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Iyyappan Valsala P, Veldmann M, Bosch D, Scheffler K, Ehses P. Submillimeter balanced SSFP BOLD-functional MRI accelerated with 3D stack-of-spirals at 9.4 T. Magn Reson Med 2024; 92:186-201. [PMID: 38440956 DOI: 10.1002/mrm.30064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/06/2024]
Abstract
PURPOSE This work aims to improve the speed of balanced SSFP (bSSFP) acquisition with segmented 3D stack-of-spirals for functional brain studies at ultrahigh field. METHODS Functional experiments were performed with an accelerated 3D stack-of-spirals sequence with water excitation for fat suppression. The resulting data were reconstructed using an iterative algorithm with corrections for system imperfections such as trajectory deviations and B0 inhomogeneity. In the first set of experiments, we evaluated the signal change and stability with respect to echo and TR for a full-field checkerboard stimulus. To demonstrate the high spatio-temporal resolution of the developed method, the results of three optimized protocols at submillimeter resolution (0.6-mm isotropic and 0.8-mm isotropic) and at 1.2 mm isotropic resolution for whole-brain coverage were shown. RESULTS Water excitation and the model-based iterative reconstruction improved image quality. The BOLD-related signal changes increased with longer TE and longer TR. We observed an increase in thermal noise performance at lower TE and higher TR. However, signal stability deteriorates at higher TE and TR. Therefore, optimized protocols used shorter TE and moderately long TR to maximize the sensitivity and speed. Reproducible activations were detected along the gray-matter gyri in the submillimeter protocols with a median signal change of approximately 4% across subjects. CONCLUSIONS Three-dimensional stack-of-spirals enables passband balanced SSFP functional imaging at a much higher spatial and temporal scale, compared with conventional spoiled gradient-echo train sequences.
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Affiliation(s)
| | - Marten Veldmann
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Dario Bosch
- Magnetic Resonance Center, Max-Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Klaus Scheffler
- Magnetic Resonance Center, Max-Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Aghaeifar A, Bosch D, Heule R, Williams S, Ehses P, Mauconduit F, Scheffler K. Intra-scan RF power amplifier drift correction. Magn Reson Med 2024. [PMID: 38469935 DOI: 10.1002/mrm.30078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/18/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024]
Abstract
PURPOSE The drift in radiofrequency (RF) power amplifiers (RFPAs) is assessed and several contributing factors are investigated. Two approaches for prospective correction of drift are proposed and their effectiveness is evaluated. METHODS RFPA drift assessment encompasses both intra-pulse and inter-pulse drift analyses. Scan protocols with varying flip angle (FA), RF length, and pulse repetition time (TR) are used to gauge the influence of these parameters on drift. Directional couplers (DICOs) monitor the forward waveforms of the RFPA outputs. DICOs data is stored for evaluation, allowing calculation of correction factors to adjust RFPAs' transmit voltage. Two correction methods, predictive and run-time, are employed: predictive correction necessitates a calibration scan, while run-time correction calculates factors during the ongoing scan. RESULTS RFPA drift is indeed influenced by the RF duty-cycle, and in the cases examined with a maximum duty-cycle of 66%, the potential drift is approximately 41% or 15%, depending on the specific RFPA revision. Notably, in low transmit voltage scenarios, FA has minimal impact on RFPA drift. The application of predictive and run-time drift correction techniques effectively reduces the average drift from 10.0% to less than 1%, resulting in enhanced MR signal stability. CONCLUSION Utilizing DICO recordings and implementing a feedback mechanism enable the prospective correction of RFPA drift. Having a calibration scan, predictive correction can be utilized with fewer complexity; for enhanced performance, a run-time approach can be employed.
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Affiliation(s)
- Ali Aghaeifar
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany
| | - Dario Bosch
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany
- Department of Biomedical Magnetic Resonance, University of Tuebingen, Tuebingen, Germany
| | - Rahel Heule
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany
- Department of Biomedical Magnetic Resonance, University of Tuebingen, Tuebingen, Germany
- Center for MR Research, University Children's Hospital, Zurich, Switzerland
| | - Sydney Williams
- Imaging Centre of Excellence, University of Glasgow, Glasgow, UK
| | - Philipp Ehses
- MR Physics, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Klaus Scheffler
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany
- Department of Biomedical Magnetic Resonance, University of Tuebingen, Tuebingen, Germany
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Chandrasekaran J, Petit E, Park YW, Tezenas du Montcel S, Joers JM, Deelchand DK, Považan M, Banan G, Valabregue R, Ehses P, Faber J, Coupé P, Onyike CU, Barker PB, Schmahmann JD, Ratai EM, Subramony SH, Mareci TH, Bushara KO, Paulson H, Durr A, Klockgether T, Ashizawa T, Lenglet C, Öz G. Clinically Meaningful Magnetic Resonance Endpoints Sensitive to Preataxic Spinocerebellar Ataxia Types 1 and 3. Ann Neurol 2023; 93:686-701. [PMID: 36511514 PMCID: PMC10261544 DOI: 10.1002/ana.26573] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/18/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVE This study was undertaken to identify magnetic resonance (MR) metrics that are most sensitive to early changes in the brain in spinocerebellar ataxia type 1 (SCA1) and type 3 (SCA3) using an advanced multimodal MR imaging (MRI) protocol in the multisite trial setting. METHODS SCA1 or SCA3 mutation carriers and controls (n = 107) underwent MR scanning in the US-European READISCA study to obtain structural, diffusion MRI, and MR spectroscopy data using an advanced protocol at 3T. Morphometric, microstructural, and neurochemical metrics were analyzed blinded to diagnosis and compared between preataxic SCA (n = 11 SCA1, n = 28 SCA3), ataxic SCA (n = 14 SCA1, n = 37 SCA3), and control (n = 17) groups using nonparametric testing accounting for multiple comparisons. MR metrics that were most sensitive to preataxic abnormalities were identified using receiver operating characteristic (ROC) analyses. RESULTS Atrophy and microstructural damage in the brainstem and cerebellar peduncles and neurochemical abnormalities in the pons were prominent in both preataxic groups, when patients did not differ from controls clinically. MR metrics were strongly associated with ataxia symptoms, activities of daily living, and estimated ataxia duration. A neurochemical measure was the most sensitive metric to preataxic changes in SCA1 (ROC area under the curve [AUC] = 0.95), and a microstructural metric was the most sensitive metric to preataxic changes in SCA3 (AUC = 0.92). INTERPRETATION Changes in cerebellar afferent and efferent pathways underlie the earliest symptoms of both SCAs. MR metrics collected with a harmonized advanced protocol in the multisite trial setting allow detection of disease effects in individuals before ataxia onset with potential clinical trial utility for subject stratification. ANN NEUROL 2023;93:686-701.
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Affiliation(s)
- Jayashree Chandrasekaran
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Emilien Petit
- Sorbonne Université, Paris Brain Institute, Inserm, INRIA, CNRS, APHP, 75013 Paris, France
| | - Young-Woo Park
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - James M. Joers
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dinesh K. Deelchand
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michal Považan
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Guita Banan
- Norman Fixel Center for Neurological Disorders, College of Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Romain Valabregue
- Sorbonne Université, Paris Brain Institute, Inserm, INRIA, CNRS, APHP, 75013 Paris, France
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Jennifer Faber
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
- Department of Neurology, University Hospital Bonn, 53127 Bonn, Germany
| | - Pierrick Coupé
- Laboratoire Bordelais de Recherche en Informatique, Université de Bordeaux, 33405 France
| | - Chiadi U. Onyike
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Peter B. Barker
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeremy D. Schmahmann
- Ataxia Center, Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Eva-Maria Ratai
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA 02114, USA
| | - S. H. Subramony
- Norman Fixel Center for Neurological Disorders, College of Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Thomas H. Mareci
- Norman Fixel Center for Neurological Disorders, College of Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Khalaf O. Bushara
- Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Henry Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute, Inserm, INRIA, CNRS, APHP, 75013 Paris, France
| | - Thomas Klockgether
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
- Department of Neurology, University Hospital Bonn, 53127 Bonn, Germany
| | - Tetsuo Ashizawa
- The Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Christophe Lenglet
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gülin Öz
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, USA
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Veldmann M, Ehses P, Chow K, Nielsen JF, Zaitsev M, Stöcker T. Open-source MR imaging and reconstruction workflow. Magn Reson Med 2022; 88:2395-2407. [PMID: 35968675 PMCID: PMC10054460 DOI: 10.1002/mrm.29384] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/25/2022] [Accepted: 06/21/2022] [Indexed: 11/06/2022]
Abstract
PURPOSE This work presents an end-to-end open-source MR imaging workflow. It is highly flexible in rapid prototyping across the whole imaging process and integrates vendor-independent openly available tools. The whole workflow can be shared and executed on different MR platforms. It is also integrated in the JEMRIS simulation framework, which makes it possible to generate simulated data from the same sequence that runs on the MRI scanner using the same pipeline for image reconstruction. METHODS MRI sequences can be designed in Python or JEMRIS using the Pulseq framework, allowing simplified integration of new sequence design tools. During the sequence design process, acquisition metadata required for reconstruction is stored in the MR raw data format. Data acquisition is possible on MRI scanners supported by Pulseq and in simulations through JEMRIS. An image reconstruction and postprocessing pipeline was implemented into a Python server that allows real-time processing of data as it is being acquired. The Berkeley Advanced Reconstruction Toolbox is integrated into this framework for image reconstruction. The reconstruction pipeline supports online integration through a vendor-dependent interface. RESULTS The flexibility of the workflow is demonstrated with different examples, containing 3D parallel imaging with controlled aliasing in volumetric parallel imaging (CAIPIRINHA) acceleration, spiral imaging, and B0 mapping. All sequences, data, and the corresponding processing pipelines are publicly available. CONCLUSION The proposed workflow is highly flexible and allows integration of advanced tools at all stages of the imaging process. All parts of this workflow are open-source, simplifying collaboration across different MR platforms or sites and improving reproducibility of results.
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Affiliation(s)
- Marten Veldmann
- MR Physics, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Philipp Ehses
- MR Physics, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Kelvin Chow
- MR R&D Collaborations, Siemens Medical Solutions USA Inc, Chicago, Illinois
| | - Jon-Fredrik Nielsen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Maxim Zaitsev
- Division of Medical Physics, Department of Radiology, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Tony Stöcker
- MR Physics, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Physics & Astronomy, University of Bonn, Bonn, Germany
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Wang D, Ehses P, Stöcker T, Stirnberg R. Reproducibility of rapid multi-parameter mapping at 3T and 7T with highly segmented and accelerated 3D-EPI. Magn Reson Med 2022; 88:2217-2232. [PMID: 35877781 DOI: 10.1002/mrm.29383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 11/11/2022]
Abstract
PURPOSE Quantitative multi-parameter mapping (MPM) has been shown to provide good longitudinal and cross-sectional reproducibility for clinical research. Unfortunately, acquisition times (TAs) are typically infeasible for routine scanning at high resolutions. METHODS A fast whole-brain MPM protocol based on interleaved multi-shot 3D-EPI with controlled aliasing (SC-EPI) at 3T and 7T is proposed and compared with MPM using a standard spoiled gradient echo (FLASH) sequence. Four parameters (R1 , PD, R 2 * $$ {R}_2^{\ast } $$ , and MTsat) were measured in less than 3 min at 1 mm isotropic resolution. Five subjects went through the same scanning sessions twice at each scanner. The intra-subject coefficient of variation (scan-rescan) (CoV) was estimated for each protocol and scanner to assess the longitudinal reproducibility. RESULTS At 3T, the CoV of SC-EPI ranged between 1.2%-4.8% for PD and R1 , 2.8%-10.6% for R 2 * $$ {R}_2^{\ast } $$ and MTsat, which was comparable with FLASH (0.6%-4.9% for PD and R1 , 2.6%-11.3% for R 2 * $$ {R}_2^{\ast } $$ and MTsat). At 7T, where the SC-EPI TA was reduced to ∼2 min, the CoV of SC-EPI (1.4%-10.6% for PD, R1 , and R 2 * $$ {R}_2^{\ast } $$ ) was 1.2-2.4 times larger than the CoV of FLASH (1.0%-15%) and MTsat showed much higher variability across subjects. The SC-EPI-MPM protocol at 3T showed high reproducibility and yielded stable quantitative maps at a clinically feasible resolution and scan time, whereas at 7T, MT saturation homogeneity needs to be improved. CONCLUSION SC-EPI-based MPM is feasible as an additional MRI modality in clinical or population studies where the parameters offer great potential as biomarkers.
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Affiliation(s)
- Difei Wang
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Tony Stöcker
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Physics and Astronomy, University of Bonn, Bonn, Germany
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Birk F, Glang F, Loktyushin A, Birkl C, Ehses P, Scheffler K, Heule R. High-resolution neural network-driven mapping of multiple diffusion metrics leveraging asymmetries in the balanced steady-state free precession frequency profile. NMR Biomed 2022; 35:e4669. [PMID: 34964998 DOI: 10.1002/nbm.4669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
We propose to utilize the rich information content about microstructural tissue properties entangled in asymmetric balanced steady-state free precession (bSSFP) profiles to estimate multiple diffusion metrics simultaneously by neural network (NN) parameter quantification. A 12-point bSSFP phase-cycling scheme with high-resolution whole-brain coverage is employed at 3 and 9.4 T for NN input. Low-resolution target diffusion data are derived based on diffusion-weighted spin-echo echo-planar-imaging (SE-EPI) scans, that is, mean, axial, and radial diffusivity (MD, AD, and RD), fractional anisotropy (FA), as well as the spherical coordinates (azimuth Φ and inclination ϴ) of the principal diffusion eigenvector. A feedforward NN is trained with incorporated probabilistic uncertainty estimation. The NN predictions yielded highly reliable results in white matter (WM) and gray matter structures for MD. The quantification of FA, AD, and RD was overall in good agreement with the reference but the dependence of these parameters on WM anisotropy was somewhat biased (e.g. in corpus callosum). The inclination ϴ was well predicted for anisotropic WM structures, while the azimuth Φ was overall poorly predicted. The findings were highly consistent across both field strengths. Application of the optimized NN to high-resolution input data provided whole-brain maps with rich structural details. In conclusion, the proposed NN-driven approach showed potential to provide distortion-free high-resolution whole-brain maps of multiple diffusion metrics at high to ultrahigh field strengths in clinically relevant scan times.
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Affiliation(s)
- Florian Birk
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Felix Glang
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Alexander Loktyushin
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Empirical Inference, Max Planck Institute for Intelligent Systems, Tübingen, Germany
| | - Christoph Birkl
- Department of Neuroradiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Klaus Scheffler
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany
| | - Rahel Heule
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany
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8
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Vaculčiaková L, Podranski K, Edwards LJ, Ocal D, Veale T, Fox NC, Haak R, Ehses P, Callaghan MF, Pine KJ, Weiskopf N. Combining navigator and optical prospective motion correction for high-quality 500 μm resolution quantitative multi-parameter mapping at 7T. Magn Reson Med 2022; 88:787-801. [PMID: 35405027 DOI: 10.1002/mrm.29253] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 12/15/2022]
Abstract
PURPOSE High-resolution quantitative multi-parameter mapping shows promise for non-invasively characterizing human brain microstructure but is limited by physiological artifacts. We implemented corrections for rigid head movement and respiration-related B0-fluctuations and evaluated them in healthy volunteers and dementia patients. METHODS Camera-based optical prospective motion correction (PMC) and FID navigator correction were implemented in a gradient and RF-spoiled multi-echo 3D gradient echo sequence for mapping proton density (PD), longitudinal relaxation rate (R1) and effective transverse relaxation rate (R2*). We studied their effectiveness separately and in concert in young volunteers and then evaluated the navigator correction (NAVcor) with PMC in a group of elderly volunteers and dementia patients. We used spatial homogeneity within white matter (WM) and gray matter (GM) and scan-rescan measures as quality metrics. RESULTS NAVcor and PMC reduced artifacts and improved the homogeneity and reproducibility of parameter maps. In elderly participants, NAVcor improved scan-rescan reproducibility of parameter maps (coefficient of variation decreased by 14.7% and 11.9% within WM and GM respectively). Spurious inhomogeneities within WM were reduced more in the elderly than in the young cohort (by 9% vs. 2%). PMC increased regional GM/WM contrast and was especially important in the elderly cohort, which moved twice as much as the young cohort. We did not find a significant interaction between the two corrections. CONCLUSION Navigator correction and PMC significantly improved the quality of PD, R1, and R2* maps, particularly in less compliant elderly volunteers and dementia patients.
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Affiliation(s)
- Lenka Vaculčiaková
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Kornelius Podranski
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Luke J Edwards
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Dilek Ocal
- The Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Thomas Veale
- The Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.,UK Dementia Research Institute at UCL, UCL, London, UK
| | - Nick C Fox
- The Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.,UK Dementia Research Institute at UCL, UCL, London, UK
| | - Rainer Haak
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Philipp Ehses
- Department of MR Physics, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Martina F Callaghan
- The Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Kerrin J Pine
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Nikolaus Weiskopf
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.,The Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, University College London, London, UK.,Felix Bloch Institute for Solid State Physics, Faculty of Physics and Earth Sciences, Leipzig University, Leipzig, Germany
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9
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Estrada S, Lu R, Diers K, Zeng W, Ehses P, Stöcker T, Breteler MMB, Reuter M. Automated olfactory bulb segmentation on high resolutional T2-weighted MRI. Neuroimage 2021; 242:118464. [PMID: 34389442 PMCID: PMC8473894 DOI: 10.1016/j.neuroimage.2021.118464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/09/2021] [Accepted: 08/09/2021] [Indexed: 11/09/2022] Open
Abstract
The neuroimage analysis community has neglected the automated segmentation of the olfactory bulb (OB) despite its crucial role in olfactory function. The lack of an automatic processing method for the OB can be explained by its challenging properties (small size, location, and poor visibility on traditional MRI scans). Nonetheless, recent advances in MRI acquisition techniques and resolution have allowed raters to generate more reliable manual annotations. Furthermore, the high accuracy of deep learning methods for solving semantic segmentation problems provides us with an option to reliably assess even small structures. In this work, we introduce a novel, fast, and fully automated deep learning pipeline to accurately segment OB tissue on sub-millimeter T2-weighted (T2w) whole-brain MR images. To this end, we designed a three-stage pipeline: (1) Localization of a region containing both OBs using FastSurferCNN, (2) Segmentation of OB tissue within the localized region through four independent AttFastSurferCNN - a novel deep learning architecture with a self-attention mechanism to improve modeling of contextual information, and (3) Ensemble of the predicted label maps. For this work, both OBs were manually annotated in a total of 620 T2w images for training (n=357) and testing. The OB pipeline exhibits high performance in terms of boundary delineation, OB localization, and volume estimation across a wide range of ages in 203 participants of the Rhineland Study (Dice Score (Dice): 0.852, Volume Similarity (VS): 0.910, and Average Hausdorff Distance (AVD): 0.215 mm). Moreover, it also generalizes to scans of an independent dataset never encountered during training, the Human Connectome Project (HCP), with different acquisition parameters and demographics, evaluated in 30 cases at the native 0.7 mm HCP resolution (Dice: 0.738, VS: 0.790, and AVD: 0.340 mm), and the default 0.8 mm pipeline resolution (Dice: 0.782, VS: 0.858, and AVD: 0.268 mm). We extensively validated our pipeline not only with respect to segmentation accuracy but also to known OB volume effects, where it can sensitively replicate age effects (β=-0.232, p<.01). Furthermore, our method can analyze a 3D volume in less than a minute (GPU) in an end-to-end fashion, providing a validated, efficient, and scalable solution for automatically assessing OB volumes.
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Affiliation(s)
- Santiago Estrada
- Image Analysis, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ran Lu
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Kersten Diers
- Image Analysis, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Weiyi Zeng
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Philipp Ehses
- MR Physics, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Tony Stöcker
- MR Physics, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; Department of Physics and Astronomy, University of Bonn, Germany
| | - Monique M B Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Martin Reuter
- Image Analysis, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston MA, USA; Department of Radiology, Harvard Medical School, Boston MA, USA.
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10
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Jamil R, Mauconduit F, Le Ster C, Ehses P, Poser BA, Vignaud A, Boulant N. Temporal SNR optimization through RF coil combination in fMRI: The more, the better? PLoS One 2021; 16:e0259592. [PMID: 34748584 PMCID: PMC8575292 DOI: 10.1371/journal.pone.0259592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
For functional MRI with a multi-channel receiver RF coil, images are often reconstructed channel by channel, resulting into multiple images per time frame. The final image to analyze usually is the result of the covariance Sum-of-Squares (covSoS) combination across these channels. Although this reconstruction is quasi-optimal in SNR, it is not necessarily the case in terms of temporal SNR (tSNR) of the time series, which is yet a more relevant metric for fMRI data quality. In this work, we investigated tSNR optimality through voxel-wise RF coil combination and its effects on BOLD sensitivity. An analytical solution for an optimal RF coil combination is described, which is somewhat tied to the extended Krueger-Glover model involving both thermal and physiological noise covariance matrices. Compared experimentally to covSOS on four volunteers at 7T, the method yielded great improvement of tSNR but, surprisingly, did not result into higher BOLD sensitivity. Solutions to improve the method such as for example the t-score for the mean recently proposed are also explored, but result into similar observations once the statistics are corrected properly. Overall, the work shows that data-driven RF coil combinations based on tSNR considerations alone should be avoided unless additional and unbiased assumptions can be made.
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Affiliation(s)
- Redouane Jamil
- CEA, CNRS, BAOBAB, NeuroSpin, Paris-Saclay University, Gif-sur-Yvette, France
| | - Franck Mauconduit
- CEA, CNRS, BAOBAB, NeuroSpin, Paris-Saclay University, Gif-sur-Yvette, France
| | - Caroline Le Ster
- CEA, CNRS, BAOBAB, NeuroSpin, Paris-Saclay University, Gif-sur-Yvette, France
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Benedikt A. Poser
- Department of Cognitive Neuroscience, Maastricht Brain Imaging Centre, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Alexandre Vignaud
- CEA, CNRS, BAOBAB, NeuroSpin, Paris-Saclay University, Gif-sur-Yvette, France
| | - Nicolas Boulant
- CEA, CNRS, BAOBAB, NeuroSpin, Paris-Saclay University, Gif-sur-Yvette, France
- * E-mail:
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11
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Voelker MN, Kraff O, Goerke S, Laun FB, Hanspach J, Pine KJ, Ehses P, Zaiss M, Liebert A, Straub S, Eckstein K, Robinson S, Nagel AN, Stefanescu MR, Wollrab A, Klix S, Felder J, Hock M, Bosch D, Weiskopf N, Speck O, Ladd ME, Quick HH. The traveling heads 2.0: Multicenter reproducibility of quantitative imaging methods at 7 Tesla. Neuroimage 2021; 232:117910. [PMID: 33647497 DOI: 10.1016/j.neuroimage.2021.117910] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/25/2021] [Accepted: 02/20/2021] [Indexed: 12/14/2022] Open
Abstract
OBJECT This study evaluates inter-site and intra-site reproducibility at ten different 7 T sites for quantitative brain imaging. MATERIAL AND METHODS Two subjects - termed the "traveling heads" - were imaged at ten different 7 T sites with a harmonized quantitative brain MR imaging protocol. In conjunction with the system calibration, MP2RAGE, QSM, CEST and multi-parametric mapping/relaxometry were examined. RESULTS Quantitative measurements with MP2RAGE showed very high reproducibility across sites and subjects, and errors were in concordance with previous results and other field strengths. QSM had high inter-site reproducibility for relevant subcortical volumes. CEST imaging revealed systematic differences between the sites, but reproducibility was comparable to results in the literature. Relaxometry had also very high agreement between sites, but due to the high sensitivity, differences caused by different applications of the B1 calibration of the two RF coil types used were observed. CONCLUSION Our results show that quantitative brain imaging can be performed with high reproducibility at 7 T and with similar reliability as found at 3 T for multicenter studies of the supratentorial brain.
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Affiliation(s)
- Maximilian N Voelker
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University Duisburg-Essen, Essen, Germany; High-Field and Hybrid MR Imaging, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
| | - Oliver Kraff
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University Duisburg-Essen, Essen, Germany
| | - Steffen Goerke
- Division of Medical Physics in Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frederik B Laun
- Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jannis Hanspach
- Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Kerrin J Pine
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Moritz Zaiss
- Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Andrzej Liebert
- Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sina Straub
- Division of Medical Physics in Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Korbinian Eckstein
- High Field MR Center, Department for Biomedical Imaging and Image guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Simon Robinson
- High Field MR Center, Department for Biomedical Imaging and Image guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Armin N Nagel
- Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Maria R Stefanescu
- Chair of Cellular and Molecular Imaging, Comprehensive Heart Failure Center (CHFC), University Hospital Wuerzburg, Wuerzburg, Germany
| | - Astrid Wollrab
- Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Sabrina Klix
- Berlin Ultrahigh Field Facility (B.U.F.F.), Max-Delbrueck-Center for Molecular Medicine, Berlin-Buch, Germany
| | - Jörg Felder
- Institute of Neuroscience and Medicine (INM-4), Forschungszentrum Jülich, Jülich, Germany
| | - Michael Hock
- Chair of Cellular and Molecular Imaging, Comprehensive Heart Failure Center (CHFC), University Hospital Wuerzburg, Wuerzburg, Germany
| | - Dario Bosch
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Nikolaus Weiskopf
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; Felix Bloch Institute for Solid State Physics, Faculty of Physics and Earth Sciences, Leipzig University, Leipzig, Germany
| | - Oliver Speck
- Otto-von-Guericke-University Magdeburg, Magdeburg, Germany; Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Mark E Ladd
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University Duisburg-Essen, Essen, Germany; Division of Medical Physics in Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and Faculty of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Harald H Quick
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University Duisburg-Essen, Essen, Germany; High-Field and Hybrid MR Imaging, University Hospital Essen, University Duisburg-Essen, Essen, Germany
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12
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Mueller S, Stirnberg R, Akbey S, Ehses P, Scheffler K, Stöcker T, Zaiss M. Whole brain snapshot CEST at 3T using 3D‐EPI: Aiming for speed, volume, and homogeneity. Magn Reson Med 2020; 84:2469-2483. [DOI: 10.1002/mrm.28298] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/16/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Sebastian Mueller
- High‐field Magnetic Resonance Center Max Planck Institute for Biological Cybernetics Tuebingen Germany
| | | | - Suzan Akbey
- German Center for Neurodegenerative Diseases (DZNE) Bonn Germany
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE) Bonn Germany
| | - Klaus Scheffler
- High‐field Magnetic Resonance Center Max Planck Institute for Biological Cybernetics Tuebingen Germany
- Department of Biomedical Magnetic Resonance Eberhard Karls University Tuebingen Tuebingen Germany
| | - Tony Stöcker
- German Center for Neurodegenerative Diseases (DZNE) Bonn Germany
- Department of Physics and Astronomy University of Bonn Bonn Germany
| | - Moritz Zaiss
- High‐field Magnetic Resonance Center Max Planck Institute for Biological Cybernetics Tuebingen Germany
- Department of Neuroradiology University Hospital Erlangen Erlangen Germany
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13
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Heule R, Deshmane A, Zaiss M, Herz K, Ehses P, Scheffler K. Structure or Exchange? On the Feasibility of Chemical Exchange Detection with Balanced Steady-State Free Precession in Tissue - An In Vitro Study. NMR Biomed 2020; 33:e4200. [PMID: 31833130 DOI: 10.1002/nbm.4200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/15/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
Balanced steady-state free precession imaging has recently been suggested for chemical exchange detection (bSSFPX). The objective of this work is to investigate the contributions of microstructural, chemical shift and chemical exchange effects to the asymmetry of the bSSFP profile at field strengths of 3 T and 9.4 T. To this end, in vitro bSSFPX experiments are performed for a range of repetition times and flip angles in glucose water solutions with different MnCl2 concentrations and tissue homogenates obtained from the brainstem of pig brains. The experimental results are compared to multi-pool Bloch-McConnell simulations. Additionally, the influence of white matter tract geometry is analyzed ex vivo in pig brain hemispheres measured at two different angles with respect to B0 . The detectable bSSFP profile asymmetry in glucose solutions with tissue-like relaxation times and white matter homogenates was consistent with Bloch-McConnell simulations but relatively small. In intact white matter tracts, the asymmetry was dominated by structural effects with a strong dependency on tract orientation relative to B0 . In tracts perpendicular to B0 , the asymmetry was ≈ 3-4 times higher than in the homogenates, thus barely affected by chemical exchange effects. In conclusion, chemical exchange-related bSSFP profile asymmetries are detectable in tissue homogenates, however, the observed asymmetry level is generally low and prone to confounding structural effects rendering in vivo chemical exchange detection with bSSFP challenging in the brain.
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Affiliation(s)
- Rahel Heule
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Anagha Deshmane
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Moritz Zaiss
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Kai Herz
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Klaus Scheffler
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany
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14
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Bause J, Polimeni JR, Stelzer J, In MH, Ehses P, Kraemer-Fernandez P, Aghaeifar A, Lacosse E, Pohmann R, Scheffler K. Impact of prospective motion correction, distortion correction methods and large vein bias on the spatial accuracy of cortical laminar fMRI at 9.4 Tesla. Neuroimage 2020; 208:116434. [DOI: 10.1016/j.neuroimage.2019.116434] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 11/08/2019] [Accepted: 12/02/2019] [Indexed: 01/24/2023] Open
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15
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Akbey S, Ehses P, Stirnberg R, Zaiss M, Stöcker T. Whole‐brain snapshot CEST imaging at 7 T using 3D‐EPI. Magn Reson Med 2019; 82:1741-1752. [DOI: 10.1002/mrm.27866] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/06/2019] [Accepted: 05/24/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Suzan Akbey
- German Center for Neurodegenerative Diseases (DZNE) Bonn Germany
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE) Bonn Germany
| | | | - Moritz Zaiss
- Max‐Planck Institute for Biological Cybernetics Tübingen Germany
| | - Tony Stöcker
- German Center for Neurodegenerative Diseases (DZNE) Bonn Germany
- Department of Physics and Astronomy University of Bonn Bonn Germany
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16
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Ehses P, Brenner D, Stirnberg R, Pracht ED, Stöcker T. Whole‐brain B
1
‐mapping using three‐dimensional DREAM. Magn Reson Med 2019; 82:924-934. [DOI: 10.1002/mrm.27773] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/22/2019] [Accepted: 03/24/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE)Bonn Germany
| | - Daniel Brenner
- German Center for Neurodegenerative Diseases (DZNE)Bonn Germany
| | | | | | - Tony Stöcker
- German Center for Neurodegenerative Diseases (DZNE)Bonn Germany
- Department of Physics and Astronomy University of Bonn Bonn Germany
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17
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Zaiss M, Deshmane A, Schuppert M, Herz K, Glang F, Ehses P, Lindig T, Bender B, Ernemann U, Scheffler K. DeepCEST: 9.4 T Chemical exchange saturation transfer MRI contrast predicted from 3 T data - a proof of concept study. Magn Reson Med 2019; 81:3901-3914. [DOI: 10.1002/mrm.27690] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/11/2019] [Accepted: 01/23/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Moritz Zaiss
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics; Tübingen Germany
| | - Anagha Deshmane
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics; Tübingen Germany
| | - Mark Schuppert
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics; Tübingen Germany
| | - Kai Herz
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics; Tübingen Germany
| | - Felix Glang
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics; Tübingen Germany
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE); Bonn Germany
| | - Tobias Lindig
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics; Tübingen Germany
- Department of Diagnostic and Interventional Neuroradiology; Eberhard-Karls University Tübingen; Tübingen Germany
| | - Benjamin Bender
- Department of Diagnostic and Interventional Neuroradiology; Eberhard-Karls University Tübingen; Tübingen Germany
| | - Ulrike Ernemann
- Department of Diagnostic and Interventional Neuroradiology; Eberhard-Karls University Tübingen; Tübingen Germany
| | - Klaus Scheffler
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics; Tübingen Germany
- Department of Biomedical Magnetic Resonance; Eberhard-Karls University Tübingen; Tübingen Germany
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18
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Zaiss M, Schuppert M, Deshmane A, Herz K, Ehses P, Füllbier L, Lindig T, Bender B, Ernemann U, Scheffler K. Chemical exchange saturation transfer MRI contrast in the human brain at 9.4 T. Neuroimage 2018; 179:144-155. [DOI: 10.1016/j.neuroimage.2018.06.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 01/06/2023] Open
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19
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Göksu C, Hanson LG, Siebner HR, Ehses P, Scheffler K, Thielscher A. [OA019] Human in-vivo Magnetic Resonance Current Density Imaging (MRCDI) and MR Electrical Impedance Tomography (MREIT). Phys Med 2018. [DOI: 10.1016/j.ejmp.2018.06.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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20
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Windschuh J, Zaiss M, Ehses P, Lee JS, Jerschow A, Regatte RR. Assessment of frequency drift on CEST MRI and dynamic correction: application to gagCEST at 7 T. Magn Reson Med 2018; 81:573-582. [PMID: 29851141 DOI: 10.1002/mrm.27367] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 02/02/2023]
Abstract
PURPOSE To investigate the effect of a frequency drift of the static magnetic field on 3D CEST MRI based on glycosaminoglycans (GAGs) of articular cartilage at 7 T and to introduce a retrospective correction method that uses the phase images of the gradient-echo readout. METHODS Repeated gagCEST and B0 measurements were performed in a glucose model solution and in vivo in the knee joint of 3 healthy volunteers at 7 T. Phase images of the modified 3D rectangular spiral centric-reordered gradient-echo CEST sequence were used to quantify and compensate the apparent frequency drift in repeated gagCEST measurements. RESULTS The frequency drift of the MRI scanner strongly influences the gagCEST signal in the articular cartilage of the human knee joint. The gagCEST signal in the articular cartilage is changed by 0.18%/Hz while an average drift of 0.7 ± 0.2 Hz/minute was observed. The proposed correction method can be applied retrospectively without the need of additional measurements and provides improved comparability and reproducibility for gagCEST studies. This correction method may also be of interest for other applications of CEST MRI. CONCLUSION Prospective or retrospective correction of the frequency drift of the MRI scanner is essential for reproducible gagCEST measurements. The proposed retrospective correction method fulfills this requirement without the need of additional measurements.
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Affiliation(s)
- Johannes Windschuh
- New York University Langone Medical Center, Department of Radiology, Center for Biomedical Imaging, New York, New York
| | - Moritz Zaiss
- Max Planck Institute for Biological Cybernetics, High-Field Magnetic Resonance Center, Tübingen, Germany
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases, Department of MR Physics, Bonn, Germany
| | - Jae-Seung Lee
- New York University Langone Medical Center, Department of Radiology, Center for Biomedical Imaging, New York, New York.,New York University, Department of Chemistry, New York, New York
| | - Alexej Jerschow
- New York University, Department of Chemistry, New York, New York
| | - Ravinder R Regatte
- New York University Langone Medical Center, Department of Radiology, Center for Biomedical Imaging, New York, New York
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21
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Zaiss M, Ehses P, Scheffler K. Snapshot-CEST: Optimizing spiral-centric-reordered gradient echo acquisition for fast and robust 3D CEST MRI at 9.4 T. NMR Biomed 2018; 31:e3879. [PMID: 29372571 DOI: 10.1002/nbm.3879] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
Gradient echo (GRE)-based acquisition provides a robust readout method for chemical exchange saturation transfer (CEST) at ultrahigh field (UHF). To develop a snapshot-CEST approach, the transient GRE signal and point spread function were investigated in detail, leading to optimized measurement parameters and reordering schemes for fast and robust volumetric CEST imaging. Simulation of the transient GRE signal was used to determine the optimal sequence parameters and the maximum feasible number of k-space lines. Point spread function analysis provided an insight into the induced k-space filtering and the performance of different rectangular reordering schemes in terms of blurring, signal-to-noise ratio (SNR) and relaxation dependence. Simulation results were confirmed in magnetic resonance imaging (MRI) measurements of healthy subjects. Minimal repetition time (TR) is beneficial for snapshot-GRE readout. At 9.4 T, for TR = 4 ms and optimal flip angle close to the Ernst angle, a maximum of 562 k-space lines can be acquired after a single presaturation, providing decent SNR with high image quality. For spiral-centric reordered k-space acquisition, the image quality can be further improved using a rectangular spiral reordering scheme adjusted to the field of view. Application of the derived snapshot-CEST sequence for fast imaging acquisition in the human brain at 9.4 T shows excellent image quality in amide and nuclear Overhauser enhancement (NOE), and enables guanidyl CEST detection. The proposed snapshot-CEST establishes a fast and robust volumetric CEST approach ready for the imaging of known and novel exchange-weighted contrasts at UHF.
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Affiliation(s)
- Moritz Zaiss
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Philipp Ehses
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Klaus Scheffler
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, Eberhard-Karls University Tübingen, Tübingen, Germany
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22
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Loktyushin A, Ehses P, Schölkopf B, Scheffler K. Autofocusing-based phase correction. Magn Reson Med 2018; 80:958-968. [DOI: 10.1002/mrm.27092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Alexander Loktyushin
- Max Planck Institute for Intelligent Systems; Tübingen Germany
- Max Planck Institute for Biological Cybernetics; Tübingen Germany
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association; Bonn Germany
| | | | - Klaus Scheffler
- Max Planck Institute for Biological Cybernetics; Tübingen Germany
- University of Tübingen, Geschwister-Scholl-Platz; Tübingen Germany
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23
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Göksu C, Hanson LG, Siebner HR, Ehses P, Scheffler K, Thielscher A. Human in-vivo brain magnetic resonance current density imaging (MRCDI). Neuroimage 2017; 171:26-39. [PMID: 29288869 DOI: 10.1016/j.neuroimage.2017.12.075] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/19/2017] [Accepted: 12/22/2017] [Indexed: 10/18/2022] Open
Abstract
Magnetic resonance current density imaging (MRCDI) and MR electrical impedance tomography (MREIT) are two emerging modalities, which combine weak time-varying currents injected via surface electrodes with magnetic resonance imaging (MRI) to acquire information about the current flow and ohmic conductivity distribution at high spatial resolution. The injected current flow creates a magnetic field in the head, and the component of the induced magnetic field ΔBz,c parallel to the main scanner field causes small shifts in the precession frequency of the magnetization. The measured MRI signal is modulated by these shifts, allowing to determine ΔBz,c for the reconstruction of the current flow and ohmic conductivity. Here, we demonstrate reliable ΔBz,c measurements in-vivo in the human brain based on multi-echo spin echo (MESE) and steady-state free precession free induction decay (SSFP-FID) sequences. In a series of experiments, we optimize their robustness for in-vivo measurements while maintaining a good sensitivity to the current-induced fields. We validate both methods by assessing the linearity of the measured ΔBz,c with respect to the current strength. For the more efficient SSFP-FID measurements, we demonstrate a strong influence of magnetic stray fields on the ΔBz,c images, caused by non-ideal paths of the electrode cables, and validate a correction method. Finally, we perform measurements with two different current injection profiles in five subjects. We demonstrate reliable recordings of ΔBz,c fields as weak as 1 nT, caused by currents of 1 mA strength. Comparison of the ΔBz,c measurements with simulated ΔBz,c images based on FEM calculations and individualized head models reveals significant linear correlations in all subjects, but only for the stray field-corrected data. As final step, we reconstruct current density distributions from the measured and simulated ΔBz,c data. Reconstructions from non-corrected ΔBz,c measurements systematically overestimate the current densities. Comparing the current densities reconstructed from corrected ΔBz,c measurements and from simulated ΔBz,c images reveals an average coefficient of determination R2 of 71%. In addition, it shows that the simulations underestimated the current strength on average by 24%. Our results open up the possibility of using MRI to systematically validate and optimize numerical field simulations that play an important role in several neuroscience applications, such as transcranial brain stimulation, and electro- and magnetoencephalography.
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Affiliation(s)
- Cihan Göksu
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Denmark; Center for Magnetic Resonance, DTU Elektro, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Lars G Hanson
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Denmark; Center for Magnetic Resonance, DTU Elektro, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Hartwig R Siebner
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Denmark; Department of Neurology, Copenhagen University Hospital, Bispebjerg, Denmark
| | - Philipp Ehses
- High-Field Magnetic Resonance Center, Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Klaus Scheffler
- High-Field Magnetic Resonance Center, Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany; Department of Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany
| | - Axel Thielscher
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Denmark; Center for Magnetic Resonance, DTU Elektro, Technical University of Denmark, Kgs Lyngby, Denmark; High-Field Magnetic Resonance Center, Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany.
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24
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Pracht ED, Feiweier T, Ehses P, Brenner D, Roebroeck A, Weber B, Stöcker T. SAR and scan-time optimized 3D whole-brain double inversion recovery imaging at 7T. Magn Reson Med 2017; 79:2620-2628. [PMID: 28905416 DOI: 10.1002/mrm.26913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/28/2017] [Accepted: 08/18/2017] [Indexed: 11/10/2022]
Abstract
PURPOSE The aim of this project was to implement an ultra-high field (UHF) optimized double inversion recovery (DIR) sequence for gray matter (GM) imaging, enabling whole brain coverage in short acquisition times ( ≈5 min, image resolution 1 mm3 ). METHODS A 3D variable flip angle DIR turbo spin echo (TSE) sequence was optimized for UHF application. We implemented an improved, fast, and specific absorption rate (SAR) efficient TSE imaging module, utilizing improved reordering. The DIR preparation was tailored to UHF application. Additionally, fat artifacts were minimized by employing water excitation instead of fat saturation. RESULTS GM images, covering the whole brain, were acquired in 7 min scan time at 1 mm isotropic resolution. SAR issues were overcome by using a dedicated flip angle calculation considering SAR and SNR efficiency. Furthermore, UHF related artifacts were minimized. CONCLUSION The suggested sequence is suitable to generate GM images with whole-brain coverage at UHF. Due to the short total acquisition times and overall robustness, this approach can potentially enable DIR application in a routine setting and enhance lesion detection in neurological diseases. Magn Reson Med 79:2620-2628, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
| | | | - Philipp Ehses
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Daniel Brenner
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Alard Roebroeck
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht, Maastricht University, The Netherlands
| | - Bernd Weber
- Department of Epileptology, University Hospital Bonn, Bonn, Germany
| | - Tony Stöcker
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Physics and Astronomy, University of Bonn, Bonn, Germany
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25
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Göksu C, Scheffler K, Ehses P, Hanson LG, Thielscher A. Sensitivity analysis of magnetic field measurements for magnetic resonance electrical impedance tomography (MREIT). Magn Reson Med 2017; 79:748-760. [DOI: 10.1002/mrm.26727] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/02/2017] [Accepted: 03/29/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Cihan Göksu
- Danish Research Center for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research; Copenhagen University Hospital; Hvidovre Denmark
- Center for Magnetic Resonance, DTU Elektro; Technical University of Denmark; Kgs Lyngby Denmark
| | - Klaus Scheffler
- High-Field Magnetic Resonance Center, Max-Planck-Institute for Biological Cybernetics; Tübingen Germany
- Department of Biomedical Magnetic Resonance; University of Tübingen; Tübingen Germany
| | - Philipp Ehses
- High-Field Magnetic Resonance Center, Max-Planck-Institute for Biological Cybernetics; Tübingen Germany
- Department of Biomedical Magnetic Resonance; University of Tübingen; Tübingen Germany
| | - Lars G. Hanson
- Danish Research Center for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research; Copenhagen University Hospital; Hvidovre Denmark
- Center for Magnetic Resonance, DTU Elektro; Technical University of Denmark; Kgs Lyngby Denmark
| | - Axel Thielscher
- Danish Research Center for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research; Copenhagen University Hospital; Hvidovre Denmark
- Center for Magnetic Resonance, DTU Elektro; Technical University of Denmark; Kgs Lyngby Denmark
- High-Field Magnetic Resonance Center, Max-Planck-Institute for Biological Cybernetics; Tübingen Germany
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26
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Ehses P, Scheffler K. Multiline balanced SSFP for rapid functional imaging at ultrahigh field. Magn Reson Med 2017; 79:994-1000. [PMID: 28547846 DOI: 10.1002/mrm.26761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 04/23/2017] [Accepted: 05/02/2017] [Indexed: 11/11/2022]
Abstract
PURPOSE The goal of this study is to develop and evaluate a multiline balanced steady-state free-precession (bSSFP) sequence for passband functional MRI at ultrahigh field. METHODS Passband bSSFP functional MRI experiments using a visual task were performed on a 9.4 T system with echo trains ranging from one up to seven echoes. We analyze the acquisition efficiency, temporal and thermal signal-to-noise ratio, as well as the observed blood oxygen-level-dependent (BOLD) signal changes. RESULTS With increasing repetition time and echo train length, the BOLD-related signal change as well as the thermal and temporal noise were improved. Activation patterns and signal changes were stable and reproducible across subjects. CONCLUSIONS We propose a multiline bSSFP for functional BOLD imaging that approaches the speed of echo-planar imaging and that shows an increased BOLD sensitivity compared with single-line bSSFP. Magn Reson Med 79:994-1000, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Philipp Ehses
- Department for Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany.,High-Field MR Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Klaus Scheffler
- Department for Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany.,High-Field MR Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
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27
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Hagberg GE, Bause J, Ethofer T, Ehses P, Dresler T, Herbert C, Pohmann R, Shajan G, Fallgatter A, Pavlova MA, Scheffler K. Whole brain MP2RAGE-based mapping of the longitudinal relaxation time at 9.4T. Neuroimage 2017; 144:203-216. [DOI: 10.1016/j.neuroimage.2016.09.047] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 09/16/2016] [Accepted: 09/20/2016] [Indexed: 11/16/2022] Open
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28
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Chadzynski GL, Bause J, Shajan G, Pohmann R, Scheffler K, Ehses P. Fast and efficient free induction decay MR spectroscopic imaging of the human brain at 9.4 Tesla. Magn Reson Med 2016; 78:1281-1295. [PMID: 27900794 DOI: 10.1002/mrm.26539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 12/14/2022]
Abstract
PURPOSE The purpose of this work was to develop a fast and efficient MRSI-FID acquisition scheme and test its performance in vivo. The aim was to find a trade-off between the minimal total acquisition time and signal-to-noise ratio of the acquired spectra. METHODS Measurements were performed on a 9.4 Tesla system. Sequence optimization included redesign of water suppression, optimization of the sequence gradients, and improvement of the sampling efficiency by minimizing the read-out time. This resulted in an acquisition time of 2:47 and 22:13 minutes for 2D (TR = 57 ms; 3-mm in-plane resolution) and 3D MRSI (TR = 57 ms; 16 slices; 3-mm isotropic resolution), respectively. RESULTS Despite strong T1 weighting and first-order phase problems, it was possible to obtain spectra of an acceptable quality. The average line width calculated for the tCr peak across the entire field of view was 26.9 ± 9.6 Hz for 2D and 30.0 ± 11.3 Hz for 3D MRSI. In 3D measurements, the percent fraction of voxels fitted with Cramer-Rao lower bounds below 10% was 53.3 ± 4.1%, 63.4 ± 8.4%, and 81.0 ± 2.9% for Glu, tCr, and tNAA, respectively. CONCLUSION Considering the typically long duration of high-resolution MRSI, the proposed technique may be of interest for clinical applications and/or studies that focus on following the biochemistry of dynamic processes. Magn Reson Med 78:1281-1295, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Grzegorz L Chadzynski
- Department of Biomedical Magnetic Resonance, Eberhard-Karls University of Tübingen, Tübingen, Germany.,High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Jonas Bause
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,Graduate Training Centre of Neuroscience, Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Gunamony Shajan
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Rolf Pohmann
- High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Klaus Scheffler
- Department of Biomedical Magnetic Resonance, Eberhard-Karls University of Tübingen, Tübingen, Germany.,High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Philipp Ehses
- Department of Biomedical Magnetic Resonance, Eberhard-Karls University of Tübingen, Tübingen, Germany.,High-field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
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29
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Loureiro JR, Hagberg GE, Ethofer T, Erb M, Bause J, Ehses P, Scheffler K, Himmelbach M. Depth-dependence of visual signals in the human superior colliculus at 9.4 T. Hum Brain Mapp 2016; 38:574-587. [PMID: 27659062 DOI: 10.1002/hbm.23404] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 09/04/2016] [Accepted: 09/06/2016] [Indexed: 11/08/2022] Open
Abstract
The superior colliculus (SC) is a layered structure located in the midbrain. We exploited the improved spatial resolution and BOLD signal strength available at 9.4 T to investigate the depth profile of visual BOLD responses in the human SC based on distortion-corrected EPI data with a 1 mm isotropic resolution. We used high resolution (350 µm in-plane) anatomical images to determine regions-of-interest of the SC and applied a semi-automated method to segment it into superficial, intermediate, and deep zones. A greater than linear increase in sensitivity of the functional signal at 9.4 T allowed us to detect a statistically significant depth pattern in a group analysis with a 20 min stimulation paradigm. Descriptive data showed consistent depth profiles also in single individuals. The highest signals were localized to the superficial layers of the right and left SC during contralateral stimulation, which was in good agreement with its functional architecture known from non-human primates. This study thus demonstrates the potential of 9.4 T MRI for functional neuroimaging even in deeply located, particularly challenging brain structures such as the SC. Hum Brain Mapp 38:574-587, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Joana R Loureiro
- High-Field MR, Max Planck Institute for Biological Cybernetics, Tuebingen, DE, Germany.,Biomedical Magnetic Resonance, University Hospital Tuebingen, Tuebingen, DE, Germany.,Graduate School of Neural and Behavioural Sciences/International Max Planck Research School, University of Tuebingen, Tuebingen, DE, Germany.,Division of Neuropsychology, Centre for Neurology, Hertie-Institute for Clinical Brain Research, Tuebingen, DE, Germany
| | - Gisela E Hagberg
- High-Field MR, Max Planck Institute for Biological Cybernetics, Tuebingen, DE, Germany.,Biomedical Magnetic Resonance, University Hospital Tuebingen, Tuebingen, DE, Germany
| | - Thomas Ethofer
- Biomedical Magnetic Resonance, University Hospital Tuebingen, Tuebingen, DE, Germany.,Department of Psychiatry and Psychotherapy, University of Tuebingen, Tuebingen, DE, Germany
| | - Michael Erb
- Biomedical Magnetic Resonance, University Hospital Tuebingen, Tuebingen, DE, Germany
| | - Jonas Bause
- High-Field MR, Max Planck Institute for Biological Cybernetics, Tuebingen, DE, Germany
| | - Philipp Ehses
- High-Field MR, Max Planck Institute for Biological Cybernetics, Tuebingen, DE, Germany.,Biomedical Magnetic Resonance, University Hospital Tuebingen, Tuebingen, DE, Germany
| | - Klaus Scheffler
- High-Field MR, Max Planck Institute for Biological Cybernetics, Tuebingen, DE, Germany.,Biomedical Magnetic Resonance, University Hospital Tuebingen, Tuebingen, DE, Germany
| | - Marc Himmelbach
- Graduate School of Neural and Behavioural Sciences/International Max Planck Research School, University of Tuebingen, Tuebingen, DE, Germany.,Division of Neuropsychology, Centre for Neurology, Hertie-Institute for Clinical Brain Research, Tuebingen, DE, Germany
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30
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Weick S, Völker M, Hemberger K, Meyer C, Ehses P, Polat B, Breuer FA, Blaimer M, Fink C, Schad LR, Sauer OA, Flentje M, Jakob PM. Desynchronization of Cartesian k-space sampling and periodic motion for improved retrospectively self-gated 3D lung MRI using quasi-random numbers. Magn Reson Med 2016; 77:787-793. [PMID: 26968124 DOI: 10.1002/mrm.26159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 11/10/2022]
Abstract
PURPOSE To demonstrate that desynchronization between Cartesian k-space sampling and periodic motion in free-breathing lung MRI improves the robustness and efficiency of retrospective respiratory self-gating. METHODS Desynchronization was accomplished by reordering the phase (ky ) and partition (kz ) encoding of a three-dimensional FLASH sequence according to two-dimensional, quasi-random (QR) numbers. For retrospective respiratory self-gating, the k-space center signal (DC signal) was acquired separately after each encoded k-space line. QR sampling results in a uniform distribution of k-space lines after gating. Missing lines resulting from the gating process were reconstructed using iterative GRAPPA. Volunteer measurements were performed to compare quasi-random with conventional sampling. Patient measurements were performed to demonstrate the feasibility of QR sampling in a clinical setting. RESULTS The uniformly sampled k-space after retrospective gating allows for a more stable iterative GRAPPA reconstruction and improved ghost artifact reduction compared with conventional sampling. It is shown that this stability can either be used to reduce the total scan time or to reconstruct artifact-free data sets in different respiratory phases, both resulting in an improved efficiency of retrospective respiratory self-gating. CONCLUSION QR sampling leads to desynchronization between repeated data acquisition and periodic respiratory motion. This results in an improved motion artifact reduction in shorter scan time. Magn Reson Med 77:787-793, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Stefan Weick
- Department of Radiation Oncology, University of Würzburg, Germany.,Department of Experimental Physics 5, University of Würzburg, Germany
| | - Michael Völker
- Department of Experimental Physics 5, University of Würzburg, Germany
| | | | - Cord Meyer
- Department of Experimental Physics 5, University of Würzburg, Germany
| | - Philipp Ehses
- Max-Planck-Institute for Biological Cybernetics, University of Tübingen, Germany
| | - Bülent Polat
- Department of Radiation Oncology, University of Würzburg, Germany
| | - Felix A Breuer
- Research Center for Magnetic Resonance Bavaria, Würzburg, Germany
| | - Martin Blaimer
- Research Center for Magnetic Resonance Bavaria, Würzburg, Germany
| | - Christian Fink
- Department of Radiology, Allgemeines Krankenhaus Celle, Germany
| | - Lothar R Schad
- Computer Assisted Clinical Medicine, Medical Faculty Mannheim, Heidelberg University, Germany
| | - Otto A Sauer
- Department of Radiation Oncology, University of Würzburg, Germany
| | - Michael Flentje
- Department of Radiation Oncology, University of Würzburg, Germany
| | - Peter M Jakob
- Department of Experimental Physics 5, University of Würzburg, Germany.,Department of Radiology, Allgemeines Krankenhaus Celle, Germany
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31
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Bause J, Ehses P, Mirkes C, Shajan G, Scheffler K, Pohmann R. Quantitative and functional pulsed arterial spin labeling in the human brain at 9.4 t. Magn Reson Med 2016; 75:1054-63. [DOI: 10.1002/mrm.25671] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Jonas Bause
- Max Planck Institute for Biological Cybernetics, High‐Field Magnetic Resonance CenterTübingen Germany
- Graduate Training Center of Neuronal SciencesInternational Max Planck Research SchoolUniversity of TübingenTübingen Germany
| | - Philipp Ehses
- Max Planck Institute for Biological Cybernetics, High‐Field Magnetic Resonance CenterTübingen Germany
- Department of Biomedical Magnetic ResonanceUniversity of TübingenTübingen Germany
| | - Christian Mirkes
- Max Planck Institute for Biological Cybernetics, High‐Field Magnetic Resonance CenterTübingen Germany
- Department of Biomedical Magnetic ResonanceUniversity of TübingenTübingen Germany
| | - G. Shajan
- Max Planck Institute for Biological Cybernetics, High‐Field Magnetic Resonance CenterTübingen Germany
| | - Klaus Scheffler
- Max Planck Institute for Biological Cybernetics, High‐Field Magnetic Resonance CenterTübingen Germany
- Department of Biomedical Magnetic ResonanceUniversity of TübingenTübingen Germany
| | - Rolf Pohmann
- Max Planck Institute for Biological Cybernetics, High‐Field Magnetic Resonance CenterTübingen Germany
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32
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Scheffler K, Ehses P. High-resolution mapping of neuronal activation with balanced SSFP at 9.4 tesla. Magn Reson Med 2015; 76:163-71. [DOI: 10.1002/mrm.25890] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/10/2015] [Accepted: 07/24/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Klaus Scheffler
- Department for Biomedical Magnetic Resonance; University of Tübingen; Tübingen Germany
- High-Field MR Center, Max Planck Institute for Biological Cybernetics; Tübingen Germany
| | - Philipp Ehses
- Department for Biomedical Magnetic Resonance; University of Tübingen; Tübingen Germany
- High-Field MR Center, Max Planck Institute for Biological Cybernetics; Tübingen Germany
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33
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Ehses P, Bause J, Shajan G, Scheffler K. Efficient generation of T2*-weighted contrast by interslice echo-shifting for human functional and anatomical imaging at 9.4 Tesla. Magn Reson Med 2014; 74:1698-704. [DOI: 10.1002/mrm.25570] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/21/2014] [Accepted: 11/02/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Philipp Ehses
- Department of Biomedical Magnetic Resonance; University of Tübingen; Tübingen Germany
- High-Field Magnetic Resonance Center; Max Planck Institute for Biological Cybernetics; Tübingen Germany
| | - Jonas Bause
- High-Field Magnetic Resonance Center; Max Planck Institute for Biological Cybernetics; Tübingen Germany
| | - G. Shajan
- High-Field Magnetic Resonance Center; Max Planck Institute for Biological Cybernetics; Tübingen Germany
| | - Klaus Scheffler
- Department of Biomedical Magnetic Resonance; University of Tübingen; Tübingen Germany
- High-Field Magnetic Resonance Center; Max Planck Institute for Biological Cybernetics; Tübingen Germany
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34
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Benkert T, Ehses P, Blaimer M, Jakob PM, Breuer FA. Dynamically phase-cycled radial balanced SSFP imaging for efficient banding removal. Magn Reson Med 2014; 73:182-94. [PMID: 24478187 DOI: 10.1002/mrm.25113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/09/2013] [Accepted: 12/12/2013] [Indexed: 11/07/2022]
Abstract
PURPOSE Balanced steady-state free precession (bSSFP) imaging suffers from banding artifacts due to its inherent sensitivity to inhomogeneities in the main magnetic field. These artifacts can be removed by the acquisition of multiple images at different frequency offsets. However, conventional phase-cycling is hindered by a long scan time. The purpose of this work is to present a novel approach for efficient banding removal in bSSFP imaging. THEORY AND METHODS To this end, the phase-cycle during a single-shot radial acquisition of an image was dynamically changed. Thus, each projection is acquired with a different frequency offset. Using conventional radial gridding, an artifact-free image can be reconstructed out of this dataset. RESULTS The approach is validated at clinical field strength [3.0 Tesla (T)] as well as at ultrahigh field (9.4T). Robust elimination of banding artifacts was obtained for different imaging regions, including brain imaging at ultrahigh field with an in-plane resolution of 0.25 × 0.25 mm(2). Besides banding artifact-free imaging, the applicability of the proposed technique for fat-water separation is demonstrated. CONCLUSION Dynamically phase-cycled radial bSSFP has the potential for banding-free bSSFP imaging in a short scan time, in the presence of severe field inhomogeneities and at high resolution.
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Affiliation(s)
- Thomas Benkert
- Research Center Magnetic Resonance Bavaria (MRB), Würzburg, Germany
| | - Philipp Ehses
- Department of Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany.,High-Field MR Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Martin Blaimer
- Research Center Magnetic Resonance Bavaria (MRB), Würzburg, Germany
| | - Peter M Jakob
- Research Center Magnetic Resonance Bavaria (MRB), Würzburg, Germany.,Department of Experimental Physics 5, University of Würzburg, Würzburg, Germany
| | - Felix A Breuer
- Research Center Magnetic Resonance Bavaria (MRB), Würzburg, Germany
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35
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Wright KL, Lee GR, Ehses P, Griswold MA, Gulani V, Seiberlich N. Three-dimensional through-time radial GRAPPA for renal MR angiography. J Magn Reson Imaging 2014; 40:864-74. [PMID: 24446211 DOI: 10.1002/jmri.24439] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 09/07/2013] [Indexed: 11/11/2022] Open
Abstract
PURPOSE To achieve high temporal and spatial resolution for contrast-enhanced time-resolved MR angiography exams (trMRAs), fast imaging techniques such as non-Cartesian parallel imaging must be used. In this study, the three-dimensional (3D) through-time radial generalized autocalibrating partially parallel acquisition (GRAPPA) method is used to reconstruct highly accelerated stack-of-stars data for time-resolved renal MRAs. MATERIALS AND METHODS Through-time radial GRAPPA has been recently introduced as a method for non-Cartesian GRAPPA weight calibration, and a similar concept can also be used in 3D acquisitions. By combining different sources of calibration information, acquisition time can be reduced. Here, different GRAPPA weight calibration schemes are explored in simulation, and the results are applied to reconstruct undersampled stack-of-stars data. RESULTS Simulations demonstrate that an accurate and efficient approach to 3D calibration is to combine a small number of central partitions with as many temporal repetitions as exam time permits. These findings were used to reconstruct renal trMRA data with an in-plane acceleration factor as high as 12.6 with respect to the Nyquist sampling criterion, where the lowest root mean squared error value of 16.4% was achieved when using a calibration scheme with 8 partitions, 16 repetitions, and a 4 projection × 8 read point segment size. CONCLUSION 3D through-time radial GRAPPA can be used to successfully reconstruct highly accelerated non-Cartesian data. By using in-plane radial undersampling, a trMRA can be acquired with a temporal footprint less than 4s/frame with a spatial resolution of approximately 1.5 mm × 1.5 mm × 3 mm.
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Affiliation(s)
- Katherine L Wright
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
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Hopfgartner AJ, Tymofiyeva O, Ehses P, Rottner K, Boldt J, Richter EJ, Jakob PM. Dynamic MRI of the TMJ under physical load. Dentomaxillofac Radiol 2013; 42:20120436. [PMID: 23975114 DOI: 10.1259/dmfr.20120436] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVES The objective of this study was to examine the kinematics of structures of the temporomandibular joint (TMJ) under physiological load while masticating. METHODS Radial MRI was chosen as a fast imaging method to dynamically capture the motions of the joint's anatomy. The technique included a golden ratio-based increment angle and a sliding window reconstruction. The measurements were performed on 22 subjects with and without deformation/displacement of the intra-articular disc while they were biting on a cooled caramel toffee. RESULTS The reconstructed dynamic images provided sufficient information about the size and localization of the disc as well as the change of the intra-articular distance with and without loading. CONCLUSIONS The feasibility of the golden ratio-based radial MRI technique to dynamically capture the anatomy of the TMJ under physical load was demonstrated in this initial study.
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Affiliation(s)
- A J Hopfgartner
- Department of Experimental Physics 5, University of Wuerzburg, Wuerzburg, Germany
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Weick S, Breuer FA, Ehses P, Völker M, Hintze C, Biederer J, Jakob PM. DC-gated high resolution three-dimensional lung imaging during free-breathing. J Magn Reson Imaging 2012; 37:727-32. [PMID: 22987283 DOI: 10.1002/jmri.23798] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 08/02/2012] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To use the acquisition of the k-space center signal (DC signal) implemented into a Cartesian three-dimensional (3D) FLASH sequence for retrospective respiratory self-gating and, thus, for the examination of the whole human lung in high spatial resolution during free breathing. MATERIALS AND METHODS Volunteer as well as patient measurements were performed under free breathing conditions. The DC signal is acquired after the actual image data acquisition within each excitation of a 3D FLASH sequence. The DC signal is then used to track respiratory motion for retrospective respiratory gating. RESULTS It is shown that the acquisition of the DC signal after the imaging module can be used in a 3D FLASH sequence to extract respiratory motion information for retrospective respiratory self-gating and allows for shorter echo times (TE) and therefore increased lung parenchyma SNR. CONCLUSION The acquisition of the DC signal after image signal acquisition allows successful retrospective gating, enabling the reconstruction of high resolution images of the whole human lung under free breathing conditions.
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Affiliation(s)
- Stefan Weick
- Department of Experimental Physics 5, University of Wuerzburg, Germany.
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Ehses P, Seiberlich N, Ma D, Breuer FA, Jakob PM, Griswold MA, Gulani V. IR TrueFISP with a golden-ratio-based radial readout: Fast quantification of T
1
, T
2
, and proton density. Magn Reson Med 2012; 69:71-81. [PMID: 22378141 DOI: 10.1002/mrm.24225] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 01/27/2012] [Accepted: 02/05/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Philipp Ehses
- High-Field MR Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.
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Gensler D, Fidler F, Ehses P, Warmuth M, Reiter T, Düring M, Ritter O, Ladd ME, Quick HH, Jakob PM, Bauer WR, Nordbeck P. MR safety: Fast T
1
thermometry of the RF-induced heating of medical devices. Magn Reson Med 2012; 68:1593-9. [PMID: 22287286 DOI: 10.1002/mrm.24171] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 12/01/2011] [Accepted: 12/29/2011] [Indexed: 11/11/2022]
Affiliation(s)
- D Gensler
- Research Center for Magnetic Resonance Bavaria e.V., Würzburg, Germany.
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Seiberlich N, Lee G, Ehses P, Duerk JL, Gilkeson R, Griswold M. Improved temporal resolution in cardiac imaging using through-time spiral GRAPPA. Magn Reson Med 2011; 66:1682-8. [PMID: 21523823 DOI: 10.1002/mrm.22952] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/11/2011] [Accepted: 03/14/2011] [Indexed: 11/06/2022]
Abstract
Previous work has shown that the use of radial GRAPPA for the reconstruction of undersampled real-time free-breathing cardiac data allows for frame rates of up to 30 images/s. It is well known that the spiral trajectory offers a higher scan efficiency compared to radial trajectories. For this reason, we have developed a novel through-time spiral GRAPPA method and demonstrate its application to real-time cardiac imaging. By moving from the radial trajectory to the spiral trajectory, the temporal resolution can be further improved at lower acceleration factors compared to radial GRAPPA. In addition, the image quality is improved compared to those generated using the radial trajectory due to the lower acceleration factor. Here, we show that 2D frame rates of up to 56 images/s can be achieved using this parallel imaging method with the spiral trajectory.
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Affiliation(s)
- Nicole Seiberlich
- Department of Radiology, University Hospitals of Cleveland, Cleveland, Ohio 44106, USA.
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Seiberlich N, Ehses P, Duerk J, Gilkeson R, Griswold M. Improved radial GRAPPA calibration for real-time free-breathing cardiac imaging. Magn Reson Med 2010; 65:492-505. [PMID: 20872865 DOI: 10.1002/mrm.22618] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 07/21/2010] [Accepted: 07/03/2010] [Indexed: 11/07/2022]
Abstract
To generate real-time, nongated, free-breathing cardiac images, the undersampled radial trajectory combined with parallel imaging in the form of radial GRAPPA has shown promise. However, this method starts to fail at high undersampling factors due to the assumptions that must be made for the purposes of calibrating the GRAPPA weight sets. In this manuscript, a novel through-time radial GRAPPA calibration scheme is proposed which greatly improves image quality for the high acceleration factors required for real-time cardiac imaging. This through-time calibration method offers better image quality than standard radial GRAPPA, but it requires many additional calibration frames to be acquired. By combining the through-time calibration method proposed here with the standard through-k-space radial GRAPPA calibration method, images with high acceleration factors can be reconstructed using few calibration frames. Both the through-time and the hybrid through-time/through-k-space methods are investigated to determine the most advantageous calibration parameters for an R = 6 in vivo short-axis cardiac image. Once the calibration parameters have been established, they are then used to reconstruct several in vivo real-time, free-breathing cardiac datasets with temporal resolutions better than 45 msec, including one with a temporal resolution of 35 msec and an in-plane resolution of 1.56 mm(2) .
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Affiliation(s)
- Nicole Seiberlich
- Department of Radiology, University Hospitals of Cleveland, Cleveland, USA.
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Seiberlich N, Breuer FA, Ehses P, Moriguchi H, Blaimer M, Jakob PM, Griswold MA. Using the GRAPPA operator and the generalized sampling theorem to reconstruct undersampled non-Cartesian data. Magn Reson Med 2009; 61:705-15. [PMID: 19145634 DOI: 10.1002/mrm.21891] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
As expected from the generalized sampling theorem of Papoulis, the use of a bunched sampling acquisition scheme in conjunction with a conjugate gradient (CG) reconstruction algorithm can decrease scan time by reducing the number of phase-encoding lines needed to generate an unaliased image at a given resolution. However, the acquisition of such bunched data requires both modified pulse sequences and high gradient performance. A novel method of generating the "bunched" data using self-calibrating GRAPPA operator gridding (GROG), a parallel imaging method that shifts data points by small distances in k-space (with Deltak usually less than 1.0, depending on the receiver coil) using the GRAPPA operator, is presented here. With the CG reconstruction method, these additional "bunched" points can then be used to reconstruct an image with reduced artifacts from undersampled data. This method is referred to as GROG-facilitated bunched phase encoding (BPE), or GROG-BPE. To better understand how the patterns of bunched points, maximal blip size, and number of bunched points affect the reconstruction quality, a number of simulations were performed using the GROG-BPE approach. Finally, to demonstrate that this method can be combined with a variety of trajectories, examples of images with reduced artifacts reconstructed from undersampled in vivo radial, spiral, and rosette data are shown.
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Affiliation(s)
- Nicole Seiberlich
- Department of Radiology, University Hospitals of Cleveland, Cleveland, Ohio 44106, USA.
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Nordbeck P, Weiss I, Ehses P, Ritter O, Warmuth M, Fidler F, Herold V, Jakob PM, Ladd ME, Quick HH, Bauer WR. Measuring RF-induced currents inside implants: Impact of device configuration on MRI safety of cardiac pacemaker leads. Magn Reson Med 2009; 61:570-8. [DOI: 10.1002/mrm.21881] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Nordbeck P, Fidler F, Weiss I, Warmuth M, Friedrich MT, Ehses P, Geistert W, Ritter O, Jakob PM, Ladd ME, Quick HH, Bauer WR. Spatial distribution of RF-induced E-fields and implant heating in MRI. Magn Reson Med 2008; 60:312-9. [PMID: 18666101 DOI: 10.1002/mrm.21475] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Peter Nordbeck
- Medizinische Klinik und Poliklinik I, Universität Würzburg, Würzburg, Germany.
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Ehses P, Fidler F, Nordbeck P, Pracht ED, Warmuth M, Jakob PM, Bauer WR. MRI thermometry: Fast mapping of RF-induced heating along conductive wires. Magn Reson Med 2008; 60:457-61. [PMID: 18570323 DOI: 10.1002/mrm.21417] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Philipp Ehses
- Physikalisches Institut (EP 5), Universität Würzburg, Würzburg, Germany.
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Ceymann A, Horstmann M, Ehses P, Schweimer K, Paschke AK, Steinert M, Faber C. Solution structure of the Legionella pneumophila Mip-rapamycin complex. BMC Struct Biol 2008; 8:17. [PMID: 18366641 PMCID: PMC2311308 DOI: 10.1186/1472-6807-8-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Accepted: 03/17/2008] [Indexed: 11/28/2022]
Abstract
Background Legionella pneumphila is the causative agent of Legionnaires' disease. A major virulence factor of the pathogen is the homodimeric surface protein Mip. It shows peptidyl-prolyl cis/trans isomerase activty and is a receptor of FK506 and rapamycin, which both inhibit its enzymatic function. Insight into the binding process may be used for the design of novel Mip inhibitors as potential drugs against Legionnaires' disease. Results We have solved the solution structure of free Mip77–213 and the Mip77–213-rapamycin complex by NMR spectroscopy. Mip77–213 showed the typical FKBP-fold and only minor rearrangements upon binding of rapamycin. Apart from the configuration of a flexible hairpin loop, which is partly stabilized upon binding, the solution structure confirms the crystal structure. Comparisons to the structures of free FKBP12 and the FKBP12-rapamycin complex suggested an identical binding mode for both proteins. Conclusion The structural similarity of the Mip-rapamycin and FKBP12-rapamycin complexes suggests that FKBP12 ligands may be promising starting points for the design of novel Mip inhibitors. The search for a novel drug against Legionnaires' disease may therefore benefit from the large variety of known FKBP12 inhibitors.
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Affiliation(s)
- Andreas Ceymann
- Department of Experimental Physics 5, University of Würzburg, Würzburg, Germany.
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Horstmann M, Ehses P, Schweimer K, Steinert M, Kamphausen T, Fischer G, Hacker J, Rösch P, Faber C. Domain motions of the Mip protein from Legionella pneumophila. Biochemistry 2006; 45:12303-11. [PMID: 17014083 DOI: 10.1021/bi060818i] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The homodimeric 45.6 kDa (total mass) Mip protein, a virulence factor from Legionella pneumophila, was investigated with solution NMR spectroscopy and molecular dynamics (MD) simulations. Two Mip monomers are dimerized via an N-terminal helix bundle that is connected via a long alpha-helix to a C-terminal FKBP domain in each subunit. More than 85% of the amino acids were identified in triple-resonance NMR spectra. (15)N relaxation analysis showed a bimodal distribution of R(1)/R(2) values, with the lower ratio in the N-terminal domain. Relaxation dispersion measurements confirmed that these reduced ratios did not originate from conformational exchange. Thus, two different correlation times (tau(c)) can be deduced, reflecting partly uncoupled motions of both domains. Relaxation data of a Mip(77)(-)(213) monomer mutant were similar to those observed in the dimer, corroborating that the FKBP domain, including part of the connecting helix, behaves as one dynamic entity. MD simulations (18 ns) of the Mip dimer also yielded two different correlation times for the two domains and thus confirm the independence of the domain motions. Principal component analysis of the dihedral space covariance matrix calculated from the MD trajectory suggests a flexible region in the long connecting helix that acts as a hinge between the two domains. Such motion provides a possible explanation of how Mip can bind to complex molecular components of the extracellular matrix and mediate alveolar damage and bacterial spread in the lung.
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Affiliation(s)
- Martin Horstmann
- Lehrstuhl für Experimentelle Physik 5, Universität Würzburg, Würzburg, Germany
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