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Marchetto E, Gallichan D. Analysis of the effect of motion on highly accelerated 3D FatNavs in 3D brain images acquired at 3T. PLoS One 2024; 19:e0306078. [PMID: 39052654 PMCID: PMC11271950 DOI: 10.1371/journal.pone.0306078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/11/2024] [Indexed: 07/27/2024] Open
Abstract
PURPOSE 3D FatNavs are rapid acquisitions of MRI fat-volumes within the head that can be used for retrospective motion correction for brain MRI. 3D FatNavs typically use very high acceleration factors and are reconstructed with the GRAPPA parallel imaging technique. However, the GRAPPA reconstruction is not expected to perform well on 3D FatNavs volumes in the presence of strong motion due to the mismatched calibration data acquired once at the start of the scan, leading to motion-parameter misestimation. This study aims to assess the accuracy and precision of 3D FatNav-derived motion-estimates in the presence of large changes in head position. METHODS Rigid motion parameters were simulated and applied retrospectively to the 3D FatNav volumes from MPRAGE datasets acquired at 3T. The transformed images were then re-reconstructed using GRAPPA to simulate real motion deterioration of the fat-navigator, and used to estimate the motion applied and evaluate the tracking inaccuracy. This information was then used to estimate the residual motion after 3D FatNav-based motion correction and applied to the original MPRAGE volumes. The effect of the misestimation was assessed using an image quality metric and the evaluation scores from two observers. Quality boundaries were then estimated to assess the motion tolerance when 3D FatNavs are used. RESULTS The GRAPPA reconstruction was shown to deteriorate for large changes in the head position, affecting the quality of 3D FatNav volumes and consequently degrading the accuracy of the motion-estimates. Based on our simulations, the estimated threshold of motion that led to a noticeable degradation in the MPRAGE image quality was up to RMS values of 3.7° and 3 mm for rotations and translations respectively. CONCLUSIONS 3D FatNavs were shown to be able to correct for a wide range of motion levels and types. Boundaries of acceptable motion magnitudes for different levels of acceptable loss of image quality were determined.
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Affiliation(s)
- Elisa Marchetto
- CUBRIC/School of Engineering, Cardiff University, Cardiff, United Kingdom
- Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York, United States of America
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Daniel Gallichan
- CUBRIC/School of Engineering, Cardiff University, Cardiff, United Kingdom
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Brackenier Y, Wang N, Liao C, Cao X, Schauman S, Yurt M, Cordero-Grande L, Malik SJ, Kerr A, Hajnal JV, Setsompop K. Rapid and accurate navigators for motion and B 0 tracking using QUEEN: Quantitatively enhanced parameter estimation from navigators. Magn Reson Med 2024; 91:2028-2043. [PMID: 38173304 DOI: 10.1002/mrm.29976] [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: 06/17/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
PURPOSE To develop a framework that jointly estimates rigid motion and polarizing magnetic field (B0 ) perturbations (δ B 0 $$ \delta {\mathbf{B}}_{\mathbf{0}} $$ ) for brain MRI using a single navigator of a few milliseconds in duration, and to additionally allow for navigator acquisition at arbitrary timings within any type of sequence to obtain high-temporal resolution estimates. THEORY AND METHODS Methods exist that match navigator data to a low-resolution single-contrast image (scout) to estimate either motion orδ B 0 $$ \delta {\mathbf{B}}_{\mathbf{0}} $$ . In this work, called QUEEN (QUantitatively Enhanced parameter Estimation from Navigators), we propose combined motion andδ B 0 $$ \delta {\mathbf{B}}_{\mathbf{0}} $$ estimation from a fast, tailored trajectory with arbitrary-contrast navigator data. To this end, the concept of a quantitative scout (Q-Scout) acquisition is proposed from which contrast-matched scout data is predicted for each navigator. Finally, navigator trajectories, contrast-matched scout, andδ B 0 $$ \delta {\mathbf{B}}_{\mathbf{0}} $$ are integrated into a motion-informed parallel-imaging framework. RESULTS Simulations and in vivo experiments show the need to modelδ B 0 $$ \delta {\mathbf{B}}_{\mathbf{0}} $$ to obtain accurate motion parameters estimated in the presence of strongδ B 0 $$ \delta {\mathbf{B}}_{\mathbf{0}} $$ . Simulations confirm that tailored navigator trajectories are needed to robustly estimate both motion andδ B 0 $$ \delta {\mathbf{B}}_{\mathbf{0}} $$ . Furthermore, experiments show that a contrast-matched scout is needed for parameter estimation from multicontrast navigator data. A retrospective, in vivo reconstruction experiment shows improved image quality when using the proposed Q-Scout and QUEEN estimation. CONCLUSIONS We developed a framework to jointly estimate rigid motion parameters andδ B 0 $$ \delta {\mathbf{B}}_{\mathbf{0}} $$ from navigators. Combing a contrast-matched scout with the proposed trajectory allows for navigator deployment in almost any sequence and/or timing, which allows for higher temporal-resolution motion andδ B 0 $$ \delta {\mathbf{B}}_{\mathbf{0}} $$ estimates.
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Affiliation(s)
| | - Nan Wang
- Department of Radiology, Stanford University, Stanford, California, USA
| | - Congyu Liao
- Department of Radiology, Stanford University, Stanford, California, USA
| | - Xiaozhi Cao
- Department of Radiology, Stanford University, Stanford, California, USA
| | - Sophie Schauman
- Department of Radiology, Stanford University, Stanford, California, USA
| | - Mahmut Yurt
- Department of Radiology, Stanford University, Stanford, California, USA
- Department of Electrical Engineering, Stanford University, Stanford, California, USA
| | - Lucilio Cordero-Grande
- Biomedical Image Technologies, ETSI Telecomunicación, Universidad Politécnica de Madrid and CIBER-BNN, Madrid, Spain
| | - Shaihan J Malik
- Biomedical Engineering Department, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- Center for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Adam Kerr
- Department of Electrical Engineering, Stanford University, Stanford, California, USA
- Cognitive and Neurobiological Imaging, Stanford University, Stanford, California, USA
| | - Joseph V Hajnal
- Biomedical Engineering Department, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- Center for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Kawin Setsompop
- Department of Radiology, Stanford University, Stanford, California, USA
- Department of Electrical Engineering, Stanford University, Stanford, California, USA
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Marchetto E, Murphy K, Glimberg SL, Gallichan D. Robust retrospective motion correction of head motion using navigator-based and markerless motion tracking techniques. Magn Reson Med 2023; 90:1297-1315. [PMID: 37183791 PMCID: PMC7615144 DOI: 10.1002/mrm.29705] [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: 12/22/2022] [Revised: 04/05/2023] [Accepted: 04/26/2023] [Indexed: 05/16/2023]
Abstract
PURPOSE This study investigated the artifacts arising from different types of head motion in brain MR images and how well these artifacts can be compensated using retrospective correction based on two different motion-tracking techniques. METHODS MPRAGE images were acquired using a 3 T MR scanner on a cohort of nine healthy participants. Subjects moved their head to generate circular motion (4 or 6 cycles/min), stepwise motion (small and large) and "simulated realistic" motion (nodding and slow diagonal motion), based on visual instructions. One MPRAGE scan without deliberate motion was always acquired as a "no motion" reference. Three dimensional fat-navigator (FatNavs) and a Tracoline markerless device (TracInnovations) were used to obtain motion estimates and images were separately reconstructed retrospectively from the raw data based on these different motion estimates. RESULTS Image quality was recovered from both motion tracking techniques in our stepwise and slow diagonal motion scenarios in almost all cases, with the apparent visual image quality comparable to the no-motion case. FatNav-based motion correction was further improved in the case of stepwise motion using a skull masking procedure to exclude non-rigid motion of the neck from the co-registration step. In the case of circular motion, both methods struggled to correct for all motion artifacts. CONCLUSION High image quality could be recovered in cases of stepwise and slow diagonal motion using both motion estimation techniques. The circular motion scenario led to more severe image artifacts that could not be fully compensated by the retrospective motion correction techniques used.
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Affiliation(s)
- Elisa Marchetto
- CUBRIC/School of Engineering, Cardiff University, Cardiff, UK
| | - Kevin Murphy
- CUBRIC/School of Physics and Astronomy, Cardiff University, Cardiff, UK
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Mesoscopic in vivo human T 2* dataset acquired using quantitative MRI at 7 Tesla. Neuroimage 2022; 264:119733. [PMID: 36375782 DOI: 10.1016/j.neuroimage.2022.119733] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/15/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022] Open
Abstract
Mesoscopic (0.1-0.5 mm) interrogation of the living human brain is critical for advancing neuroscience and bridging the resolution gap with animal models. Despite the variety of MRI contrasts measured in recent years at the mesoscopic scale, in vivo quantitative imaging of T2* has not been performed. Here we provide a dataset containing empirical T2* measurements acquired at 0.35 × 0.35 × 0.35 mm3 voxel resolution using 7 Tesla MRI. To demonstrate unique features and high quality of this dataset, we generate flat map visualizations that reveal fine-scale cortical substructures such as layers and vessels, and we report quantitative depth-dependent T2* (as well as R2*) values in primary visual cortex and auditory cortex that are highly consistent across subjects. This dataset is freely available at https://doi.org/10.17605/OSF.IO/N5BJ7, and may prove useful for anatomical investigations of the human brain, as well as for improving our understanding of the basis of the T2*-weighted (f)MRI signal.
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Andersen M, Laustsen M, Boer V. Accuracy investigations for volumetric head-motion navigators with and without EPI at 7 T. Magn Reson Med 2022; 88:1198-1211. [PMID: 35576128 PMCID: PMC9325528 DOI: 10.1002/mrm.29296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/31/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022]
Abstract
PURPOSE Accuracy investigation of volumetric navigators for motion correction, with emphasis on geometric EPI distortions at ultrahigh field. METHODS High-resolution Dixon images were collected in different head positions and reconstructed to water, fat, T2 *, and B0 maps. Resolution reduction was performed, and the T2 * and B0 maps were used to apply effects of TE and EPI distortions to simulate various volumetric water and fat navigators. Registrations of the simulated navigators were compared with registrations of the original high-resolution images. RESULTS Increased accuracy was observed with increased spatial resolution for non-EPI navigators. When using EPI, the distortions had a negative effect on registration accuracy, which was most noticeable for high-resolution navigators. Parallel imaging helped to alleviate those caveats to a certain extent, and 5-fold acceleration gave close to similar accuracy to non-EPI in most cases. Shortening the TE by partial Fourier sampling was shown to be mostly beneficial, except for water navigators with long readout durations. The EPI blip direction had an influence on navigator accuracy, and positive blip gradient polarities (yielding mostly image stretching frontally) typically gave the best accuracy for water navigators, whereas no clear recommendation could be made for fat navigators. Generally, fat EPI navigators had lower accuracy than water EPI navigators with otherwise similar parameters. CONCLUSIONS Echo planar imaging has been widely used for MRI navigators, but the induced distortions reduce navigator accuracy at ultrahigh field. This study can help protocol optimization and guide the complex tradeoff between resolution and EPI acceleration in navigator parameter setup.
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Affiliation(s)
- Mads Andersen
- Philips HealthcareCopenhagenDenmark
- Lund University Bioimaging Center, Lund UniversityLundSweden
| | - Malte Laustsen
- Center for Magnetic Resonance, Department of Health TechnologyTechnical University of DenmarkLyngbyDenmark
- Danish Research Center for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and ResearchCopenhagen University Hospital – Amager and HvidovreCopenhagenDenmark
| | - Vincent Boer
- Danish Research Center for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and ResearchCopenhagen University Hospital – Amager and HvidovreCopenhagenDenmark
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Dong Z, Wang F, Setsompop K. Motion-corrected 3D-EPTI with efficient 4D navigator acquisition for fast and robust whole-brain quantitative imaging. Magn Reson Med 2022; 88:1112-1125. [PMID: 35481604 PMCID: PMC9246907 DOI: 10.1002/mrm.29277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 12/14/2022]
Abstract
PURPOSE To develop a motion estimation and correction method for motion-robust three-dimensional (3D) quantitative imaging with 3D-echo-planar time-resolved imaging. THEORY AND METHODS The 3D-echo-planar time-resolved imaging technique was designed with additional four-dimensional navigator acquisition (x-y-z-echoes) to achieve fast and motion-robust quantitative imaging of the human brain. The four-dimensional-navigator is inserted into the relaxation-recovery deadtime of the sequence in every pulse TR (∼2 s) to avoid extra scan time, and to provide continuous tracking of the 3D head motion and B0 -inhomogeneity changes. By using an optimized spatiotemporal encoding combined with a partial-Fourier scheme, the navigator acquires a large central k-t data block for accurate motion estimation using only four small-flip-angle excitations and readouts, resulting in negligible signal-recovery reduction to the 3D-echo-planar time-resolved imaging acquisition. By incorporating the estimated motion and B0 -inhomogeneity changes into the reconstruction, multi-contrast images can be recovered with reduced motion artifacts. RESULTS Simulation shows the cost to the SNR efficiency from the added navigator acquisitions is <1%. Both simulation and in vivo retrospective experiments were conducted, that demonstrate the four-dimensional navigator provided accurate estimation of the 3D motion and B0 -inhomogeneity changes, allowing effective reduction of image artifacts in quantitative maps. Finally, in vivo prospective undersampling acquisition was performed with and without head motion, in which the motion corrupted data after correction show close image quality and consistent quantifications to the motion-free scan, providing reliable quantitative measurements even with head motion. CONCLUSION The proposed four-dimensional navigator acquisition provides reliable tracking of the head motion and B0 change with negligible SNR cost, equips the 3D-echo-planar time-resolved imaging technique for motion-robust and efficient quantitative imaging.
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Affiliation(s)
- Zijing Dong
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Fuyixue Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Kawin Setsompop
- Department of Radiology, Stanford University, Stanford, CA, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
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Slipsager JM, Glimberg SL, Højgaard L, Paulsen RR, Wighton P, Tisdall MD, Jaimes C, Gagoski BA, Grant PE, van der Kouwe A, Olesen OV, Frost R. Comparison of prospective and retrospective motion correction in 3D-encoded neuroanatomical MRI. Magn Reson Med 2022; 87:629-645. [PMID: 34490929 PMCID: PMC8635810 DOI: 10.1002/mrm.28991] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/17/2021] [Accepted: 08/10/2021] [Indexed: 02/03/2023]
Abstract
PURPOSE To compare prospective motion correction (PMC) and retrospective motion correction (RMC) in Cartesian 3D-encoded MPRAGE scans and to investigate the effects of correction frequency and parallel imaging on the performance of RMC. METHODS Head motion was estimated using a markerless tracking system and sent to a modified MPRAGE sequence, which can continuously update the imaging FOV to perform PMC. The prospective correction was applied either before each echo train (before-ET) or at every sixth readout within the ET (within-ET). RMC was applied during image reconstruction by adjusting k-space trajectories according to the measured motion. The motion correction frequency was retrospectively increased with RMC or decreased with reverse RMC. Phantom and in vivo experiments were used to compare PMC and RMC, as well as to compare within-ET and before-ET correction frequency during continuous motion. The correction quality was quantitatively evaluated using the structural similarity index measure with a reference image without motion correction and without intentional motion. RESULTS PMC resulted in superior image quality compared to RMC both visually and quantitatively. Increasing the correction frequency from before-ET to within-ET reduced the motion artifacts in RMC. A hybrid PMC and RMC correction, that is, retrospectively increasing the correction frequency of before-ET PMC to within-ET, also reduced motion artifacts. Inferior performance of RMC compared to PMC was shown with GRAPPA calibration data without intentional motion and without any GRAPPA acceleration. CONCLUSION Reductions in local Nyquist violations with PMC resulted in superior image quality compared to RMC. Increasing the motion correction frequency to within-ET reduced the motion artifacts in both RMC and PMC.
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Affiliation(s)
- Jakob M. Slipsager
- DTU Compute, Technical University of Denmark, Denmark
- Dept. of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, University of Copenhagen, Denmark
- TracInnovations, Ballerup, Denmark
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
| | | | - Liselotte Højgaard
- Dept. of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, University of Copenhagen, Denmark
| | | | - Paul Wighton
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
| | - M. Dylan Tisdall
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Camilo Jaimes
- Boston Children’s Hospital, Boston, Massachusetts
- Dept. of Radiology, Harvard Medical School, Boston, Massachusetts
| | - Borjan A. Gagoski
- Dept. of Radiology, Harvard Medical School, Boston, Massachusetts
- Fetal-Neonatal Neuroimaging & Developmental Science Center, Boston Children’s Hospital, Boston, Massachusetts
| | - P. Ellen Grant
- Dept. of Radiology, Harvard Medical School, Boston, Massachusetts
- Fetal-Neonatal Neuroimaging & Developmental Science Center, Boston Children’s Hospital, Boston, Massachusetts
| | - André van der Kouwe
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
- Dept. of Radiology, Harvard Medical School, Boston, Massachusetts
| | - Oline V. Olesen
- DTU Compute, Technical University of Denmark, Denmark
- Dept. of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, University of Copenhagen, Denmark
- TracInnovations, Ballerup, Denmark
| | - Robert Frost
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
- Dept. of Radiology, Harvard Medical School, Boston, Massachusetts
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Sciarra A, Mattern H, Yakupov R, Chatterjee S, Stucht D, Oeltze-Jafra S, Godenschweger F, Speck O. Quantitative evaluation of prospective motion correction in healthy subjects at 7T MRI. Magn Reson Med 2022; 87:646-657. [PMID: 34463376 PMCID: PMC8663924 DOI: 10.1002/mrm.28998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/28/2021] [Accepted: 08/16/2021] [Indexed: 02/03/2023]
Abstract
PURPOSE Quantitative assessment of prospective motion correction (PMC) capability at 7T MRI for compliant healthy subjects to improve high-resolution images in the absence of intentional motion. METHODS Twenty-one healthy subjects were imaged at 7 T. They were asked not to move, to consider only unintentional motion. An in-bore optical tracking system was used to monitor head motion and consequently update the imaging volume. For all subjects, high-resolution T1 (3D-MPRAGE), T2 (2D turbo spin echo), proton density (2D turbo spin echo), and T2∗ (2D gradient echo) weighted images were acquired with and without PMC. The images were evaluated through subjective and objective analysis. RESULTS Subjective evaluation overall has shown a statistically significant improvement (5.5%) in terms of image quality with PMC ON. In a separate evaluation of every contrast, three of the four contrasts (T1 , T2 , and proton density) have shown a statistically significant improvement (9.62%, 9.85%, and 9.26%), whereas the fourth one ( T2∗ ) has shown improvement, although not statistically significant. In the evaluation with objective metrics, average edge strength has shown an overall improvement of 6% with PMC ON, which was statistically significant; and gradient entropy has shown an overall improvement of 2%, which did not reach statistical significance. CONCLUSION Based on subjective assessment, PMC improved image quality in high-resolution images of healthy compliant subjects in the absence of intentional motion for all contrasts except T2∗ , in which no significant differences were observed. Quantitative metrics showed an overall trend for an improvement with PMC, but not all differences were significant.
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Affiliation(s)
- A. Sciarra
- Medicine and Digitalization - MedDigit, Medical Faculty, Univ. Dept. of Neurology, Otto von Guericke University, Magdeburg, 39120, Germany, Dept. of Biomedical Magnetic Resonance, Otto von Guericke University, Magdeburg,39120, Germany, Institute for Physics, Otto von Guericke University, Magdeburg, 39106, Germany
| | - H. Mattern
- Dept. of Biomedical Magnetic Resonance, Otto von Guericke University, Magdeburg,39120, Germany
| | - R. Yakupov
- German Centre for Neurodegenerative Diseases (DZNE), Magdeburg, 39120, Germany
| | - S. Chatterjee
- Dept. of Biomedical Magnetic Resonance, Otto von Guericke University, Magdeburg,39120, Germany, Data and Knowledge Engineering Group, Faculty of Computer Science, Otto von Guericke University, Magdeburg
| | - D. Stucht
- Dept. of Biomedical Magnetic Resonance, Otto von Guericke University, Magdeburg,39120, Germany
| | - S. Oeltze-Jafra
- Medicine and Digitalization - MedDigit, Medical Faculty, Univ. Dept. of Neurology, Otto von Guericke University, Magdeburg, 39120, Germany, German Centre for Neurodegenerative Diseases (DZNE), Magdeburg, 39120, Germany, Center for Behavioral Brain Sciences, Magdeburg, 39120, Germany
| | - F. Godenschweger
- Dept. of Biomedical Magnetic Resonance, Otto von Guericke University, Magdeburg,39120, Germany
| | - O. Speck
- Dept. of Biomedical Magnetic Resonance, Otto von Guericke University, Magdeburg,39120, Germany, Institute for Physics, Otto von Guericke University, Magdeburg, 39106, Germany, German Centre for Neurodegenerative Diseases (DZNE), Magdeburg, 39120, Germany, Leibniz Institute for Neurobiology, Magdeburg, 39120, Germany, Center for Behavioral Brain Sciences, Magdeburg, 39120, Germany
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Lüsebrink F, Mattern H, Yakupov R, Acosta-Cabronero J, Ashtarayeh M, Oeltze-Jafra S, Speck O. Comprehensive ultrahigh resolution whole brain in vivo MRI dataset as a human phantom. Sci Data 2021; 8:138. [PMID: 34035308 PMCID: PMC8149725 DOI: 10.1038/s41597-021-00923-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/13/2021] [Indexed: 11/09/2022] Open
Abstract
Here, we present an extension to our previously published structural ultrahigh resolution T1-weighted magnetic resonance imaging (MRI) dataset with an isotropic resolution of 250 µm, consisting of multiple additional ultrahigh resolution contrasts. Included are up to 150 µm Time-of-Flight angiography, an updated 250 µm structural T1-weighted reconstruction, 330 µm quantitative susceptibility mapping, up to 450 µm structural T2-weighted imaging, 700 µm T1-weighted back-to-back scans, 800 µm diffusion tensor imaging, one hour continuous resting-state functional MRI with an isotropic spatial resolution of 1.8 mm as well as more than 120 other structural T1-weighted volumes together with multiple corresponding proton density weighted acquisitions collected over ten years. All data are from the same participant and were acquired on the same 7 T scanner. The repository contains the unprocessed data as well as (pre-)processing results. The data were acquired in multiple studies with individual goals. This is a unique and comprehensive collection comprising a "human phantom" dataset. Therefore, we compiled, processed, and structured the data, making them publicly available for further investigation.
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Affiliation(s)
- Falk Lüsebrink
- Medicine and Digitalization, Department of Neurology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany.
- Biomedical Magnetic Resonance, Faculty of Natural Sciences, Otto-von-Guericke University, Magdeburg, Germany.
| | - Hendrik Mattern
- Biomedical Magnetic Resonance, Faculty of Natural Sciences, Otto-von-Guericke University, Magdeburg, Germany
| | - Renat Yakupov
- German Center of Neurodegenerative Diseases (DZNE), site Magdeburg, Germany
| | | | - Mohammad Ashtarayeh
- Department of Systems Neuroscience, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Steffen Oeltze-Jafra
- Medicine and Digitalization, Department of Neurology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
- German Center of Neurodegenerative Diseases (DZNE), site Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Oliver Speck
- Biomedical Magnetic Resonance, Faculty of Natural Sciences, Otto-von-Guericke University, Magdeburg, Germany
- German Center of Neurodegenerative Diseases (DZNE), site Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
- Leibniz Institute for Neurobiology, Magdeburg, Germany
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10
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Hucker P, Dacko M, Zaitsev M. Combining prospective and retrospective motion correction based on a model for fast continuous motion. Magn Reson Med 2021; 86:1284-1298. [PMID: 33829538 DOI: 10.1002/mrm.28783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 11/08/2022]
Abstract
PURPOSE Prospective motion correction (PMC) and retrospective motion correction (RMC) have different advantages and limitations. The present work aims to combine the advantages of both for rigid body motion, aiming at correcting for faster motions than was previously achievable. Additionally, it provides insights into the effects of motion on pulse sequences and MR signals with a goal of further improving motion correction in the future. METHODS The effective encoding trajectory and a global phase offset in a moving object are calculated based on complete gradient waveforms of an arbitrary sequence and a continuous motion model. These data are used to feed the forward signal model, which is then used in iterative image reconstruction to suppress the artifacts still present after the PMC. RESULTS Verification experiments with a rotation phantom and in vivo were performed. Predictions of simulated motion artifacts for PMC based on sequence waveforms are very accurate. The performance at combined PMC+RMC is limited by Nyquist violations in the sampled k-space and can be compensated by oversampling. CONCLUSION The combined correction results in better images than pure PMC in the presence of fast motion. The predictions of artifacts are very accurate, allowing for comparing sequences or protocols in simulations. The observed artifacts due to Nyquist violations are expected to be corrected by utilizing parallel imaging.
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Affiliation(s)
- Patrick Hucker
- Center for Diagnostic and Therapeutic Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Dacko
- Center for Diagnostic and Therapeutic Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maxim Zaitsev
- Center for Diagnostic and Therapeutic Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,High Field Magnetic Resonance Center, Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
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11
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Wallace TE, Afacan O, Jaimes C, Rispoli J, Pelkola K, Dugan M, Kober T, Warfield SK. Free induction decay navigator motion metrics for prediction of diagnostic image quality in pediatric MRI. Magn Reson Med 2021; 85:3169-3181. [PMID: 33404086 PMCID: PMC7904595 DOI: 10.1002/mrm.28649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/05/2020] [Accepted: 11/25/2020] [Indexed: 12/23/2022]
Abstract
Purpose To investigate the ability of free induction decay navigator (FIDnav)‐based motion monitoring to predict diagnostic utility and reduce the time and cost associated with acquiring diagnostically useful images in a pediatric patient cohort. Methods A study was carried out in 102 pediatric patients (aged 0‐18 years) at 3T using a 32‐channel head coil array. Subjects were scanned with an FID‐navigated MPRAGE sequence and images were graded by two radiologists using a five‐point scale to evaluate the impact of motion artifacts on diagnostic image quality. The correlation between image quality and four integrated FIDnav motion metrics was investigated, as well as the sensitivity and specificity of each FIDnav‐based metric to detect different levels of motion corruption in the images. Potential time and cost savings were also assessed by retrospectively applying an optimal detection threshold to FIDnav motion scores. Results A total of 12% of images were rated as non‐diagnostic, while a further 12% had compromised diagnostic value due to motion artifacts. FID‐navigated metrics exhibited a moderately strong correlation with image grade (Spearman's rho ≥ 0.56). Integrating the cross‐correlation between FIDnav signal vectors achieved the highest sensitivity and specificity for detecting non‐diagnostic images, yielding total time savings of 7% across all scans. This corresponded to a financial benefit of $2080 in this study. Conclusions Our results indicate that integrated motion metrics from FIDnavs embedded in structural MRI are a useful predictor of diagnostic image quality, which translates to substantial time and cost savings when applied to pediatric MRI examinations.
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Affiliation(s)
- Tess E Wallace
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, MA, USA.,Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Onur Afacan
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, MA, USA.,Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Camilo Jaimes
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, MA, USA.,Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Joanne Rispoli
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, MA, USA.,Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Kristina Pelkola
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, MA, USA
| | - Monet Dugan
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, MA, USA
| | - Tobias Kober
- Advanced Clinical Imaging Technology, Siemens Healthcare AG, Lausanne, Switzerland.,Department of Radiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.,LTS5, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Simon K Warfield
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, MA, USA.,Department of Radiology, Harvard Medical School, Boston, MA, USA
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12
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Driver ID, Traat M, Fasano F, Wise RG. Most Small Cerebral Cortical Veins Demonstrate Significant Flow Pulsatility: A Human Phase Contrast MRI Study at 7T. Front Neurosci 2020; 14:415. [PMID: 32431591 PMCID: PMC7214844 DOI: 10.3389/fnins.2020.00415] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/06/2020] [Indexed: 12/22/2022] Open
Abstract
Phase contrast MRI (pcMRI) has been used to investigate flow pulsatility in cerebral arteries, larger cerebral veins, and the cerebrospinal fluid (CSF). Such measurements of intracranial pulsatility and compliance are beginning to inform understanding of the pathophysiology of conditions including normal pressure hydrocephalus, multiple sclerosis, and dementias. We demonstrate the presence of flow pulsatility in small cerebral cortical veins, for the first time using pcMRI at 7 T, with the aim of improving our understanding of the hemodynamics of this little-studied vascular compartment. A method for establishing where venous flow is pulsatile is introduced, revealing significant pulsatility in 116 out of 146 veins, across eight healthy participants, assessed in parietal and frontal regions. Distributions of pulsatility index (PI) and pulse waveform delay were characterized, indicating a small, but statistically significant (p < 0.05), delay of 59 ± 41 ms in cortical veins with respect to the superior sagittal sinus, but no differences between veins draining different arterial supply territories. Measurements of pulsatility in smaller cortical veins, a hitherto unstudied compartment closer to the capillary bed, could lead to a better understanding of intracranial compliance and cerebrovascular (patho)physiology.
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Affiliation(s)
- Ian D Driver
- Cardiff University Brain Research Imaging Centre, School of Psychology, Cardiff University, Cardiff, United Kingdom
| | - Maarika Traat
- Cardiff University Brain Research Imaging Centre, School of Psychology, Cardiff University, Cardiff, United Kingdom.,Institute of Psychology, University of Tartu, Tartu, Estonia
| | | | - Richard G Wise
- Cardiff University Brain Research Imaging Centre, School of Psychology, Cardiff University, Cardiff, United Kingdom.,Department of Neuroscience, Imaging and Clinical Sciences, "G. D'Annunzio University" of Chieti-Pescara, Chieti, Italy.,Institute for Advanced Biomedical Technologies, "G. D'Annunzio University" of Chieti-Pescara, Chieti, Italy
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13
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Slipsager JM, Glimberg SL, Søgaard J, Paulsen RR, Johannesen HH, Martens PC, Seth A, Marner L, Henriksen OM, Olesen OV, Højgaard L. Quantifying the Financial Savings of Motion Correction in Brain MRI: A Model‐Based Estimate of the Costs Arising From Patient Head Motion and Potential Savings From Implementation of Motion Correction. J Magn Reson Imaging 2020; 52:731-738. [DOI: 10.1002/jmri.27112] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 11/08/2022] Open
Affiliation(s)
- Jakob M. Slipsager
- DTU ComputeTechnical University of Denmark Lyngby Denmark
- Department of Clinical Physiology, Nuclear Medicine & PETRigshospitalet, University of Copenhagen Copenhagen Denmark
- TracInnovations Ballerup Denmark
| | | | - Jes Søgaard
- Institute of Clinical Research, HealthUniversity of Southern Denmark Odense Denmark
| | | | - Helle H. Johannesen
- Department of Clinical Physiology, Nuclear Medicine & PETRigshospitalet, University of Copenhagen Copenhagen Denmark
| | - Pernille C. Martens
- Department of RadiologyRigshospitalet, University of Copenhagen Copenhagen Denmark
| | - Alka Seth
- Department of RadiologyRigshospitalet, University of Copenhagen Copenhagen Denmark
| | - Lisbeth Marner
- Department of Clinical Physiology, Nuclear Medicine & PETRigshospitalet, University of Copenhagen Copenhagen Denmark
- Department of Clinical Physiology and Nuclear MedicineCopenhagen University Hospital Bispebjerg Copenhagen Denmark
| | - Otto M. Henriksen
- Department of Clinical Physiology, Nuclear Medicine & PETRigshospitalet, University of Copenhagen Copenhagen Denmark
| | - Oline V. Olesen
- DTU ComputeTechnical University of Denmark Lyngby Denmark
- Department of Clinical Physiology, Nuclear Medicine & PETRigshospitalet, University of Copenhagen Copenhagen Denmark
- TracInnovations Ballerup Denmark
| | - Liselotte Højgaard
- Department of Clinical Physiology, Nuclear Medicine & PETRigshospitalet, University of Copenhagen Copenhagen Denmark
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14
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Jorge J, Gretsch F, Najdenovska E, Tuleasca C, Levivier M, Maeder P, Gallichan D, Marques JP, Bach Cuadra M. Improved susceptibility-weighted imaging for high contrast and resolution thalamic nuclei mapping at 7T. Magn Reson Med 2020; 84:1218-1234. [PMID: 32052486 DOI: 10.1002/mrm.28197] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
PURPOSE The thalamus is an important brain structure and neurosurgical target, but its constituting nuclei are challenging to image non-invasively. Recently, susceptibility-weighted imaging (SWI) at ultra-high field has shown promising capabilities for thalamic nuclei mapping. In this work, several methodological improvements were explored to enhance SWI quality and contrast, and specifically its ability for thalamic imaging. METHODS High-resolution SWI was performed at 7T in healthy participants, and the following techniques were applied: (a) monitoring and retrospective correction of head motion and B0 perturbations using integrated MR navigators, (b) segmentation and removal of venous vessels on the SWI data using vessel enhancement filtering, and (c) contrast enhancement by tuning the parameters of the SWI phase-magnitude combination. The resulting improvements were evaluated with quantitative metrics of image quality, and by comparison to anatomo-histological thalamic atlases. RESULTS Even with sub-millimeter motion and natural breathing, motion and field correction produced clear improvements in both magnitude and phase data quality (76% and 41%, respectively). The improvements were stronger in cases of larger motion/field deviations, mitigating the dependence of image quality on subject performance. Optimizing the SWI phase-magnitude combination yielded substantial improvements in image contrast, particularly in the thalamus, well beyond previously reported SWI results. The atlas comparisons provided compelling evidence of anatomical correspondence between SWI features and several thalamic nuclei, for example, the ventral intermediate nucleus. Vein detection performed favorably inside the thalamus, and vein removal further improved visualization. CONCLUSION Altogether, the proposed developments substantially improve high-resolution SWI, particularly for thalamic nuclei imaging.
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Affiliation(s)
- João Jorge
- Medical Image Analysis Laboratory, Center for Biomedical Imaging (CIBM), University of Lausanne, Lausanne, Switzerland.,Laboratory for Functional and Metabolic Imaging, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Frédéric Gretsch
- Laboratory for Functional and Metabolic Imaging, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Elena Najdenovska
- Medical Image Analysis Laboratory, Center for Biomedical Imaging (CIBM), University of Lausanne, Lausanne, Switzerland.,Department of Radiology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Constantin Tuleasca
- Department of Clinical Neurosciences, Neurosurgery Service and Gamma Knife Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.,Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Marc Levivier
- Department of Clinical Neurosciences, Neurosurgery Service and Gamma Knife Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.,Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Philippe Maeder
- Department of Radiology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Daniel Gallichan
- Cardiff University Brain Research Imaging Centre, School of Engineering, Cardiff University, Cardiff, UK
| | - José P Marques
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Meritxell Bach Cuadra
- Medical Image Analysis Laboratory, Center for Biomedical Imaging (CIBM), University of Lausanne, Lausanne, Switzerland.,Department of Radiology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland.,Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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