1
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Afzali M, Pieciak T, Newman S, Garyfallidis E, Özarslan E, Cheng H, Jones DK. The sensitivity of diffusion MRI to microstructural properties and experimental factors. J Neurosci Methods 2021; 347:108951. [PMID: 33017644 PMCID: PMC7762827 DOI: 10.1016/j.jneumeth.2020.108951] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/27/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022]
Abstract
Diffusion MRI is a non-invasive technique to study brain microstructure. Differences in the microstructural properties of tissue, including size and anisotropy, can be represented in the signal if the appropriate method of acquisition is used. However, to depict the underlying properties, special care must be taken when designing the acquisition protocol as any changes in the procedure might impact on quantitative measurements. This work reviews state-of-the-art methods for studying brain microstructure using diffusion MRI and their sensitivity to microstructural differences and various experimental factors. Microstructural properties of the tissue at a micrometer scale can be linked to the diffusion signal at a millimeter-scale using modeling. In this paper, we first give an introduction to diffusion MRI and different encoding schemes. Then, signal representation-based methods and multi-compartment models are explained briefly. The sensitivity of the diffusion MRI signal to the microstructural components and the effects of curvedness of axonal trajectories on the diffusion signal are reviewed. Factors that impact on the quality (accuracy and precision) of derived metrics are then reviewed, including the impact of random noise, and variations in the acquisition parameters (i.e., number of sampled signals, b-value and number of acquisition shells). Finally, yet importantly, typical approaches to deal with experimental factors are depicted, including unbiased measures and harmonization. We conclude the review with some future directions and recommendations on this topic.
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Affiliation(s)
- Maryam Afzali
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom.
| | - Tomasz Pieciak
- AGH University of Science and Technology, Kraków, Poland; LPI, ETSI Telecomunicación, Universidad de Valladolid, Valladolid, Spain.
| | - Sharlene Newman
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA; Program of Neuroscience, Indiana University, Bloomington, IN 47405, USA.
| | - Eleftherios Garyfallidis
- Program of Neuroscience, Indiana University, Bloomington, IN 47405, USA; Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47408, USA.
| | - Evren Özarslan
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden; Center for Medical Image Science and Visualization, Linköping University, Linköping, Sweden.
| | - Hu Cheng
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA; Program of Neuroscience, Indiana University, Bloomington, IN 47405, USA.
| | - Derek K Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom.
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2
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Fair MJ, Liao C, Manhard MK, Setsompop K. Diffusion-PEPTIDE: Distortion- and blurring-free diffusion imaging with self-navigated motion-correction and relaxometry capabilities. Magn Reson Med 2020; 85:2417-2433. [PMID: 33314281 DOI: 10.1002/mrm.28579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022]
Abstract
PURPOSE To implement the time-resolved relaxometry PEPTIDE technique into a diffusion acquisition to provide self-navigated, distortion- and blurring-free diffusion imaging that is robust to motion, while simultaneously providing T2 and T 2 ∗ mapping. THEORY AND METHODS The PEPTIDE readout was implemented into a spin-echo diffusion acquisition, enabling reconstruction of a time-series of T2 - and T 2 ∗ -weighted images, free from conventional echo planar imaging (EPI) distortion and blurring, for each diffusion-encoding. Robustness of PEPTIDE to motion and shot-to-shot phase variation was examined through a deliberate motion-corrupted diffusion experiment. Two diffusion-relaxometry in vivo brain protocols were also examined: (1)1 × 1 × 3 mm3 across 32 diffusion directions in 20 min, (2)1.5 × 1.5 × 3.0 mm3 across 6 diffusion-weighted images in 3.4 min. T2 , T 2 ∗ , and diffusion parameter maps were calculated from these data. As initial exploration of the rich diffusion-relaxometry data content for use in multi-compartment modeling, PEPTIDE data were acquired of a gadolinium-doped asparagus phantom. These datasets contained two compartments with different relaxation parameters and different diffusion orientation properties, and T2 relaxation variations across these diffusion directions were explored. RESULTS Diffusion-PEPTIDE showed the capability to provide high quality diffusion images and T2 and T 2 ∗ maps from both protocols. The reconstructions were distortion-free, avoided potential resolution losses exceeding 100% in equivalent EPI acquisitions, and showed tolerance to nearly 30° of rotational motion. Expected variation in T2 values as a function of diffusion direction was observed in the two-compartment asparagus phantom (P < .01), demonstrating potential to explore diffusion-PEPTIDE data for multi-compartment modeling. CONCLUSIONS Diffusion-PEPTIDE provides highly robust diffusion and relaxometry data and offers potential for future applications in diffusion-relaxometry multi-compartment modeling.
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Affiliation(s)
- Merlin J Fair
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Congyu Liao
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mary Kate Manhard
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Kawin Setsompop
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Harvard-MIT Health Sciences and Technology, MIT, Cambridge, Massachusetts, USA
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3
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Montrazi ET, Monaretto T, Bonagamba TJ, Colnago LA. New and rapid pulse sequences for two-dimensional D-T 1 correlation measurements. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 315:106749. [PMID: 32438311 DOI: 10.1016/j.jmr.2020.106749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Longitudinal relaxation time (T1), transverse relaxation time (T2) and diffusion coefficient (D) values have been widely used for the characterizations of materials using low field Time Domain Nuclear Magnetic Resonance (TD-NMR). Each parameter can be determined using one-dimensional techniques or their values and correlations by multi-dimensional experiments such as T1-T2, D-T2, and T1-D-T2. In this work, we studied four D-T1 sequences for TD-NMR combining Stejskal-Tanner Pulse Gradient Spin Echo (PGSE) diffusion measurement with Inversion-Recovery (IR), Saturation-Recovery (SR), Small-Angle Continuous Wave Free Precession (CWFP-T1) and Small-Angle Flip-Flop (SAFF) for T1 measurement. The results show that rapid D-T1 measurements can be obtained with single shot CWFP-T1 and SAFF sequences. The two sequences were two and eight time fast than sequences based on SR and IR, respectively. Although the two fast sequences yield low signal-to-noise ratio signal, they can be as fast as the traditional D-T2 experiment, or even faster, because it is not necessary to wait a recycle delay of 5 T1. Another advantage of the CWFP-T1 and SAFF methods, when compared to the one based on SR or CPMG (for D-T2) are the low specific absorption rate (SAR) of these sequences due the low flip angles in the sequences, that reduces the sample heating problem. These sequences were initially studied using phantom samples. They also were used to study plant tissues to observe the anisotropic diffusion in asparagus. Therefore, they can be useful methods for practical application in TD-NMR.
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Affiliation(s)
- Elton Tadeu Montrazi
- São Carlos Institute of Physics, University of São Paulo, PO Box 369, 13560-970 São Carlos, SP, Brazil.
| | - Tatiana Monaretto
- São Carlos Institute of Chemistry, University of São Paulo, PO Box 780, 13560-970 São Carlos, SP, Brazil
| | - Tito José Bonagamba
- São Carlos Institute of Physics, University of São Paulo, PO Box 369, 13560-970 São Carlos, SP, Brazil
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4
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Alexander DC, Dyrby TB, Nilsson M, Zhang H. Imaging brain microstructure with diffusion MRI: practicality and applications. NMR IN BIOMEDICINE 2019; 32:e3841. [PMID: 29193413 DOI: 10.1002/nbm.3841] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 07/09/2017] [Accepted: 09/11/2017] [Indexed: 05/22/2023]
Abstract
This article gives an overview of microstructure imaging of the brain with diffusion MRI and reviews the state of the art. The microstructure-imaging paradigm aims to estimate and map microscopic properties of tissue using a model that links these properties to the voxel scale MR signal. Imaging techniques of this type are just starting to make the transition from the technical research domain to wide application in biomedical studies. We focus here on the practicalities of both implementing such techniques and using them in applications. Specifically, the article summarizes the relevant aspects of brain microanatomy and the range of diffusion-weighted MR measurements that provide sensitivity to them. It then reviews the evolution of mathematical and computational models that relate the diffusion MR signal to brain tissue microstructure, as well as the expanding areas of application. Next we focus on practicalities of designing a working microstructure imaging technique: model selection, experiment design, parameter estimation, validation, and the pipeline of development of this class of technique. The article concludes with some future perspectives on opportunities in this topic and expectations on how the field will evolve in the short-to-medium term.
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Affiliation(s)
- Daniel C Alexander
- Centre for Medical Image Computing (CMIC), Department of Computer Science, UCL (University College London), Gower Street, London, UK
| | - Tim B Dyrby
- Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Markus Nilsson
- Clinical Sciences Lund, Department of Radiology, Lund University, Lund, Sweden
| | - Hui Zhang
- Centre for Medical Image Computing (CMIC), Department of Computer Science, UCL (University College London), Gower Street, London, UK
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de Souza EM, Costa ET, Castellano G. Investigation of anisotropic fishing line-based phantom as tool in quality control of diffusion tensor imaging. Radiol Phys Technol 2019; 12:161-171. [PMID: 30877555 DOI: 10.1007/s12194-019-00507-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 12/14/2022]
Abstract
This work proposes a low-cost, fishing line-based phantom for quality control of diffusion tensor imaging (DTI). The device was applied to investigate the relationship between DTI indexes (DTIi) and imaging acquisition parameters. A Dyneema® fishing line phantom was built with fiber bundles of different thicknesses. DTI acquisitions were performed in a 3T magnetic resonance imaging scanner using an 8-channel and a 32-channel head coil. For each coil, the following acquisition parameters were changed, one at a time: diffusion sensitivity factor (b value), echo time, sensitivity encoding, voxel size, number of signal averages, and number of diffusion gradient directions (NDGD). DTIi including fractional anisotropy, relative anisotropy (RA), linear anisotropy (CL), and planar anisotropy (CP) were calculated for each image; the data were analyzed using the coefficient of variation (CV) and distributions of DTIi values. The 32-channel head coil presented higher CV values for the DTIi RA, CL, and CP when voxel size was changed. Using the phantom, dependences between diffusion-related parameters (b value and NDGD) and DTIi were also observed; the majority of these were for the smaller thickness fiber bundles. The device proved to be useful for the verification of the DTI performance over time.
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Affiliation(s)
- Edna Marina de Souza
- Biomedical Engineering Center, University of Campinas (UNICAMP), 163 Alexander Fleming St, Cidade Universitária, Campinas, SP, 13083 881, Brazil. .,Biomedical Engineering Department, School of Electrical and Computer Engineering, University of Campinas (UNICAMP), Campinas, Brazil. .,Neurophysics Group, Gleb Wataghin Physics Institute, University of Campinas (UNICAMP), 777 Sergio Buarque de Holanda St, University City, Campinas, SP, 13083 859, Brazil. .,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil.
| | - Eduardo Tavares Costa
- Biomedical Engineering Center, University of Campinas (UNICAMP), 163 Alexander Fleming St, Cidade Universitária, Campinas, SP, 13083 881, Brazil.,Biomedical Engineering Department, School of Electrical and Computer Engineering, University of Campinas (UNICAMP), Campinas, Brazil
| | - Gabriela Castellano
- Neurophysics Group, Gleb Wataghin Physics Institute, University of Campinas (UNICAMP), 777 Sergio Buarque de Holanda St, University City, Campinas, SP, 13083 859, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
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6
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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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7
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Souza EMD, Costa ET, Castellano G. Phantoms for diffusion-weighted imaging and diffusion tensor imaging quality control: a review and new perspectives. ACTA ACUST UNITED AC 2017. [DOI: 10.1590/2446-4740.07816] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | | | - Gabriela Castellano
- University of Campinas, Brazil; Brazilian Institute of Neuroscience and Neurotechnology, Brazil
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8
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Morozov D, Tal I, Pisanty O, Shani E, Cohen Y. Studying microstructure and microstructural changes in plant tissues by advanced diffusion magnetic resonance imaging techniques. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2245-2257. [PMID: 28398563 PMCID: PMC5447889 DOI: 10.1093/jxb/erx106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
As sessile organisms, plants must respond to the environment by adjusting their growth and development. Most of the plant body is formed post-embryonically by continuous activity of apical and lateral meristems. The development of lateral adventitious roots is a complex process, and therefore the development of methods that can visualize, non-invasively, the plant microstructure and organ initiation that occur during growth and development is of paramount importance. In this study, relaxation-based and advanced diffusion magnetic resonance imaging (MRI) methods including diffusion tensor (DTI), q-space diffusion imaging (QSI), and double-pulsed-field-gradient (d-PFG) MRI, at 14.1 T, were used to characterize the hypocotyl microstructure and the microstructural changes that occurred during the development of lateral adventitious roots in tomato. Better contrast was observed in relaxation-based MRI using higher in-plane resolution but this also resulted in a significant reduction in the signal-to-noise ratio of the T2-weighted MR images. Diffusion MRI revealed that water diffusion is highly anisotropic in the vascular cylinder. QSI and d-PGSE MRI showed that in the vascular cylinder some of the cells have sizes in the range of 6-10 μm. The MR images captured cell reorganization during adventitious root formation in the periphery of the primary vascular bundles, adjacent to the xylem pole that broke through the cortex and epidermis layers. This study demonstrates that MRI and diffusion MRI methods allow the non-invasive study of microstructural features of plants, and enable microstructural changes associated with adventitious root formation to be followed.
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Affiliation(s)
- Darya Morozov
- School of Chemistry, The Sackler Faculty of Exact Sciences, and
| | - Iris Tal
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Ramat Aviv, Tel Aviv 66978, Israel
| | - Odelia Pisanty
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Ramat Aviv, Tel Aviv 66978, Israel
| | - Eilon Shani
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Ramat Aviv, Tel Aviv 66978, Israel
| | - Yoram Cohen
- School of Chemistry, The Sackler Faculty of Exact Sciences, and
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9
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Perrone D, Jeurissen B, Aelterman J, Roine T, Sijbers J, Pizurica A, Leemans A, Philips W. D-BRAIN: Anatomically Accurate Simulated Diffusion MRI Brain Data. PLoS One 2016; 11:e0149778. [PMID: 26930054 PMCID: PMC4773122 DOI: 10.1371/journal.pone.0149778] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/04/2016] [Indexed: 12/13/2022] Open
Abstract
Diffusion Weighted (DW) MRI allows for the non-invasive study of water diffusion inside living tissues. As such, it is useful for the investigation of human brain white matter (WM) connectivity in vivo through fiber tractography (FT) algorithms. Many DW-MRI tailored restoration techniques and FT algorithms have been developed. However, it is not clear how accurately these methods reproduce the WM bundle characteristics in real-world conditions, such as in the presence of noise, partial volume effect, and a limited spatial and angular resolution. The difficulty lies in the lack of a realistic brain phantom on the one hand, and a sufficiently accurate way of modeling the acquisition-related degradation on the other. This paper proposes a software phantom that approximates a human brain to a high degree of realism and that can incorporate complex brain-like structural features. We refer to it as a Diffusion BRAIN (D-BRAIN) phantom. Also, we propose an accurate model of a (DW) MRI acquisition protocol to allow for validation of methods in realistic conditions with data imperfections. The phantom model simulates anatomical and diffusion properties for multiple brain tissue components, and can serve as a ground-truth to evaluate FT algorithms, among others. The simulation of the acquisition process allows one to include noise, partial volume effects, and limited spatial and angular resolution in the images. In this way, the effect of image artifacts on, for instance, fiber tractography can be investigated with great detail. The proposed framework enables reliable and quantitative evaluation of DW-MR image processing and FT algorithms at the level of large-scale WM structures. The effect of noise levels and other data characteristics on cortico-cortical connectivity and tractography-based grey matter parcellation can be investigated as well.
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Affiliation(s)
- Daniele Perrone
- iMinds - IPI - TELIN, Ghent University, Ghent, Belgium
- * E-mail:
| | - Ben Jeurissen
- iMinds - Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium
| | - Jan Aelterman
- iMinds - IPI - TELIN, Ghent University, Ghent, Belgium
| | - Timo Roine
- iMinds - Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium
| | - Jan Sijbers
- iMinds - Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium
| | | | - Alexander Leemans
- Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands
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10
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SUZUKI Y, HORI M, KAMIYA K, FUKUNAGA I, AOKI S, VAN CAUTEREN M. Estimation of the Mean Axon Diameter and Intra-axonal Space Volume Fraction of the Human Corpus Callosum: Diffusion q-space Imaging with Low q-values. Magn Reson Med Sci 2016; 15:83-93. [DOI: 10.2463/mrms.2014-0141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Yuriko SUZUKI
- Philips Electronics Japan, Ltd., Healthcare
- Department of Radiology, Graduate School of Medicine, Juntendo University
| | - Masaaki HORI
- Department of Radiology, Graduate School of Medicine, Juntendo University
| | - Kouhei KAMIYA
- Department of Radiology, Graduate School of Medicine, The University of Tokyo
| | - Issei FUKUNAGA
- Department of Radiology, Graduate School of Medicine, Juntendo University
| | - Shigeki AOKI
- Department of Radiology, Graduate School of Medicine, Juntendo University
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11
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Kan H, Miyati T, Mase M, Osawa T, Ohno N, Kasai H, Arai N, Kawano M, Shibamoto Y. Dynamic state of water molecular displacement of the brain during the cardiac cycle in idiopathic normal pressure hydrocephalus. Comput Med Imaging Graph 2015; 40:88-93. [PMID: 25614094 DOI: 10.1016/j.compmedimag.2014.12.004] [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: 06/10/2014] [Revised: 12/07/2014] [Accepted: 12/24/2014] [Indexed: 11/29/2022]
Abstract
The predictive accuracy of iNPH diagnoses could be increased using a combination of supplemental tests for iNPH. To evaluate the dynamic state of water displacement during the cardiac cycle in idiopathic normal pressure hydrocephalus (iNPH), we determined the change in water displacement using q-space analysis of diffusion magnetic resonance image. ECG-triggered single-shot diffusion echo planar imaging was used. Water displacement was obtained from the displacement probability profile calculated by Fourier transform of the signal decay fitted as a function of the reciprocal spatial vector q. Then maximum minus minimum displacement (delta-displacement), of all cardiac phase images was calculated. We assessed the delta-displacement in white matter in patients with iNPH and atrophic ventricular dilation (atrophic VD), and in healthy volunteers (control group). Delta-displacement in iNPH was significantly higher than those in the atrophic VD and control. This shows that water molecules of the white matter in iNPH are easily fluctuated by volume loading of the cranium during the cardiac cycle, due to the decrease in intracranial compliance. There was no significant correlation between delta-displacement and displacement. The delta-displacement and the displacement do not necessarily yield the same kind of information. Delta-displacement demonstrated to obtain biophysical information about fluctuation. This analysis may be helpful in the understanding physiology and pathological condition in iNPH and the assisting in the diagnosis.
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Affiliation(s)
- Hirohito Kan
- Department of Radiology, Nagoya City University Hospital, 1-Kawasumi, Mizuho-cho Mizuho-ku, Nagoya 4678602, Aichi, Japan; Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa 9200942, Ishikawa, Japan.
| | - Tosiaki Miyati
- Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa 9200942, Ishikawa, Japan.
| | - Mitsuhito Mase
- Department of Neurosurgery, Nagoya City University Hospital, 1-Kawasumi, Mizuho-cho Mizuho-ku, Nagoya 4678602, Aichi, Japan.
| | - Tomoshi Osawa
- Department of Neurosurgery, Nagoya City University Hospital, 1-Kawasumi, Mizuho-cho Mizuho-ku, Nagoya 4678602, Aichi, Japan.
| | - Naoki Ohno
- Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa 9200942, Ishikawa, Japan.
| | - Harumasa Kasai
- Department of Radiology, Nagoya City University Hospital, 1-Kawasumi, Mizuho-cho Mizuho-ku, Nagoya 4678602, Aichi, Japan.
| | - Nobuyuki Arai
- Department of Radiology, Nagoya City University Hospital, 1-Kawasumi, Mizuho-cho Mizuho-ku, Nagoya 4678602, Aichi, Japan.
| | - Makoto Kawano
- Department of Radiology, Nagoya City University Hospital, 1-Kawasumi, Mizuho-cho Mizuho-ku, Nagoya 4678602, Aichi, Japan.
| | - Yuta Shibamoto
- Department of Radiology, Nagoya City University Hospital, 1-Kawasumi, Mizuho-cho Mizuho-ku, Nagoya 4678602, Aichi, Japan.
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12
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Dean RJ, Stait-Gardner T, Clarke SJ, Rogiers SY, Bobek G, Price WS. Use of diffusion magnetic resonance imaging to correlate the developmental changes in grape berry tissue structure with water diffusion patterns. PLANT METHODS 2014; 10:35. [PMID: 25400688 PMCID: PMC4232727 DOI: 10.1186/1746-4811-10-35] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/21/2014] [Indexed: 05/13/2023]
Abstract
BACKGROUND Over the course of grape berry development, the tissues of the berry undergo numerous morphological transformations in response to processes such as water and solute accumulation and cell division, growth and senescence. These transformations are expected to produce changes to the diffusion of water through these tissues detectable using diffusion magnetic resonance imaging (MRI). To assess this non-invasive technique diffusion was examined over the course of grape berry development, and in plant tissues with contrasting oil content. RESULTS In this study, the fruit of Vitis vinfera L. cv. Semillon at seven different stages of berry development, from four weeks post-anthesis to over-ripe, were imaged using diffusion tensor and transverse relaxation MRI acquisition protocols. Variations in diffusive motion between these stages of development were then linked to known events in the morphological development of the grape berry. Within the inner mesocarp of the berry, preferential directions of diffusion became increasingly apparent as immature berries increased in size and then declined as berries progressed through the ripening and senescence phases. Transverse relaxation images showed radial striation patterns throughout the sub-tissue, initiating at the septum and vascular systems located at the centre of the berry, and terminating at the boundary between the inner and outer mesocarp. This study confirms that these radial patterns are due to bands of cells of alternating width that extend across the inner mesocarp. Preferential directions of diffusion were also noted in young grape seed nucelli prior to their dehydration. These observations point towards a strong association between patterns of diffusion within grape berries and the underlying tissue structures across berry development. A diffusion tensor image of a post-harvest olive demonstrated that the technique is applicable to tissues with high oil content. CONCLUSION This study demonstrates that diffusion MRI is a powerful and information rich technique for probing the internal microstructure of plant tissues. It was shown that macroscopic diffusion anisotropy patterns correlate with the microstructure of the major pericarp tissues of cv. Semillon grape berries, and that changes in grape berry tissue structure during berry development can be observed.
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Affiliation(s)
- Ryan J Dean
- />Nanoscale Organisation and Dynamics Group, University of Western Sydney, Penrith, NSW 2751 Australia
| | - Timothy Stait-Gardner
- />Nanoscale Organisation and Dynamics Group, University of Western Sydney, Penrith, NSW 2751 Australia
| | - Simon J Clarke
- />National Wine & Grape Industry Centre, Charles Sturt University, Locked Bag 588, Wagga Wagga, New South Wales, 2678 Australia
| | - Suzy Y Rogiers
- />National Wine & Grape Industry Centre, Charles Sturt University, Locked Bag 588, Wagga Wagga, New South Wales, 2678 Australia
- />New South Wales Department of Primary Industries, Locked Bag 588, Wagga Wagga, New South Wales, 2678 Australia
| | - Gabriele Bobek
- />School of Medicine, University of Western Sydney, Penrith, NSW 2751 Australia
| | - William S Price
- />Nanoscale Organisation and Dynamics Group, University of Western Sydney, Penrith, NSW 2751 Australia
- />National Wine & Grape Industry Centre, Charles Sturt University, Locked Bag 588, Wagga Wagga, New South Wales, 2678 Australia
- />School of Medicine, University of Western Sydney, Penrith, NSW 2751 Australia
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Zemmoura I, Serres B, Andersson F, Barantin L, Tauber C, Filipiak I, Cottier JP, Venturini G, Destrieux C. FIBRASCAN: a novel method for 3D white matter tract reconstruction in MR space from cadaveric dissection. Neuroimage 2014; 103:106-118. [PMID: 25234114 DOI: 10.1016/j.neuroimage.2014.09.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 08/27/2014] [Accepted: 09/04/2014] [Indexed: 01/13/2023] Open
Abstract
INTRODUCTION Diffusion tractography relies on complex mathematical models that provide anatomical information indirectly, and it needs to be validated. In humans, up to now, tractography has mainly been validated by qualitative comparison with data obtained from dissection. No quantitative comparison was possible because Magnetic Resonance Imaging (MRI) and dissection data are obtained in different reference spaces, and because fiber tracts are progressively destroyed by dissection. Here, we propose a novel method and software (FIBRASCAN) that allow accurate reconstruction of fiber tracts from dissection in MRI reference space. METHOD Five human hemispheres, obtained from four formalin-fixed brains were prepared for Klingler's dissection, placed on a holder with fiducial markers, MR scanned, and then dissected to expose the main association tracts. During dissection, we performed iterative acquisitions of the surface and texture of the specimens using a laser scanner and two digital cameras. Each texture was projected onto the corresponding surface and the resulting set of textured surfaces was coregistered thanks to the fiducial holders. The identified association tracts were then interactively segmented on each textured surface and reconstructed from the pile of surface segments. Finally, the reconstructed tracts were coregistered onto ex vivo MRI space thanks to the fiducials. Each critical step of the process was assessed to measure the precision of the method. RESULTS We reconstructed six fiber tracts (long, anterior and posterior segments of the superior longitudinal fasciculus; Inferior fronto-occipital, Inferior longitudinal and uncinate fasciculi) from cadaveric dissection and ported them into ex vivo MRI reference space. The overall accuracy of the method was of the order of 1mm: surface-to-surface registration=0.138mm (standard deviation (SD)=0.058mm), deformation of the specimen during dissection=0.356mm (SD=0.231mm), and coregistration surface-MRI=0.6mm (SD=0.274mm). The spatial resolution of the method (distance between two consecutive surface acquisitions) was 0.345mm (SD=0.115mm). CONCLUSION This paper presents the robustness of a novel method, FIBRASCAN, for accurate reconstruction of fiber tracts from dissection in the ex vivo MR reference space. This is a major step toward quantitative comparison of MR tractography with dissection results.
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Affiliation(s)
- Ilyess Zemmoura
- INSERM U930 Imagerie et Cerveau, Université François-Rabelais de Tours, Tours, France; Université François-Rabelais de Tours, Laboratoire d'Anatomie, Tours, France; CHRU de Tours, Service de Neurochirurgie, Tours, France.
| | - Barthélémy Serres
- INSERM U930 Imagerie et Cerveau, Université François-Rabelais de Tours, Tours, France; Université François-Rabelais de Tours, Laboratoire d'Informatique, EA6300 Tours, France
| | - Frédéric Andersson
- INSERM U930 Imagerie et Cerveau, Université François-Rabelais de Tours, Tours, France
| | - Laurent Barantin
- INSERM U930 Imagerie et Cerveau, Université François-Rabelais de Tours, Tours, France
| | - Clovis Tauber
- INSERM U930 Imagerie et Cerveau, Université François-Rabelais de Tours, Tours, France
| | - Isabelle Filipiak
- INSERM U930 Imagerie et Cerveau, Université François-Rabelais de Tours, Tours, France
| | - Jean-Philippe Cottier
- INSERM U930 Imagerie et Cerveau, Université François-Rabelais de Tours, Tours, France; CHRU de Tours, Service de Neuroradiologie, Tours, France
| | - Gilles Venturini
- Université François-Rabelais de Tours, Laboratoire d'Informatique, EA6300 Tours, France
| | - Christophe Destrieux
- INSERM U930 Imagerie et Cerveau, Université François-Rabelais de Tours, Tours, France; Université François-Rabelais de Tours, Laboratoire d'Anatomie, Tours, France; CHRU de Tours, Service de Neurochirurgie, Tours, France
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The role of tissue microstructure and water exchange in biophysical modelling of diffusion in white matter. MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE 2013; 26:345-70. [PMID: 23443883 PMCID: PMC3728433 DOI: 10.1007/s10334-013-0371-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 01/28/2013] [Accepted: 02/01/2013] [Indexed: 12/27/2022]
Abstract
Biophysical models that describe the outcome of white matter diffusion MRI experiments have various degrees of complexity. While the simplest models assume equal-sized and parallel axons, more elaborate ones may include distributions of axon diameters and axonal orientation dispersions. These microstructural features can be inferred from diffusion-weighted signal attenuation curves by solving an inverse problem, validated in several Monte Carlo simulation studies. Model development has been paralleled by microscopy studies of the microstructure of excised and fixed nerves, confirming that axon diameter estimates from diffusion measurements agree with those from microscopy. However, results obtained in vivo are less conclusive. For example, the amount of slowly diffusing water is lower than expected, and the diffusion-encoded signal is apparently insensitive to diffusion time variations, contrary to what may be expected. Recent understandings of the resolution limit in diffusion MRI, the rate of water exchange, and the presence of microscopic axonal undulation and axonal orientation dispersions may, however, explain such apparent contradictions. Knowledge of the effects of biophysical mechanisms on water diffusion in tissue can be used to predict the outcome of diffusion tensor imaging (DTI) and of diffusion kurtosis imaging (DKI) studies. Alterations of DTI or DKI parameters found in studies of pathologies such as ischemic stroke can thus be compared with those predicted by modelling. Observations in agreement with the predictions strengthen the credibility of biophysical models; those in disagreement could provide clues of how to improve them. DKI is particularly suited for this purpose; it is performed using higher b-values than DTI, and thus carries more information about the tissue microstructure. The purpose of this review is to provide an update on the current understanding of how various properties of the tissue microstructure and the rate of water exchange between microenvironments are reflected in diffusion MRI measurements. We focus on the use of biophysical models for extracting tissue-specific parameters from data obtained with single PGSE sequences on clinical MRI scanners, but results obtained with animal MRI scanners are also considered. While modelling of white matter is the central theme, experiments on model systems that highlight important aspects of the biophysical models are also reviewed.
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Nilsson M, Lätt J, Ståhlberg F, van Westen D, Hagslätt H. The importance of axonal undulation in diffusion MR measurements: a Monte Carlo simulation study. NMR IN BIOMEDICINE 2012; 25:795-805. [PMID: 22020832 DOI: 10.1002/nbm.1795] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 08/31/2011] [Accepted: 09/02/2011] [Indexed: 05/12/2023]
Abstract
Many axons follow wave-like undulating courses. This is a general feature of extracranial nerve segments, but is also found in some intracranial nervous tissue. The importance of axonal undulation has previously been considered, for example, in the context of biomechanics, where it has been shown that posture affects undulation properties. However, the importance of axonal undulation in the context of diffusion MR measurements has not been investigated. Using an analytical model and Monte Carlo simulations of water diffusion, this study compared undulating and straight axons in terms of diffusion propagators, diffusion-weighted signal intensities and parameters derived from diffusion tensor imaging, such as the mean diffusivity (MD), the eigenvalues and the fractional anisotropy (FA). All parameters were strongly affected by the presence of undulation. The diffusivity perpendicular to the undulating axons increased with the undulation amplitude, thus resembling that of straight axons with larger diameters. Consequently, models assuming straight axons for the estimation of the axon diameter from diffusion MR measurements might overestimate the diameter if undulation is present. FA decreased from approximately 0.7 to 0.5 when axonal undulation was introduced into the simulation model structure. Our results indicate that axonal undulation may play a role in diffusion measurements when investigating, for example, the optic and sciatic nerves and the spinal cord. The simulations also demonstrate that the stretching or compression of neuronal tissue comprising undulating axons alters the observed water diffusivity, suggesting that posture may be of importance for the outcome of diffusion MRI measurements.
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Affiliation(s)
- Markus Nilsson
- Department of Medical Radiation Physics, Lund University, Lund, Sweden.
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Panagiotaki E, Hall MG, Zhang H, Siow B, Lythgoe MF, Alexander DC. High-fidelity meshes from tissue samples for diffusion MRI simulations. ACTA ACUST UNITED AC 2010; 13:404-11. [PMID: 20879341 DOI: 10.1007/978-3-642-15745-5_50] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
This paper presents a method for constructing detailed geometric models of tissue microstructure for synthesizing realistic diffusion MRI data. We construct three-dimensional mesh models from confocal microscopy image stacks using the marching cubes algorithm. Random-walk simulations within the resulting meshes provide synthetic diffusion MRI measurements. Experiments optimise simulation parameters and complexity of the meshes to achieve accuracy and reproducibility while minimizing computation time. Finally we assess the quality of the synthesized data from the mesh models by comparison with scanner data as well as synthetic data from simple geometric models and simplified meshes that vary only in two dimensions. The results support the extra complexity of the three-dimensional mesh compared to simpler models although sensitivity to the mesh resolution is quite robust.
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Affiliation(s)
- Eleftheria Panagiotaki
- Centre for Medical Image Computing, Department of Computer Science, University College London, UK.
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Nilsson M, Alerstam E, Wirestam R, Ståhlberg F, Brockstedt S, Lätt J. Evaluating the accuracy and precision of a two-compartment Kärger model using Monte Carlo simulations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 206:59-67. [PMID: 20594881 DOI: 10.1016/j.jmr.2010.06.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 05/27/2010] [Accepted: 06/02/2010] [Indexed: 05/29/2023]
Abstract
Specific parameters of the neuronal tissue microstructure, such as axonal diameters, membrane permeability and intracellular water fractions are assessable using diffusion MRI. These parameters are commonly estimated using analytical models, which may introduce bias in the estimated parameters due to the approximations made when deriving the models. As an alternative to using analytical models, a database of signal curves generated by fast Monte Carlo simulations can be employed. Simulated diffusion MRI measurements were generated and evaluated using the two-compartment Kärger model as well as the simulation model based on a database containing signal curves from approximately 60000 simulations performed with different combinations of microstructural parameters. A protocol based on a pulsed gradient spin echo sequence with diffusion times of 30 and 60 ms and with gradient amplitudes obtainable with a clinical MRI scanner was employed for the investigations. When using the analytical model, a major negative bias (up to approximately 25%) in the estimated intracellular volume fraction was observed for short exchange times, while almost no bias was seen for the simulation model. In general, the simulation model improved the accuracy of the estimated parameters as compared to the analytical model, except for the exchange time parameter.
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Affiliation(s)
- M Nilsson
- Department of Medical Radiation Physics, Lund University, Lund, Sweden.
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Feng S, Hong Y, Zhou Z, Jinsong Z, Xiaofeng D, Zaizhong W, Yali G, Ying L, Yingjuan C, Yi H. Monitoring of acute axonal injury in the swine spinal cord with EAE by diffusion tensor imaging. J Magn Reson Imaging 2009; 30:277-85. [PMID: 19629996 DOI: 10.1002/jmri.21825] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To evaluate the ability of diffusion tensor imaging (DTI) to detect and monitor acute axonal injury in swine spinal cord with acute experimental allergic encephalomyelitis (EAE). MATERIALS AND METHODS Magnetic resonance imaging of the cervical spinal cord was performed in vivo at different time points through the onset and progression of EAE using a 3 Tesla clinical scanner. The DTI parameters were calculated in four separate regions of interest at the C2/C3 level. The quantitative DTI-pathology and DTI-clinical correlations were verified. RESULTS In the monophasic acute course of EAE onset and progression, axial diffusivity (AD) decrease correlates with acute axonal injury (r = -0.84; P < 0.001). By contrast, radial diffusivity does not change and no demyelination in histopathology was detected. Moreover, a clear correlation between clinical disease and axial diffusivity was found in two swine EAE models (r = -0.86; P < 0.001 and r = -0.92; P < 0.001). CONCLUSION AD corresponds with axonal injury in the absence of demyelination and may be a useful noninvasive tool to investigate the underlying pathogenic processes of multiple sclerosis and to monitor the effects of experimental treatments for axonal injury.
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Affiliation(s)
- Song Feng
- Department of Medical Imaging, The First Military Hospital OF PLA, LanZhou, GanShu, China
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Lätt J, Nilsson M, van Westen D, Wirestam R, Ståhlberg F, Brockstedt S. Diffusion-weighted MRI measurements on stroke patients reveal water-exchange mechanisms in sub-acute ischaemic lesions. NMR IN BIOMEDICINE 2009; 22:619-628. [PMID: 19306340 DOI: 10.1002/nbm.1376] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The aim of this study was to investigate the diffusion time dependence of signal-versus-b curves obtained from diffusion-weighted magnetic resonance imaging (DW-MRI) of sub-acute ischaemic lesions in stroke patients. In this case series study, 16 patients with sub-acute ischaemic stroke were examined with DW-MRI using two different diffusion times (60 and 260 ms). Nine of these patients showed sufficiently large lesions without artefacts to merit further analysis. The signal-versus-b curves from the lesions were plotted and analysed using a two-compartment model including compartmental exchange. To validate the model and to aid the interpretation of the estimated model parameters, Monte Carlo simulations were performed. In eight cases, the plotted signal-versus-b curves, obtained from the lesions, showed a signal-curve split-up when data for the two diffusion times were compared, revealing effects of compartmental water exchange. For one of the patients, parametric maps were generated based on the extracted model parameters. These novel observations suggest that water exchange between different water pools is measurable and thus potentially useful for clinical assessment. The information can improve the understanding of the relationship between the DW-MRI signal intensity and the microstructural properties of the lesions.
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Affiliation(s)
- J Lätt
- Department of Medical Radiation Physics, Lund University, Lund, Sweden.
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Nilsson M, Lätt J, Nordh E, Wirestam R, Ståhlberg F, Brockstedt S. On the effects of a varied diffusion time in vivo: is the diffusion in white matter restricted? Magn Reson Imaging 2009; 27:176-87. [DOI: 10.1016/j.mri.2008.06.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Revised: 06/04/2008] [Accepted: 06/12/2008] [Indexed: 11/29/2022]
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Fieremans E, De Deene Y, Delputte S, Özdemir MS, Achten E, Lemahieu I. The design of anisotropic diffusion phantoms for the validation of diffusion weighted magnetic resonance imaging. Phys Med Biol 2008; 53:5405-19. [DOI: 10.1088/0031-9155/53/19/009] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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