive at the most accurate and grounded interpretation of the data. In practice, the researcher/clinician must choose, from many available options, the most suitable software tool for each stage of the fMRI analysis pipeline. Herein we provide a straightforward guide designed to address, for each of the major stages, the techniques, and tools involved in the process. We have developed this guide both to help those new to the technique to overcome the most critical difficulties in its use, as well as to serve as a resource for the neuroimaging community.
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Affiliation(s)
- José M. Soares
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal
- ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal
| | - Ricardo Magalhães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal
- ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal
| | - Pedro S. Moreira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal
- ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal
| | - Alexandre Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal
- ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal
- Department of Informatics, University of MinhoBraga, Portugal
| | - Edward Ganz
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal
- ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal
| | - Adriana Sampaio
- Neuropsychophysiology Lab, CIPsi, School of Psychology, University of MinhoBraga, Portugal
| | - Victor Alves
- Department of Informatics, University of MinhoBraga, Portugal
| | - Paulo Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal
- ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal
| | - Nuno Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of MinhoBraga, Portugal
- ICVS/3B's - PT Government Associate LaboratoryBraga, Portugal
- Clinical Academic Center – BragaBraga, Portugal
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