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Shin S, Yun SD, Shah NJ. T2* quantification using multi-echo gradient echo sequences: a comparative study of different readout gradients. Sci Rep 2023; 13:1138. [PMID: 36670286 PMCID: PMC9860026 DOI: 10.1038/s41598-023-28265-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
To quantify T2*, multiple echoes are typically acquired with a multi-echo gradient echo sequence using either monopolar or bipolar readout gradients. The use of bipolar readout gradients achieves a shorter echo spacing time, enabling the acquisition of a larger number of echoes in the same scan time. However, despite their relative time efficiency and the potential for more accurate quantification, a comparative investigation of these readout gradients has not yet been addressed. This work aims to compare the performance of monopolar and bipolar readout gradients for T2* quantification. The differences in readout gradients were theoretically investigated with a Cramér-Rao lower bound and validated with computer simulations with respect to the various imaging parameters (e.g., flip angle, TR, TE, TE range, and BW). The readout gradients were then compared at 3 T using phantom and in vivo experiments. The bipolar readout gradients provided higher precision than monopolar readout gradients in both computer simulations and experimental results. The difference between the two readout gradients increased for a lower SNR and smaller TE range, consistent with the prediction made using Cramér-Rao lower bound. The use of bipolar readout gradients is advantageous for regions or situations where a lower SNR is expected or a shorter acquisition time is required.
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Affiliation(s)
- Seonyeong Shin
- grid.8385.60000 0001 2297 375XInstitute of Neuroscience and Medicine 4, Forschungszentrum Jülich, INM-4, 52428 Jülich, Germany ,grid.1957.a0000 0001 0728 696XRWTH Aachen University, Aachen, Germany
| | - Seong Dae Yun
- grid.8385.60000 0001 2297 375XInstitute of Neuroscience and Medicine 4, Forschungszentrum Jülich, INM-4, 52428 Jülich, Germany
| | - N. Jon Shah
- grid.8385.60000 0001 2297 375XInstitute of Neuroscience and Medicine 4, Forschungszentrum Jülich, INM-4, 52428 Jülich, Germany ,grid.1957.a0000 0001 0728 696XRWTH Aachen University, Aachen, Germany ,grid.494742.8Institute of Neuroscience and Medicine 11, JARA, Forschungszentrum Jülich, INM-11, Jülich, Germany ,JARA-BRAIN-Translational Medicine, Aachen, Germany ,grid.1957.a0000 0001 0728 696XDepartment of Neurology, RWTH Aachen University, Aachen, Germany
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2
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C Thomas D, Oros-Peusquens AM, Poot D, Shah NJ. Whole-Brain Water Content Mapping Using Super-Resolution Reconstruction with MRI Acquisition in 3 Orthogonal Orientations. Magn Reson Med 2022; 88:2117-2130. [PMID: 35861258 DOI: 10.1002/mrm.29377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/11/2022]
Abstract
PURPOSE Brain water content provides rich tissue contrast comparable to that of longitudinal relaxation time T1 , but mapping is usually performed at modest resolution. In particular, the slice thickness in 2D mapping methods is limited. Here, we combine super-resolution reconstruction techniques with a fast water content mapping method to acquire high and isotropic resolution (0.75 mm) water content maps at 3 Tesla. METHODS A high-resolution multi-echo gradient echo image is super-resolution-reconstructed from 3 low-resolution, orthogonal multi-echo gradient echo image acquisitions, followed by water content mapping. The mapping accuracy and SNR of the proposed method are assessed using numerical simulations, phantom studies, and in vivo data acquired from 6 healthy volunteers at 3 Tesla. A high-resolution acquisition with an established mapping method is used as a reference. RESULTS Whole-brain water content maps with 0.75 mm isotropic resolution are demonstrated. No bias in the water content values was seen following super-resolution reconstruction. In the in vivo experiments, a lower SD of the mean water content values was observed with the proposed method compared to the reference method. CONCLUSIONS Super-resolution reconstruction of multi-echo gradient echo data is demonstrated, enabling whole-brain water content mapping with high and isotropic resolution. The accuracy of the proposed method is shown using phantoms and 6 healthy volunteers and was found to be unchanged compared to the conventional acquisition. The proposed method could increase the sensitivity of water content mapping sufficiently to enable the detection of very small lesions, such as cortical lesions in multiple sclerosis.
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Affiliation(s)
- Dennis C Thomas
- Institute of Neuroscience and Medicine 4, Jülich, Germany.,Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | | | - Dirk Poot
- Department of Radiology and Nuclear medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - N Jon Shah
- Institute of Neuroscience and Medicine 4, Jülich, Germany.,Institute of Neuroscience and Medicine 11, INM-11, JARA, Jülich, Germany.,JARA - BRAIN - Translational Medicine, Aachen, Germany.,Department of Neurology, RWTH Aachen University, Aachen, Germany
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3
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Küppers F, Yun SD, Shah NJ. Development of a novel 10-echo multi-contrast sequence based on EPIK to deliver simultaneous quantification of T 2 and T 2 * with application to oxygen extraction fraction. Magn Reson Med 2022; 88:1608-1623. [PMID: 35657054 DOI: 10.1002/mrm.29305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/14/2022] [Accepted: 04/26/2022] [Indexed: 11/05/2022]
Abstract
PURPOSE The simultaneous quantification of T2 and T2 * maps based on fast sequences for combined GE and SE acquisition has rekindled research and clinical interest by offering a wide range of attractive applications, e.g., dynamic tracking of oxygen extraction fraction (OEF). However, previously published methods based on EPI-readouts have been hindered by resolution and the number of acquired echoes. METHODS This work presents a novel 10-echo GE-SE EPIK (EPI with keyhole) sequence for the rapid quantification of T2 '. T2 /T2 * maps from the GE-SE EPIK sequence were validated using three phantoms and 15 volunteers at 3T. The incorporation of a sliding window approach, combined with the full sampling of the k-space center inherent to EPIK, enables a high effective temporal resolution. That is, for an eight-slice breath-hold experiment, a temporal sampling rate of eight reconstructed slices per 1.1 s. RESULTS In comparison with repeated single-echo SE, multi-echo GE, and spectroscopy methods, the GE-SE EPIK sequence shows good agreement in quantifying T2 /T2 * values, while the gray matter/white matter separation yielded the expected contrast differentiation. The OEF was calculated with a view to an initial application with clinical relevance, producing results comparable to those in the literature and with good sensitivity in breath-hold experiments. CONCLUSIONS GE-SE EPIK provides increased resolution and more echoes, including two SEs, than comparable sequences. Moreover, GE-SE EPIK achieves this within an acquisition time of 57 s for 20 slices (matrix size = 128×128; FOV = 24 cm) and with a reasonably short TE for the final echo (114 ms). The sequence can dynamically track OEF changes in a breath-hold experiment.
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Affiliation(s)
- Fabian Küppers
- Institute of Neuroscience and Medicine 4, INM-4, Forschungszentrum Jülich, Jülich, Germany.,RWTH Aachen University, Aachen, Germany
| | - Seong Dae Yun
- Institute of Neuroscience and Medicine 4, INM-4, Forschungszentrum Jülich, Jülich, Germany
| | - N Jon Shah
- Institute of Neuroscience and Medicine 4, INM-4, Forschungszentrum Jülich, Jülich, Germany.,Institute of Neuroscience and Medicine 11, INM-11, JARA, Forschungszentrum Jülich, Jülich, Germany.,JARA - BRAIN - Translational Medicine, Aachen, Germany.,Department of Neurology, RWTH Aachen University, Aachen, Germany
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4
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Trotier AJ, Dilharreguy B, Anandra S, Corbin N, Lefrançois W, Ozenne V, Miraux S, Ribot EJ. The Compressed Sensing MP2RAGE as a Surrogate to the MPRAGE for Neuroimaging at 3 T. Invest Radiol 2022; 57:366-378. [PMID: 35030106 PMCID: PMC9390231 DOI: 10.1097/rli.0000000000000849] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/08/2021] [Indexed: 11/26/2022]
Abstract
OBJECTIVES The magnetization-prepared 2 rapid acquisition gradient echo (MP2RAGE) sequence provides quantitative T1 maps in addition to high-contrast morphological images. Advanced acceleration techniques such as compressed sensing (CS) allow its acquisition time to be compatible with clinical applications. To consider its routine use in future neuroimaging protocols, the repeatability of the segmented brain structures was evaluated and compared with the standard morphological sequence (magnetization-prepared rapid gradient echo [MPRAGE]). The repeatability of the T1 measurements was also assessed. MATERIALS AND METHODS Thirteen healthy volunteers were scanned either 3 or 4 times at several days of interval, on a 3 T clinical scanner, with the 2 sequences (CS-MP2RAGE and MPRAGE), set with the same spatial resolution (0.8-mm isotropic) and scan duration (6 minutes 21 seconds). The reconstruction time of the CS-MP2RAGE outputs (including the 2 echo images, the MP2RAGE image, and the T1 map) was 3 minutes 33 seconds, using an open-source in-house algorithm implemented in the Gadgetron framework.Both precision and variability of volume measurements obtained from CAT12 and VolBrain were assessed. The T1 accuracy and repeatability were measured on phantoms and on humans and were compared with literature.Volumes obtained from the CS-MP2RAGE and the MPRAGE images were compared using Student t tests (P < 0.05 was considered significant). RESULTS The CS-MP2RAGE acquisition provided morphological images of the same quality and higher contrasts than the standard MPRAGE images. Similar intravolunteer variabilities were obtained with the CS-MP2RAGE and the MPRAGE segmentations. In addition, high-resolution T1 maps were obtained from the CS-MP2RAGE. T1 times of white and gray matters and several deep gray nuclei are consistent with the literature and show very low variability (<1%). CONCLUSIONS The CS-MP2RAGE can be used in future protocols to rapidly obtain morphological images and quantitative T1 maps in 3-dimensions while maintaining high repeatability in volumetry and relaxation times.
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Affiliation(s)
- Aurélien J. Trotier
- From the Centre de Résonance Magnétique des Systèmes Biologiques, UMR5536, CNRS/Université de Bordeaux
| | - Bixente Dilharreguy
- Biomedical Imaging Facility (pIBIO), UMS3767, CNRS/Université de Bordeaux, Bordeaux, France
| | - Serge Anandra
- Biomedical Imaging Facility (pIBIO), UMS3767, CNRS/Université de Bordeaux, Bordeaux, France
| | - Nadège Corbin
- From the Centre de Résonance Magnétique des Systèmes Biologiques, UMR5536, CNRS/Université de Bordeaux
- UCL Queen Square Institute of Neurology, Wellcome Centre for Human Neuroimaging, University College of London, London, United Kingdom
| | - William Lefrançois
- From the Centre de Résonance Magnétique des Systèmes Biologiques, UMR5536, CNRS/Université de Bordeaux
| | - Valery Ozenne
- From the Centre de Résonance Magnétique des Systèmes Biologiques, UMR5536, CNRS/Université de Bordeaux
| | - Sylvain Miraux
- From the Centre de Résonance Magnétique des Systèmes Biologiques, UMR5536, CNRS/Université de Bordeaux
| | - Emeline J. Ribot
- From the Centre de Résonance Magnétique des Systèmes Biologiques, UMR5536, CNRS/Université de Bordeaux
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5
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O'Reilly T, Webb AG. In vivo T 1 and T 2 relaxation time maps of brain tissue, skeletal muscle, and lipid measured in healthy volunteers at 50 mT. Magn Reson Med 2021; 87:884-895. [PMID: 34520068 PMCID: PMC9292835 DOI: 10.1002/mrm.29009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/12/2021] [Accepted: 08/27/2021] [Indexed: 11/10/2022]
Abstract
PURPOSE Low-field (B0 < 0.1 T) MRI has generated much interest as a means of increased accessibility via reduced cost and improved portability compared to conventional clinical systems (B0 ≥ 1.5 Tesla). Here we measure MR relaxation times at 50 mT and compare results with commonly used models based on both in vivo and ex vivo measurements. METHODS Using 3D turbo spin echo readouts, T1 and T2 maps of the human brain and lower leg were acquired on a custom-built 50 mT MRI scanner using inversion-recovery and multi-echo-based sequences, respectively. Image segmentation was performed based on a histogram analysis of the relaxation times. RESULTS The average T1 times of gray matter, white matter, and cerebrospinal fluid (CSF) were 327 ± 10 ms, 275 ± 5 ms, and 3695 ± 287 ms, respectively. Corresponding values of T2 were 102 ± 6 ms, 102 ± 6 ms, and 1584 ± 124 ms. T1 times in the calf muscle were measured to be 171 ± 11 ms and were 130 ± 5 ms in subcutaneous and bone marrow lipid. Corresponding T2 times were 39 ± 2 ms in muscle and 90 ± 13 ms in lipid. CONCLUSIONS For tissues except for CSF, the measured T1 times are much shorter than reported at higher fields and generally lie within the range of different models in the literature. As expected, T2 times are similar to those seen at typical clinical field strengths. Analysis of the relaxation maps indicates that segmentation of white and gray matter based purely on T1 or T2 will be quite challenging at low field given the relatively small difference in relaxation times.
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Affiliation(s)
- Thomas O'Reilly
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Andrew G Webb
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
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6
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Kobayashi N, Parkinson B, Idiyatullin D, Adriany G, Theilenberg S, Juchem C, Garwood M. Development and validation of 3D MP-SSFP to enable MRI in inhomogeneous magnetic fields. Magn Reson Med 2020; 85:831-844. [PMID: 32892400 DOI: 10.1002/mrm.28469] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/19/2020] [Accepted: 07/16/2020] [Indexed: 01/27/2023]
Abstract
PURPOSE We demonstrate the feasibility of MRI with missing-pulse steady-state free precession (MP-SSFP) in a 4T magnet with artificially degraded homogeneity. METHODS T1 , T2 , and diffusion contrast of MP-SSFP was simulated with constant and alternate radiofrequency (RF) phase using an extended phase graph. To validate MP-SSFP performance in human brain imaging, MP-SSFP was tested with two types of artificially introduced inhomogeneous magnetic fields: (1) a pure linear gradient field, and (2) a pseudo-linear gradient field introduced by mounting a head-gradient set at 36 cm from the magnet isocenter. Image distortion induced by the nonlinear inhomogeneous field was corrected using B0 mapping measured with MP-SSFP. RESULTS The maximum flip angle in MP-SSFP was limited to ≤10° because of the large range of resonance frequencies in the inhomogeneous magnetic fields tested in this study. Under this flip-angle limitation, MP-SSFP with constant RF phase provided advantages of higher signal-to-noise ratio and insensitivity to B1 + field inhomogeneity as compared with an alternate RF phase. In diffusion simulation, the steady-state magnetization in constant RF phase MP-SSFP increased with an increase of static field gradient up to 8 to 21 mT/m depending on simulation parameters. Experimental results at 4T validated these findings. In human brain imaging, MP-SSFP preserved sufficient signal intensities, but images showed severe image distortion from the pseudo-linear inhomogeneous field. However, following distortion correction, good-quality brain images were achieved. CONCLUSION MP-SSFP appears to be a feasible MRI technique for brain imaging in an inhomogeneous magnetic field.
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Affiliation(s)
- Naoharu Kobayashi
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ben Parkinson
- Robinson Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Djaudat Idiyatullin
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Gregor Adriany
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Christoph Juchem
- Department of Biomedical Engineering, Columbia University, New York, New York, USA.,Department of Radiology, Columbia University, New York, New York, USA
| | - Michael Garwood
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
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7
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Chanet N, Guillot G, Willoquet G, Jourdain L, Dubuisson RM, Reganha G, de Rochefort L. Design of a fast field-cycling magnetic resonance imaging system, characterization and methods for relaxation dispersion measurements around 1.5 T. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:024102. [PMID: 32113406 DOI: 10.1063/1.5128851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
The dependence of the nuclear magnetic resonance relaxation rate on the magnetic field has been widely studied, in particular, in biomedical areas with the objectives to better understand the underlying microscopic mechanisms in tissues and provide biomarkers of diseases. By combining fast-field cycling (FFC) and magnetic resonance imaging (MRI), it is possible to provide localized relaxation dispersion measurements in heterogeneous systems with recent demonstrations in solutions, biological samples, human beings, and small animals. We report here the developments and performances of a device designed for small animal FFC-MRI comprising a resistive insert technology operating inside a 1.5 T MRI system. Specific measurement methods were developed to characterize the system efficiency, response time, homogeneity, stability, and compensation. By adding a non-linear element in the system and using a dual amplifier strategy, it is shown that large field offsets can be produced during relaxation periods while maintaining precise field control during detection periods. The measurement of longitudinal nuclear magnetic relaxation dispersion (NMRD) profiles in the range of 1.08 T-1.92 T is reported, essentially displaying a linear variation in this range for common MRI contrast agents. The slopes of both the longitudinal and transverse relaxation dispersion profiles at 1.5 T are measured and validated, extending the capabilities of previous approaches. The performances of a longitudinal relaxation dispersion mapping method are finally reported, opening the way to quantitative preclinical dispersion imaging studies at a high FFC-MRI field.
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Affiliation(s)
- Nicolas Chanet
- Imagerie par Résonance Magnétique Médicale et Multi-Modalités (UMR8081) IR4M, CNRS, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Geneviève Guillot
- Imagerie par Résonance Magnétique Médicale et Multi-Modalités (UMR8081) IR4M, CNRS, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Georges Willoquet
- Imagerie par Résonance Magnétique Médicale et Multi-Modalités (UMR8081) IR4M, CNRS, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Laurène Jourdain
- Imagerie par Résonance Magnétique Médicale et Multi-Modalités (UMR8081) IR4M, CNRS, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Rose-Marie Dubuisson
- Imagerie par Résonance Magnétique Médicale et Multi-Modalités (UMR8081) IR4M, CNRS, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Gaël Reganha
- Imagerie par Résonance Magnétique Médicale et Multi-Modalités (UMR8081) IR4M, CNRS, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Ludovic de Rochefort
- Aix-Marseille University, CNRS, CRMBM (Center for Magnetic Resonance in Biology and Medicine-UMR 7339), Marseille, France
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8
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Oros-Peusquens AM, Loução R, Abbas Z, Gras V, Zimmermann M, Shah NJ. A Single-Scan, Rapid Whole-Brain Protocol for Quantitative Water Content Mapping With Neurobiological Implications. Front Neurol 2019; 10:1333. [PMID: 31920951 PMCID: PMC6934004 DOI: 10.3389/fneur.2019.01333] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 12/02/2019] [Indexed: 12/16/2022] Open
Abstract
Water concentration is tightly regulated in the healthy human brain and changes only slightly with age and gender in healthy subjects. Consequently, changes in water content are important for the characterization of disease. MRI can be used to measure changes in brain water content, but as these changes are usually in the low percentage range, highly accurate and precise methods are required for detection. The method proposed here is based on a long-TR (10 s) multiple-echo gradient-echo measurement with an acquisition time of 7:21 min. Using such a long TR ensures that there is no T1 weighting, meaning that the image intensity at zero echo time is only proportional to the water content, the transmit field, and to the receive field. The receive and transmit corrections, which are increasingly large at higher field strengths and for highly segmented coil arrays, are multiplicative and can be approached heuristically using a bias field correction. The method was tested on 21 healthy volunteers at 3T field strength. Calibration using cerebral-spinal fluid values (~100% water content) resulted in mean values and standard deviations of the water content distribution in white matter and gray matter of 69.1% (1.7%) and 83.7% (1.2%), respectively. Measured distributions were coil-independent, as seen by using either a 12-channel receiver coil or a 32-channel receiver coil. In a test-retest investigation using 12 scans on one volunteer, the variation in the mean value of water content for different tissue types was ~0.3% and the mean voxel variability was ~1%. Robustness against reduced SNR was assessed by comparing results for 5 additional volunteers at 1.5T and 3T. Furthermore, water content distribution in gray matter is investigated and regional contrast reported for the first time. Clinical applicability is illustrated with data from one stroke patient and one brain tumor patient. It is anticipated that this fast, stable, easy-to-use, high-quality mapping method will facilitate routine quantitative MR imaging of water content.
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Affiliation(s)
| | - Ricardo Loução
- Institute of Neurosciences and Medicine 4 (INM-4), Forschungszentrum Jülich, Jülich, Germany
| | - Zaheer Abbas
- Institute of Neurosciences and Medicine 4 (INM-4), Forschungszentrum Jülich, Jülich, Germany
| | - Vincent Gras
- Institute of Neurosciences and Medicine 4 (INM-4), Forschungszentrum Jülich, Jülich, Germany
| | - Markus Zimmermann
- Institute of Neurosciences and Medicine 4 (INM-4), Forschungszentrum Jülich, Jülich, Germany
| | - N J Shah
- Institute of Neurosciences and Medicine 4 (INM-4), Forschungszentrum Jülich, Jülich, Germany.,Institute of Neurosciences and Medicine 11 (INM-11), JARA, Forschungszentrum Jülich, Jülich, Germany.,JARA - BRAIN - Translational Medicine, Aachen, Germany.,Department of Neurology, RWTH Aachen University, Aachen, Germany
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9
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Zimmermann M, Oros-Peusquens AM, Iordanishvili E, Shin S, Yun SD, Abbas Z, Shah NJ. Multi-Exponential Relaxometry Using l 1 -Regularized Iterative NNLS (MERLIN) With Application to Myelin Water Fraction Imaging. IEEE TRANSACTIONS ON MEDICAL IMAGING 2019; 38:2676-2686. [PMID: 30990178 DOI: 10.1109/tmi.2019.2910386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A new parameter estimation algorithm, MERLIN, is presented for accurate and robust multi-exponential relaxometry using magnetic resonance imaging, a tool that can provide valuable insight into the tissue microstructure of the brain. Multi-exponential relaxometry is used to analyze the myelin water fraction and can help to detect related diseases. However, the underlying problem is ill-conditioned, and as such, is extremely sensitive to noise and measurement imperfections, which can lead to less precise and more biased parameter estimates. MERLIN is a fully automated, multi-voxel approach that incorporates state-of-the-art l1 -regularization to enforce sparsity and spatial consistency of the estimated distributions. The proposed method is validated in simulations and in vivo experiments, using a multi-echo gradient-echo (MEGE) sequence at 3 T. MERLIN is compared to the conventional single-voxel l2 -regularized NNLS (rNNLS) and a multi-voxel extension with spatial priors (rNNLS + SP), where it consistently showed lower root mean squared errors of up to 70 percent for all parameters of interest in these simulations.
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10
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Liao Y, Oros-Peusquens AM, Lindemeyer J, Lechea N, Weiß-Lucas C, Langen KJ, Shah NJ. An MR technique for simultaneous quantitative imaging of water content, conductivity and susceptibility, with application to brain tumours using a 3T hybrid MR-PET scanner. Sci Rep 2019; 9:88. [PMID: 30643159 PMCID: PMC6331621 DOI: 10.1038/s41598-018-36435-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 11/21/2018] [Indexed: 12/29/2022] Open
Abstract
Approaches for the quantitative mapping of water content, electrical conductivity and susceptibility have been developed independently. The purpose of this study is to develop a method for simultaneously acquiring quantitative water content, electrical conductivity and susceptibility maps based on a 2D multi-echo gradient echo sequence. Another purpose is to investigate the changes in these properties caused by brain tumours. This was done using a 3T hybrid magnetic resonance imaging and positron emission tomography (MR-PET) scanner. Water content maps were derived after performing T2* and transmit-receive field bias corrections to magnitude images essentially reflecting only the H2O content contrast. Phase evolution during the multi-echo train was used to generate field maps and derive quantitative susceptibility, while the conductivity maps were retrieved from the phase value at zero echo time. Performance of the method is demonstrated on phantoms and two healthy volunteers. In addition, the method was applied to three patients with brain tumours and a comparison to maps obtained from PET using O-(2-[18 F]fluoroethyl)-L-tyrosine and clinical MR images is presented. The combined information of the water content, conductivity and susceptibility may provide additional information about the tissue viability. Future studies can benefit from the evaluation of these contrasts with shortened acquisition times.
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Affiliation(s)
- Yupeng Liao
- Institute of Neuroscience and Medicine-4, Forschungszentrum Jülich, Jülich, Germany
| | | | - Johannes Lindemeyer
- Institute of Neuroscience and Medicine-4, Forschungszentrum Jülich, Jülich, Germany
| | - Nazim Lechea
- Institute of Neuroscience and Medicine-4, Forschungszentrum Jülich, Jülich, Germany
| | - Carolin Weiß-Lucas
- Department of Neurosurgery, University Hospital Cologne, Cologne, Germany
| | - Karl-Josef Langen
- Institute of Neuroscience and Medicine-4, Forschungszentrum Jülich, Jülich, Germany.,Department of Nuclear Medicine, RWTH Aachen University Clinic, Aachen, Germany.,JARA-Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - N Jon Shah
- Institute of Neuroscience and Medicine-4, Forschungszentrum Jülich, Jülich, Germany.,Department of Neurology, RWTH Aachen University Clinic, Aachen, Germany.,JARA-Faculty of Medicine, RWTH Aachen University, Aachen, Germany
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11
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Fieremans E, Lee HH. Physical and numerical phantoms for the validation of brain microstructural MRI: A cookbook. Neuroimage 2018; 182:39-61. [PMID: 29920376 PMCID: PMC6175674 DOI: 10.1016/j.neuroimage.2018.06.046] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 06/08/2018] [Accepted: 06/13/2018] [Indexed: 12/24/2022] Open
Abstract
Phantoms, both numerical (software) and physical (hardware), can serve as a gold standard for the validation of MRI methods probing the brain microstructure. This review aims to provide guidelines on how to build, implement, or choose the right phantom for a particular application, along with an overview of the current state-of-the-art of phantoms dedicated to study brain microstructure with MRI. For physical phantoms, we discuss the essential requirements and relevant characteristics of both the (NMR visible) liquid and (NMR invisible) phantom materials that induce relevant microstructural features detectable via MRI, based on diffusion, intra-voxel incoherent motion, magnetization transfer or magnetic susceptibility weighted contrast. In particular, for diffusion MRI, many useful phantoms have been proposed, ranging from simple liquids to advanced biomimetic phantoms consisting of hollow or plain microfibers and capillaries. For numerical phantoms, the focus is on Monte Carlo simulations of random walk, for which the basic principles, along with useful criteria to check and potential pitfalls are reviewed, in addition to a literature overview highlighting recent advances. While many phantoms exist already, the current review aims to stimulate further research in the field and to address remaining needs.
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Affiliation(s)
- Els Fieremans
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA.
| | - Hong-Hsi Lee
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA
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12
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Schall M, Zimmermann M, Iordanishvili E, Gu Y, Shah NJ, Oros-Peusquens AM. A 3D two-point method for whole-brain water content and relaxation time mapping: Comparison with gold standard methods. PLoS One 2018; 13:e0201013. [PMID: 30161125 PMCID: PMC6116981 DOI: 10.1371/journal.pone.0201013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/06/2018] [Indexed: 12/23/2022] Open
Abstract
Quantitative imaging of the human brain is of great interest in clinical research as it enables the identification of a range of MR biomarkers useful in diagnosis, treatment and prognosis of a wide spectrum of diseases. Here, a 3D two-point method for water content and relaxation time mapping is presented and compared to established gold standard methods. The method determines free water content, H2O, and the longitudinal relaxation time, T1, quantitatively from a two-point fit to the signal equation including corrections of the transmit and receive fields. In addition, the effective transverse relaxation time, T2*, is obtained from an exponential fit to the multi-echo signal train and its influence on H2O values is corrected. The phantom results obtained with the proposed method show good agreement for H2O and T1 values with known and spectroscopically measured values, respectively. The method is compared in vivo to already established gold standard quantitative methods. For H2O and T2* mapping, the 3D two-point results were compared to a measurement conducted with a multiple-echo GRE with long TR and T1 is compared to results from a Look-Locker method, TAPIR. In vivo results show good overall agreement between the methods, but some systematic deviations are present. Besides an expected dependence of T2* on voxel size, T1 values are systematically larger in the 3D approach than those obtained with the gold standard method. This behaviour might be due to imperfect spoiling, influencing each method differently. Results for H2O differ due to differences in the saturation of cerebrospinal fluid and partial volume effects. In addition, ground truth values of in vivo studies are unknown, even when comparing to in vivo gold standard methods. A detailed region-of-interest analysis for H2O and T1 matches well published literature values.
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Affiliation(s)
- Melissa Schall
- Institute of Neuroscience and Medicine 4 (INM-4), Research Centre Jülich, Jülich, Germany
| | - Markus Zimmermann
- Institute of Neuroscience and Medicine 4 (INM-4), Research Centre Jülich, Jülich, Germany
| | - Elene Iordanishvili
- Institute of Neuroscience and Medicine 4 (INM-4), Research Centre Jülich, Jülich, Germany
| | - Yun Gu
- Institute of Neuroscience and Medicine 4 (INM-4), Research Centre Jülich, Jülich, Germany
| | - N. Jon Shah
- Institute of Neuroscience and Medicine 4 (INM-4), Research Centre Jülich, Jülich, Germany
- Institute of Neuroscience and Medicine 11 (INM-11), Research Centre Jülich, Jülich, Germany
- Jülich Aachen Research Alliance (JARA-BRAIN)—TranslationalMedicine, Aachen, Germany
- Department of Neurology of the RWTH Aachen University, Aachen, Germany
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13
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Oros-Peusquens A, Loução R, Zimmermann M, Langen KJ, Shah N. Methods for molecular imaging of brain tumours in a hybrid MR-PET context: Water content, T 2 ∗ , diffusion indices and FET-PET. Methods 2017; 130:135-151. [DOI: 10.1016/j.ymeth.2017.07.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/22/2017] [Accepted: 07/27/2017] [Indexed: 11/27/2022] Open
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14
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Baudrexel S, Nöth U, Schüre JR, Deichmann R. T1
mapping with the variable flip angle technique: A simple correction for insufficient spoiling of transverse magnetization. Magn Reson Med 2017; 79:3082-3092. [DOI: 10.1002/mrm.26979] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Simon Baudrexel
- Brain Imaging Center; Goethe University Frankfurt; Frankfurt/Main Germany
- Department of Neurology; Goethe University Frankfurt; Frankfurt/Main Germany
| | - Ulrike Nöth
- Brain Imaging Center; Goethe University Frankfurt; Frankfurt/Main Germany
| | - Jan-Rüdiger Schüre
- Department of Neuroradiology; Goethe University Frankfurt; Frankfurt/Main Germany
| | - Ralf Deichmann
- Brain Imaging Center; Goethe University Frankfurt; Frankfurt/Main Germany
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15
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Jiang Y, Liu F, Fan M, Li X, Zhao Z, Zeng Z, Wang Y, Xu D. Deducing magnetic resonance neuroimages based on knowledge from samples. Comput Med Imaging Graph 2017; 62:1-14. [PMID: 28807363 DOI: 10.1016/j.compmedimag.2017.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 05/25/2017] [Accepted: 07/27/2017] [Indexed: 10/19/2022]
Abstract
PURPOSE Because individual variance always exists, using the same set of predetermined parameters for magnetic resonance imaging (MRI) may not be exactly suitable for each participant. We propose a knowledge-based method that can repair MRI data of undesired contrast as if a new scan were acquired using imaging parameters that had been individually optimized. METHODS The method employed a strategy called analogical reasoning to deduce voxel-wise relaxation properties using morphological and biological similarity. The proposed framework involves steps of intensity normalization, tissue segmentation, relaxation time deducing, and image deducing. RESULTS This approach has been preliminarily validated using conventional MRI data at 3T from several examples, including 5 normal and 9 clinical datasets. It can effectively improve the contrast of real MRI data by deducing imaging data using optimized imaging parameters based on deduced relaxation properties. The statistics of deduced images shows a high correlation with real data that were actually collected using the same set of imaging parameters. CONCLUSION The proposed method of deducing MRI data using knowledge of relaxation times alternatively provides a way of repairing MRI data of less optimal contrast. The method is also capable of optimizing an MRI protocol for individual participants, thereby realizing personalized MR imaging.
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Affiliation(s)
- Yuwei Jiang
- Shanghai Key Laboratory of Magnetic Resonance, MOE & Shanghai Key Laboratory of Brain Functional Genomics, Institute of Cognitive Neuroscience, East China Normal University, Shanghai 200062, PR China; Department of Psychiatry, Columbia University & Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, 10032, USA
| | - Feng Liu
- Department of Psychiatry, Columbia University & Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, 10032, USA
| | - Mingxia Fan
- Shanghai Key Laboratory of Magnetic Resonance, MOE & Shanghai Key Laboratory of Brain Functional Genomics, Institute of Cognitive Neuroscience, East China Normal University, Shanghai 200062, PR China
| | - Xuzhou Li
- Shanghai Key Laboratory of Magnetic Resonance, MOE & Shanghai Key Laboratory of Brain Functional Genomics, Institute of Cognitive Neuroscience, East China Normal University, Shanghai 200062, PR China; Department of Psychiatry, Columbia University & Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, 10032, USA
| | - Zhiyong Zhao
- Shanghai Key Laboratory of Magnetic Resonance, MOE & Shanghai Key Laboratory of Brain Functional Genomics, Institute of Cognitive Neuroscience, East China Normal University, Shanghai 200062, PR China
| | - Zhaoling Zeng
- Shanghai University of Electric Power, Shanghai 200090, PR China
| | - Yi Wang
- MRI Research Institute, Radiology Department, Cornell University, New York, NY 10012, USA
| | - Dongrong Xu
- Department of Psychiatry, Columbia University & Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, 10032, USA.
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16
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Nöth U, Shrestha M, Schüre JR, Deichmann R. Quantitative in vivo T2 mapping using fast spin echo techniques - A linear correction procedure. Neuroimage 2017; 157:476-485. [PMID: 28602814 DOI: 10.1016/j.neuroimage.2017.06.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 11/16/2022] Open
Abstract
A method is presented for correcting the effects of stimulated and indirect echoes on quantitative T2 mapping data acquired with multiple spin echo techniques, such as turbo spin echo. In contrast to similar correction techniques proposed in the literature, the method does not require a priori knowledge of the radio frequency (RF) pulse profiles. In a first step, for the T2 mapping protocol under investigation, signal decay curves S(TE) are simulated for a range of different RF pulse profiles. The actual signal decay S(TE) is then measured on a phantom with known T2, so the approximate RF pulse profiles can be derived via comparison with the simulated decay curves. In a second step, with the RF pulses obtained from step one, signal decay curves S(TE) are simulated for different T2 values and fitted mono-exponentially, thus allowing to deduce the relationship between true T2 and the apparent T2 (T2app) values. Results show that this relationship is approximately linear, allowing for a direct correction of T2app maps. If the amplitude of the transmitted RF field (B1) does not exceed the nominal value by more than 10%, it is shown that a B1-independent correction of T2app maps yields sufficiently accurate results for T2. A B1-dependent version is also presented. The method is tested in vitro on a phantom with different T2 values and in vivo on healthy subjects.
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Affiliation(s)
- Ulrike Nöth
- Brain Imaging Center (BIC), Goethe University Frankfurt, Schleusenweg 2-16, D-60528 Frankfurt am Main, Germany.
| | - Manoj Shrestha
- Brain Imaging Center (BIC), Goethe University Frankfurt, Schleusenweg 2-16, D-60528 Frankfurt am Main, Germany
| | - Jan-Rüdiger Schüre
- Department of Neuroradiology, Goethe University Frankfurt, Schleusenweg 2-16, D-60528 Frankfurt am Main, Germany
| | - Ralf Deichmann
- Brain Imaging Center (BIC), Goethe University Frankfurt, Schleusenweg 2-16, D-60528 Frankfurt am Main, Germany
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17
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Segmenting and validating brain tissue definitions in the presence of varying tissue contrast. Magn Reson Imaging 2016; 35:98-116. [PMID: 27569366 DOI: 10.1016/j.mri.2016.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 08/06/2016] [Accepted: 08/20/2016] [Indexed: 11/23/2022]
Abstract
We propose a method for segmenting brain tissue as either gray matter or white matter in the presence of varying tissue contrast, which can derive from either differential changes in tissue water content or increasing myelin content of white matter. Our method models the spatial distribution of intensities as a Markov Random Field (MRF) and estimates the parameters for the MRF model using a maximum likelihood approach. Although previously described methods have used similar models to segment brain tissue, accurate model of the conditional probabilities of tissue intensities and adaptive estimates of tissue properties to local intensities generates tissue definitions that are accurate and robust to variations in tissue contrast with age and across illnesses. Robustness to variations in tissue contrast is important to understand normal brain development and to identify the brain bases of neurological and psychiatric illnesses. We used simulated brains of varying tissue contrast to compare both visually and quantitatively the performance of our method with the performance of prior methods. We assessed validity of the cortical definitions by associating cortical thickness with various demographic features, clinical measures, and medication use in our three large cohorts of participants who were either healthy or who had Bipolar Disorder (BD), Autism Spectrum Disorder (ASD), or familial risk for Major Depressive Disorder (MDD). We assessed validity of the tissue definitions using synthetic brains and data for three large cohort of individuals with various neuropsychiatric disorders. Visual inspection and quantitative analyses showed that our method accurately and robustly defined the cortical mantle in brain images with varying contrast. Furthermore, associating the thickness with various demographic and clinical measures generated findings that were novel and supported by histological analyses or were supported by previous MRI studies, thereby validating the cortical definitions generated by the proposed method: (1) Although cortical thickness decreased with age in adolescents, in adults cortical thickness did not correlate significantly with age. Our synthetic data showed that the previously reported thinning of cortex in adults is likely due to decease in tissue contrast, thereby suggesting that the method generated cortical definitions in adults that were invariant to tissue contrast. In adolescents, cortical thinning with age was preserved likely due to widespread dendritic and synaptic pruning, even though the effects of decreasing tissue contrast were minimized. (3) The method generated novel finding of both localized increases and decreases in thickness of males compared to females after controlling for the differing brain sizes, which are supported by the histological analyses of brain tissue in males and females. (4) The proposed method, unlike prior methods, defined thicker cortex in BD individuals using lithium. The novel finding is supported by the studies that showed lithium treatment increased dendritic arborization and neurogenesis, thereby leading to thickening of cortex. (5) In both BD and ASD participants, associations of more severe symptoms with thinner cortex showed that correcting for the effects of tissue contrast preserved the biological consequences of illnesses. Therefore, consistency of the findings across the three large cohorts of participants, in images acquired on either 1.5T or 3T MRI scanners, and with findings from prior histological analyses provides strong evidence that the proposed method generated valid and accurate definitions of the cortex while controlling for the effects of tissue contrast.
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18
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Lauzon ML, McCreary CR, Frayne R. Multislice T1 -prepared 2D single-shot EPI: analysis of a clinical T1 mapping method unbiased by B0 or B1 inhomogeneity. NMR IN BIOMEDICINE 2016; 29:1056-1069. [PMID: 27331861 DOI: 10.1002/nbm.3566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 06/06/2023]
Abstract
Quantitative MR imaging is as sensitive in detecting lesions as qualitative imaging, but it is potentially more specific in differentiating disease. T1 mapping in particular might help to assess acute ischemic stroke, multiple sclerosis, epilepsy and Alzheimer's disease better. Thus, a rapid and robust clinical technique is vital. In 1990, Ordidge and colleagues developed the multislice T1 -prepared two-dimensional (2D) single-shot echo planar imaging technique. Subsequent studies demonstrated its clinical viability, but none performed an in-depth analysis of the strengths and advantages of this T1 mapping method. Herein, theoretical and experimental evidence shows that the technique accounts for 2D slice profile effects and is unbiased by B0 or B1 inhomogeneity. This is verified explicitly by varying the linear shims, the T1 preparation flip angle and the excitation flip angle. Furthermore, it is shown that the repetition time (and hence scan time) can be reduced without a loss of T1 accuracy. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- M Louis Lauzon
- Seaman Family MR Research Centre, Foothills Medical Centre, Calgary, AB, Canada
- Depts of Radiology and Clinical Neurosciences, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Cheryl R McCreary
- Seaman Family MR Research Centre, Foothills Medical Centre, Calgary, AB, Canada
- Depts of Radiology and Clinical Neurosciences, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Richard Frayne
- Seaman Family MR Research Centre, Foothills Medical Centre, Calgary, AB, Canada
- Depts of Radiology and Clinical Neurosciences, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
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19
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Gras V, Farrher E, Grinberg F, Shah NJ. Diffusion-weighted DESS protocol optimization for simultaneous mapping of the mean diffusivity, proton density and relaxation times at 3 Tesla. Magn Reson Med 2016; 78:130-141. [PMID: 27476684 DOI: 10.1002/mrm.26353] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 06/16/2016] [Accepted: 07/01/2016] [Indexed: 01/09/2023]
Abstract
PURPOSE To design a general framework for the optimization of an MRI protocol based on the the diffusion-weighted dual-echo steady-state (DW-DESS) sequence, enabling quantitative and simultaneous mapping of proton density (PD), relaxation times T1 and T2 and diffusion coefficient D. METHODS A parameterization of the DW-DESS sequence minimizing the Cramér-Rao lower bound of each parameter estimate was proposed and tested in a phantom experiment. An extension of the protocol was implemented for brain imaging to return the rotationally invariant mean diffusivity (MD). RESULTS In an NiCl2 -doped agar gel phantom wherein T1/T2=920/65 ms, the parameter estimation errors were below 3% for PD and T1 and below 7% for T2 and D while the measured signal-to-noise ratio always exceeded 20. In the human brain, the in vivo parametric maps obtained were overall in reasonable agreement with gold standard measurements, despite a broadening of the distributions due to physiological motion. CONCLUSION Within the optimization framework presented here, DW-DESS images can be quantitatively interpreted to yield four intrinsic parameters of the tissue. Currently, the method is limited by the sensitivity of the DW-DESS sequence in terms of physiological motion. Magn Reson Med 78:130-141, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Vincent Gras
- Institute of Neuroscience and Medicine - 4, Medical Imaging Physics, Forschungszentrum Jülich GmbH, Jülich, Germany.,UNIRS, Institut d'Imagerie Biomédicale, Neurospin, CEA Saclay, Gif-sur-Yvette, France
| | - Ezequiel Farrher
- Institute of Neuroscience and Medicine - 4, Medical Imaging Physics, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Farida Grinberg
- Institute of Neuroscience and Medicine - 4, Medical Imaging Physics, Forschungszentrum Jülich GmbH, Jülich, Germany.,Department of Neurology, Faculty of Medicine, JARA, RWTH Aachen University, Aachen, Germany
| | - N Jon Shah
- Institute of Neuroscience and Medicine - 4, Medical Imaging Physics, Forschungszentrum Jülich GmbH, Jülich, Germany.,Department of Neurology, Faculty of Medicine, JARA, RWTH Aachen University, Aachen, Germany
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20
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Jutras JD, Wachowicz K, Gilbert G, De Zanche N. SNR efficiency of combined bipolar gradient echoes: Comparison of three-dimensional FLASH, MPRAGE, and multiparameter mapping with VFA-FLASH and MP2RAGE. Magn Reson Med 2016; 77:2186-2202. [DOI: 10.1002/mrm.26306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Jean-David Jutras
- Department of Oncology; University of Alberta; Edmonton Alberta Canada
| | - Keith Wachowicz
- Department of Oncology; University of Alberta; Edmonton Alberta Canada
- Department of Medical Physics; Cross Cancer Institute; Edmonton Alberta Canada
| | - Guillaume Gilbert
- MR Clinical Science; Philips Healthcare Canada; Markham Ontario Canada
| | - Nicola De Zanche
- Department of Oncology; University of Alberta; Edmonton Alberta Canada
- Department of Medical Physics; Cross Cancer Institute; Edmonton Alberta Canada
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21
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Gracien RM, Nürnberger L, Hok P, Hof SM, Reitz SC, Rüb U, Steinmetz H, Hilker-Roggendorf R, Klein JC, Deichmann R, Baudrexel S. Evaluation of brain ageing: a quantitative longitudinal MRI study over 7 years. Eur Radiol 2016; 27:1568-1576. [PMID: 27379992 DOI: 10.1007/s00330-016-4485-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/27/2016] [Accepted: 06/21/2016] [Indexed: 12/31/2022]
Abstract
OBJECTIVES T1 relaxometry is a promising tool for the assessment of microstructural changes during brain ageing. Previous cross-sectional studies demonstrated increasing T1 values in white and decreasing T1 values in grey matter over the lifetime. However, these findings have not yet been confirmed on the basis of a longitudinal study. In this longitudinal study over 7 years, T1 relaxometry was used to investigate the dynamics of age-related microstructural changes in older healthy subjects. METHODS T1 mapping was performed in 17 healthy subjects (range 51-77 years) at baseline and after 7 years. Advanced cortical and white matter segmentation was used to determine mean T1 values in the cortex and white matter. RESULTS The analysis revealed a decrease of mean cortical T1 values over 7 years, the rate of T1 reduction being more prominent in subjects with higher age. T1 decreases were predominantly localized in the lateral frontal, parietal and temporal cortex. In contrast, mean white matter T1 values remained stable. CONCLUSIONS T1 mapping is shown to be sensitive to age-related microstructural changes in healthy ageing subjects in a longitudinal setting. Data of a cohort in late adulthood and the senescence period demonstrate a decrease of cortical T1 values over 7 years, most likely reflecting decreasing water content and increased iron concentrations. KEY POINTS • T1 mapping is sensitive to age-related microstructural changes in a longitudinal setting. • T1 decreases were predominantly localized in the lateral frontal, parietal and temporal cortex. • The rate of T1 reduction was more prominent in subjects with higher age. • These changes most likely reflect decreasing cortical water and increasing iron concentrations.
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Affiliation(s)
- René-Maxime Gracien
- Department of Neurology, Goethe University, Frankfurt/Main, Germany. .,Brain Imaging Center, Goethe University, Frankfurt/Main, Germany.
| | - Lucas Nürnberger
- Department of Neurology, Goethe University, Frankfurt/Main, Germany.,Brain Imaging Center, Goethe University, Frankfurt/Main, Germany
| | - Pavel Hok
- Department of Neurology, Goethe University, Frankfurt/Main, Germany.,Brain Imaging Center, Goethe University, Frankfurt/Main, Germany.,Department of Neurology, Palacky University, Olomouc, Czech Republic
| | - Stephanie-Michelle Hof
- Department of Neurology, Goethe University, Frankfurt/Main, Germany.,Brain Imaging Center, Goethe University, Frankfurt/Main, Germany
| | - Sarah C Reitz
- Department of Neurology, Goethe University, Frankfurt/Main, Germany.,Brain Imaging Center, Goethe University, Frankfurt/Main, Germany
| | - Udo Rüb
- Dr. Senckenberg Chronomedical Institute, Goethe University, Frankfurt/Main, Germany
| | | | - Rüdiger Hilker-Roggendorf
- Department of Neurology, Goethe University, Frankfurt/Main, Germany.,Brain Imaging Center, Goethe University, Frankfurt/Main, Germany
| | - Johannes C Klein
- Department of Neurology, Goethe University, Frankfurt/Main, Germany.,Brain Imaging Center, Goethe University, Frankfurt/Main, Germany.,Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Ralf Deichmann
- Brain Imaging Center, Goethe University, Frankfurt/Main, Germany
| | - Simon Baudrexel
- Department of Neurology, Goethe University, Frankfurt/Main, Germany.,Brain Imaging Center, Goethe University, Frankfurt/Main, Germany
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22
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Van Steenkiste G, Poot DHJ, Jeurissen B, den Dekker AJ, Vanhevel F, Parizel PM, Sijbers J. Super‐resolution
T
1
estimation: Quantitative high resolution
T
1
mapping from a set of low resolution
T
1
‐weighted images with different slice orientations. Magn Reson Med 2016; 77:1818-1830. [DOI: 10.1002/mrm.26262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 04/11/2016] [Accepted: 04/11/2016] [Indexed: 11/06/2022]
Affiliation(s)
| | - Dirk H. J. Poot
- Imaging Science and Technology, Delft University of Technology2628 CJDelft The Netherlands
- BIGR (Department of Medical informatics and Radiology)Erasmus Medical Center RotterdamRotterdam The Netherlands
| | - Ben Jeurissen
- iMinds‐Vision LabDepartment of Physics, University of AntwerpAntwerp Belgium
| | - Arnold J. den Dekker
- iMinds‐Vision LabDepartment of Physics, University of AntwerpAntwerp Belgium
- Delft Center for Systems and Control, Delft University of Technology2628CD Delft The Netherlands
| | - Floris Vanhevel
- Department of RadiologyUniversity of Antwerp, Antwerp University Hospital Belgium
| | - Paul M. Parizel
- Department of RadiologyUniversity of Antwerp, Antwerp University Hospital Belgium
| | - Jan Sijbers
- iMinds‐Vision LabDepartment of Physics, University of AntwerpAntwerp Belgium
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23
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Jutras JD, Wachowicz K, De Zanche N. Analytical corrections of banding artifacts in driven equilibrium single pulse observation of T2 (DESPOT2). Magn Reson Med 2015; 76:1790-1804. [PMID: 26714609 DOI: 10.1002/mrm.26074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/05/2015] [Accepted: 11/15/2015] [Indexed: 11/10/2022]
Abstract
PURPOSE DESPOT2 is a single-component T2 mapping technique based on bSSFP imaging. It has seen limited application because of banding artifacts and magnetization transfer (MT) effects. In this work, acquisitions are optimized to minimize MT effects, while exact and approximate analytical equations enable automatic correction of banding artifacts within the T2 maps in mere seconds. THEORY AND METHODS The technique was verified on an agar phantom at 3 tesla. The T2 resulting from four different data combination techniques was compared with the T2 from CPMG. Two comparable DESPOT2 scan protocols (short vs. long TR/TRF ) designed to minimize MT effects, were tested both in the phantom and in vivo. A third protocol was tested in the brain of 8 volunteers and analytical correction schemes were compared with DESPOT2-FM. RESULTS The T2 measurements in agar agree with CPMG within ∼7% and in vivo results agree with values reported in the literature. The approximate analytical solutions provide increased robustness to hardware imperfections and higher T2 -to-noise ratio than the exact solutions. CONCLUSION New analytical solutions enable fast and accurate whole-brain T2 mapping from previously measured T1 and B1 maps, and bSSFP images with at least two phase offsets and two flip angles (=4 datasets, 8 min scan). Magn Reson Med 76:1790-1804, 2016. © 2015 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Jean-David Jutras
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Keith Wachowicz
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Physics, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Nicola De Zanche
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Physics, Cross Cancer Institute, Edmonton, Alberta, Canada
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24
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Kim J, Wu Y, Guo Y, Zheng H, Sun PZ. A review of optimization and quantification techniques for chemical exchange saturation transfer MRI toward sensitive in vivo imaging. CONTRAST MEDIA & MOLECULAR IMAGING 2015; 10:163-178. [PMID: 25641791 DOI: 10.1002/cmmi.1628] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/26/2014] [Accepted: 09/10/2014] [Indexed: 01/10/2023]
Abstract
Chemical exchange saturation transfer (CEST) MRI is a versatile imaging method that probes the chemical exchange between bulk water and exchangeable protons. CEST imaging indirectly detects dilute labile protons via bulk water signal changes following selective saturation of exchangeable protons, which offers substantial sensitivity enhancement and has sparked numerous biomedical applications. Over the past decade, CEST imaging techniques have rapidly evolved owing to contributions from multiple domains, including the development of CEST mathematical models, innovative contrast agent designs, sensitive data acquisition schemes, efficient field inhomogeneity correction algorithms, and quantitative CEST (qCEST) analysis. The CEST system that underlies the apparent CEST-weighted effect, however, is complex. The experimentally measurable CEST effect depends not only on parameters such as CEST agent concentration, pH and temperature, but also on relaxation rate, magnetic field strength and more importantly, experimental parameters including repetition time, RF irradiation amplitude and scheme, and image readout. Thorough understanding of the underlying CEST system using qCEST analysis may augment the diagnostic capability of conventional imaging. In this review, we provide a concise explanation of CEST acquisition methods and processing algorithms, including their advantages and limitations, for optimization and quantification of CEST MRI experiments.
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Affiliation(s)
- Jinsuh Kim
- Department of Radiology, University of Iowa, Iowa City, IA, USA
| | - Yin Wu
- Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Key Laboratory for MRI, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Yingkun Guo
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Hairong Zheng
- Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Key Laboratory for MRI, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Phillip Zhe Sun
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
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IVIM analysis of brain tumors: an investigation of the relaxation effects of CSF, blood, and tumor tissue on the estimated perfusion fraction. MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE 2014; 28:377-83. [PMID: 25475914 DOI: 10.1007/s10334-014-0474-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 11/16/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
Abstract
OBJECT We sought to investigate the dependence of intravoxel incoherent motion (IVIM)-related perfusion fraction (f) estimates on the transverse relaxation of brain tissue, blood, and cerebrospinal fluid (CSF), attempting to overcome the influence of CSF on conventional f maps. MATERIALS AND METHODS Eighteen patients with gliomas underwent DWI with 14 b-values (0-1,300 s/mm(2)) and two distinct echo times (TEs). Regions of interest representing tumour and normal brain tissue were analysed by calculating the f values for both TEs. A mask for pixels with relevant CSF partial volume was subsequently created. The f values were tested for significant differences. RESULTS We found statistically significant differences between the two TEs in the f values for cortical and juxtacortical structures and non-enhancing areas of the tumour /oedema. Normal white matter and gadolinium-enhancing tumour tissue appeared insensitive to TE variation. In all tissue types examined, the masking of voxels with considerable CSF content was able to overcome issues of erroneous f estimation and calculation of f values insensitive to TE changes was feasible. CONCLUSION Due to the complex interaction in the relaxation rates of CSF, blood, and tumour tissue, the estimation of f values is affected by the choice of TE. Only f values in normal white matter and tumour tissue--which largely comprise blood voxels with minor CSF partial volume--may be clinically applicable in the present form of IVIM-based DWI analysis. Going a step further, and after removing voxels with heavily TE-susceptible f values, we were able to obtain accurate and TE-independent f values in contrast-enhancing tumour tissue, white matter, and grey matter, which were essentially consistent with those reported in the literature.
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Brynolfsson P, Yu J, Wirestam R, Karlsson M, Garpebring A. Combining phase and magnitude information for contrast agent quantification in dynamic contrast-enhanced MRI using statistical modeling. Magn Reson Med 2014; 74:1156-64. [DOI: 10.1002/mrm.25490] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/10/2014] [Accepted: 09/17/2014] [Indexed: 02/04/2023]
Affiliation(s)
| | - Jun Yu
- Department of Mathematics and Mathematical Statistics; Umeå University; Umeå Sweden
| | - Ronnie Wirestam
- Department of Medical Radiation Physics; Lund University; Lund Sweden
| | - Mikael Karlsson
- Department of Radiation Physics; Umeå University; Umeå Sweden
| | - Anders Garpebring
- Department of Radiation Physics; Umeå University; Umeå Sweden
- CJ Gorter Center for High Field MRI; Leiden University Medical Center; Leiden Netherlands
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Hirsch NM, Toth V, Förschler A, Kooijman H, Zimmer C, Preibisch C. Technical considerations on the validity of blood oxygenation level-dependent-based MR assessment of vascular deoxygenation. NMR IN BIOMEDICINE 2014; 27:853-862. [PMID: 24809665 DOI: 10.1002/nbm.3131] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 06/03/2023]
Abstract
A blood oxygenation level-dependent (BOLD)-based apparent relative oxygen extraction fraction (rOEF) as a semi-quantitative marker of vascular deoxygenation has recently been introduced in clinical studies of patients with glioma and stroke, yielding promising results. These rOEF measurements are based on independent quantification of the transverse relaxation times T2 and T2* and relative cerebral blood volume (rCBV). Simulations demonstrate that small errors in any of the underlying measures may result in a large deviation of the calculated rOEF. Therefore, we investigated the validity of such measurements. For this, we evaluated the quantitative measurements of T2 and T2* at 3 T in a gel phantom, in healthy subjects and in healthy tissue of patients with brain tumors. We calculated rOEF maps covering large portions of the brain from T2, T2* and rCBV [routinely measured in patients using dynamic susceptibility contrast (DSC)], and obtained rOEF values of 0.63 ± 0.16 and 0.90 ± 0.21 in healthy-appearing gray matter (GM) and white matter (WM), respectively; values of about 0.4 are usually reported. Quantitative T2 mapping using the fast, clinically feasible, multi-echo gradient spin echo (GRASE) approach yields significantly higher values than much slower multiple single spin echo (SE) experiments. Although T2* mapping is reliable in magnetically homogeneous tissues, uncorrectable macroscopic background gradients and other effects (e.g. iron deposition) shorten T2*. Cerebral blood volume (CBV) measurement using DSC and normalization to WM yields robust estimates of rCBV in healthy-appearing brain tissue; absolute quantification of the venous fraction of CBV, however, is difficult to achieve. Our study demonstrates that quantitative measurements of rOEF are currently biased by inherent difficulties in T2 and CBV quantification, but also by inadequacies of the underlying model. We argue, however, that standardized, reproducible measurements of apparent T2, T2* and rCBV may still allow the estimation of a meaningful apparent rOEF, which requires further validation in clinical studies.
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Affiliation(s)
- Nuria M Hirsch
- Department of Neuroradiology, Technische Universität München, Munich, Germany
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Hocq A, Luhmer M, Saussez S, Louryan S, Gillis P, Gossuin Y. Effect of magnetic field and iron content on NMR proton relaxation of liver, spleen and brain tissues. CONTRAST MEDIA & MOLECULAR IMAGING 2014; 10:144-52. [PMID: 24954138 DOI: 10.1002/cmmi.1610] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 05/02/2014] [Accepted: 05/22/2014] [Indexed: 12/13/2022]
Abstract
Iron accumulation is observed in liver and spleen during hemochromatosis and important neurodegenerative diseases involve iron overload in brain. Storage of iron is ensured by ferritin, which contains a magnetic core. It causes a darkening on T2 -weighted MR images. This work aims at improving the understanding of the NMR relaxation of iron-loaded human tissues, which is necessary to develop protocols of iron content measurements by MRI. Relaxation times measurements on brain, liver and spleen samples were realized at different magnetic fields. Iron content was determined by atomic emission spectroscopy. For all samples, the longitudinal relaxation rate (1/T1 ) of tissue protons decreases with the magnetic field up to 1 T, independently of iron content, while their transverse relaxation rate (1/T2 ) strongly increases with the field, either linearly or quadratically, or a combination thereof. The extent of the inter-echo time dependence of 1/T2 also varies according to the sample. A combination of theoretical models is necessary to describe the relaxation of iron-containing tissues. This can be due to the presence, inside tissues, of ferritin clusters of different sizes and densities. When considering all samples, a correlation (r(2) = 0.6) between 1/T1 and iron concentration is observed at 7.0 T. In contrast the correlation between 1/T2 and iron content is poor, even at high field (r(2) = 0.14 at 7.0 T). Our results show that MRI methods based on T1 or T2 measurements will easily detect an iron overloading at high magnetic field, but will not provide an accurate quantification of tissue iron content at low iron concentrations.
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Affiliation(s)
- Aline Hocq
- Biomedical Physics Department, UMONS, 7000, Mons, Belgium
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Abbas Z, Gras V, Möllenhoff K, Keil F, Oros-Peusquens AM, Shah NJ. Analysis of proton-density bias corrections based on T1 measurement for robust quantification of water content in the brain at 3 Tesla. Magn Reson Med 2014; 72:1735-45. [PMID: 24436248 DOI: 10.1002/mrm.25086] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 11/25/2013] [Accepted: 11/25/2013] [Indexed: 11/07/2022]
Abstract
PURPOSE Estimating tissue water content using high field MRI, such as 3 Tesla (T), is challenging due to the difficulty in dissociating the radio frequency inhomogeneity pattern from the signal arising from tissue intrinsic proton density (PD) variations. To overcome this problem the longitudinal relaxation time T1 can be combined with an initial guess of the PD to yield the desired PD bias correction. However, it is necessary to know whether T1 effects, i.e., any effect contributing to T1 while being independent of tissue hydration, influence the estimated correction. METHODS Twenty-five healthy subjects underwent a quantitative 3T MRI protocol enabling acquisition of 64 slices with 1 mm in-plane resolution and 2 mm slice thickness in 14 min. Influence of T1 effects on the estimated water content map is evaluated using a dedicated method including T1 and T2 * information and region of interest-based water content values are compared with the literature. RESULTS Our analysis indicates that the PD bias correction based on T1 is largely insensitive to T1 effects. Besides, water content results are in good agreement with literature values obtained at 1.5T. CONCLUSION This study demonstrates the applicability of a PD bias correction based on T1 to yield tissue water content at 3T.
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Affiliation(s)
- Zaheer Abbas
- Institute of Neuroscience and Medicine-4, Medical Imaging Physics (INM-4), Research Centre Jülich, Jülich, Germany
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Bansal R, Hao X, Liu F, Xu D, Liu J, Peterson BS. The effects of changing water content, relaxation times, and tissue contrast on tissue segmentation and measures of cortical anatomy in MR images. Magn Reson Imaging 2013; 31:1709-30. [PMID: 24055410 PMCID: PMC4241465 DOI: 10.1016/j.mri.2013.07.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 11/23/2022]
Abstract
Water content is the dominant chemical compound in the brain and it is the primary determinant of tissue contrast in magnetic resonance (MR) images. Water content varies greatly between individuals, and it changes dramatically over time from birth through senescence of the human life span. We hypothesize that the effects that individual- and age-related variations in water content have on contrast of the brain in MR images also have important, systematic effects on in vivo, MRI-based measures of regional brain volumes. We also hypothesize that changes in water content and tissue contrast across time may account for age-related changes in regional volumes, and that differences in water content or tissue contrast across differing neuropsychiatric diagnoses may account for differences in regional volumes across diagnostic groups. We demonstrate in several complementary ways that subtle variations in water content across age and tissue compartments alter tissue contrast, and that changing tissue contrast in turn alters measures of the thickness and volume of the cortical mantle: (1) We derive analytic relations describing how age-related changes in tissue relaxation times produce age-related changes in tissue gray-scale intensity values and tissue contrast; (2) We vary tissue contrast in computer-generated images to assess its effects on tissue segmentation and volumes of gray matter and white matter; and (3) We use real-world imaging data from adults with either Schizophrenia or Bipolar Disorder and age- and sex-matched healthy adults to assess the ways in which variations in tissue contrast across diagnoses affects group differences in tissue segmentation and associated volumes. We conclude that in vivo MRI-based morphological measures of the brain, including regional volumes and measures of cortical thickness, are a product of, or at least are confounded by, differences in tissue contrast across individuals, ages, and diagnostic groups, and that differences in tissue contrast in turn likely derive from corresponding differences in water content of the brain across individuals, ages, and diagnostic groups.
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Affiliation(s)
- Ravi Bansal
- Department of Psychiatry, Columbia College of Physicians and Surgeons and the New York State Psychiatric Institute, New York, NY 10032.
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Stöcker T, Keil F, Vahedipour K, Brenner D, Pracht E, Shah NJ. MR parameter quantification with magnetization-prepared double echo steady-state (MP-DESS). Magn Reson Med 2013; 72:103-11. [PMID: 23913587 DOI: 10.1002/mrm.24901] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/12/2013] [Accepted: 07/02/2013] [Indexed: 11/09/2022]
Abstract
PURPOSE The mapping of MR relaxation times and proton density has been the subject of research in medical imaging for many years, as it offers the possibility for longitudinal investigation of disease and the correlation with related biochemical processes. The purpose of this study is to provide a fast mapping protocol, which simultaneously acquires MR relaxation times and relative proton density without compromising accuracy and precision. METHODS This work presents a novel magnetization-prepared double echo steady-state (MP-DESS) sequence, which was designed to be sensitive to parameter variations of interest, and insensitive to variations of confounding variables. It provides high sensitivity against variations of the MR relaxation times, high acquisition efficiency, and it is insensitive to off-resonance. Accurate phase graph modeling of the MP-DESS signal is used to obtain unbiased parameter estimates. RESULTS The approach is validated in phantom and in vivo measurements. A whole-brain acquisition of 1.4-mm isotropic resolution was acquired in 15 min. Comparisons to gold-standard methods suggest a mapping precision of 5% for T1 and M0 , and below 10% for T2. CONCLUSION A new quantitative imaging technique is introduced that allows fast and isotropic simultaneous MR parameter mapping of T1, T2, and M0.
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Affiliation(s)
- Tony Stöcker
- Institute of Neuroscience and Medicine - 4, Forschungszentrum Juelich, Juelich, Germany
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Diakite M, Odéen H, Todd N, Payne A, Parker DL. Toward real-time temperature monitoring in fat and aqueous tissue during magnetic resonance-guided high-intensity focused ultrasound using a three-dimensional proton resonance frequency T1 method. Magn Reson Med 2013; 72:178-87. [PMID: 23901014 DOI: 10.1002/mrm.24900] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 07/01/2013] [Accepted: 07/01/2013] [Indexed: 11/05/2022]
Abstract
PURPOSE To present a three-dimensional (3D) segmented echoplanar imaging (EPI) pulse sequence implementation that provides simultaneously the proton resonance frequency shift temperature of aqueous tissue and the longitudinal relaxation time (T1 ) of fat during thermal ablation. METHODS The hybrid sequence was implemented by combining a 3D segmented flyback EPI sequence, the extended two-point Dixon fat and water separation, and the double flip angle T1 mapping techniques. High-intensity focused ultrasound (HIFU) heating experiments were performed at three different acoustic powers on excised human breast fat embedded in ex vivo porcine muscle. Furthermore, T1 calibrations with temperature in four different excised breast fat samples were performed, yielding an estimate of the average and variation of dT1 /dT across subjects. RESULTS The water only images were used to mask the complex original data before computing the proton resonance frequency shift. T1 values were calculated from the fat-only images. The relative temperature coefficients were found in five fat tissue samples from different patients and ranged from 1.2% to 2.6%/°C. CONCLUSION The results demonstrate the capability of real-time simultaneous temperature mapping in aqueous tissue and T1 mapping in fat during HIFU ablation, providing a potential tool for treatment monitoring in organs with large fat content, such as the breast.
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Affiliation(s)
- Mahamadou Diakite
- Department of Physics & Astronomy, University of Utah, Salt Lake City, Utah, USA; Department of Radiology, University of Utah, Salt Lake City, Utah, USA
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Ford AA, Colon-Perez L, Triplett WT, Gullett JM, Mareci TH, Fitzgerald DB. Imaging white matter in human brainstem. Front Hum Neurosci 2013; 7:400. [PMID: 23898254 PMCID: PMC3721683 DOI: 10.3389/fnhum.2013.00400] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 07/08/2013] [Indexed: 12/03/2022] Open
Abstract
The human brainstem is critical for the control of many life-sustaining functions, such as consciousness, respiration, sleep, and transfer of sensory and motor information between the brain and the spinal cord. Most of our knowledge about structure and organization of white and gray matter within the brainstem is derived from ex vivo dissection and histology studies. However, these methods cannot be applied to study structural architecture in live human participants. Tractography from diffusion-weighted magnetic resonance imaging (MRI) may provide valuable insights about white matter organization within the brainstem in vivo. However, this method presents technical challenges in vivo due to susceptibility artifacts, functionally dense anatomy, as well as pulsatile and respiratory motion. To investigate the limits of MR tractography, we present results from high angular resolution diffusion imaging of an intact excised human brainstem performed at 11.1 T using isotropic resolution of 0.333, 1, and 2 mm, with the latter reflecting resolution currently used clinically. At the highest resolution, the dense fiber architecture of the brainstem is evident, but the definition of structures degrades as resolution decreases. In particular, the inferred corticopontine/corticospinal tracts (CPT/CST), superior (SCP) and middle cerebellar peduncle (MCP), and medial lemniscus (ML) pathways are clearly discernable and follow known anatomical trajectories at the highest spatial resolution. At lower resolutions, the CST/CPT, SCP, and MCP pathways are artificially enlarged due to inclusion of collinear and crossing fibers not inherent to these three pathways. The inferred ML pathways appear smaller at lower resolutions, indicating insufficient spatial information to successfully resolve smaller fiber pathways. Our results suggest that white matter tractography maps derived from the excised brainstem can be used to guide the study of the brainstem architecture using diffusion MRI in vivo.
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Affiliation(s)
- Anastasia A Ford
- Department of Veterans Affairs Rehabilitation Research and Development Brain Rehabilitation Research Center, Malcom Randall VA Medical Center , Gainesville, FL , USA ; Department of Psychology, University of Florida , Gainesville, FL , USA
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Weiskopf N, Suckling J, Williams G, Correia MM, Inkster B, Tait R, Ooi C, Bullmore ET, Lutti A. Quantitative multi-parameter mapping of R1, PD(*), MT, and R2(*) at 3T: a multi-center validation. Front Neurosci 2013; 7:95. [PMID: 23772204 PMCID: PMC3677134 DOI: 10.3389/fnins.2013.00095] [Citation(s) in RCA: 336] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/18/2013] [Indexed: 02/02/2023] Open
Abstract
Multi-center studies using magnetic resonance imaging facilitate studying small effect sizes, global population variance and rare diseases. The reliability and sensitivity of these multi-center studies crucially depend on the comparability of the data generated at different sites and time points. The level of inter-site comparability is still controversial for conventional anatomical T1-weighted MRI data. Quantitative multi-parameter mapping (MPM) was designed to provide MR parameter measures that are comparable across sites and time points, i.e., 1 mm high-resolution maps of the longitudinal relaxation rate (R1 = 1/T1), effective proton density (PD(*)), magnetization transfer saturation (MT) and effective transverse relaxation rate (R2(*) = 1/T2(*)). MPM was validated at 3T for use in multi-center studies by scanning five volunteers at three different sites. We determined the inter-site bias, inter-site and intra-site coefficient of variation (CoV) for typical morphometric measures [i.e., gray matter (GM) probability maps used in voxel-based morphometry] and the four quantitative parameters. The inter-site bias and CoV were smaller than 3.1 and 8%, respectively, except for the inter-site CoV of R2(*) (<20%). The GM probability maps based on the MT parameter maps had a 14% higher inter-site reproducibility than maps based on conventional T1-weighted images. The low inter-site bias and variance in the parameters and derived GM probability maps confirm the high comparability of the quantitative maps across sites and time points. The reliability, short acquisition time, high resolution and the detailed insights into the brain microstructure provided by MPM makes it an efficient tool for multi-center imaging studies.
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Affiliation(s)
- Nikolaus Weiskopf
- Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, University College LondonLondon, UK,*Correspondence: Nikolaus Weiskopf, Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, University College London, 12 Queen Square, London WC1N 3BG, UK e-mail:
| | - John Suckling
- Department of Psychiatry, University of CambridgeCambridge, UK,Behavioural and Clinical Neuroscience Institute, University of CambridgeCambridge, UK,Cambridgeshire and Peterborough NHS Foundation TrustCambridge, UK
| | - Guy Williams
- Behavioural and Clinical Neuroscience Institute, University of CambridgeCambridge, UK,Department of Clinical Neuroscience, Wolfson Brain Imaging Centre, University of CambridgeCambridge, UK
| | | | - Becky Inkster
- Department of Psychiatry, University of CambridgeCambridge, UK
| | - Roger Tait
- Behavioural and Clinical Neuroscience Institute, University of CambridgeCambridge, UK
| | - Cinly Ooi
- Department of Psychiatry, University of CambridgeCambridge, UK,Behavioural and Clinical Neuroscience Institute, University of CambridgeCambridge, UK
| | - Edward T. Bullmore
- Department of Psychiatry, University of CambridgeCambridge, UK,Behavioural and Clinical Neuroscience Institute, University of CambridgeCambridge, UK,Cambridgeshire and Peterborough NHS Foundation TrustCambridge, UK,GlaxoSmithKline, Clinical Unit Cambridge, Addenbrooke's HospitalCambridge, UK
| | - Antoine Lutti
- Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, University College LondonLondon, UK,Laboratoire de recherche en neuroimagerie, Département des neurosciences cliniques, CHUV, University of LausanneLausanne, Switzerland
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Glasser MF, Goyal MS, Preuss TM, Raichle ME, Van Essen DC. Trends and properties of human cerebral cortex: correlations with cortical myelin content. Neuroimage 2013; 93 Pt 2:165-75. [PMID: 23567887 DOI: 10.1016/j.neuroimage.2013.03.060] [Citation(s) in RCA: 267] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 03/12/2013] [Accepted: 03/23/2013] [Indexed: 10/27/2022] Open
Abstract
"In vivo Brodmann mapping" or non-invasive cortical parcellation using MRI, especially by measuring cortical myelination, has recently become a popular research topic, though myeloarchitectonic cortical parcellation in humans previously languished in favor of cytoarchitecture. We review recent in vivo myelin mapping studies and discuss some of the different methods for estimating myelin content. We discuss some ways in which myelin maps may improve surface registration and be useful for cross-modal and cross-species comparisons, including some preliminary cross-species results. Next, we consider neurobiological aspects of why some parts of cortex are more myelinated than others. Myelin content is inversely correlated with intracortical circuit complexity - in general, more myelin content means simpler and perhaps less dynamic intracortical circuits. Using existing PET data and functional network parcellations, we examine metabolic differences in the differently myelinated cortical functional networks. Lightly myelinated cognitive association networks tend to have higher aerobic glycolysis than heavily myelinated early sensory-motor ones, perhaps reflecting greater ongoing dynamic anabolic cortical processes. This finding is consistent with the hypothesis that intracortical myelination may stabilize intracortical circuits and inhibit synaptic plasticity. Finally, we discuss the future of the in vivo myeloarchitectural field and cortical parcellation--"in vivo Brodmann mapping"--in general.
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Affiliation(s)
- Matthew F Glasser
- Department of Anatomy and Neurobiology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA.
| | - Manu S Goyal
- Department of Radiology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA.
| | - Todd M Preuss
- Division of Neuropharmacology and Neurologic Diseases, Emory University, Atlanta, GA 30329, USA; Center for Translational and Social Neuroscience, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology, Emory University School of Medicine, Atlanta, GA 30329, USA.
| | - Marcus E Raichle
- Department of Anatomy and Neurobiology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Department of Radiology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA.
| | - David C Van Essen
- Department of Anatomy and Neurobiology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA.
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Abstract
In contrast to vision, where retinotopic mapping alone can define areal borders, primary auditory areas such as A1 are best delineated by combining in vivo tonotopic mapping with postmortem cyto- or myeloarchitectonics from the same individual. We combined high-resolution (800 μm) quantitative T(1) mapping with phase-encoded tonotopic methods to map primary auditory areas (A1 and R) within the "auditory core" of human volunteers. We first quantitatively characterize the highly myelinated auditory core in terms of shape, area, cortical depth profile, and position, with our data showing considerable correspondence to postmortem myeloarchitectonic studies, both in cross-participant averages and in individuals. The core region contains two "mirror-image" tonotopic maps oriented along the same axis as observed in macaque and owl monkey. We suggest that these two maps within the core are the human analogs of primate auditory areas A1 and R. The core occupies a much smaller portion of tonotopically organized cortex on the superior temporal plane and gyrus than is generally supposed. The multimodal approach to defining the auditory core will facilitate investigations of structure-function relationships, comparative neuroanatomical studies, and promises new biomarkers for diagnosis and clinical studies.
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Kara F, Chen F, Ronen I, de Groot HJM, Matysik J, Alia A. In vivo measurement of transverse relaxation time in the mouse brain at 17.6 T. Magn Reson Med 2012; 70:985-93. [PMID: 23161407 DOI: 10.1002/mrm.24533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 11/09/2022]
Abstract
PURPOSE To establish regional T1 and T2 values of the healthy mouse brain at ultra-high magnetic field strength of 17.6 T and to follow regional brain T1 and T2 changes with age. METHODS In vivo T1 and T2 values in the C57BL/6J mouse brain were followed with age using multislice-multiecho sequence and multiple spin echo saturation recovery with variable repetition time sequence, respectively, at 9.4 and 17.6 T. Gadolinium-tetra-azacyclo-dodecane-tetra-acetic acid phantoms were used to validate in vivo T2 measurements. Student's t-test was used to compare mean relaxation values. RESULTS A field-dependent decrease in T2 is shown and validated with phantom measurements. T2 values at 17.6 T typically increased with age in multiple brain regions except in the hypothalamus and the caudate-putamen, where a slight decrease was observed. Furthermore, T1 values in various brain regions of young and old mice are presented at 17.6 T. A large gain in signal-to-noise ratio was observed at 17.6 T. CONCLUSIONS This study establishes for the first time the normative T1 and T2 values at 17.6 T over different mouse brain regions with age. The estimates of in vivo T1 and T2 will be useful to optimize pulse sequences for optimal image contrast at 17.6 T and will serve as baseline values against which disease-related relaxation changes can be assessed in mice.
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Affiliation(s)
- Firat Kara
- Solid State NMR, Leiden Institute of Chemistry, Gorlaeus Laboratoria, Leiden, The Netherlands
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He L, Parikh NA. Automated detection of white matter signal abnormality using T2 relaxometry: application to brain segmentation on term MRI in very preterm infants. Neuroimage 2012; 64:328-40. [PMID: 22974556 DOI: 10.1016/j.neuroimage.2012.08.081] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 08/27/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022] Open
Abstract
Hyperintense white matter signal abnormalities, also called diffuse excessive high signal intensity (DEHSI), are observed in up to 80% of very preterm infants on T2-weighted MRI scans at term-equivalent age. DEHSI may represent a developmental stage or diffuse microstructural white matter abnormalities. Automated quantitative assessment of DEHSI severity may help resolve this debate and improve neonatal brain tissue segmentation. For T2-weighted sequence without fluid attenuation, the signal intensity distribution of DEHSI greatly overlaps with that of cerebrospinal fluid (CSF) making its detection difficult. Furthermore, signal intensities of T2-weighted images are susceptible to magnetic field inhomogeneity. Increased signal intensities caused by field inhomogeneity may be confused with DEHSI. To overcome these challenges, we propose an algorithm to detect DEHSI using T2 relaxometry, whose reflection of the rapid changes in free water content provides improved distinction between CSF and DEHSI over that of conventional T2-weighted imaging. Moreover, the parametric transverse relaxation time T2 is invulnerable to magnetic field inhomogeneity. We conducted computer simulations to select an optimal detection parameter and to validate the proposed method. We also demonstrated that brain tissue segmentation is further enhanced by incorporating DEHSI detection for both simulated preterm infant brain images and in vivo in very preterm infants imaged at term-equivalent age.
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Affiliation(s)
- Lili He
- Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43215, USA.
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Investigation of the spatial correlation in human white matter and the influence of age using 3-dimensional variography applied to MP-RAGE data. Neuroimage 2012; 63:1374-83. [PMID: 22836175 DOI: 10.1016/j.neuroimage.2012.07.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 07/11/2012] [Indexed: 10/28/2022] Open
Abstract
A novel method for the quantification of heterogeneity and spatial correlation in 3D MP-RAGE images of white matter is presented. The technique is based on the variogram, a tool commonly used in geosciences for the analysis of spatial data, and was tailored to the special requirements of MR image analysis. Influences from intensity non-uniformities, noise and arbitrary greyscale were quantified and considered in the calculations. The obtained variograms were fitted with spherical model functions to infer parameters that quantify heterogeneity and size of the correlation structures of the tissue. Numerically generated samples with well-defined correlation properties were employed to validate the estimation process and to provide an interpretation of the parameters obtained. It is shown that the method gives reliable results in an interval of correlation structures sized between 2mm and 20mm. The method was applied to 24 MP-RAGE datasets of healthy female volunteers ranging in age from 19 to 73 years. White matter was found to have two prominent correlation structures with sizes of approximately 3mm and 23 mm. The heterogeneity of the smaller structure increases significantly with age (r=0.83, p<10(-6)).
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Chow AM, Gao DS, Fan SJ, Qiao Z, Lee FY, Yang J, Man K, Wu EX. Measurement of liver T1 and T2 relaxation times in an experimental mouse model of liver fibrosis. J Magn Reson Imaging 2012; 36:152-8. [DOI: 10.1002/jmri.23606] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Accepted: 01/10/2012] [Indexed: 12/14/2022] Open
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Brain iron deposition and sequence characteristics in Parkinsonism: comparison of SWI, T₂* maps, T₂-weighted-, and FLAIR-SPACE. Invest Radiol 2011; 45:795-802. [PMID: 20829707 DOI: 10.1097/rli.0b013e3181ec9c96] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To compare quantitatively T2- and T2*-based magnetic resonance imaging sequences in patients with symptoms of Parkinson disease and to evaluate the information content of those sequences regarding brain iron concentration. MATERIALS AND METHODS We imaged 51 patients with symptoms of Parkinson disease on 3-T magnetic resonance imaging with T2-weighted sampling perfection with application optimized contrasts using different flip-angle evolution (SPACE), fluid attenuation inversion recovery (FLAIR)-SPACE, susceptibility-weighted imaging (SWI), and parametric T2* sequence (MapIt). Signal analysis was performed in 22 regions of interest in the brain. RESULTS Correlations (r2 = 0.82...0.96) with brain iron concentration were excellent. Contrast and tissue separability ratios were best in the T2* maps and FLAIR-SPACE, respectively. Good correlations of contrast were reached between SWI and both T2-weighted SPACE and FLAIR-SPACE. Their relation to quantitative T2* values was reminiscent of a quadratic curve shape. However, separation into gray and white matter revealed a linear positive and negative correlation, respectively. CONCLUSIONS SWI showed potential in differentiating illnesses characterized by brain iron deposition. Closely similar information was given by T2-weighted SPACE and FLAIR-SPACE, whereas other sequence comparisons revealed dispersion from intersequence agreement.
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In vivo quantification of T₂ anisotropy in white matter fibers in marmoset monkeys. Neuroimage 2011; 59:979-85. [PMID: 21906687 DOI: 10.1016/j.neuroimage.2011.08.064] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 08/10/2011] [Accepted: 08/21/2011] [Indexed: 12/11/2022] Open
Abstract
T₂-weighted MRI at high field is a promising approach for studying noninvasively the tissue structure and composition of the brain. However, the biophysical origin of T₂ contrast, especially in white matter, remains poorly understood. Recent work has shown that R₂ (=1/T₂) may depend on the tissue's orientation relative to the static magnetic field (B(0)) and suggested that this dependence could be attributed to local anisotropy in the magnetic properties of brain tissue. In the present work, we analyzed high-resolution, multi-gradient-echo images of in vivo marmoset brains at 7T, and compared them with ex vivo diffusion tensor images, to show that R₂ relaxation in white matter is highly sensitive to the fiber orientation relative to the main field. We directly demonstrate this orientation dependence by performing in vivo multi-gradient-echo experiments in two orthogonal brain positions, uncovering a nearly 50% change in the R₂ relaxation rate constant of the optic radiations. We attribute this substantial R₂ anisotropy to local subvoxel susceptibility effects arising from the highly ordered and anisotropic structure of the myelin sheath.
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Croitor Sava AR, Sima DM, Poullet JB, Wright AJ, Heerschap A, Van Huffel S. Exploiting spatial information to estimate metabolite levels in two-dimensional MRSI of heterogeneous brain lesions. NMR IN BIOMEDICINE 2011; 24:824-835. [PMID: 21834006 DOI: 10.1002/nbm.1628] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Revised: 07/15/2010] [Accepted: 09/21/2010] [Indexed: 05/31/2023]
Abstract
MRSI provides MR spectra from multiple adjacent voxels within a body volume represented as a two- or three-dimensional matrix, allowing the measurement of the distribution of metabolites over this volume. The spectra of these voxels are usually analyzed one by one, without exploiting their spatial context. In this article, we present an advanced metabolite quantification method for MRSI data, in which the available spatial information is considered. A nonlinear least-squares algorithm is proposed in which prior knowledge is included in the form of proximity constraints on the spectral parameters within a grid and optimized starting values. A penalty term that promotes a spatially smooth spectral parameter map is added to the fitting algorithm. This method is adaptive, in the sense that several sweeps through the grid are performed and each solution may tune some hyperparameters at run-time. Simulation studies of MRSI data showed significantly improved metabolite estimates after the inclusion of spatial information. Improved metabolite maps were also demonstrated by applying the method to in vivo MRSI data. Overlapping peaks or peaks of compounds present at low concentration can be better quantified with the proposed method than with single-voxel approaches. The new approach compares favorably against the multivoxel approach embedded in the well-known quantification software LCModel.
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Affiliation(s)
- Anca R Croitor Sava
- Department of Electrical Engineering, ESAT-SCD, Katholieke Universiteit Leuven, Leuven, Belgium.
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Shah NJ, Ermer V, Oros-Peusquens AM. Measuring the absolute water content of the brain using quantitative MRI. Methods Mol Biol 2011; 711:29-64. [PMID: 21279597 DOI: 10.1007/978-1-61737-992-5_3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Methods for quantitative imaging of the brain are presented and compared. Highly precise and accurate mapping of the absolute water content and distribution, as presented here, requires a significant number of corrections and also involves mapping of other MR parameters. Here, either T(1) and T(2)(*) or T(2) is mapped, and several corrections involving the measurement of temperature, transmit and receive B(1) inhomogeneities and signal extrapolation to zero TE are applied. Information about the water content of the whole brain can be acquired in clinically acceptable measurement times (10 or 20 min). Since water content is highly regulated in the healthy brain, pathological changes can be easily identified and their evolution or correlation with other manifestations of the disease investigated. In addition to voxel-based total water content, information about the different environments of water can be gleaned from qMRI. The myelin water fraction can be extracted from the fit of very high-SNR multiple-echo T(2) decay curves with a superposition of a large number of exponentials. Diseases involving de- or dysmyelination can be investigated and lead to novel observations regarding the water compartmentalisation in tissue, despite the limited spatial coverage. In conclusion, quantitative MRI is emerging as an unparalleled tool for the study of the normal and diseased brain, replacing the customary time-space environment of the sequential mixed-contrast MRI with a multi-NMR-parametric space in which tissue microscopy is increasingly revealed.
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Affiliation(s)
- Nadim Joni Shah
- Institute of Neuroscience and Medicine (INM-4), Research Centre Juelich, Juelich, Germany.
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45
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Werz K, Braun H, Vitha D, Bruno G, Martirosian P, Steidle G, Schick F. [Relaxation times T1, T2, and T2* of apples, pears, citrus fruits, and potatoes with a comparison to human tissues]. Z Med Phys 2011; 21:206-15. [PMID: 21530199 DOI: 10.1016/j.zemedi.2010.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 11/24/2010] [Accepted: 12/22/2010] [Indexed: 10/17/2022]
Abstract
The aim of the project was a systematic assessment of relaxation times of different fruits and vegetables and a comparison to values of human tissues. Results provide an improved basis for selection of plant phantoms for development of new MR techniques and sequences. Vessels filled with agar gel are mostly used for this purpose, preparation of which is effortful and time-consuming. In the presented study apples, (malus, 8 species), pears, (pyrus, 2 species), citrus fruits (citrus, 5 species) and uncooked potatoes (solanum tuberosum, 8 species) from the supermarket were examined which are easily available nearly all-the-year. T1, T2 and T2* relaxation times of these nature products were measured on a 1.5 Tesla MR system with adapted examination protocols and mono-exponential fitting, and compared to literature data of human parenchyma tissues, fatty tissue and body fluid (cerebrospinal fluid). Resulting values were as follows: apples: T1: 1486-1874 ms, T2: 163-281 ms, T2*: 2.3-3.2 ms; pears: T1: 1631-1969 ms, T2: 119-133 ms, T2* : 10.1-10.6 ms, citrus fruits (pulp) T1: 2055-2632 ms, T2: 497-998 ms, T2* : 151-182 ms; citrus fruits (skin) T1: 561-1669 ms, T2: 93-119 ms; potatoes: T1: 1011-1459 ms, T2: 166 - 210 ms, T2* : 20 - 30 ms. All T1-values of the examined objects (except for potatoes and skins of citrus fruits) were longer than T1 values of human tissues. Also T2 values (except for pears and skins of citrus fruits) of the fruits and the potatoes tended to be longer. T2* values of apples, pears and potatoes were shorter than in healthy human tissue. Results show relaxation values of many fruits to be not exactly fitting to human tissue, but with suitable selection of the fruits and optionally with an adaption of measurement parameters one can achieve suitable contrast and signal characteristics for some purposes.
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Affiliation(s)
- Karin Werz
- Sektion für Experimentelle Radiologie, Abteilung für Diagnostische und Interventionelle Radiologie Eberhard-Karls-Universität Tübingen, Deutschland
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Weiskopf N, Lutti A, Helms G, Novak M, Ashburner J, Hutton C. Unified segmentation based correction of R1 brain maps for RF transmit field inhomogeneities (UNICORT). Neuroimage 2010; 54:2116-24. [PMID: 20965260 PMCID: PMC3018573 DOI: 10.1016/j.neuroimage.2010.10.023] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 10/07/2010] [Accepted: 10/11/2010] [Indexed: 12/26/2022] Open
Abstract
Quantitative mapping of the longitudinal relaxation rate (R1 = 1/T1) in the human brain enables the investigation of tissue microstructure and macroscopic morphology which are becoming increasingly important for clinical and neuroimaging applications. R1 maps are now commonly estimated from two fast high-resolution 3D FLASH acquisitions with variable excitation flip angles, because this approach is fast and does not rely on special acquisition techniques. However, these R1 maps need to be corrected for bias due to RF transmit field (B1+) inhomogeneities, requiring additional B1+ mapping which is usually time consuming and difficult to implement. We propose a technique that simultaneously estimates the B1+ inhomogeneities and R1 values from the uncorrected R1 maps in the human brain without need for B1+ mapping. It employs a probabilistic framework for unified segmentation based correction of R1 maps for B1+ inhomogeneities (UNICORT). The framework incorporates a physically informed generative model of smooth B1+ inhomogeneities and their multiplicative effect on R1 estimates. Extensive cross-validation with the established standard using measured B1+ maps shows that UNICORT yields accurate B1+ and R1 maps with a mean deviation from the standard of less than 4.3% and 5%, respectively. The results of different groups of subjects with a wide age range and different levels of atypical brain anatomy further suggest that the method is robust and generalizes well to wider populations. UNICORT is easy to apply, as it is computationally efficient and its basic framework is implemented as part of the tissue segmentation in SPM8.
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Affiliation(s)
- Nikolaus Weiskopf
- Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, University College London, London, UK.
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Shin W, Geng X, Gu H, Zhan W, Zou Q, Yang Y. Automated brain tissue segmentation based on fractional signal mapping from inversion recovery Look-Locker acquisition. Neuroimage 2010; 52:1347-54. [PMID: 20452444 DOI: 10.1016/j.neuroimage.2010.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 04/28/2010] [Accepted: 05/01/2010] [Indexed: 12/01/2022] Open
Abstract
Most current automated segmentation methods are performed on T(1)- or T(2)-weighted MR images, relying on relative image intensity that is dependent on other MR parameters and sensitive to B(1) magnetic field inhomogeneity. Here, we propose an image segmentation method based on quantitative longitudinal magnetization relaxation time (T(1)) of brain tissues. Considering the partial volume effect, fractional volume maps of brain tissues (white matter, gray matter, and cerebrospinal fluid) were obtained by fitting the observed signal in an inversion recovery procedure to a linear combination of three exponential functions, which represents the relaxations of each of the tissue types. A Look-Locker acquisition was employed to accelerate the acquisition process. The feasibility and efficacy of this proposed method were evaluated using simulations and experiments. The potential applications of this method in the study of neurological disease as well as normal brain development and aging are discussed.
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Affiliation(s)
- Wanyong Shin
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD 21224, USA.
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48
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Kickhefel A, Roland J, Weiss C, Schick F. Accuracy of real-time MR temperature mapping in the brain: a comparison of fast sequences. Phys Med 2010; 26:192-201. [PMID: 20096617 DOI: 10.1016/j.ejmp.2009.11.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 10/29/2009] [Accepted: 11/29/2009] [Indexed: 11/15/2022] Open
Abstract
PURPOSE To compare magnetic resonance (MR) thermometry based on the proton resonance frequency (PRF) method using a single shot echoplanar imaging (ss EPI) sequence to both of the standard sequences, gradient echo (GRE) and segmented echoplanar imaging (seg EPI) in the in vivo human brain, at 1.5T and 3T. MATERIAL AND METHODS Repetitive MR thermometry was performed on the brain of six volunteers using GRE, seg EPI, and ss EPI sequences on whole-body 1.5T and 3T clinical systems using comparable acquisition parameters. Phase stability and temperature data precision in the human head were determined over 12 min for the three sequences at both field strengths. An ex-vivo swine skeletal muscle model was used to evaluate temperature accuracy of the ss EPI sequence during heating by high intensity focused ultrasound (HIFU). RESULTS In-vivo examinations of brain revealed an average temperature precision of 0.37 °C/0.39 °C/0.16 °C at 3T for the GRE/seg EPI/ss EPI sequences. At 1.5T, a precision of 0.58 °C/0.63 °C/0.21 °C was achieved. In the ex-vivo swine model, a strong correlation of temperature data derived using ss EPI and GRE sequences was found with a temperature deviation <1 °C. CONCLUSION The ss EPI sequence was the fastest and the most precise sequence for MR thermometry, with significantly higher accuracy compared to GRE.
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Affiliation(s)
- A Kickhefel
- Siemens Healthcare, H IM MR PLM AW Oncology, FH5/2008, Allee am Röthelheimpark 2, 91052 Erlangen, Germany.
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Flory GS, O'Malley J, Grant KA, Park B, Kroenke CD. Quantification of ethanol methyl (1)H magnetic resonance signal intensity following intravenous ethanol administration in primate brain. Methods 2009; 50:189-98. [PMID: 20018244 DOI: 10.1016/j.ymeth.2009.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 12/08/2009] [Accepted: 12/09/2009] [Indexed: 11/19/2022] Open
Abstract
In vivo(1)H magnetic resonance spectroscopy (MRS) can be used to directly monitor brain ethanol. Previously, studies of human subjects have lead to the suggestion that the ethanol methyl (1)H MRS signal intensity relates to tolerance to ethanol's intoxicating effects. More recently, the ethanol (1)H MRS signal intensity has been recognized to vary between brain gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) due to differences in T(2) within these environments. The methods presented here extend ethanol MRS techniques to non-human primate subjects. Twelve monkeys were administered ethanol while sedated and positioned within a 3T MRI system. Chemical shift imaging (CSI) measurements were performed following intravenous infusion of 1g/kg ethanol. Magnetic resonance imaging (MRI) data were also recorded for each monkey to provide volume fractions of GM, WM, and CSF for each CSI spectrum. To estimate co-variance of ethanol MRS intensity with GM, WM, and CSF volume fractions, the relative contribution of each tissue subtype was determined following corrections for radiofrequency pulse profile non-uniformity, chemical shift artifacts, and differences between the point spread function in the CSI data and the imaging data. The ethanol MRS intensity per unit blood ethanol concentration was found to differ between GM, WM, and CSF. Individual differences in MRS intensity were larger in GM than WM. This methodology demonstrates the feasibility of ethanol MRS experiments and analysis in non-human primate subjects, and suggests GM may be a site of significant variation in ethanol MRS intensity between individuals.
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Affiliation(s)
- Graham S Flory
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
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Qin W, Yu CS, Zhang F, Du XY, Jiang H, Yan YX, Li KC. Effects of echo time on diffusion quantification of brain white matter at 1.5 T and 3.0 T. Magn Reson Med 2009; 61:755-60. [PMID: 19191286 DOI: 10.1002/mrm.21920] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The aim was to investigate the effects of echo time (TE) on diffusion quantification of brain white matter. Seven rhesus monkeys (all males; age, 4-6 years; weight, 5-7 kg) underwent diffusion tensor imaging (DTI) with a series of TEs in 1.5 T and 3.0 T MR scanners. The mean diffusivity (MD), fractional anisotropy (FA), primary (lambda(1)), and transverse eigenvalues (lambda(23)) were measured in a region of interest at the bilateral internal capsule. Pearson correlation showed that the FA and lambda(1) increased and lambda(23) decreased with TE both at 1.5 T and 3.0 T except for the MD. Repeated measurement analysis of variance (ANOVA) also showed significantly higher FA and lower MD and lambda(23) at 3.0 T than those at 1.5 T (P<0.01), but no statistical differences were found in lambda(1) between these two field strengths (P=0.709). These findings implied that TE and field strength might influence diffusion quantification in brain white matter.
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Affiliation(s)
- Wen Qin
- Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing, China
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