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Boulant N, Le Ster C, Amadon A, Aubert G, Beckett A, Belorgey J, Bonnelye C, Bosch D, Brunner DO, Dilasser G, Dubois O, Ehses P, Feinberg D, Feizollah S, Gras V, Gross S, Guihard Q, Lannou H, Le Bihan D, Mauconduit F, Molinié F, Nunio F, Pruessmann K, Quettier L, Scheffler K, Stöcker T, Tardif C, Ugurbil K, Vignaud A, Vu A, Wu X. The possible influence of third-order shim coils on gradient-magnet interactions: an inter-field and inter-site study. MAGMA (NEW YORK, N.Y.) 2024; 37:169-183. [PMID: 38197908 PMCID: PMC10995016 DOI: 10.1007/s10334-023-01138-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/11/2024]
Abstract
OBJECTIVE To assess the possible influence of third-order shim coils on the behavior of the gradient field and in gradient-magnet interactions at 7 T and above. MATERIALS AND METHODS Gradient impulse response function measurements were performed at 5 sites spanning field strengths from 7 to 11.7 T, all of them sharing the same exact whole-body gradient coil design. Mechanical fixation and boundary conditions of the gradient coil were altered in several ways at one site to study the impact of mechanical coupling with the magnet on the field perturbations. Vibrations, power deposition in the He bath, and field dynamics were characterized at 11.7 T with the third-order shim coils connected and disconnected inside the Faraday cage. RESULTS For the same whole-body gradient coil design, all measurements differed greatly based on the third-order shim coil configuration (connected or not). Vibrations and gradient transfer function peaks could be affected by a factor of 2 or more, depending on the resonances. Disconnecting the third-order shim coils at 11.7 T also suppressed almost completely power deposition peaks at some frequencies. DISCUSSION Third-order shim coil configurations can have major impact in gradient-magnet interactions with consequences on potential hardware damage, magnet heating, and image quality going beyond EPI acquisitions.
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Affiliation(s)
- Nicolas Boulant
- CEA, CNRS, BAOBAB, NeuroSpin, University Paris-Saclay, 91191, Gif Sur Yvette Cedex, France.
| | - Caroline Le Ster
- CEA, CNRS, BAOBAB, NeuroSpin, University Paris-Saclay, 91191, Gif Sur Yvette Cedex, France
| | - Alexis Amadon
- CEA, CNRS, BAOBAB, NeuroSpin, University Paris-Saclay, 91191, Gif Sur Yvette Cedex, France
| | - Guy Aubert
- CEA, Irfu, DACM, University Paris-Saclay, Gif Sur Yvette, France
| | - Alexander Beckett
- Brain Imaging Center and Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
- Advanced MRI Technologies, Sebastopol, CA, USA
| | - Jean Belorgey
- CEA, Irfu, DIS, University Paris-Saclay, Gif Sur Yvette, France
| | - Cédric Bonnelye
- CEA, CNRS, BAOBAB, NeuroSpin, University Paris-Saclay, 91191, Gif Sur Yvette Cedex, France
| | - Dario Bosch
- Department for Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany
- High-Field MR Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | | | | | - Olivier Dubois
- CEA, Irfu, DIS, University Paris-Saclay, Gif Sur Yvette, France
| | | | - David Feinberg
- Brain Imaging Center and Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
- Advanced MRI Technologies, Sebastopol, CA, USA
| | - Sajjad Feizollah
- Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Vincent Gras
- CEA, CNRS, BAOBAB, NeuroSpin, University Paris-Saclay, 91191, Gif Sur Yvette Cedex, France
| | | | - Quentin Guihard
- CEA, Irfu, DIS, University Paris-Saclay, Gif Sur Yvette, France
| | - Hervé Lannou
- CEA, Irfu, DACM, University Paris-Saclay, Gif Sur Yvette, France
| | - Denis Le Bihan
- CEA, CNRS, BAOBAB, NeuroSpin, University Paris-Saclay, 91191, Gif Sur Yvette Cedex, France
| | - Franck Mauconduit
- CEA, CNRS, BAOBAB, NeuroSpin, University Paris-Saclay, 91191, Gif Sur Yvette Cedex, France
| | | | - François Nunio
- CEA, Irfu, DIS, University Paris-Saclay, Gif Sur Yvette, France
| | | | - Lionel Quettier
- CEA, Irfu, DACM, University Paris-Saclay, Gif Sur Yvette, France
| | - Klaus Scheffler
- Department for Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany
- High-Field MR Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Tony Stöcker
- Center for Neurogenerative Diseases, Bonn, Germany
| | - Christine Tardif
- Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Kamil Ugurbil
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - Alexandre Vignaud
- CEA, CNRS, BAOBAB, NeuroSpin, University Paris-Saclay, 91191, Gif Sur Yvette Cedex, France
| | - An Vu
- University of California, San Francisco, CA, USA
- San Francisco VA Health Care System, San Francisco, CA, USA
| | - Xiaoping Wu
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
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Amor Z, Le Ster C, Gr C, Daval-Frérot G, Boulant N, Mauconduit F, Thirion B, Ciuciu P, Vignaud A. Impact of B 0 $$ {\mathrm{B}}_0 $$ field imperfections correction on BOLD sensitivity in 3D-SPARKLING fMRI data. Magn Reson Med 2024; 91:1434-1448. [PMID: 38156952 DOI: 10.1002/mrm.29943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/07/2023] [Accepted: 11/09/2023] [Indexed: 01/03/2024]
Abstract
PURPOSE Static and dynamicB 0 $$ {\mathrm{B}}_0 $$ field imperfections are detrimental to functional MRI (fMRI) applications, especially at ultra-high magnetic fields (UHF). In this work, a field camera is used to assess the benefits of retrospectively correctingB 0 $$ {\mathrm{B}}_0 $$ field perturbations on Blood Oxygen Level Dependent (BOLD) sensitivity in non-Cartesian three-dimensional (3D)-SPARKLING fMRI acquisitions. METHODS fMRI data were acquired at 1 mm3 $$ {}^3 $$ and for a 2.4s-TR while concurrently monitoring in real-time field perturbations using a Skope Clip-on field camera in a novel experimental setting involving a shorter TR than the required minimal TR of the field probes. Measurements of the dynamic field deviations were used along with a staticΔ B 0 $$ \Delta {\mathrm{B}}_0 $$ map to retrospectively correct static and dynamic field imperfections, respectively. In order to evaluate the impact of such a correction on fMRI volumes, a comparative study was conducted on healthy volunteers. RESULTS Correction ofB 0 $$ {\mathrm{B}}_0 $$ deviations improved image quality and yielded between 20% and 30% increase in median temporal signal-to-noise ratio (tSNR).Using fMRI data collected during a retinotopic mapping experiment, we demonstrated a significant increase in sensitivity to the BOLD contrast and improved accuracy of the BOLD phase maps: 44% (resp., 159%) more activated voxels were retrieved when using a significance control level based on a p-value of 0.001 without correcting for multiple comparisons (resp., 0.05 with a false discovery rate correction). CONCLUSION 3D-SPARKLING fMRI hugely benefits from static and dynamicB 0 $$ {\mathrm{B}}_0 $$ imperfections correction. However, the proposed experimental protocol is flexible enough to be deployed on a large spectrum of encoding schemes, including arbitrary non-Cartesian readouts.
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Affiliation(s)
- Zaineb Amor
- CEA, NeuroSpin, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Caroline Le Ster
- CEA, NeuroSpin, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Chaithya Gr
- CEA, NeuroSpin, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
- Inria, MIND, Palaiseau, France
| | - Guillaume Daval-Frérot
- CEA, NeuroSpin, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
- Inria, MIND, Palaiseau, France
- Siemens Healthineers, Courbevoie, France
| | - Nicolas Boulant
- CEA, NeuroSpin, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Franck Mauconduit
- CEA, NeuroSpin, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Bertrand Thirion
- CEA, NeuroSpin, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
- Inria, MIND, Palaiseau, France
| | - Philippe Ciuciu
- CEA, NeuroSpin, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
- Inria, MIND, Palaiseau, France
| | - Alexandre Vignaud
- CEA, NeuroSpin, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
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3
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Guo T, He W, Wan C, Zhang Y, Xu Z. NMR Magnetometer Based on Dynamic Nuclear-Polarization for Low-Strength Magnetic Field Measurement. SENSORS (BASEL, SWITZERLAND) 2023; 23:4663. [PMID: 37430578 DOI: 10.3390/s23104663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/29/2023] [Accepted: 05/09/2023] [Indexed: 07/12/2023]
Abstract
Nuclear magnetic resonance (NMR) magnetometers are considered due to their ability to map magnetic fields with high precision and calibrate other magnetic field measurement devices. However, the low signal-to-noise ratio of low-strength magnetic fields limits the precision when measuring magnetic fields below 40 mT. Therefore, we developed a new NMR magnetometer that combines the dynamic nuclear polarization (DNP) technique with pulsed NMR. The dynamic pre-polarization technique enhances the SNR under a low magnetic field. Pulsed NMR was used in conjunction with DNP to improve measurement accuracy and speed. The efficacy of this approach was validated through simulation and analysis of the measurement process. Next, a complete set of equipment was constructed, and we successfully measured magnetic fields of 30 mT and 8 mT with an accuracy of only 0.5 Hz (11 nT) at 30 mT (0.4 ppm) and 1 Hz (22 nT) at 8mT (3 ppm).
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Affiliation(s)
- Taoning Guo
- School of Electrical Engineering, Chongqing University, Chongqing 400044, China
| | - Wei He
- School of Electrical Engineering, Chongqing University, Chongqing 400044, China
| | - Cai Wan
- School of Electrical Engineering, Chongqing University, Chongqing 400044, China
| | - Yuxiang Zhang
- School of Electrical Engineering, Chongqing University, Chongqing 400044, China
| | - Zheng Xu
- School of Electrical Engineering, Chongqing University, Chongqing 400044, China
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Wallace TE, Kober T, Stockmann JP, Polimeni JR, Warfield SK, Afacan O. Real-time shimming with FID navigators. Magn Reson Med 2022; 88:2548-2563. [PMID: 36093989 PMCID: PMC9529812 DOI: 10.1002/mrm.29421] [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: 06/01/2022] [Revised: 07/22/2022] [Accepted: 08/02/2022] [Indexed: 11/12/2022]
Abstract
PURPOSE To implement a method for real-time field control using rapid FID navigator (FIDnav) measurements and evaluate the efficacy of the proposed approach for mitigating dynamic field perturbations and improvingT 2 * $$ {\mathrm{T}}_2^{\ast } $$ -weighted image quality. METHODS FIDnavs were embedded in a gradient echo sequence and a subject-specific linear calibration model was generated on the scanner to facilitate rapid shim updates in response to measured FIDnav signals. To confirm the accuracy of FID-navigated field updates, phantom and volunteer scans were performed with online updates of the scanner B0 shim settings. To evaluate improvement inT 2 * $$ {\mathrm{T}}_2^{\ast } $$ -weighted image quality with real-time shimming, 10 volunteers were scanned at 3T while performing deep-breathing and nose-touching tasks designed to modulate the B0 field. Quantitative image quality metrics were compared with and without FID-navigated field control. An additional volunteer was scanned at 7T to evaluate performance at ultra-high field. RESULTS Applying measured FIDnav shim updates successfully compensated for applied global and linear field offsets in phantoms and across all volunteers. FID-navigated real-time shimming led to a substantial reduction in field fluctuations and a consequent improvement inT 2 * $$ {\mathrm{T}}_2^{\ast } $$ -weighted image quality in volunteers performing deep-breathing and nose-touching tasks, with 7.57% ± 6.01% and 8.21% ± 10.90% improvement in peak SNR and structural similarity, respectively. CONCLUSION FIDnavs facilitate rapid measurement and application of field coefficients for slice-wise B0 shimming. The proposed approach can successfully counteract spatiotemporal field perturbations and substantially improvesT 2 * $$ {\mathrm{T}}_2^{\ast } $$ -weighted image quality, which is important for a variety of clinical and research applications, particularly at ultra-high field.
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Affiliation(s)
- Tess E Wallace
- Computational Radiology Laboratory, Department of Radiology, Boston Children’s Hospital, Boston, MA, United States
- Department of Radiology, Harvard Medical School, Boston, MA, United States
| | - 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
| | - Jason P Stockmann
- Department of Radiology, Harvard Medical School, Boston, MA, United States
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
| | - Jonathan R Polimeni
- Department of Radiology, Harvard Medical School, Boston, MA, United States
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
| | - Simon K Warfield
- Computational Radiology Laboratory, Department of Radiology, Boston Children’s Hospital, Boston, MA, United States
- Department of Radiology, Harvard Medical School, Boston, MA, United States
| | - Onur Afacan
- Computational Radiology Laboratory, Department of Radiology, Boston Children’s Hospital, Boston, MA, United States
- Department of Radiology, Harvard Medical School, Boston, MA, United States
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5
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Gilbert KM, Dubovan PI, Gati JS, Menon RS, Baron CA. Integration of an RF coil and commercial field camera for ultrahigh-field MRI. Magn Reson Med 2021; 87:2551-2565. [PMID: 34932225 DOI: 10.1002/mrm.29130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/16/2021] [Accepted: 12/03/2021] [Indexed: 11/08/2022]
Abstract
PURPOSE To develop an RF coil with an integrated commercial field camera for ultrahigh field (7T) neuroimaging. The RF coil would operate within a head-only gradient coil and be subject to the corresponding design constraints. The RF coil can thereafter be used for subject-specific correction of k-space trajectories-notably in gradient-sensitive sequences such as single-shot spiral imaging. METHODS The transmit and receive performance was evaluated before and after the integration of field probes, whereas field probes were evaluated when in an optimal configuration external to the coil and after their integration. Diffusion-weighted EPI and single-shot spiral acquisitions were employed to evaluate the efficacy of correcting higher order field perturbations and the consequent effect on image quality. RESULTS Field probes had a negligible effect on RF-coil performance, including the transmit efficiency, transmit uniformity, and mean SNR over the brain. Modest reductions in field-probe signal lifetimes were observed, caused primarily by nonidealities in the gradient and shim fields of the head-only gradient coil at the probe positions. The field-monitoring system could correct up to second-order field perturbations in single-shot spiral imaging. CONCLUSION The integrated RF coil and field camera was capable of concurrent-field monitoring within a 7T head-only scanner and facilitated the subsequent correction of k-space trajectories during spiral imaging.
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Affiliation(s)
- Kyle M Gilbert
- Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, Ontario, Canada.,Department of Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
| | - Paul I Dubovan
- Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, Ontario, Canada.,Department of Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
| | - Joseph S Gati
- Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, Ontario, Canada.,Department of Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
| | - Ravi S Menon
- Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, Ontario, Canada.,Department of Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
| | - Corey A Baron
- Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, Ontario, Canada.,Department of Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
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6
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Nussbaum J, Dietrich BE, Wilm BJ, Pruessmann KP. Thermal variation in gradient response: measurement and modeling. Magn Reson Med 2021; 87:2224-2238. [PMID: 34932233 PMCID: PMC9303907 DOI: 10.1002/mrm.29123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/02/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022]
Abstract
PURPOSE Many aspects and imperfections of gradient dynamics in MRI have been successfully captured by linear time-invariant (LTI) models. Changes in gradient behavior due to heating, however, violate time invariance. The goal of this work is to study such changes at the level of transfer functions and model them by thermal extension of the LTI framework. METHODS To study the impact of gradient heating on transfer functions, a clinical MR system was heated using a range of high-amplitude DC and AC waveforms, each followed by measuring transfer functions in rapid succession while the system cooled down. Simultaneously, gradient temperature was monitored with an array of temperature sensors positioned according to initial infrared recordings of the gradient tube. The relation between temperatures and transfer functions is cast into local and global linear models. The models are analysed in terms of self-consistency, conditioning, and prediction performance. RESULTS Pronounced thermal effects are observed in the time resolved transfer functions, largely attributable to in-coil eddy currents and mechanical resonances. Thermal modeling is found to capture these effects well. The keys to good model performance are well-placed temperature sensors and suitable training data. CONCLUSION Heating changes gradient response, violating time invariance. The utility of LTI modeling can nevertheless be recovered by a linear thermal extension, relying on temperature sensing and adequate one-time training.
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Affiliation(s)
- Jennifer Nussbaum
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Benjamin E Dietrich
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Bertram J Wilm
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Klaas P Pruessmann
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
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7
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Asadi N, Olson IR, Obradovic Z. The backbone network of dynamic functional connectivity. Netw Neurosci 2021; 5:851-873. [PMID: 35024533 PMCID: PMC8746122 DOI: 10.1162/netn_a_00209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/07/2021] [Indexed: 11/04/2022] Open
Abstract
Temporal networks have become increasingly pervasive in many real-world applications, including the functional connectivity analysis of spatially separated regions of the brain. A major challenge in analysis of such networks is the identification of noise confounds, which introduce temporal ties that are nonessential, or links that are formed by chance due to local properties of the nodes. Several approaches have been suggested in the past for static networks or temporal networks with binary weights for extracting significant ties whose likelihood cannot be reduced to the local properties of the nodes. In this work, we propose a data-driven procedure to reveal the irreducible ties in dynamic functional connectivity of resting-state fMRI data with continuous weights. This framework includes a null model that estimates the latent characteristics of the distributions of temporal links through optimization, followed by a statistical test to filter the links whose formation can be reduced to the activities and local properties of their interacting nodes. We demonstrate the benefits of this approach by applying it to a resting-state fMRI dataset, and provide further discussion on various aspects and advantages of it.
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Affiliation(s)
- Nima Asadi
- Department of Computer and Information Sciences, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Ingrid R. Olson
- Department of Psychology, College of Liberal Arts, Temple University, Philadelphia, PA, USA
- Decision Neuroscience, College of Liberal Arts, Temple University, Philadelphia, PA, USA
| | - Zoran Obradovic
- Department of Computer and Information Sciences, College of Science and Technology, Temple University, Philadelphia, PA, USA
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8
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Advances in spiral fMRI: A high-resolution study with single-shot acquisition. Neuroimage 2021; 246:118738. [PMID: 34800666 DOI: 10.1016/j.neuroimage.2021.118738] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 10/23/2021] [Accepted: 11/15/2021] [Indexed: 01/15/2023] Open
Abstract
Spiral fMRI has been put forward as a viable alternative to rectilinear echo-planar imaging, in particular due to its enhanced average k-space speed and thus high acquisition efficiency. This renders spirals attractive for contemporary fMRI applications that require high spatiotemporal resolution, such as laminar or columnar fMRI. However, in practice, spiral fMRI is typically hampered by its reduced robustness and ensuing blurring artifacts, which arise from imperfections in both static and dynamic magnetic fields. Recently, these limitations have been overcome by the concerted application of an expanded signal model that accounts for such field imperfections, and its inversion by iterative image reconstruction. In the challenging ultra-high field environment of 7 Tesla, where field inhomogeneity effects are aggravated, both multi-shot and single-shot 2D spiral imaging at sub-millimeter resolution was demonstrated with high depiction quality and anatomical congruency. In this work, we further these advances towards a time series application of spiral readouts, namely, single-shot spiral BOLD fMRI at 0.8 mm in-plane resolution. We demonstrate that high-resolution spiral fMRI at 7 T is not only feasible, but delivers both excellent image quality, BOLD sensitivity, and spatial specificity of the activation maps, with little artifactual blurring. Furthermore, we show the versatility of the approach with a combined in/out spiral readout at a more typical resolution (1.5 mm), where the high acquisition efficiency allows to acquire two images per shot for improved sensitivity by echo combination.
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9
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Rischka L, Godbersen GM, Pichler V, Michenthaler P, Klug S, Klöbl M, Ritter V, Wadsak W, Hacker M, Kasper S, Lanzenberger R, Hahn A. Reliability of task-specific neuronal activation assessed with functional PET, ASL and BOLD imaging. J Cereb Blood Flow Metab 2021; 41:2986-2999. [PMID: 34078145 PMCID: PMC8545051 DOI: 10.1177/0271678x211020589] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mapping the neuronal response during cognitive processing is of crucial importance to gain new insights into human brain function. BOLD imaging and ASL are established MRI methods in this endeavor. Recently, the novel approach of functional PET (fPET) was introduced, enabling absolute quantification of glucose metabolism at rest and during task execution in a single measurement. Here, we report test-retest reliability of fPET in direct comparison to BOLD imaging and ASL. Twenty healthy subjects underwent two PET/MRI measurements, providing estimates of glucose metabolism, cerebral blood flow (CBF) and blood oxygenation. A cognitive task was employed with different levels of difficulty requiring visual-motor coordination. Task-specific neuronal activation was robustly detected with all three imaging approaches. The highest reliability was obtained for glucose metabolism at rest. Although this dropped during task performance it was still comparable to that of CBF. In contrast, BOLD imaging yielded high performance only for qualitative spatial overlap of task effects but not for quantitative comparison. Hence, the combined assessment of fPET and ASL offers reliable and simultaneous absolute quantification of glucose metabolism and CBF at rest and task.
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Affiliation(s)
- Lucas Rischka
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Godber M Godbersen
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Verena Pichler
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Vienna, Austria
| | - Paul Michenthaler
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Sebastian Klug
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Manfred Klöbl
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Vera Ritter
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Wadsak
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Vienna, Austria.,Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Marcus Hacker
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Vienna, Austria
| | - Siegfried Kasper
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Rupert Lanzenberger
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Andreas Hahn
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
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10
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Graedel NN, Kasper L, Engel M, Nussbaum J, Wilm BJ, Pruessmann KP, Vannesjo SJ. Feasibility of spiral fMRI based on an LTI gradient model. Neuroimage 2021; 245:118674. [PMID: 34718138 DOI: 10.1016/j.neuroimage.2021.118674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022] Open
Abstract
Spiral imaging is very well suited for functional MRI, however its use has been limited by the fact that artifacts caused by gradient imperfections and B0 inhomogeneity are more difficult to correct compared to EPI. Effective correction requires accurate knowledge of the traversed k-space trajectory. With the goal of making spiral fMRI more accessible, we have evaluated image reconstruction using trajectories predicted by the gradient impulse response function (GIRF), which can be determined in a one-time calibration step. GIRF-predicted reconstruction was tested for high-resolution (0.8 mm) fMRI at 7T. Image quality and functional results of the reconstructions using GIRF-prediction were compared to reconstructions using the nominal trajectory and concurrent field monitoring. The reconstructions using nominal spiral trajectories contain substantial artifacts and the activation maps contain misplaced activation. Image artifacts are substantially reduced when using the GIRF-predicted reconstruction, and the activation maps for the GIRF-predicted and monitored reconstructions largely overlap. The GIRF reconstruction provides a large increase in the spatial specificity of the activation compared to the nominal reconstruction. The GIRF-reconstruction generates image quality and fMRI results similar to using a concurrently monitored trajectory. The presented approach does not prolong or complicate the fMRI acquisition. Using GIRF-predicted trajectories has the potential to enable high-quality spiral fMRI in situations where concurrent trajectory monitoring is not available.
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Affiliation(s)
- Nadine N Graedel
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom; Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Lars Kasper
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland; Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Maria Engel
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Jennifer Nussbaum
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Bertram J Wilm
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Klaas P Pruessmann
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - S Johanna Vannesjo
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
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11
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Viessmann O, Polimeni JR. High-resolution fMRI at 7 Tesla: challenges, promises and recent developments for individual-focused fMRI studies. Curr Opin Behav Sci 2021; 40:96-104. [PMID: 33816717 DOI: 10.1016/j.cobeha.2021.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Limited detection power has been a bottleneck for subject-specific functional MRI (fMRI) studies, however the higher signal-to-noise ratio afforded by ultra-high magnetic fields (≥ 7 Tesla) provides levels of sensitivity and resolution needed to study individual subjects. What may be surprising is that higher imaging resolution may provide both higher specificity and sensitivity due to reductions in partial volume effects and reduced physiological noise. However, challenges remain to ensure high data quality and to reduce variability in ultra-high field fMRI. We discuss session-specific biases including those caused by factors related to instrumentation, anatomy, and physiology-which can translate into variability across sessions-and how to minimize these to help ultra-high field fMRI reach its full potential for individual-focused studies.
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Affiliation(s)
- Olivia Viessmann
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Radiology, Harvard Medical School, Boston, MA, USA.,Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
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12
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Wang Y, van Gelderen P, de Zwart JA, Campbell-Washburn AE, Duyn JH. FMRI based on transition-band balanced SSFP in comparison with EPI on a high-performance 0.55 T scanner. Magn Reson Med 2021; 85:3196-3210. [PMID: 33480108 DOI: 10.1002/mrm.28657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/23/2020] [Accepted: 12/05/2020] [Indexed: 02/03/2023]
Abstract
PURPOSE Low-field (<1 tesla) MRI scanners allow more widespread diagnostic use for a range of cardiac, musculoskeletal, and neurological applications. However, the feasibility of performing robust fMRI at low field has yet to be fully demonstrated. To address this gap, we investigated task-based fMRI using a highly sensitive transition-band balanced steady-state free precession approach and standard EPI on a 0.55 tesla scanner equipped with modern high-performance gradient coils and a receive array. METHODS TR and flip-angle of transition-band steady-state free precession were optimized for 0.55 tesla by simulations. Static shimming was employed to compensate for concomitant field effects. Visual task-based fMRI data were acquired from 8 healthy volunteers. For comparison, standard EPI data were also acquired with TE = T 2 ∗ . Retrospective image-based correction for physiological effects (RETROICOR) was used to quantify physiological noise effects. RESULTS Activation was robustly detected using both methods in a 4-min scan time. Transition-band steady-state free precession was found to be sensitive to interference from subtle spatial and temporal (field drift, respiration) variations in the magnetic field, counteracting potential advantages of the reduced magnetic susceptibility effects compared to its utilization at high field. These adverse effects could be partially remedied with static shimming and postprocessing approaches. Standard EPI proved more robust against the sources of interference. CONCLUSION BOLD contrast is sufficiently large at 0.55 tesla for robust detection of brain activation and may be employed to broaden the spectrum of applications of low-field MRI. Standard EPI outperforms transition-band steady-state free precession in terms of signal stability.
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Affiliation(s)
- Yicun Wang
- Advanced MRI Section, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter van Gelderen
- Advanced MRI Section, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Jacco A de Zwart
- Advanced MRI Section, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Adrienne E Campbell-Washburn
- Cardiovascular Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeff H Duyn
- Advanced MRI Section, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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13
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Kumar R, Tan L, Kriegstein A, Lithen A, Polimeni JR, Mujica-Parodi LR, Strey HH. Ground-truth "resting-state" signal provides data-driven estimation and correction for scanner distortion of fMRI time-series dynamics. Neuroimage 2020; 227:117584. [PMID: 33285328 DOI: 10.1016/j.neuroimage.2020.117584] [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: 07/14/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 10/22/2022] Open
Abstract
The fMRI community has made great strides in decoupling neuronal activity from other physiologically induced T2* changes, using sensors that provide a ground-truth with respect to cardiac, respiratory, and head movement dynamics. However, blood oxygenation level-dependent (BOLD) time-series dynamics are also confounded by scanner artifacts, in complex ways that can vary not only between scanners but even, for the same scanner, between sessions. Unfortunately, the lack of an equivalent ground truth for BOLD time-series has thus far stymied the development of reliable methods for identification and removal of scanner-induced noise, a problem that we have previously shown to severely impact detection sensitivity of resting-state brain networks. To address this problem, we first designed and built a phantom capable of providing dynamic signals equivalent to that of the resting-state brain. Using the dynamic phantom, we then compared the ground-truth time-series with its measured fMRI data. Using these, we introduce data-quality metrics: Standardized Signal-to-Noise Ratio (ST-SNR) and Dynamic Fidelity that, unlike currently used measures such as temporal SNR (tSNR), can be directly compared across scanners. Dynamic phantom data acquired from four "best-case" scenarios: high-performance scanners with MR-physicist-optimized acquisition protocols, still showed scanner instability/multiplicative noise contributions of about 6-18% of the total noise. We further measured strong non-linearity in the fMRI response for all scanners, ranging between 8-19% of total voxels. To correct scanner distortion of fMRI time-series dynamics at a single-subject level, we trained a convolutional neural network (CNN) on paired sets of measured vs. ground-truth data. The CNN learned the unique features of each session's noise, providing a customized temporal filter. Tests on dynamic phantom time-series showed a 4- to 7-fold increase in ST-SNR and about 40-70% increase in Dynamic Fidelity after denoising, with CNN denoising outperforming both the temporal bandpass filtering and denoising using Marchenko-Pastur principal component analysis. Critically, we observed that the CNN temporal denoising pushes ST-SNR to a regime where signal power is higher than that of noise (ST-SNR > 1). Denoising human-data with ground-truth-trained CNN, in turn, showed markedly increased detection sensitivity of resting-state networks. These were visible even at the level of the single-subject, as required for clinical applications of fMRI.
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Affiliation(s)
- Rajat Kumar
- Department of Biomedical Engineering, Stony Brook University, School of Medicine, Stony Brook, NY 11794-5281, USA
| | - Liang Tan
- ALA Scientific Instruments, Inc., Farmingdale, NY, USA
| | | | - Andrew Lithen
- Department of Biomedical Engineering, Stony Brook University, School of Medicine, Stony Brook, NY 11794-5281, USA
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical, School, Massachusetts General Hospital, Charlestown, MA, USA; Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Cambridge, MA, USA
| | - Lilianne R Mujica-Parodi
- Department of Biomedical Engineering, Stony Brook University, School of Medicine, Stony Brook, NY 11794-5281, USA; Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical, School, Massachusetts General Hospital, Charlestown, MA, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.
| | - Helmut H Strey
- Department of Biomedical Engineering, Stony Brook University, School of Medicine, Stony Brook, NY 11794-5281, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.
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14
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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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15
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Wallace TE, Polimeni JR, Stockmann JP, Hoge WS, Kober T, Warfield SK, Afacan O. Dynamic distortion correction for functional MRI using FID navigators. Magn Reson Med 2020; 85:1294-1307. [PMID: 32970869 DOI: 10.1002/mrm.28505] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/06/2020] [Accepted: 08/14/2020] [Indexed: 11/08/2022]
Abstract
PURPOSE To develop a method for slice-wise dynamic distortion correction for EPI using rapid spatiotemporal B0 field measurements from FID navigators (FIDnavs) and to evaluate the efficacy of this new approach relative to an established data-driven technique. METHODS A low-resolution reference image was used to create a forward model of FIDnav signal changes to enable estimation of spatiotemporal B0 inhomogeneity variations up to second order from measured FIDnavs. Five volunteers were scanned at 3 T using a 64-channel coil with FID-navigated EPI. The accuracy of voxel shift measurements and geometric distortion correction was assessed for experimentally induced magnetic field perturbations. The temporal SNR was evaluated in EPI time-series acquired at rest and with a continuous nose-touching action, before and after image realignment. RESULTS Field inhomogeneity coefficients and voxel shift maps measured using FIDnavs were in excellent agreement with multi-echo EPI measurements. The FID-navigated distortion correction accurately corrected image geometry in the presence of induced magnetic field perturbations, outperforming the data-driven approach in regions with large field offsets. In functional MRI scans with nose touching, FIDnav-based correction yielded temporal SNR gains of 30% in gray matter. Following image realignment, which accounted for global image shifts, temporal SNR gains of 3% were achieved. CONCLUSIONS Our proposed application of FIDnavs enables slice-wise dynamic distortion correction with high temporal efficiency. We achieved improved signal stability by leveraging the encoding information from multichannel coils. This approach can be easily adapted to other EPI-based sequences to improve temporal SNR for a variety of clinical and research applications.
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Affiliation(s)
- Tess E Wallace
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan R Polimeni
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jason P Stockmann
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - W Scott Hoge
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Tobias Kober
- Advanced Clinical Imaging Technology, Siemens Healthcare AG, Lausanne, Switzerland.,Department of Radiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.,LTS5, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Simon K Warfield
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Onur Afacan
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
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16
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Shrestha M, Lee HS, Nöth U, Deichmann R. A novel sequence to improve auditory functional MRI with variable silent delays. Magn Reson Med 2020; 85:883-896. [PMID: 32886374 DOI: 10.1002/mrm.28479] [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: 05/06/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022]
Abstract
PURPOSE Auditory functional MRI (fMRI) often uses silent inter-volume delays for stimulus presentation. However, maintaining the steady-state of the magnetization usually requires constant delays. Here, a novel acquisition scheme dubbed "pre-Saturated EPI using Multiple delays in Steady-state" (SEPIMS) is proposed, using spin saturation at a fixed delay before each volume to maintain steady-state conditions, independent of previous spin history. This concept allows for variable inter-volume delays and thus for flexible stimulus design in auditory fMRI. The purpose was to compare the signal stability of SEPIMS and conventional sparse EPI (CS-EPI). METHODS The saturation module comprises two non-selective adiabatic saturation pulses. The efficiency of the saturation and its effect on the SEPIMS signal stability is tested in vitro and in vivo. RESULTS Data show that SEPIMS yields the same signal stability as CS-EPI, even for extreme variations between inter-volume delay durations. However, dual saturation pulses are required to achieve sufficiently high saturation efficiency in compartments with long T1 values. Importantly, spoiler gradient pulses after the EPI readout have to be optimized to avoid eddy-current-induced image distortions. CONCLUSION The proposed SEPIMS sequence maintains high signal stability in the presence of variable inter-volume durations, thus allowing for flexible stimulus design.
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Affiliation(s)
- Manoj Shrestha
- Brain Imaging Center (BIC), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - H Sean Lee
- Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany
| | - Ulrike Nöth
- Brain Imaging Center (BIC), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ralf Deichmann
- Brain Imaging Center (BIC), Goethe University Frankfurt, Frankfurt am Main, Germany
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17
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Prando G, Zorzi M, Bertoldo A, Corbetta M, Zorzi M, Chiuso A. Sparse DCM for whole-brain effective connectivity from resting-state fMRI data. Neuroimage 2020; 208:116367. [DOI: 10.1016/j.neuroimage.2019.116367] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022] Open
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18
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Wilm BJ, Dietrich BE, Reber J, Vannesjo SJ, Pruessmann KP. Gradient Response Harvesting for Continuous System Characterization During MR Sequences. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:806-815. [PMID: 31425067 DOI: 10.1109/tmi.2019.2936107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
MRI gradient systems are required to generate magnetic field gradient waveforms with very high fidelity. This is commonly implemented by gradient system calibration and pre-emphasis. However, a number of mechanisms, particularly thermal changes, cause variation in the gradient response over time, which cannot be addressed by calibration approaches. To overcome this limitation, we present a novel method termed gradient response harvesting, where the gradient response is continuously characterized during the course of a normal MR sequence. Snippets of field measurements are repeatedly acquired during an MR sequence, and from these multiple field measurements and the known nominal MR sequence gradients, the gradient response and gradient/field offsets are calculated. The calculation is implemented in a model-based and a model-free variant. The method is demonstrated for EPI with high gradient duty-cycle, where the continuous gradient characterization is used to obtain k-space trajectory estimates that are employed in the subsequent image reconstruction. During the course of the MR sequence, changes in both the envelope and the phase of the gradient response functions were observed, including shifts of mechanical resonances. The gradient response changes were also reflected in the calculated uninterrupted gradient waveforms and thus in the k-space trajectories. Using the updated encoding information in the image reconstruction removed ghosting artifacts, that otherwise impaired the image quality. We introduced the concept of gradient response harvesting and demonstrated its feasibility. The obtained gradient response functions may be used for quality assurance/preventive maintenance, real-time adaptation of gradient pre-emphasis or to calculate uninterrupted gradient field evolutions.
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19
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Characteristics of respiratory measures in young adults scanned at rest, including systematic changes and "missed" deep breaths. Neuroimage 2019; 204:116234. [PMID: 31589990 DOI: 10.1016/j.neuroimage.2019.116234] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/04/2019] [Accepted: 09/27/2019] [Indexed: 11/20/2022] Open
Abstract
Breathing rate and depth influence the concentration of carbon dioxide in the blood, altering cerebral blood flow and thus functional magnetic resonance imaging (fMRI) signals. Such respiratory fluctuations can have substantial influence in studies of fMRI signal covariance in subjects at rest, the so-called "resting state functional connectivity" technique. If respiration is monitored during fMRI scanning, it is typically done using a belt about the subject's abdomen to record abdominal circumference. Several measures have been derived from these belt records, including the windowed envelope of the waveform (ENV), the windowed variance in the waveform (respiration variation, RV), and a measure of the amplitude of each breath divided by the cycle time of the breath (respiration volume per time, RVT). Any attempt to gauge respiratory contributions to fMRI signals requires a respiratory measure, but little is known about how these measures compare to each other, or how they perform beyond the small studies in which they were initially proposed. Here, we examine the properties of these measures in hundreds of healthy young adults scanned for an hour each at rest, a subset of the Human Connectome Project chosen for having high-quality physiological records. We find: 1) ENV, RV, and RVT are all correlated, and ENV and RV are more highly correlated to each other than to RVT; 2) respiratory events like deep breaths exhibit characteristic heart rate elevations, fMRI signal changes, head motions, and image quality abnormalities time-locked to large deflections in the belt traces; 3) all measures can "miss" deep breaths; 4) RVT "misses" deep breaths more than ENV or RV; 5) all respiratory measures change systematically over the course of a 14.4-min scan. We discuss the implications of these findings for the literature and ways to move forward in modeling respiratory influences on fMRI scans.
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20
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Kassinopoulos M, Mitsis GD. Identification of physiological response functions to correct for fluctuations in resting-state fMRI related to heart rate and respiration. Neuroimage 2019; 202:116150. [PMID: 31487547 DOI: 10.1016/j.neuroimage.2019.116150] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/30/2019] [Accepted: 08/30/2019] [Indexed: 12/31/2022] Open
Abstract
Functional magnetic resonance imaging (fMRI) is widely viewed as the gold standard for studying brain function due to its high spatial resolution and non-invasive nature. However, it is well established that changes in breathing patterns and heart rate strongly influence the blood oxygen-level dependent (BOLD) fMRI signal and this, in turn, can have considerable effects on fMRI studies, particularly resting-state studies. The dynamic effects of physiological processes are often quantified by using convolution models along with simultaneously recorded physiological data. In this context, physiological response function (PRF) curves (cardiac and respiratory response functions), which are convolved with the corresponding physiological fluctuations, are commonly employed. While it has often been suggested that the PRF curves may be region- or subject-specific, it is still an open question whether this is the case. In the present study, we propose a novel framework for the robust estimation of PRF curves and use this framework to rigorously examine the implications of using population-, subject-, session- and scan-specific PRF curves. The proposed framework was tested on resting-state fMRI and physiological data from the Human Connectome Project. Our results suggest that PRF curves vary significantly across subjects and, to a lesser extent, across sessions from the same subject. These differences can be partly attributed to physiological variables such as the mean and variance of the heart rate during the scan. The proposed methodological framework can be used to obtain robust scan-specific PRF curves from data records with duration longer than 5 min, exhibiting significantly improved performance compared to previously defined canonical cardiac and respiration response functions. Besides removing physiological confounds from the BOLD signal, accurate modeling of subject- (or session-/scan-) specific PRF curves is of importance in studies that involve populations with altered vascular responses, such as aging subjects.
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Affiliation(s)
- Michalis Kassinopoulos
- Graduate Program in Biological and Biomedical Engineering, McGill University, Montreal, QC, Canada
| | - Georgios D Mitsis
- Department of Bioengineering, McGill University, Montreal, QC, Canada.
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21
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Gross-Weege N, Nolte T, Schulz V. MR image corrections for PET-induced gradient distortions. ACTA ACUST UNITED AC 2019; 64:02NT03. [DOI: 10.1088/1361-6560/aaf97a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Grisi M, Conley GM, Sommer P, Tinembart J, Boero G. A single-chip integrated transceiver for high field NMR magnetometry. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:015001. [PMID: 30709227 DOI: 10.1063/1.5066436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/13/2018] [Indexed: 06/09/2023]
Abstract
We present the design and performance of a broad-band single-chip integrated transceiver specifically conceived for nuclear magnetic resonance magnetometry. The single-chip transceiver is realized using a standard silicon complementary metal-oxide-semiconductor integrated circuit technology. A radio-frequency (RF) transmit amplifier, a transmit/receive switch, a low noise RF receive amplifier, a quadrature (IQ)-mixer, and two intermediate frequency amplifiers are integrated on a single silicon chip of 1.8 mm2. The advantages and problematic aspects with respect to conventional discrete electronic approaches are discussed. We show the results of magnetic field measurements performed at 1.4 and 7.05 T, using solid and liquid samples having volumes from 40 μl down to 100 pl. Particular attention is devoted to the comparison of the experimentally measured magnetic field standard deviation with respect to the Cramer-Rao lower bound value. With a sample of distilled water (T1 ≅ T2 ≅ 3 s, T2 *≅ 20 ms) having a volume of 40 μl, a standard deviation of 2.5 nT at 7.05 T (i.e., 0.5 ppb) in 1 s of averaging time is achieved, with a projected Cramer-Rao lower bond of 8 pT (i.e., 1.1 ppt).
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Affiliation(s)
- Marco Grisi
- École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Pascal Sommer
- Metrolab Technology SA, CH-1228 Plan-les-Ouates, Switzerland
| | | | - Giovanni Boero
- École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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23
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Frässle S, Lomakina EI, Kasper L, Manjaly ZM, Leff A, Pruessmann KP, Buhmann JM, Stephan KE. A generative model of whole-brain effective connectivity. Neuroimage 2018; 179:505-529. [DOI: 10.1016/j.neuroimage.2018.05.058] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/16/2018] [Accepted: 05/24/2018] [Indexed: 12/17/2022] Open
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24
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Pinsard B, Boutin A, Doyon J, Benali H. Integrated fMRI Preprocessing Framework Using Extended Kalman Filter for Estimation of Slice-Wise Motion. Front Neurosci 2018; 12:268. [PMID: 29755312 PMCID: PMC5932184 DOI: 10.3389/fnins.2018.00268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/06/2018] [Indexed: 11/13/2022] Open
Abstract
Functional MRI acquisition is sensitive to subjects' motion that cannot be fully constrained. Therefore, signal corrections have to be applied a posteriori in order to mitigate the complex interactions between changing tissue localization and magnetic fields, gradients and readouts. To circumvent current preprocessing strategies limitations, we developed an integrated method that correct motion and spatial low-frequency intensity fluctuations at the level of each slice in order to better fit the acquisition processes. The registration of single or multiple simultaneously acquired slices is achieved online by an Iterated Extended Kalman Filter, favoring the robust estimation of continuous motion, while an intensity bias field is non-parametrically fitted. The proposed extraction of gray-matter BOLD activity from the acquisition space to an anatomical group template space, taking into account distortions, better preserves fine-scale patterns of activity. Importantly, the proposed unified framework generalizes to high-resolution multi-slice techniques. When tested on simulated and real data the latter shows a reduction of motion explained variance and signal variability when compared to the conventional preprocessing approach. These improvements provide more stable patterns of activity, facilitating investigation of cerebral information representation in healthy and/or clinical populations where motion is known to impact fine-scale data.
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Affiliation(s)
- Basile Pinsard
- Unité de Neuroimagerie Fonctionelle, Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montreal, QC, Canada.,UMR7371 Laboratoire d'Imagerie Biomédicale, Paris, France.,Sorbonne Universités, Paris, France
| | - Arnaud Boutin
- Unité de Neuroimagerie Fonctionelle, Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montreal, QC, Canada.,Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Julien Doyon
- Unité de Neuroimagerie Fonctionelle, Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montreal, QC, Canada.,Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Habib Benali
- UMR7371 Laboratoire d'Imagerie Biomédicale, Paris, France.,Sorbonne Universités, Paris, France.,PERFORM Center, Concordia University, Montreal, QC, Canada
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25
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Engel M, Kasper L, Barmet C, Schmid T, Vionnet L, Wilm B, Pruessmann KP. Single‐shot spiral imaging at 7
T. Magn Reson Med 2018; 80:1836-1846. [DOI: 10.1002/mrm.27176] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/15/2018] [Accepted: 02/18/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Maria Engel
- Institute for Biomedical EngineeringETH Zurich and University of ZurichZurich Switzerland
| | - Lars Kasper
- Institute for Biomedical EngineeringETH Zurich and University of ZurichZurich Switzerland
- Translational Neuromodeling Unit, Institute for Biomedical EngineeringUniversity of Zurich and ETH ZurichZurich Switzerland
| | - Christoph Barmet
- Institute for Biomedical EngineeringETH Zurich and University of ZurichZurich Switzerland
- Skope Magnetic Resonance Technologies AGZurich Switzerland
| | - Thomas Schmid
- Institute for Biomedical EngineeringETH Zurich and University of ZurichZurich Switzerland
| | - Laetitia Vionnet
- Institute for Biomedical EngineeringETH Zurich and University of ZurichZurich Switzerland
| | - Bertram Wilm
- Institute for Biomedical EngineeringETH Zurich and University of ZurichZurich Switzerland
- Skope Magnetic Resonance Technologies AGZurich Switzerland
| | - Klaas P. Pruessmann
- Institute for Biomedical EngineeringETH Zurich and University of ZurichZurich Switzerland
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26
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Serial correlations in single-subject fMRI with sub-second TR. Neuroimage 2017; 166:152-166. [PMID: 29066396 DOI: 10.1016/j.neuroimage.2017.10.043] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/16/2017] [Accepted: 10/20/2017] [Indexed: 01/29/2023] Open
Abstract
When performing statistical analysis of single-subject fMRI data, serial correlations need to be taken into account to allow for valid inference. Otherwise, the variability in the parameter estimates might be under-estimated resulting in increased false-positive rates. Serial correlations in fMRI data are commonly characterized in terms of a first-order autoregressive (AR) process and then removed via pre-whitening. The required noise model for the pre-whitening depends on a number of parameters, particularly the repetition time (TR). Here we investigate how the sub-second temporal resolution provided by simultaneous multislice (SMS) imaging changes the noise structure in fMRI time series. We fit a higher-order AR model and then estimate the optimal AR model order for a sequence with a TR of less than 600 ms providing whole brain coverage. We show that physiological noise modelling successfully reduces the required AR model order, but remaining serial correlations necessitate an advanced noise model. We conclude that commonly used noise models, such as the AR(1) model, are inadequate for modelling serial correlations in fMRI using sub-second TRs. Rather, physiological noise modelling in combination with advanced pre-whitening schemes enable valid inference in single-subject analysis using fast fMRI sequences.
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27
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Bright MG, Murphy K. Cleaning up the fMRI time series: Mitigating noise with advanced acquisition and correction strategies. Neuroimage 2017; 154:1-3. [PMID: 28365420 DOI: 10.1016/j.neuroimage.2017.03.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Molly G Bright
- Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom; Division of Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Kevin Murphy
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom; CUBRIC, School of Physics and Astronomy, Cardiff University, Cardiff, United Kingdom
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28
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Özbay PS, Duerst Y, Wilm BJ, Pruessmann KP, Nanz D. Enhanced quantitative susceptibility mapping (QSM) using real-time field control. Magn Reson Med 2017; 79:770-778. [DOI: 10.1002/mrm.26735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/31/2017] [Accepted: 04/02/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Pinar Senay Özbay
- University Hospital Zurich and University of Zurich, Institute of Diagnostic and Interventional Radiology; Zurich Switzerland
- ETH Zurich and University of Zurich, Institute for Biomedical Engineering; Zurich Switzerland
| | - Yolanda Duerst
- ETH Zurich and University of Zurich, Institute for Biomedical Engineering; Zurich Switzerland
| | - Bertram Jakob Wilm
- ETH Zurich and University of Zurich, Institute for Biomedical Engineering; Zurich Switzerland
| | - Klaas Paul Pruessmann
- ETH Zurich and University of Zurich, Institute for Biomedical Engineering; Zurich Switzerland
| | - Daniel Nanz
- University Hospital Zurich and University of Zurich, Institute of Diagnostic and Interventional Radiology; Zurich Switzerland
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