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Huber R, Stirnberg R, Morgan AT, Feinberg DA, Ehses P, Knudsen L, Gulban OF, Koiso K, Swegle S, Gephart I, Wardle SG, Persichetti A, Beckett AJ, Stöcker T, Boulant N, Poser BA, Bandettini P. Fuzzy ripple artifact in high resolution fMRI: identification, cause, and mitigation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611294. [PMID: 39314458 PMCID: PMC11418939 DOI: 10.1101/2024.09.04.611294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Purpose High resolution fMRI is a rapidly growing research field focused on capturing functional signal changes across cortical layers. However, the data acquisition is limited by low spatial frequency EPI artifacts; termed here as Fuzzy Ripples. These artifacts limit the practical applicability of acquisition protocols with higher spatial resolution, faster acquisition speed, and they challenge imaging in lower brain areas. Methods We characterize Fuzzy Ripple artifacts across commonly used sequences and distinguish them from conventional EPI Nyquist ghosts, off-resonance effects, and GRAPPA artifacts. To investigate their origin, we employ dual polarity readouts. Results Our findings indicate that Fuzzy Ripples are primarily caused by readout-specific imperfections in k-space trajectories, which can be exacerbated by inductive coupling between third-order shims and readout gradients. We also find that these artifacts can be mitigated through complex-valued averaging of dual polarity EPI or by disconnecting the third-order shim coils. Conclusion The proposed mitigation strategies allow overcoming current limitations in layer-fMRI protocols: (1)Achieving resolutions beyond 0.8mm is feasible, and even at 3T, we achieved 0.53mm voxel functional connectivity mapping.(2)Sub-millimeter sampling acceleration can be increased to allow sub-second TRs and laminar whole brain protocols with up to GRAPPA 8.(3)Sub-millimeter fMRI is achievable in lower brain areas, including the cerebellum.
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Affiliation(s)
| | | | | | - David A Feinberg
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
- Advanced MRI Technologies, Sebastopol, CA, United States
- CN, FPN, University of Maastricht, The Netherlands
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Lasse Knudsen
- Center of Functionally Integrative Neuroscience (CFIN), Department of Clinical Medicine, Aarhus University, Universitetsbyen 3, 8000 Aarhus C, Denmark
- Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101400, PR China
| | - Omer Faruk Gulban
- CN, FPN, University of Maastricht, The Netherlands
- Brain Innovation, Maastricht, The Netherlands
| | - Kenshu Koiso
- CN, FPN, University of Maastricht, The Netherlands
| | | | | | | | | | - Alexander Js Beckett
- Advanced MRI Technologies, Sebastopol, CA, United States
- CN, FPN, University of Maastricht, The Netherlands
| | - Tony Stöcker
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Nicolas Boulant
- University Paris Saclay, CEA, CNRS, NeuroSpin, BAOBAB, France
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Wu W. Dynamic field mapping and distortion correction using single-shot blip-rewound EPI and joint multi-echo reconstruction. Magn Reson Med 2024; 92:82-97. [PMID: 38308081 DOI: 10.1002/mrm.30038] [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: 08/17/2023] [Revised: 01/02/2024] [Accepted: 01/16/2024] [Indexed: 02/04/2024]
Abstract
PURPOSE To develop a method for dynamic∆ B 0 $$ \Delta {B}_0 $$ mapping and distortion correction. METHODS A blip-rewound EPI trajectory was developed to acquire multiple 2D EPI images in a single readout with an interleaved order, which allows a short TE difference. A joint multi-echo reconstruction was utilized to exploit the shared information between EPI images. The reconstructed images from each readout are combined to produce a final magnitude image. A∆ B 0 $$ \Delta {B}_0 $$ map is calculated from the phase of these images for distortion correction. The efficacy of the proposed method is assessed with phantom and in vivo experiments. The performance of the proposed method in the presence of subject motion is also investigated. RESULTS Compared to conventional multi-echo EPI, the proposed method allows dynamic∆ B 0 $$ \Delta {B}_0 $$ mapping at matched resolution with a much shorter TR. Phantom and in vivo results show that the proposed method can provide a comparable magnitude image as conventional single-shot EPI. The∆ B 0 $$ \Delta {B}_0 $$ maps calculated from the proposed method are consistent with conventional multi-echo EPI in the phantom experiment. For in vivo experiments, the proposed method provides a more accurate estimation of∆ B 0 $$ \Delta {B}_0 $$ than conventional multi-echo EPI, which is prone to phase wrapping problems due to the long TE difference. In-vivo scan with subject motion shows the proposed dynamic field mapping method can improve the temporal stability of EPI time series compared to gradient echo (GRE) based static field mapping. CONCLUSION The proposed method allows accurate dynamic∆ B 0 $$ \Delta {B}_0 $$ mapping for robust distortion correction without compromising spatial or temporal resolution.
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Affiliation(s)
- Wenchuan Wu
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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3
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Zha F, Feng C, Xu J, Zou Q, Li J, Hu D, Liu WV, Li Z, Wu S. Evaluation of multiplexed sensitivity encoding diffusion-weighted imaging in detecting uterine lesions: Image quality optimization. Magn Reson Imaging 2024; 110:17-22. [PMID: 38452829 DOI: 10.1016/j.mri.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/03/2024] [Accepted: 03/03/2024] [Indexed: 03/09/2024]
Abstract
PURPOSE To compare the image quality of multiplexed sensitivity-encoding diffusion-weighted imaging (MUSE-DWI) and single-shot echo-planar imaging (SS-EPI-DWI) techniques in uterine MRI. METHODS Eighty-eight eligible patients underwent MUSE-DWI and SS-EPI-DWI examinations simultaneously using a 3.0 T MRI system. Two radiologists independently performed quantitative and qualitative analysis of the two groups of images using a double-blind method. The weighted Kappa test was used to evaluate the interobserver agreement. Wilcoxon's rank sum test was used for qualitative parameters, and paired t-test was used for quantitative parameters. Spearman rank correlation analysis was used to obtained correlation between pathological results and mean apparent diffusion coefficient (ADC) value. RESULTS The qualitative and quantitative analysis of the images by the two radiologists were in good or excellent agreement, with weighted kappa value ranging from 0.636 to 0.981. The scores of total subjective image quality (15.4 ± 0.99) and signal-to-noise ratio (158.99 ± 60.71) of MUSE-DWI were significantly higher than those of SS-EPI-DWI (12.93 ± 1.62 P < 0.001; 130.23 ± 48.29 P < 0.05). It effectively reduced image distortion and artifact, and had better lesion conspicuity. There was no significant difference in contrast-to-noise ratio score and average ADC values between the two DWI sequences. The average ADC values of the two DWI sequences were highest in the normal uterus group and lowest in the endometrial cancer group, with statistically significant differences among groups (P < 0.01). In addition, the average ADC values of the two DWI sequences were negatively correlated with the type of lesions, decreasing with the malignancy of the lesions (r = -0.805 P < 0.01, r = -0.815 P < 0.01). CONCLUSION Compared to SS-EPI-DWI, MUSE-DWI can significantly reduce distortion, artifacts, and fuzziness in MRI of uterine lesions, which is more conducive to lesion detection.
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Affiliation(s)
- Fuxiang Zha
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, China
| | - Cui Feng
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, China
| | - Jin Xu
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, China
| | - Qian Zou
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, China
| | - Jiali Li
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, China
| | - Daoyu Hu
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, China
| | | | - Zhen Li
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, China
| | - Sisi Wu
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, China.
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Ramos-Llordén G, Park DJ, Kirsch JE, Scholz A, Keil B, Maffei C, Lee HH, Bilgic B, Edlow BL, Mekkaoui C, Yendiki A, Witzel T, Huang SY. Eddy current-induced artifact correction in high b-value ex vivo human brain diffusion MRI with dynamic field monitoring. Magn Reson Med 2024; 91:541-557. [PMID: 37753621 PMCID: PMC10842131 DOI: 10.1002/mrm.29873] [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: 02/12/2023] [Revised: 08/30/2023] [Accepted: 09/02/2023] [Indexed: 09/28/2023]
Abstract
PURPOSE To investigate whether spatiotemporal magnetic field monitoring can correct pronounced eddy current-induced artifacts incurred by strong diffusion-sensitizing gradients up to 300 mT/m used in high b-value diffusion-weighted (DW) EPI. METHODS A dynamic field camera equipped with 16 1 H NMR field probes was first used to characterize field perturbations caused by residual eddy currents from diffusion gradients waveforms in a 3D multi-shot EPI sequence on a 3T Connectom scanner for different gradient strengths (up to 300 mT/m), diffusion directions, and shots. The efficacy of dynamic field monitoring-based image reconstruction was demonstrated on high-gradient strength, submillimeter resolution whole-brain ex vivo diffusion MRI. A 3D multi-shot image reconstruction framework was developed that incorporated the nonlinear phase evolution measured with the dynamic field camera. RESULTS Phase perturbations in the readout induced by residual eddy currents from strong diffusion gradients are highly nonlinear in space and time, vary among diffusion directions, and interfere significantly with the image encoding gradients, changing the k-space trajectory. During the readout, phase modulations between odd and even EPI echoes become non-static and diffusion encoding direction-dependent. Superior reduction of ghosting and geometric distortion was achieved with dynamic field monitoring compared to ghosting reduction approaches such as navigator- and structured low-rank-based methods or MUSE followed by image-based distortion correction with the FSL tool "eddy." CONCLUSION Strong eddy current artifacts characteristic of high-gradient strength DW-EPI can be well corrected with dynamic field monitoring-based image reconstruction.
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Affiliation(s)
- Gabriel Ramos-Llordén
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Daniel J. Park
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - John E. Kirsch
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 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, Baldingerstrasse 1, 35043, Marburg, Germany
| | - Chiara Maffei
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Center for Neurotechnology and Neurorecovery, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Hong-Hsi Lee
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Berkin Bilgic
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Brian L. Edlow
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Center for Neurotechnology and Neurorecovery, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Choukri Mekkaoui
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Anastasia Yendiki
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | | | - Susie Y. Huang
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 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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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: 1] [Impact Index Per Article: 0.5] [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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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: 14] [Impact Index Per Article: 2.8] [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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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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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: 11] [Impact Index Per Article: 1.6] [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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11
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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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12
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Geraghty BJ, Lau JYC, Chen AP, Cunningham CH. Dual-Echo EPI sequence for integrated distortion correction in 3D time-resolved hyperpolarized 13 C MRI. Magn Reson Med 2017; 79:643-653. [PMID: 28394085 DOI: 10.1002/mrm.26698] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 02/15/2017] [Accepted: 03/11/2017] [Indexed: 01/24/2023]
Abstract
PURPOSE To provide built-in off-resonance correction in time-resolved, volumetric hyperpolarized 13 C metabolic imaging by implementing a novel dual-echo 3D echo-planar imaging (EPI) sequence and reconstruction. METHODS A spectral-spatial pulse for single-resonance excitation followed by a dual-echo 3D EPI readout was implemented to provide 64 × 8 × 6 cm3 coverage at 5 × 5 × 5 mm3 nominal resolution. Multiple sources of EPI distortions were encoded using a multi-echo 1 H EPI reference scan. Phase maps computed from the reference scans were combined with a bulk 13 C frequency offset encoded in the dual-echo [1-13 C]pyruvate images to correct geometric distortion and improve spatial registration. The proposed scheme was validated in a phantom study, and in vivo [1-13 C]pyruvate and [1-13 C]lactate rat images were acquired with intentional transmit frequency deviations to assess the dual-echo 3D EPI sequence. RESULTS The phantom study demonstrated improved spatial registration in off-resonance corrected images. Close agreement was observed between metabolic kidney signal and the underlying anatomy in rat imaging experiments. Relative to a single-echo acquisition, the coherent addition of the two corrected echoes provided the expected increase in signal-to-noise ratio by approximately 2. CONCLUSION A novel dual-echo 3D EPI acquisition sequence for integrated off-resonance correction in hyperpolarized 13 C imaging was developed and demonstrated. The proposed sequence offers clear advantages over flyback EPI for time-resolved metabolic mapping. Magn Reson Med 79:643-653, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Benjamin J Geraghty
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Physical Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Justin Y C Lau
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Physical Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | | | - Charles H Cunningham
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Physical Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
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13
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Lee J, Jin KH, Ye JC. Reference-free single-pass EPI Nyquist ghost correction using annihilating filter-based low rank Hankel matrix (ALOHA). Magn Reson Med 2016; 76:1775-1789. [PMID: 26887895 DOI: 10.1002/mrm.26077] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 10/20/2015] [Accepted: 11/13/2015] [Indexed: 11/09/2022]
Abstract
PURPOSE MR measurements from an echo-planar imaging (EPI) sequence produce Nyquist ghost artifacts that originate from inconsistencies between odd and even echoes. Several reconstruction algorithms have been proposed to reduce such artifacts, but most of these methods require either additional reference scans or multipass EPI acquisition. This article proposes a novel and accurate single-pass EPI ghost artifact correction method that does not require any additional reference data. THEORY AND METHODS After converting a ghost correction problem into separate k-space data interpolation problems for even and odd phase encoding, our algorithm exploits an observation that the differential k-space data between the even and odd echoes is a Fourier transform of an underlying sparse image. Accordingly, we can construct a rank-deficient Hankel structured matrix, whose missing data can be recovered using an annihilating filter-based low rank Hankel structured matrix completion approach. RESULTS The proposed method was applied to EPI data for both single and multicoil acquisitions. Experimental results using in vivo data confirmed that the proposed method can completely remove ghost artifacts successfully without prescan echoes. CONCLUSION Owing to the discovery of the annihilating filter relationship from the intrinsic EPI image property, the proposed method successfully suppresses ghost artifacts without a prescan step. Magn Reson Med 76:1775-1789, 2016. © 2016 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Juyoung Lee
- Bio-Imaging & Signal Processing Laboratory, Department of Bio and Brain Engineering, Korea Advanced Institute of Science & Technology (KAIST) 291 Daehak-ro, Yuseong-gu, Daejon, 34141, Republic of Korea
| | - Kyong Hwan Jin
- Bio-Imaging & Signal Processing Laboratory, Department of Bio and Brain Engineering, Korea Advanced Institute of Science & Technology (KAIST) 291 Daehak-ro, Yuseong-gu, Daejon, 34141, Republic of Korea
| | - Jong Chul Ye
- Bio-Imaging & Signal Processing Laboratory, Department of Bio and Brain Engineering, Korea Advanced Institute of Science & Technology (KAIST) 291 Daehak-ro, Yuseong-gu, Daejon, 34141, Republic of Korea
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14
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Lu NH, Hung CM, Liu KY, Chen TB, Huang YH. Diagnosed chest lesion on diffusion-weighted magnetic resonance images using apparent diffusion coefficients. JOURNAL OF X-RAY SCIENCE AND TECHNOLOGY 2016; 24:133-143. [PMID: 26890904 DOI: 10.3233/xst-160535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
PURPOSE A novel diagnostic method using the standard deviation (SD) value of apparent diffusion coefficient (ADC) by diffusion-weighted (DWI) magnetic resonance imaging (MRI) is applied for differential diagnosis of primary chest cancers, metastatic tumors and benign tumors. MATERIALS AND METHODS This retrospective study enrolled 27 patients (20 males, 7 female; age, 15-85; mean age, 68) who had thoracic mass lesions in the last three years and underwent an MRI chest examination at our institution. In total, 29 mass lesions were analyzed using SD of ADC and DWI. Lesions were divided into five groups: Primary lung cancers (N = 10); esophageal cancers (N = 5); metastatic tumors (N = 8); benign tumors (N = 3); and inflammatory lesions (N = 3). Quantitative assessment of MRI parameters of mass lesions was performed. The ADC value was acquired based on the average of the entire tumor area. The error-plot, t-test and the area under receiver operating characteristic (AUC) were applied for statistical analysis. RESULTS The SD of ADC value (mean±SD) was (4.867±1.359)×10-4 mm2/sec in primary lung cancers, and (3.598±0.350)×10-4 mm2/sec in metastatic tumors. The SD of ADC values of primary lung cancers and metastatic tumors (P < 0.05) were significantly different and the AUC was 0.800 (P < 0.05). The means of SD of ADC values was 4.532±1.406×10-4 mm2/sec and 2.973±0.364×10-4 mm2/sec for malignant tumors (including primary lung cancers, esophageal cancers) and benign tumors with respectively. The mean of SD of ADC values between malignant chest tumors and benign chest tumors was shown significant difference (P < 0.01). The values of AUC was 0.967 between malignant chest tumors and benign chest tumors (P < 0.05). The ADC values for primary lung cancers, metastatic tumors and benign tumors were not significantly difference (P > 0.05). CONCLUSIONS The mean of SD of ADC value by DWI can be used for differential diagnosis of chest lesions.
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Affiliation(s)
- Nan-Han Lu
- Department of Radiology, E-DA Hospital, I-Shou University, Kaohsiung City, Taiwan
- Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung City, Taiwan
| | - Chao-Ming Hung
- Department of General Sugary, E-DA Hospital, I-Shou University, Kaohsiung City, Taiwan
- The School of Medicine, I-Shou University, Kaohsiung City, Taiwan
| | - Kuo-Ying Liu
- Department of Radiology, E-DA Hospital, I-Shou University, Kaohsiung City, Taiwan
- Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung City, Taiwan
- Department of Information Engineering, I-Shou University, Kaohsiung City, Taiwan
| | - Tai-Been Chen
- Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung City, Taiwan
| | - Yung-Hui Huang
- Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung City, Taiwan
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15
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Talagala SL, Sarlls JE, Liu S, Inati SJ. Improvement of temporal signal-to-noise ratio of GRAPPA accelerated echo planar imaging using a FLASH based calibration scan. Magn Reson Med 2015; 75:2362-71. [PMID: 26192822 DOI: 10.1002/mrm.25846] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 11/10/2022]
Abstract
PURPOSE To demonstrate that the temporal signal-to-noise ratio (SNR) of generalized autocalibrating partially parallel acquisitions (GRAPPA) accelerated echo planar imaging (EPI) can be enhanced and made more spatially uniform by using a fast low angle shot (FLASH) based calibration scan. METHODS EPI of a phantom and human brains were acquired at 3 Tesla without and with GRAPPA acceleration factor of 2. The GRAPPA accelerated data were reconstructed using calibration scans acquired with EPI and FLASH acquisition schemes. The increase in temporal signal fluctuation due to GRAPPA reconstruction was quantified and compared. Simulated g-factor maps were also created for different calibration scans. RESULTS GRAPPA accelerated phantom data exhibited areas with high g values when using the EPI based calibration for reconstruction. The g-factor maps were uniform when using the FLASH calibration scan. g was greater than 1.1 in 74% of pixels in 64 × 64 data reconstructed with the EPI calibration compared with only 15% when using the FLASH calibration scan. Human data also showed abnormally high g regions when using the EPI calibration but not when using the FLASH calibration scan. Use of the FLASH calibration scan increased the whole brain temporal SNR by ∼12% without affecting the image quality. Experimental observations were confirmed by simulations. CONCLUSION A calibration scan based on a FLASH acquisition scheme can be used to improve the temporal SNR of GRAPPA accelerated EPI time series. Magn Reson Med 75:2362-2371, 2016. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- S Lalith Talagala
- NIH MRI Research Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Joelle E Sarlls
- NIH MRI Research Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Siyuan Liu
- Language Section, Voice, Speech and Language Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Souheil J Inati
- Functional MRI Facility, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
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16
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Chen L, Li J, Zhang M, Cai S, Zhang T, Cai C, Chen Z. Super-resolved enhancing and edge deghosting (SEED) for spatiotemporally encoded single-shot MRI. Med Image Anal 2015; 23:1-14. [DOI: 10.1016/j.media.2015.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 02/12/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022]
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17
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Geißler A, Matt E, Fischmeister F, Wurnig M, Dymerska B, Knosp E, Feucht M, Trattnig S, Auff E, Fitch WT, Robinson S, Beisteiner R. Differential functional benefits of ultra highfield MR systems within the language network. Neuroimage 2014; 103:163-170. [PMID: 25255049 PMCID: PMC4263528 DOI: 10.1016/j.neuroimage.2014.09.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/03/2014] [Accepted: 09/15/2014] [Indexed: 11/16/2022] Open
Abstract
Several investigations have shown limitations of fMRI reliability with the current standard field strengths. Improvement is expected from ultra highfield systems but studies on possible benefits for cognitive networks are lacking. Here we provide an initial investigation on a prominent and clinically highly-relevant cognitive function: language processing in individual brains. 26 patients evaluated for presurgical language localization were investigated with a standardized overt language fMRI paradigm on both 3T and 7T MR scanners. During data acquisition and analysis we made particular efforts to minimize effects not related to static magnetic field strength differences. Six measures relevant for functional activation showed a large dissociation between essential language network nodes: although in Wernicke's area 5/6 measures indicated a benefit of ultra highfield, in Broca's area no comparison was significant. The most important reason for this discrepancy was identified as being an increase in susceptibility-related artifacts in inferior frontal brain areas at ultra high field. We conclude that functional UHF benefits are evident, however these depend crucially on the brain region investigated and the ability to control local artifacts.
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Affiliation(s)
- A Geißler
- Study Group Clinical fMRI, Department of Neurology, Medical University of Vienna, Austria; High Field MR Center, Medical University of Vienna, Austria; Department of Neurology, Medical University of Vienna, Austria
| | - E Matt
- Study Group Clinical fMRI, Department of Neurology, Medical University of Vienna, Austria; High Field MR Center, Medical University of Vienna, Austria; Department of Neurology, Medical University of Vienna, Austria
| | - F Fischmeister
- Study Group Clinical fMRI, Department of Neurology, Medical University of Vienna, Austria; High Field MR Center, Medical University of Vienna, Austria; Department of Neurology, Medical University of Vienna, Austria
| | - M Wurnig
- Study Group Clinical fMRI, Department of Neurology, Medical University of Vienna, Austria; High Field MR Center, Medical University of Vienna, Austria; Department of Neurology, Medical University of Vienna, Austria
| | - B Dymerska
- High Field MR Center, Medical University of Vienna, Austria; Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - E Knosp
- Department of Neurosurgery, Medical University of Vienna, Austria
| | - M Feucht
- Department of Pediatrics, Medical University of Vienna, Austria
| | - S Trattnig
- High Field MR Center, Medical University of Vienna, Austria; Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - E Auff
- Department of Neurology, Medical University of Vienna, Austria
| | - W T Fitch
- Department of Cognitive Biology, University of Vienna, Vienna, Austria
| | - S Robinson
- High Field MR Center, Medical University of Vienna, Austria; Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - R Beisteiner
- Study Group Clinical fMRI, Department of Neurology, Medical University of Vienna, Austria; High Field MR Center, Medical University of Vienna, Austria; Department of Neurology, Medical University of Vienna, Austria.
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18
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Vannesjo SJ, Dietrich BE, Pavan M, Brunner DO, Wilm BJ, Barmet C, Pruessmann KP. Field camera measurements of gradient and shim impulse responses using frequency sweeps. Magn Reson Med 2013; 72:570-83. [PMID: 24105800 DOI: 10.1002/mrm.24934] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/19/2013] [Accepted: 08/01/2013] [Indexed: 11/09/2022]
Abstract
PURPOSE Applications of dynamic shimming require high field fidelity, and characterizing the shim field dynamics is therefore necessary. Modeling the system as linear and time-invariant, the purpose of this work was to measure the impulse response function with optimal sensitivity. THEORY AND METHODS Frequency-swept pulses as inputs are analyzed theoretically, showing that the sweep speed is a key factor for the measurement sensitivity. By adjusting the sweep speed it is possible to achieve any prescribed noise profile in the measured system response. Impulse response functions were obtained for the third-order shim system of a 7 Tesla whole-body MR scanner. Measurements of the shim fields were done with a dynamic field camera, yielding also cross-term responses. RESULTS The measured shim impulse response functions revealed system characteristics such as response bandwidth, eddy currents and specific resonances, possibly of mechanical origin. Field predictions based on the shim characterization were shown to agree well with directly measured fields, also in the cross-terms. CONCLUSION Frequency sweeps provide a flexible tool for shim or gradient system characterization. This may prove useful for applications involving dynamic shimming by yielding accurate estimates of the shim fields and a basis for setting shim pre-emphasis.
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Affiliation(s)
- S Johanna Vannesjo
- Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
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19
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Robinson SD, Schöpf V, Cardoso P, Geissler A, Fischmeister FPS, Wurnig M, Trattnig S, Beisteiner R. Applying independent component analysis to clinical FMRI at 7 t. Front Hum Neurosci 2013; 7:496. [PMID: 24032007 PMCID: PMC3759034 DOI: 10.3389/fnhum.2013.00496] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 08/05/2013] [Indexed: 11/24/2022] Open
Abstract
Increased BOLD sensitivity at 7 T offers the possibility to increase the reliability of fMRI, but ultra-high field is also associated with an increase in artifacts related to head motion, Nyquist ghosting, and parallel imaging reconstruction errors. In this study, the ability of independent component analysis (ICA) to separate activation from these artifacts was assessed in a 7 T study of neurological patients performing chin and hand motor tasks. ICA was able to isolate primary motor activation with negligible contamination by motion effects. The results of General Linear Model (GLM) analysis of these data were, in contrast, heavily contaminated by motion. Secondary motor areas, basal ganglia, and thalamus involvement were apparent in ICA results, but there was low capability to isolate activation in the same brain regions in the GLM analysis, indicating that ICA was more sensitive as well as more specific. A method was developed to simplify the assessment of the large number of independent components. Task-related activation components could be automatically identified via these intuitive and effective features. These findings demonstrate that ICA is a practical and sensitive analysis approach in high field fMRI studies, particularly where motion is evoked. Promising applications of ICA in clinical fMRI include presurgical planning and the study of pathologies affecting subcortical brain areas.
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Affiliation(s)
- Simon Daniel Robinson
- High Field Magnetic Resonance Imaging Centre of Excellence, Medical University of Vienna , Vienna , Austria ; Department of Radiology, Medical University of Vienna , Vienna , Austria
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20
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Geißler A, Fischmeister FPS, Grabner G, Wurnig M, Rath J, Foki T, Matt E, Trattnig S, Beisteiner R, Robinson SD. Comparing the Microvascular Specificity of the 3- and 7-T BOLD Response Using ICA and Susceptibility-Weighted Imaging. Front Hum Neurosci 2013; 7:474. [PMID: 23950744 PMCID: PMC3739379 DOI: 10.3389/fnhum.2013.00474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 07/29/2013] [Indexed: 11/28/2022] Open
Abstract
In functional MRI it is desirable for the blood-oxygenation level dependent (BOLD) signal to be localized to the tissue containing activated neurons rather than the veins draining that tissue. This study addresses the dependence of the specificity of the BOLD signal – the relative contribution of the BOLD signal arising from tissue compared to venous vessels – on magnetic field strength. To date, studies of specificity have been based on models or indirect measures of BOLD sensitivity such as signal to noise ratio and relaxation rates, and assessment has been made in isolated vein and tissue voxels. The consensus has been that ultra-high field systems not only significantly increase BOLD sensitivity but also specificity, that is, there is a proportionately reduced signal contribution from draining veins. Specificity was not quantified in prior studies, however, due to the difficulty of establishing a reliable network of veins in the activated volume. In this study we use a map of venous vessel networks extracted from 7 T high resolution Susceptibility-Weighted Images to quantify the relative contributions of micro- and macro-vasculature to functional MRI results obtained at 3 and 7 T. High resolution measurements made here minimize the contribution of physiological noise and Independent Component Analysis (ICA) is used to separate activation from technical, physiological, and motion artifacts. ICA also avoids the possibility of timing-dependent bias from different micro- and macro-vasculature responses. We find a significant increase in the number of activated voxels at 7 T in both the veins and the microvasculature – a BOLD sensitivity increase – with the increase in the microvasculature being higher. However, the small increase in sensitivity at 7 T was not significant. For the experimental conditions of this study, our findings do not support the hypothesis of an increased specificity of the BOLD response at ultra-high field.
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Affiliation(s)
- Alexander Geißler
- Study Group Clinical fMRI, Department of Neurology, Medical University of Vienna , Vienna , Austria ; High Field Magnetic Resonance Imaging Center of Excellence, Medical University of Vienna , Vienna , Austria
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Xu J, Moeller S, Auerbach EJ, Strupp J, Smith SM, Feinberg DA, Yacoub E, Uğurbil K. Evaluation of slice accelerations using multiband echo planar imaging at 3 T. Neuroimage 2013; 83:991-1001. [PMID: 23899722 DOI: 10.1016/j.neuroimage.2013.07.055] [Citation(s) in RCA: 360] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/16/2013] [Accepted: 07/20/2013] [Indexed: 10/26/2022] Open
Abstract
We evaluate residual aliasing among simultaneously excited and acquired slices in slice accelerated multiband (MB) echo planar imaging (EPI). No in-plane accelerations were used in order to maximize and evaluate achievable slice acceleration factors at 3 T. We propose a novel leakage (L-) factor to quantify the effects of signal leakage between simultaneously acquired slices. With a standard 32-channel receiver coil at 3 T, we demonstrate that slice acceleration factors of up to eight (MB=8) with blipped controlled aliasing in parallel imaging (CAIPI), in the absence of in-plane accelerations, can be used routinely with acceptable image quality and integrity for whole brain imaging. Spectral analyses of single-shot fMRI time series demonstrate that temporal fluctuations due to both neuronal and physiological sources were distinguishable and comparable up to slice-acceleration factors of nine (MB=9). The increased temporal efficiency could be employed to achieve, within a given acquisition period, higher spatial resolution, increased fMRI statistical power, multiple TEs, faster sampling of temporal events in a resting state fMRI time series, increased sampling of q-space in diffusion imaging, or more quiet time during a scan.
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Affiliation(s)
- Junqian Xu
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, USA.
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22
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Theysohn N, Qin S, Maderwald S, Poser BA, Theysohn JM, Ladd ME, Norris DG, Gizewski ER, Fernandez G, Tendolkar I. Memory-related hippocampal activity can be measured robustly using FMRI at 7 tesla. J Neuroimaging 2013; 23:445-51. [PMID: 23751153 DOI: 10.1111/jon.12036] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 11/08/2012] [Accepted: 02/23/2013] [Indexed: 11/28/2022] Open
Abstract
High field strength functional magnetic resonance imaging (fMRI) has developed rapidly. However, it suffers from increased artifacts in brain regions such as the medial temporal lobe (MTL), challenging functional imaging of the hippocampus with the objective of high-spatial resolution, which is particularly useful for this region both from a clinical and cognitive neuroscience perspective. We set out to compare a BOLD sequence at 7 T versus 3 T to visualize the MTL activity during an associative memory-encoding task. Twenty-eight healthy volunteers underwent a blocked-design fMRI at either 3 T or 7 T while performing a face-profession associative memory encoding task. Qualitative analyses of overall image quality revealed that functional images at 7 T were of high quality, showing a good white/gray matter contrast, with reasonably acceptable signal dropouts and artifacts at the lower portion of the temporal lobe. Analyses of task-related fMRI data revealed robust activations in the bilateral MTL during associative memory encoding at both field strengths. Notably, we observed significantly stronger memory-related hippocampal activation at 7 T than at 3 T, suggesting higher BOLD sensitivity at 7 T. These results are discussed in the light of the feasibility of 7 T scanning protocols for the MTL.
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Affiliation(s)
- Nina Theysohn
- University Hospital Essen, Department of Diagnostic and Interventional Radiology and Neuroradiology, Essen, Germany; University Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen, Germany
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