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Dabbagh A, Horn U, Kaptan M, Mildner T, Müller R, Lepsien J, Weiskopf N, Brooks JCW, Finsterbusch J, Eippert F. Reliability of task-based fMRI in the dorsal horn of the human spinal cord. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.572825. [PMID: 38187724 PMCID: PMC10769329 DOI: 10.1101/2023.12.22.572825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The application of functional magnetic resonance imaging (fMRI) to the human spinal cord is still a relatively small field of research and faces many challenges. Here we aimed to probe the limitations of task-based spinal fMRI at 3T by investigating the reliability of spinal cord blood oxygen level dependent (BOLD) responses to repeated nociceptive stimulation across two consecutive days in 40 healthy volunteers. We assessed the test-retest reliability of subjective ratings, autonomic responses, and spinal cord BOLD responses to short heat pain stimuli (1s duration) using the intraclass correlation coefficient (ICC). At the group level, we observed robust autonomic responses as well as spatially specific spinal cord BOLD responses at the expected location, but no spatial overlap in BOLD response patterns across days. While autonomic indicators of pain processing showed good-to-excellent reliability, both β-estimates and z-scores of task-related BOLD responses showed poor reliability across days in the target region (gray matter of the ipsilateral dorsal horn). When taking into account the sensitivity of gradient-echo echo planar imaging (GE-EPI) to draining vein signals by including the venous plexus in the analysis, we observed BOLD responses with good reliability across days. Taken together, these results demonstrate that heat pain stimuli as short as one second are able to evoke a robust and spatially specific BOLD response, which is however strongly variable within participants across time, resulting in low reliability in the dorsal horn gray matter. Further improvements in data acquisition and analysis techniques are thus necessary before event-related spinal cord fMRI as used here can be reliably employed in longitudinal designs or clinical settings.
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Affiliation(s)
- Alice Dabbagh
- Max Planck Research Group Pain Perception, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Ulrike Horn
- Max Planck Research Group Pain Perception, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Merve Kaptan
- Max Planck Research Group Pain Perception, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, CA, USA
| | - Toralf Mildner
- Methods & Development Group Nuclear Magnetic Resonance, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Roland Müller
- Methods & Development Group Nuclear Magnetic Resonance, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Jöran Lepsien
- Methods & Development Group Nuclear Magnetic Resonance, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Nikolaus Weiskopf
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Felix Bloch Institute for Solid State Physics, Faculty of Physics and Earth Sciences, University of Leipzig, Leipzig, Germany
- Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London, London, UK
| | - Jonathan C W Brooks
- School of Psychology, University of East Anglia Wellcome Wolfson Brain Imaging Centre (UWWBIC), Norwich, United Kingdom
| | - Jürgen Finsterbusch
- Department of Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Falk Eippert
- Max Planck Research Group Pain Perception, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
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2
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Theilenberg S, Shang Y, Ghazouani J, Kumaragamage C, Nixon TW, McIntyre S, Vaughan JT, Parkinson B, Garwood M, de Graaf RA, Juchem C. Design and realization of a multi-coil array for B 0 field control in a compact 1.5T head-only MRI scanner. Magn Reson Med 2023; 90:1228-1241. [PMID: 37145035 PMCID: PMC10330274 DOI: 10.1002/mrm.29692] [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: 12/17/2022] [Revised: 03/27/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
Abstract
PURPOSE To design and implement a multi-coil (MC) array for B0 field generation for image encoding and simultaneous advanced shimming in a novel 1.5T head-only MRI scanner. METHODS A 31-channel MC array was designed following the unique constraints of this scanner design: The vertically oriented magnet is very short, stopping shortly above the shoulders of a sitting subject, and includes a window for the subject to see through. Key characteristics of the MC hardware, the B0 field generation capabilities, and thermal behavior, were optimized in simulations prior to its construction. The unit was characterized via bench testing. B0 field generation capabilities were validated on a human 4T MR scanner by analysis of experimental B0 fields and by comparing images for several MRI sequences acquired with the MC array to those acquired with the system's linear gradients. RESULTS The MC system was designed to produce a multitude of linear and nonlinear magnetic fields including linear gradients of up to 10 kHz/cm (23.5 mT/m) with MC currents of 5 A per channel. With water cooling it can be driven with a duty cycle of up to 74% and ramp times of 500 μs. MR imaging experiments encoded with the developed multi-coil hardware were largely artifact-free; residual imperfections were predictable, and correctable. CONCLUSION The presented compact multi-coil array is capable of generating image encoding fields with amplitudes and quality comparable to clinical systems at very high duty cycles, while additionally enabling high-order B0 shimming capabilities and the potential for nonlinear encoding fields.
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Affiliation(s)
- Sebastian Theilenberg
- Department of Biomedical Engineering, Columbia University, New York, NY, United States
| | - Yun Shang
- Department of Biomedical Engineering, Columbia University, New York, NY, United States
| | - Jalal Ghazouani
- Department of Biomedical Engineering, Columbia University, New York, NY, United States
| | - Chathura Kumaragamage
- Department of Radiology and Biomedical Imaging, Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, United States
| | - Terence W. Nixon
- Department of Radiology and Biomedical Imaging, Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, United States
| | - Scott McIntyre
- Department of Radiology and Biomedical Imaging, Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, United States
| | - J. Thomas Vaughan
- Department of Biomedical Engineering, Columbia University, New York, NY, United States
- Department of Radiology, Columbia University Medical Center, New York, NY, United States
| | - Ben Parkinson
- Robinson Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Mike Garwood
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, United States
| | - Robin A. de Graaf
- Department of Radiology and Biomedical Imaging, Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, United States
| | - Christoph Juchem
- Department of Biomedical Engineering, Columbia University, New York, NY, United States
- Department of Radiology, Columbia University Medical Center, New York, NY, United States
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3
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Finsterbusch J, Chu Y. Simultaneous multislice imaging with slice-specific z-shim. Magn Reson Med 2023; 90:633-642. [PMID: 37093986 DOI: 10.1002/mrm.29673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/26/2023]
Abstract
PURPOSE To implement slice-specific z-shim in simultaneous multislice (SMS) imaging in order to minimize signal losses in slice-accelerated T2 *-weighted acquisitions, such as for spinal cord functional neuroimaging. METHODS The RF envelopes of the individual slice bands are temporally shifted on the plateau of the slice-selection gradient pulse before being combined to the multiband RF envelope. Thus, optimum z-shims can be realized for each slice of an SMS excitation, which is in contrast to conventional z-shimming. EPI with 2-fold SMS acceleration was performed on a 3T whole-body MR system in phantoms and the cervical spinal cord of healthy volunteers (i) without z-shim, (ii) with conventional z-shim using the average value of the slices of the SMS excitation, and (iii) with optimal, slice-specific z-shims for each slice using envelope shifts. RESULTS Phantom experiments demonstrate the equivalence of the envelope shift and conventional z-shimming for non-SMS excitations. With SMS, the best image quality is obtained with "mixed" z-shim, where only the z-shim differences of the slices of an SMS excitation are implemented by an envelope shift while their mean z-shim is applied conventionally with a gradient pulse after the echoes acquired for N/2 ghost correction. In phantoms and in vivo, this setup outperforms the approaches without slice-specific z-shim with respect to signal amplitude and temporal SNR at the expense of slight TE differences (<1 ms) between the slices. CONCLUSION With RF envelope shifts, slice-specific z-shims can be combined with SMS imaging, which could improve slice-accelerated functional neuroimaging in the spinal cord.
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Affiliation(s)
- Jürgen Finsterbusch
- Department of Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ying Chu
- Department of Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Alonso-Ortiz E, Papp D, D'Astous A, Cohen-Adad J. Dynamic shimming in the cervical spinal cord for multi-echo gradient-echo imaging at 3 T. NEUROIMAGE: REPORTS 2023. [DOI: 10.1016/j.ynirp.2022.100150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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5
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Cuthbertson JD, Truong TK, Stormont R, Robb F, Song AW, Darnell D. An iPRES-W Coil Array for Simultaneous Imaging and Wireless Localized B 0 Shimming of the Cervical Spinal Cord. Magn Reson Med 2022; 88:1002-1014. [PMID: 35468243 PMCID: PMC10445458 DOI: 10.1002/mrm.29257] [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: 01/07/2022] [Revised: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 11/07/2022]
Abstract
PURPOSE To develop a wireless integrated parallel reception, excitation, and shimming (iPRES-W) coil array for simultaneous imaging and wireless localized B0 shimming, and to demonstrate its ability to correct for distortions in DTI of the spinal cord in vivo. METHODS A 4-channel coil array was modified to allow an RF current at the Larmor frequency and a direct current to flow on each coil element, enabling imaging and localized B0 shimming, respectively. One coil element was further modified to allow additional RF currents within a wireless communication band to flow on it to wirelessly control the direct currents for shimming, which were supplied from a battery pack within the scanner bore. The RF signals for imaging were transferred via conventional wired connections. Experiments were conducted to evaluate the RF, B0 shimming, and wireless performance of this coil design. RESULTS The coil modifications did not degrade the SNR. Wireless localized B0 shimming with the iPRES-W coil array substantially reduced the B0 RMSE (-57.5% on average) and DTI distortions in the spinal cord. The antenna radiation efficiency, antenna gain pattern, and battery power consumption of an iPRES-W coil measured in an anechoic chamber were minimally impacted by the introduction of a saline phantom representing tissue. CONCLUSION The iPRES-W coil array can perform imaging and wireless localized B0 shimming of the spinal cord with no SNR degradation, with minimal change in wireless performance and without any scanner modifications or additional antenna systems within the scanner bore.
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Affiliation(s)
- Jonathan D. Cuthbertson
- Brain Imaging and Analysis Center, Duke University, Durham, North Carolina
- Medical Physics Graduate Program, Duke University, Durham, North Carolina
| | - Trong-Kha Truong
- Brain Imaging and Analysis Center, Duke University, Durham, North Carolina
- Medical Physics Graduate Program, Duke University, Durham, North Carolina
| | | | | | - Allen W. Song
- Brain Imaging and Analysis Center, Duke University, Durham, North Carolina
- Medical Physics Graduate Program, Duke University, Durham, North Carolina
| | - Dean Darnell
- Brain Imaging and Analysis Center, Duke University, Durham, North Carolina
- Medical Physics Graduate Program, Duke University, Durham, North Carolina
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6
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Dehghani H, Oghabian MA, Batouli SAH, Arab Kheradmand J, Khatibi A. Effect of Physiological Noise on Thoracolumbar Spinal Cord Functional Magnetic Resonance Imaging in 3T Magnetic Field. Basic Clin Neurosci 2020; 11:737-751. [PMID: 33850611 PMCID: PMC8019845 DOI: 10.32598/bcn.11.6.1395.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/10/2018] [Accepted: 02/19/2019] [Indexed: 11/20/2022] Open
Abstract
Introduction: Functional Magnetic Resonance Imaging (fMRI) methods have been used to study sensorimotor processing in the spinal cord. However, these techniques confront unwanted noises to the measured signal from the physiological fluctuations. In the spinal cord imaging, most of the challenges are consequences of cardiac and respiratory movement artifacts that are considered as significant sources of noise, especially in the thoracolumbar region. In this study, we investigated the effect of each source of physiological noise and their contribution to the outcome of the analysis of the blood-oxygen-level-dependent signal in the human thoracolumbar spinal cord. Methods: Fifteen young healthy male volunteers participated in the study, and pain stimuli were delivered on the L5 dermatome between the two malleoli. Respiratory and cardiac signals were recorded during the imaging session, and the generated respiration and cardiac regressors were included in the general linear model for quantification of the effect of each of them on the task-analysis results. The sum of active voxels of the clusters was calculated in the spinal cord in three correction states (respiration correction only, cardiac correction only, and respiration and cardiac noise corrections) and analyzed with analysis of variance statistical test and receiver operating characteristic curve. Results: The results illustrated that cardiac noise correction had an effective role in increasing the active voxels (Mean±SD = 23.46±9.46) compared to other noise correction methods. Cardiac effects were higher than other physiological noise sources Conclusion: In summary, our results indicate great respiration effects on the lumbar and thoracolumbar spinal cord fMRI, and its contribution to the heartbeat effect can be a significant variable in the individual fMRI data analysis. Displacement of the spinal cord and the effects of this noise in the thoracolumbar and lumbar spinal cord fMRI results are significant and cannot be ignored.
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Affiliation(s)
- Hamed Dehghani
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Tehran University of Medical Science, Tehran, Iran.,Research Center for Molecular and Cellular Imaging (RCMCI), Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Oghabian
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Tehran University of Medical Science, Tehran, Iran.,Research Center for Molecular and Cellular Imaging (RCMCI), Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Amir Hosein Batouli
- Research Center for Molecular and Cellular Imaging (RCMCI), Tehran University of Medical Sciences, Tehran, Iran.,Department of Neuroscience, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Jalil Arab Kheradmand
- Shefa Neuroscience Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Khatibi
- Centre of Precision Rehabilitation for Spinal Pain (CPR Spine), School of Sport, Exercise and Rehabilitation Sciences, University of Birmingham, Birmingham, United Kingdom.,Centre for Human Brain Health, University of Birmingham, Birmingham, United Kingdom
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7
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Tinnermann A, Büchel C, Cohen-Adad J. Cortico-spinal imaging to study pain. Neuroimage 2020; 224:117439. [PMID: 33039624 DOI: 10.1016/j.neuroimage.2020.117439] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/21/2020] [Accepted: 10/01/2020] [Indexed: 12/15/2022] Open
Abstract
Functional magnetic resonance imaging of the brain has helped to reveal mechanisms of pain perception in health and disease. Recently, imaging approaches have been developed that allow recording neural activity simultaneously in the brain and in the spinal cord. These approaches offer the possibility to examine pain perception in the entire central pain system and in addition, to investigate cortico-spinal interactions during pain processing. Although cortico-spinal imaging is a promising technique, it bears challenges concerning data acquisition and data analysis strategies. In this review, we discuss studies that applied simultaneous imaging of the brain and spinal cord to explore central pain processing. Furthermore, we describe different MR-related acquisition techniques, summarize advantages and disadvantages of approaches that have been implemented so far and present software that has been specifically developed for the analysis of spinal fMRI data to address challenges of spinal data analysis.
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Affiliation(s)
- Alexandra Tinnermann
- Department for Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Max Planck School of Cognition, Leipzig, Germany.
| | - Christian Büchel
- Department for Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Max Planck School of Cognition, Leipzig, Germany
| | - Julien Cohen-Adad
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, Quebec, Canada; Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, Quebec, Canada.
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8
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Geldschläger O, Bosch D, Avdievich NI, Henning A. Ultrahigh-resolution quantitative spinal cord MRI at 9.4T. Magn Reson Med 2020; 85:1013-1027. [PMID: 32789980 DOI: 10.1002/mrm.28455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 11/08/2022]
Abstract
PURPOSE To present the results of the first human spinal cord in vivo MRI scans at 9.4T. METHODS A human brain coil was used to image the human spinal cord at 9.4T. All anatomical images were acquired with a T2 *-weighted gradient-echo sequence. A comparison of the influence of four different B0 shimming routines on the image quality was performed. Intrinsic signal-to-noise-ratio maps were determined using a pseudo-multiple replica approach. Measurements with different echo times were compared and processed to one multiecho data image combination image. Based on the multiecho acquisitions, T2 *-relaxation time maps were calculated. Algorithmic spinal cord detection and gray matter/white matter segmentation were tested. RESULTS An echo time between 9 and 13.8 ms compromised best between gray matter/white matter contrast and image quality. A maximum in-plane resolution of 0.15 × 0.15 mm2 was achieved for anatomical images. These images offered excellent image quality and made small structures of the spinal cord visible. The scanner vendor implemented B0 shimming routine performed best during this work. Intrinsic signal-to-noise-ratio values of between 6600 and 8060 at the upper cervical spinal cord were achieved. Detection and segmentation worked reliably. An average T2 *-time of 24.88 ms ± 6.68 ms for gray matter and 19.37 ms ± 8.66 ms for white matter was calculated. CONCLUSION The proposed human brain coil can be used to image the spinal cord. The maximum in-plane resolution in this work was higher compared with the 7T results from the literature. The 9.4T acquisitions made the small structures of the spinal cord clearly visible.
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Affiliation(s)
- Ole Geldschläger
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Dario Bosch
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,Biomedical Magnetic Resonance, University Hospital Tübingen, Tübingen, Germany
| | - Nikolai I Avdievich
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Anke Henning
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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9
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Geiger Y, Tal A. Optimal echo times for multi-gradient echo-based B 0 field-mapping. NMR IN BIOMEDICINE 2020; 33:e4316. [PMID: 32339348 DOI: 10.1002/nbm.4316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 03/28/2020] [Accepted: 04/05/2020] [Indexed: 06/11/2023]
Abstract
B0 field maps are used ubiquitously in neuroimaging, in disciplines ranging from magnetic resonance spectroscopy to temperature mapping and susceptibility-weighted imaging. Most B0 maps are acquired using standard gradient-echo-based vendor-provided sequences, often comprised of two echoes spaced a few milliseconds apart. Herein, we analyze the optimal spacing of echo times, defined as those maximizing precision-minimizing the standard deviation-for a fixed total acquisition time. Field estimation is carried out using a weighted least squares estimator. The standard deviation is shown to be approximately inversely proportional to the total acquisition time, suggesting a law of diminishing returns, whereby substantial gains are obtained up to a certain point, with little improvement beyond that point. Validations are provided in a phantom and a group of volunteers. Multi-gradient echo sequences are readily available on all manufacturer platforms, making our recommendations straightforward to implement on any modern scanner.
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Affiliation(s)
- Yasmin Geiger
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Israel
| | - Assaf Tal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Israel
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10
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Juchem C, Theilenberg S, Kumaragamage C, Mullen M, DelaBarre L, Adriany G, Brown PB, McIntyre S, Nixon TW, Garwood M, de Graaf RA. Dynamic multicoil technique (DYNAMITE) MRI on human brain. Magn Reson Med 2020; 84:2953-2963. [PMID: 32544274 DOI: 10.1002/mrm.28323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/23/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022]
Abstract
PURPOSE Spatial encoding for MRI is generally based on linear x, y, and z magnetic field gradients generated by a set of dedicated gradient coils. We recently introduced the dynamic multicoil technique (DYNAMITE) for B0 field control and demonstrated DYNAMITE MRI in a preclinical MR environment. In this study, we report the first realization of DYNAMITE MRI of the in vivo human head. METHODS Gradient fields for DYNAMITE MRI were generated with a 28-channel multicoil hardware arranged in 4 rows of 7 coils on a cylindrical surface (length 359 mm, diameter 344 mm, maximum 5 A per coil). DYNAMITE MRIs of a resolution phantom and in vivo human heads were acquired with multislice gradient-echo, multislice spin-echo, and 3D gradient-echo sequences. The resultant image fidelity was compared to that obtained with conventional gradient coil technology. RESULTS DYNAMITE field control enabled the realization of all imaging sequences with average gradient errors ≤ 1%. DYNAMITE MRI provided image quality and sensitivity comparable to conventional gradient technology without any obvious artifacts. Some minor geometric deformations were noticed primarily in the image periphery as the result of regional field imperfections. The imperfections can be readily approximated theoretically through numerical integration of the Biot-Savart law and removed through image distortion correction. CONCLUSION The first realization of DYNAMITE MRI of the in vivo human head has been presented. The obtained image fidelity is comparable to MRI with conventional gradient coils, paving the way for full-fledged DYNAMITE MRI and B0 shim systems for human applications.
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Affiliation(s)
- Christoph Juchem
- Department of Biomedical Engineering, Columbia University, New York, New York, USA.,Department of Radiology, Columbia University, New York, New York, USA
| | | | - Chathura Kumaragamage
- Department of Radiology and Biomedical Imaging, Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael Mullen
- Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Lance DelaBarre
- Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Gregor Adriany
- Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Peter B Brown
- Department of Radiology and Biomedical Imaging, Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Scott McIntyre
- Department of Radiology and Biomedical Imaging, Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Terence W Nixon
- Department of Radiology and Biomedical Imaging, Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael Garwood
- Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Robin A de Graaf
- Department of Radiology and Biomedical Imaging, Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, Connecticut, USA
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11
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Chuhutin A, Hansen B, Wlodarczyk A, Owens T, Shemesh N, Jespersen SN. Diffusion Kurtosis Imaging maps neural damage in the EAE model of multiple sclerosis. Neuroimage 2019; 208:116406. [PMID: 31830588 PMCID: PMC9358435 DOI: 10.1016/j.neuroimage.2019.116406] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 01/22/2023] Open
Abstract
Diffusion kurtosis imaging (DKI) is an imaging modality that yields novel
disease biomarkers and in combination with nervous tissue modeling, provides
access to microstructural parameters. Recently, DKI and subsequent estimation of
microstructural model parameters has been used for assessment of tissue changes
in neurodegenerative diseases and associated animal models. In this study, mouse
spinal cords from the experimental autoimmune encephalomyelitis (EAE) model of
multiple sclerosis (MS) were investigated for the first time using DKI in
combination with biophysical modeling to study the relationship between
microstructural metrics and degree of animal dysfunction. Thirteen spinal cords
were extracted from animals with varied grades of disability and scanned in a
high-field MRI scanner along with five control specimen. Diffusion weighted data
were acquired together with high resolution T2*
images. Diffusion data were fit to estimate diffusion and kurtosis tensors and
white matter modeling parameters, which were all used for subsequent statistical
analysis using a linear mixed effects model. T2*
images were used to delineate focal demyelination/inflammation. Our results
reveal a strong relationship between disability and measured microstructural
parameters in normal appearing white matter and gray matter. Relationships
between disability and mean of the kurtosis tensor, radial kurtosis, radial
diffusivity were similar to what has been found in other hypomyelinating MS
models, and in patients. However, the changes in biophysical modeling parameters
and in particular in extra-axonal axial diffusivity were clearly different from
previous studies employing other animal models of MS. In conclusion, our data
suggest that DKI and microstructural modeling can provide a unique contrast
capable of detecting EAE-specific changes correlating with clinical
disability.
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Affiliation(s)
| | | | - Agnieszka Wlodarczyk
- Department of Neurobiology Research, Institute for Molecular Medicine,University of South Denmark, Odense, Denmark
| | - Trevor Owens
- Department of Neurobiology Research, Institute for Molecular Medicine,University of South Denmark, Odense, Denmark
| | - Noam Shemesh
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Sune Nørhøj Jespersen
- CFIN, Aarhus University, Aarhus, Denmark; Department of Physics, Aarhus University, Aarhus, Denmark
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12
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Cadotte DW, Akbar MA, Fehlings MG, Stroman PW, Cohen-Adad J. What Has Been Learned from Magnetic Resonance Imaging Examination of the Injured Human Spinal Cord: A Canadian Perspective. J Neurotrauma 2019; 35:1942-1957. [PMID: 30074873 DOI: 10.1089/neu.2018.5903] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Magnetic resonance imaging (MRI) has transformed the way surgeons and researchers study and treat spinal cord injury. In this narrative review, we explore the historical context of imaging the human spinal cord and describe how MRI has evolved from providing the first visualization of the human spinal cord in the 1980s to a remarkable set of imaging tools today. The article focuses in particular on the role of Canadian researchers to this field. We begin by outlining the clinical context of traumatic injury to the human spinal cord and describe why current MRI standards fall short when it comes to treating this disabling condition. Parts 2 and 3 of this work explore an exciting and dramatic shift in the use of MRI technology to aid in our understanding and treatment of traumatic injury to the spinal cord. We explore the use of functional imaging (part 2) and structural imaging (part 3) and explore how these techniques have evolved, how they are used, and the challenges that we face for continued refinement and application to patients who live with the neurological and functional deficits caused by injury to the delicate spinal cord.
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Affiliation(s)
- David W Cadotte
- 1 University of Calgary Spine Program, Division of Neurosurgery, Department of Clinical Neurosciences, University of Calgary , Foothills Medical Centre, Calgary, Alberta, Canada
| | - M Ali Akbar
- 2 Department of Surgery, Division of Neurosurgery and Spinal Program, Toronto Western Hospital, University of Toronto , Toronto, Ontario, Canada
| | - Michael G Fehlings
- 2 Department of Surgery, Division of Neurosurgery and Spinal Program, Toronto Western Hospital, University of Toronto , Toronto, Ontario, Canada
| | - Patrick W Stroman
- 3 Centre for Neuroscience Studies, Queens University , Kingston, Ontario, Canada
| | - Julien Cohen-Adad
- 4 NeuroPoly Lab, Institute of Biomedical Engineering , Polytechnique Montreal, Montreal, Quebéc, Canada .,5 Functional Neuroimaging Unit, CRIUGM, Université de Montréal , Montreal, Quebéc, Canada
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13
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Vannesjo SJ, Clare S, Kasper L, Tracey I, Miller KL. A method for correcting breathing-induced field fluctuations in T2*-weighted spinal cord imaging using a respiratory trace. Magn Reson Med 2019; 81:3745-3753. [PMID: 30737825 PMCID: PMC6492127 DOI: 10.1002/mrm.27664] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/01/2018] [Accepted: 12/27/2018] [Indexed: 02/04/2023]
Abstract
PURPOSE Spinal cord MRI at ultrahigh field is hampered by time-varying magnetic fields associated with the breathing cycle, giving rise to ghosting artifacts in multi-shot acquisitions. Here, we suggest a correction approach based on linking the signal from a respiratory bellows to field changes inside the spinal cord. The information is used to correct the data at the image reconstruction level. METHODS The correction was demonstrated in the context of multi-shot T2*-weighted imaging of the cervical spinal cord at 7T. A respiratory trace was acquired during a high-resolution multi-echo gradient-echo sequence, used for structural imaging and quantitative T2* mapping, and a multi-shot EPI time series, as would be suitable for fMRI. The coupling between the trace and the breathing-induced fields was determined by a short calibration scan in each individual. Images were reconstructed with and without trace-based correction. RESULTS In the multi-echo acquisition, breathing-induced fields caused severe ghosting in images with long TE, which led to a systematic underestimation of T2* in the spinal cord. The trace-based correction reduced the ghosting and increased the estimated T2* values. Breathing-related ghosting was also observed in the multi-shot EPI images. The correction largely removed the ghosting, thereby improving the temporal signal-to-noise ratio of the time series. CONCLUSIONS Trace-based retrospective correction of breathing-induced field variations can reduce ghosting and improve quantitative metrics in multi-shot structural and functional T2*-weighted imaging of the spinal cord. The method is straightforward to implement and does not rely on sequence modifications or additional hardware beyond a respiratory bellows.
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Affiliation(s)
- S. Johanna Vannesjo
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
| | - Stuart Clare
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
| | - Lars Kasper
- Institute for Biomedical EngineeringETH Zurich and University of ZurichZurichSwitzerland
- Translational Neuromodeling Unit, Institute for Biomedical EngineeringUniversity of Zurich and ETH ZurichZurichSwitzerland
| | - Irene Tracey
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
| | - Karla L. Miller
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
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14
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Ertan K, Taraghinia S, Atalar E. Driving mutually coupled gradient array coils in magnetic resonance imaging. Magn Reson Med 2019; 82:1187-1198. [PMID: 30989710 DOI: 10.1002/mrm.27768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/13/2019] [Accepted: 03/20/2019] [Indexed: 11/08/2022]
Abstract
PURPOSE In contrast to conventional linear gradients, gradient coil arrays with arbitrary spatial dependency might experience strong mutual coupling. Although conventional gradient power amplifiers with feedback loop might compensate the effect of coupling, required voltages for the compensation are generally unknown and has to be considered beforehand to ensure that amplifier voltage limits are not exceeded. A first-order circuit model is proposed to be used as a feedforward model which enables analytical formulas of required voltages to drive the mutually coupled gradient coil arrays. THEORY AND METHODS A first-order circuit model including the mutual couplings is provided to analytically calculate the input voltages and minimum achievable rise times for a given set of gradient array currents and amplifier limitations. Previously designed 9-channel Z-gradient coil array and home-built gradient amplifiers (50 V and 20 A) are used in the experiments. Three sets of currents optimized for linear Z-gradient, second-order Z2, and third-order Z3 fields are used in the bench-top experiments. The current weightings for the linear Z-gradient are also used as the readout gradient in the 3T MRI experiments. RESULTS Current measurements for the example magnetic field profiles with minimum rise times are demonstrated for the simultaneous use of 9-channel gradient coils and amplifiers. MRI experiments verify that a linear Z-gradient field with a desired time waveform can be generated using a mutually coupled array coils. CONCLUSION Bench-top and MRI experiments demonstrate the feasibility of the proposed circuit model and analytical formulas to drive the mutually coupled gradient coils.
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Affiliation(s)
- Koray Ertan
- National Magnetic Resonance Research Center (UMRAM), Bilkent University, Bilkent, Ankara, Turkey.,Department of Electrical and Electronics Engineering, Bilkent University, Bilkent, Ankara, Turkey
| | - Soheil Taraghinia
- National Magnetic Resonance Research Center (UMRAM), Bilkent University, Bilkent, Ankara, Turkey.,Department of Electrical and Electronics Engineering, Bilkent University, Bilkent, Ankara, Turkey
| | - Ergin Atalar
- National Magnetic Resonance Research Center (UMRAM), Bilkent University, Bilkent, Ankara, Turkey.,Department of Electrical and Electronics Engineering, Bilkent University, Bilkent, Ankara, Turkey
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15
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Gros C, De Leener B, Badji A, Maranzano J, Eden D, Dupont SM, Talbott J, Zhuoquiong R, Liu Y, Granberg T, Ouellette R, Tachibana Y, Hori M, Kamiya K, Chougar L, Stawiarz L, Hillert J, Bannier E, Kerbrat A, Edan G, Labauge P, Callot V, Pelletier J, Audoin B, Rasoanandrianina H, Brisset JC, Valsasina P, Rocca MA, Filippi M, Bakshi R, Tauhid S, Prados F, Yiannakas M, Kearney H, Ciccarelli O, Smith S, Treaba CA, Mainero C, Lefeuvre J, Reich DS, Nair G, Auclair V, McLaren DG, Martin AR, Fehlings MG, Vahdat S, Khatibi A, Doyon J, Shepherd T, Charlson E, Narayanan S, Cohen-Adad J. Automatic segmentation of the spinal cord and intramedullary multiple sclerosis lesions with convolutional neural networks. Neuroimage 2019; 184:901-915. [PMID: 30300751 PMCID: PMC6759925 DOI: 10.1016/j.neuroimage.2018.09.081] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/05/2018] [Accepted: 09/28/2018] [Indexed: 12/12/2022] Open
Abstract
The spinal cord is frequently affected by atrophy and/or lesions in multiple sclerosis (MS) patients. Segmentation of the spinal cord and lesions from MRI data provides measures of damage, which are key criteria for the diagnosis, prognosis, and longitudinal monitoring in MS. Automating this operation eliminates inter-rater variability and increases the efficiency of large-throughput analysis pipelines. Robust and reliable segmentation across multi-site spinal cord data is challenging because of the large variability related to acquisition parameters and image artifacts. In particular, a precise delineation of lesions is hindered by a broad heterogeneity of lesion contrast, size, location, and shape. The goal of this study was to develop a fully-automatic framework - robust to variability in both image parameters and clinical condition - for segmentation of the spinal cord and intramedullary MS lesions from conventional MRI data of MS and non-MS cases. Scans of 1042 subjects (459 healthy controls, 471 MS patients, and 112 with other spinal pathologies) were included in this multi-site study (n = 30). Data spanned three contrasts (T1-, T2-, and T2∗-weighted) for a total of 1943 vol and featured large heterogeneity in terms of resolution, orientation, coverage, and clinical conditions. The proposed cord and lesion automatic segmentation approach is based on a sequence of two Convolutional Neural Networks (CNNs). To deal with the very small proportion of spinal cord and/or lesion voxels compared to the rest of the volume, a first CNN with 2D dilated convolutions detects the spinal cord centerline, followed by a second CNN with 3D convolutions that segments the spinal cord and/or lesions. CNNs were trained independently with the Dice loss. When compared against manual segmentation, our CNN-based approach showed a median Dice of 95% vs. 88% for PropSeg (p ≤ 0.05), a state-of-the-art spinal cord segmentation method. Regarding lesion segmentation on MS data, our framework provided a Dice of 60%, a relative volume difference of -15%, and a lesion-wise detection sensitivity and precision of 83% and 77%, respectively. In this study, we introduce a robust method to segment the spinal cord and intramedullary MS lesions on a variety of MRI contrasts. The proposed framework is open-source and readily available in the Spinal Cord Toolbox.
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Affiliation(s)
- Charley Gros
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Benjamin De Leener
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Atef Badji
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada
- Department of Neuroscience, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - Josefina Maranzano
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
| | - Dominique Eden
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Sara M. Dupont
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada
- Department of Radiology and Biomedical Imaging, Zuckerberg San Francisco General Hospital, University of California, San Francisco, CA, USA
| | - Jason Talbott
- Department of Radiology and Biomedical Imaging, Zuckerberg San Francisco General Hospital, University of California, San Francisco, CA, USA
| | - Ren Zhuoquiong
- Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053, P. R. China
| | - Yaou Liu
- Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053, P. R. China
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P. R. China
| | - Tobias Granberg
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, USA
| | - Russell Ouellette
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, USA
| | | | | | | | - Lydia Chougar
- Juntendo University Hospital, Tokyo, Japan
- Hospital Cochin, Paris, France
| | - Leszek Stawiarz
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Jan Hillert
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Elise Bannier
- CHU Rennes, Radiology Department
- Univ Rennes, Inria, CNRS, Inserm, IRISA UMR 6074, Visages U1128, France
| | - Anne Kerbrat
- Univ Rennes, Inria, CNRS, Inserm, IRISA UMR 6074, Visages U1128, France
- CHU Rennes, Neurology Department
| | - Gilles Edan
- Univ Rennes, Inria, CNRS, Inserm, IRISA UMR 6074, Visages U1128, France
- CHU Rennes, Neurology Department
| | - Pierre Labauge
- MS Unit. DPT of Neurology. University Hospital of Montpellier
| | - Virginie Callot
- Aix Marseille Univ, CNRS, CRMBM, Marseille, France
- APHM, CHU Timone, CEMEREM, Marseille, France
| | - Jean Pelletier
- APHM, CHU Timone, CEMEREM, Marseille, France
- APHM, Department of Neurology, CHU Timone, APHM, Marseille
| | - Bertrand Audoin
- APHM, CHU Timone, CEMEREM, Marseille, France
- APHM, Department of Neurology, CHU Timone, APHM, Marseille
| | | | - Jean-Christophe Brisset
- Observatoire Français de la Sclérose en Plaques (OFSEP) ; Univ Lyon, Université Claude Bernard Lyon 1 ; Hospices Civils de Lyon ; CREATIS-LRMN, UMR 5220 CNRS & U 1044 INSERM ; Lyon, France
| | - Paola Valsasina
- Neuroimaging Research Unit, INSPE, Division of Neuroscience, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Maria A. Rocca
- Neuroimaging Research Unit, INSPE, Division of Neuroscience, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Massimo Filippi
- Neuroimaging Research Unit, INSPE, Division of Neuroscience, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Rohit Bakshi
- Brigham and Women’s Hospital, Harvard Medical School, Boston, USA
| | - Shahamat Tauhid
- Brigham and Women’s Hospital, Harvard Medical School, Boston, USA
| | - Ferran Prados
- Queen Square MS Centre, UCL Institute of Neurology, Faculty of Brain Sciences, University College London, London (UK)
- Center for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Marios Yiannakas
- Queen Square MS Centre, UCL Institute of Neurology, Faculty of Brain Sciences, University College London, London (UK)
| | - Hugh Kearney
- Queen Square MS Centre, UCL Institute of Neurology, Faculty of Brain Sciences, University College London, London (UK)
| | - Olga Ciccarelli
- Queen Square MS Centre, UCL Institute of Neurology, Faculty of Brain Sciences, University College London, London (UK)
| | | | | | - Caterina Mainero
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, USA
| | - Jennifer Lefeuvre
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, USA
| | - Daniel S. Reich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, USA
| | - Govind Nair
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, USA
| | | | | | - Allan R. Martin
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Michael G. Fehlings
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Shahabeddin Vahdat
- Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, QC, Canada
- Neurology Department, Stanford University, US
| | - Ali Khatibi
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
- Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, QC, Canada
| | - Julien Doyon
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
- Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, QC, Canada
| | | | | | - Sridar Narayanan
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
| | - Julien Cohen-Adad
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada
- Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, QC, Canada
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16
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Cohen-Adad J. Microstructural imaging in the spinal cord and validation strategies. Neuroimage 2018; 182:169-183. [PMID: 29635029 DOI: 10.1016/j.neuroimage.2018.04.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 03/02/2018] [Accepted: 04/06/2018] [Indexed: 12/13/2022] Open
Abstract
In vivo histology using magnetic resonance imaging (MRI) is a newly emerging research field that aims to non-invasively characterize tissue microstructure. The implications of in vivo histology are many, from discovering novel biomarkers to studying human development, to providing tools for disease diagnosis and monitoring the effects of novel treatments on tissue. This review focuses on quantitative MRI (qMRI) techniques that are used to map spinal cord microstructure. Opening with a rationale for non-invasive imaging of the spinal cord, this article continues with a brief overview of the existing MRI techniques for axon and myelin imaging, followed by the specific challenges and potential solutions for acquiring and processing such data. The final part of this review focuses on histological validation, with suggested tissue preparation, acquisition and processing protocols for large-scale microscopy.
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Affiliation(s)
- J Cohen-Adad
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada; Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, QC, Canada.
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17
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Stockmann JP, Wald LL. In vivo B 0 field shimming methods for MRI at 7T. Neuroimage 2018; 168:71-87. [PMID: 28602943 PMCID: PMC5760477 DOI: 10.1016/j.neuroimage.2017.06.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 05/19/2017] [Accepted: 06/06/2017] [Indexed: 01/12/2023] Open
Abstract
Functional MRI (fMRI) at 7T and above provides improved Signal-to-Noise Ratio and Contrast-to-Noise Ratio compared to 3T acquisitions. In addition to the beneficial effects on spin polarization and magnetization of deoxyhemoglobin, the increased applied field also further magnetizes air and tissue. While the magnets themselves typically provide a static B0 field with sufficient spatial homogeneity, the diamagnetism of tissue and the paramagnetism of air causes local field deviations inside the human head. These spatially-varying field offsets (ΔB0) cause image artifacts, especially in single shot EPI, including geometric distortion, signal dropout, and blurring. These effects are particularly strong near air-tissue interfaces such as the frontal sinus, and ear canals. Furthermore, if the field offsets are dynamically modulated through physiological processes such as respiration or motion, then the effect on the image time-series can be even more problematic. While post-processing methods have been developed to mitigate these effects, the ideal solution would be to reduce the ΔB0 variations at their source. Typically 7T scanners contain 2nd and some 3rd order spherical harmonic shim coil terms to cancel static ΔB0 variations of low spatial order. In this article, we will motivate the need for improved, higher-order compensation for B0 inhomogeneity and potentially add dynamic control of these fields. We discuss and compare several promising hardware approaches for static and dynamic B0 shimming using either higher-order spherical harmonic shim coils or multi-coil shim arrays as well as passive shimming approaches, and active variants such and adaptive current networks.
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Affiliation(s)
- Jason P Stockmann
- A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA 02129, United States.
| | - Lawrence L Wald
- A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA 02129, United States; Harvard Medical School, Boston, MA, United States
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18
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Barry RL, Vannesjo SJ, By S, Gore JC, Smith SA. Spinal cord MRI at 7T. Neuroimage 2018; 168:437-451. [PMID: 28684332 PMCID: PMC5894871 DOI: 10.1016/j.neuroimage.2017.07.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 06/30/2017] [Accepted: 07/02/2017] [Indexed: 11/25/2022] Open
Abstract
Magnetic resonance imaging (MRI) of the human spinal cord at 7T has been demonstrated by a handful of research sites worldwide, and the spinal cord remains one of the areas in which higher fields and resolution could have high impact. The small diameter of the cord (∼1 cm) necessitates high spatial resolution to minimize partial volume effects between gray and white matter, and so MRI of the cord can greatly benefit from increased signal-to-noise ratio and contrasts at ultra-high field (UHF). Herein we review the current state of UHF spinal cord imaging. Technical challenges to successful UHF spinal cord MRI include radiofrequency (B1) nonuniformities and a general lack of optimized radiofrequency coils, amplified physiological noise, and an absence of methods for robust B0 shimming along the cord to mitigate image distortions and signal losses. Numerous solutions to address these challenges have been and are continuing to be explored, and include novel approaches for signal excitation and acquisition, dynamic shimming and specialized shim coils, and acquisitions with increased coverage or optimal slice angulations.
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Affiliation(s)
- Robert L Barry
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA; Department of Radiology, Harvard Medical School, Boston, MA, USA.
| | - S Johanna Vannesjo
- Oxford Centre for Functional MRI of the Brain (FMRIB), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Samantha By
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - John C Gore
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Seth A Smith
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
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19
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Topfer R, Foias A, Stikov N, Cohen-Adad J. Real-time correction of respiration-induced distortions in the human spinal cord using a 24-channel shim array. Magn Reson Med 2018; 80:935-946. [DOI: 10.1002/mrm.27089] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 12/22/2017] [Accepted: 12/24/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Ryan Topfer
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal; Montreal Quebec Canada
| | - Alexandru Foias
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal; Montreal Quebec Canada
| | - Nikola Stikov
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal; Montreal Quebec Canada
- Montreal Heart Institute, Université de Montréal; Montreal Quebec Canada
| | - Julien Cohen-Adad
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal; Montreal Quebec Canada
- Functional Neuroimaging Unit, CRIUGM, Université de Montréal; Montreal Quebec Canada
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20
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Gros C, De Leener B, Dupont SM, Martin AR, Fehlings MG, Bakshi R, Tummala S, Auclair V, McLaren DG, Callot V, Cohen-Adad J, Sdika M. Automatic spinal cord localization, robust to MRI contrasts using global curve optimization. Med Image Anal 2017; 44:215-227. [PMID: 29288983 DOI: 10.1016/j.media.2017.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/29/2017] [Accepted: 12/02/2017] [Indexed: 12/14/2022]
Abstract
During the last two decades, MRI has been increasingly used for providing valuable quantitative information about spinal cord morphometry, such as quantification of the spinal cord atrophy in various diseases. However, despite the significant improvement of MR sequences adapted to the spinal cord, automatic image processing tools for spinal cord MRI data are not yet as developed as for the brain. There is nonetheless great interest in fully automatic and fast processing methods to be able to propose quantitative analysis pipelines on large datasets without user bias. The first step of most of these analysis pipelines is to detect the spinal cord, which is challenging to achieve automatically across the broad range of MRI contrasts, field of view, resolutions and pathologies. In this paper, a fully automated, robust and fast method for detecting the spinal cord centerline on MRI volumes is introduced. The algorithm uses a global optimization scheme that attempts to strike a balance between a probabilistic localization map of the spinal cord center point and the overall spatial consistency of the spinal cord centerline (i.e. the rostro-caudal continuity of the spinal cord). Additionally, a new post-processing feature, which aims to automatically split brain and spine regions is introduced, to be able to detect a consistent spinal cord centerline, independently from the field of view. We present data on the validation of the proposed algorithm, known as "OptiC", from a large dataset involving 20 centers, 4 contrasts (T2-weighted n = 287, T1-weighted n = 120, T2∗-weighted n = 307, diffusion-weighted n = 90), 501 subjects including 173 patients with a variety of neurologic diseases. Validation involved the gold-standard centerline coverage, the mean square error between the true and predicted centerlines and the ability to accurately separate brain and spine regions. Overall, OptiC was able to cover 98.77% of the gold-standard centerline, with a mean square error of 1.02 mm. OptiC achieved superior results compared to a state-of-the-art spinal cord localization technique based on the Hough transform, especially on pathological cases with an averaged mean square error of 1.08 mm vs. 13.16 mm (Wilcoxon signed-rank test p-value < .01). Images containing brain regions were identified with a 99% precision, on which brain and spine regions were separated with a distance error of 9.37 mm compared to ground-truth. Validation results on a challenging dataset suggest that OptiC could reliably be used for subsequent quantitative analyses tasks, opening the door to more robust analysis on pathological cases.
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Affiliation(s)
- Charley Gros
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Benjamin De Leener
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Sara M Dupont
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Allan R Martin
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Michael G Fehlings
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Rohit Bakshi
- Laboratory for Neuroimaging Research, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Subhash Tummala
- Laboratory for Neuroimaging Research, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | | | | | - Virginie Callot
- Aix Marseille Univ, CNRS, CRMBM, Marseille, France; APHM, Hôpital de la Timone, Pôle d'imagerie médicale, CEMEREM, Marseille, France
| | - Julien Cohen-Adad
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada; Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, QC, Canada
| | - Michaël Sdika
- Univ. Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, UJM-Saint Etienne, CNRS, Inserm, CREATIS UMR 5220, U1206, F-69100, Lyon, France.
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21
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Spatiotemporal characterization of breathing-induced B 0 field fluctuations in the cervical spinal cord at 7T. Neuroimage 2017; 167:191-202. [PMID: 29175497 PMCID: PMC5854299 DOI: 10.1016/j.neuroimage.2017.11.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/09/2017] [Accepted: 11/15/2017] [Indexed: 01/31/2023] Open
Abstract
Magnetic resonance imaging and spectroscopy of the spinal cord stand to benefit greatly from the increased signal-to-noise ratio of ultra-high field. However, ultra-high field also poses considerable technical challenges, especially related to static and dynamic B0 fields. Breathing causes the field to fluctuate with the respiratory cycle, giving rise to artifacts such as ghosting and apparent motion in images. We here investigated the spatial and temporal characteristics of breathing-induced B0 fields in the cervical spinal cord at 7T. We analyzed the magnitude and spatial profile of breathing-induced fields during breath-holds in an expired and inspired breathing state. We also measured the temporal field evolution during free breathing by acquiring a time series of fast phase images, and a principal component analysis was performed on the measured field evolution. In all subjects, the field shift was largest around the vertebral level of C7 and lowest at the top of the spinal cord. At C7, we measured peak-to-peak field fluctuations of 36 Hz on average during normal free breathing; increasing to on average 113 Hz during deep breathing. The first principal component could explain more than 90% of the field variations along the foot-head axis inside the spinal cord in all subjects. We further implemented a proof-of-principle shim correction, demonstrating the feasibility of using the shim system to compensate for the breathing-induced fields inside the spinal cord. Effective correction strategies will be crucial to unlock the full potential of ultra-high field for spinal cord imaging. The B0 field in the spinal cord fluctuates with the breathing cycle. Average peak-to-peak ΔB0 of 36/113 Hz at C7 during normal/deep breathing at 7T. The first principal component explains more than 90% of the field variance. Respiratory trace correlates well with field fluctuations during normal breathing. Proof-of-principle correction using 2nd-order shims was demonstrated.
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Darnell D, Ma Y, Wang H, Robb F, Song AW, Truong TK. Adaptive integrated parallel reception, excitation, and shimming (iPRES-A) with microelectromechanical systems switches. Magn Reson Med 2017; 80:371-379. [PMID: 29148102 DOI: 10.1002/mrm.27007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/20/2017] [Accepted: 10/23/2017] [Indexed: 11/09/2022]
Abstract
PURPOSE Integrated parallel reception, excitation, and shimming coil arrays with N shim loops per radio-frequency (RF) coil element (iPRES(N)) allow an RF current and N direct currents (DC) to flow in each coil element, enabling simultaneous reception/excitation and shimming of highly localized B0 inhomogeneities. The purpose of this work was to reduce the cost and complexity of this design by reducing the number of DC power supplies required by a factor N, while maintaining a high RF and shimming performance. METHODS In the proposed design, termed adaptive iPRES(N) (iPRES(N)-A), each coil element only requires one DC power supply, but uses microelectromechanical systems switches to adaptively distribute the DC current into the appropriate shim loops to generate the desired magnetic field for B0 shimming. Proof-of-concept phantom experiments with an iPRES(2)-A coil and simulations in the human abdomen with an 8-channel iPRES(4)-A body coil array were performed to demonstrate the advantages of this innovative design. RESULTS The iPRES(2)-A coil showed no loss in signal-to-noise ratio and provided a much more effective correction of highly localized B0 inhomogeneities and geometric distortions than an equivalent iPRES(1) coil (88.2% vs. 32.2% lower B0 root-mean-square error). The iPRES(4)-A coil array showed a comparable shimming performance as that of an equivalent iPRES(4) coil array (52.6% vs. 54.2% lower B0 root-mean-square error), while only requiring 8 instead of 32 power supplies. CONCLUSION The iPRES(N)-A design retains the ability of the iPRES(N) design to shim highly localized B0 inhomogeneities, while drastically reducing its cost and complexity. Magn Reson Med 80:371-379, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Dean Darnell
- Brain Imaging and Analysis Center, Duke University, Durham, North Carolina, USA.,Medical Physics Graduate Program, Duke University, Durham, North Carolina, USA
| | - Yixin Ma
- Brain Imaging and Analysis Center, Duke University, Durham, North Carolina, USA.,Medical Physics Graduate Program, Duke University, Durham, North Carolina, USA
| | - Hongyuan Wang
- Brain Imaging and Analysis Center, Duke University, Durham, North Carolina, USA.,Medical Physics Graduate Program, Duke Kunshan University, Kunshan, China
| | | | - Allen W Song
- Brain Imaging and Analysis Center, Duke University, Durham, North Carolina, USA.,Medical Physics Graduate Program, Duke University, Durham, North Carolina, USA
| | - Trong-Kha Truong
- Brain Imaging and Analysis Center, Duke University, Durham, North Carolina, USA.,Medical Physics Graduate Program, Duke University, Durham, North Carolina, USA.,Medical Physics Graduate Program, Duke Kunshan University, Kunshan, China
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Choe AS. Advances in Spinal Functional Magnetic Resonance Imaging in the Healthy and Injured Spinal Cords. CURRENT PHYSICAL MEDICINE AND REHABILITATION REPORTS 2017; 5:143-150. [PMID: 29255645 DOI: 10.1007/s40141-017-0161-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Purpose of Review This review provides an overview of the current spinal functional magnetic resonance imaging (fMRI) studies that investigate the healthy and injured spinal cords. Recent Findings Spinal fMRI-derived outcome measures have previously been suggested to be sensitive to changes in neurological function in the spinal cord. A body of recent task-activated fMRI studies seems to confirm that detecting neural activity in the spinal cord using spinal fMRI may be feasible as well as reliable. Furthermore, a growing number of studies has shown that resting state fMRI in the spinal cord is also feasible, demonstrating that the investigation of changes in neural activity can also be performed in the absence of explicit tasks. Summary Current task-activated and resting state fMRI studies suggest that spinal fMRI has a strong potential to provide novel imaging biomarkers that can be used to investigate plastic changes in the injured spinal cord.
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Affiliation(s)
- Ann S Choe
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD 21205 USA
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Cohen-Adad J. Functional Magnetic Resonance Imaging of the Spinal Cord: Current Status and Future Developments. Semin Ultrasound CT MR 2017; 38:176-186. [DOI: 10.1053/j.sult.2016.07.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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De Tillieux P, Topfer R, Foias A, Leroux I, El Maâchi I, Leblond H, Stikov N, Cohen-Adad J. A pneumatic phantom for mimicking respiration-induced artifacts in spinal MRI. Magn Reson Med 2017; 79:600-605. [DOI: 10.1002/mrm.26679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/13/2017] [Accepted: 02/21/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Philippe De Tillieux
- NeuroPoly Lab; Institute of Biomedical Engineering, Polytechnique Montreal; Montreal Quebec Canada
| | - Ryan Topfer
- NeuroPoly Lab; Institute of Biomedical Engineering, Polytechnique Montreal; Montreal Quebec Canada
| | - Alexandru Foias
- NeuroPoly Lab; Institute of Biomedical Engineering, Polytechnique Montreal; Montreal Quebec Canada
| | - Iris Leroux
- NeuroPoly Lab; Institute of Biomedical Engineering, Polytechnique Montreal; Montreal Quebec Canada
| | - Imanne El Maâchi
- NeuroPoly Lab; Institute of Biomedical Engineering, Polytechnique Montreal; Montreal Quebec Canada
| | - Hugues Leblond
- Department of Anatomy; Université du Québec à Trois-Rivières; Trois-Rivières Quebec Canada
| | - Nikola Stikov
- NeuroPoly Lab; Institute of Biomedical Engineering, Polytechnique Montreal; Montreal Quebec Canada
- Montreal Heart Institute, Université de Montréal; Montreal Quebec Canada
| | - Julien Cohen-Adad
- NeuroPoly Lab; Institute of Biomedical Engineering, Polytechnique Montreal; Montreal Quebec Canada
- Functional Neuroimaging Unit, CRIUGM, Université de Montréal; Montreal Quebec Canada
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