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Canales-Rodríguez EJ, Pizzolato M, Zhou FL, Barakovic M, Thiran JP, Jones DK, Parker GJM, Dyrby TB. Pore size estimation in axon-mimicking microfibers with diffusion-relaxation MRI. Magn Reson Med 2024; 91:2579-2596. [PMID: 38192108 DOI: 10.1002/mrm.29991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024]
Abstract
PURPOSE This study aims to evaluate two distinct approaches for fiber radius estimation using diffusion-relaxation MRI data acquired in biomimetic microfiber phantoms that mimic hollow axons. The methods considered are the spherical mean power-law approach and a T2-based pore size estimation technique. THEORY AND METHODS A general diffusion-relaxation theoretical model for the spherical mean signal from water molecules within a distribution of cylinders with varying radii was introduced, encompassing the evaluated models as particular cases. Additionally, a new numerical approach was presented for estimating effective radii (i.e., MRI-visible mean radii) from the ground truth radii distributions, not reliant on previous theoretical approximations and adaptable to various acquisition sequences. The ground truth radii were obtained from scanning electron microscope images. RESULTS Both methods show a linear relationship between effective radii estimated from MRI data and ground-truth radii distributions, although some discrepancies were observed. The spherical mean power-law method overestimated fiber radii. Conversely, the T2-based method exhibited higher sensitivity to smaller fiber radii, but faced limitations in accurately estimating the radius in one particular phantom, possibly because of material-specific relaxation changes. CONCLUSION The study demonstrates the feasibility of both techniques to predict pore sizes of hollow microfibers. The T2-based technique, unlike the spherical mean power-law method, does not demand ultra-high diffusion gradients, but requires calibration with known radius distributions. This research contributes to the ongoing development and evaluation of neuroimaging techniques for fiber radius estimation, highlights the advantages and limitations of both methods, and provides datasets for reproducible research.
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Affiliation(s)
- Erick J Canales-Rodríguez
- Signal Processing Laboratory 5 (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Danish Research Centre for Magnetic Resonance (DRCMR), Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
| | - Marco Pizzolato
- Danish Research Centre for Magnetic Resonance (DRCMR), Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
- Department of Applied Mathematics and Computer Science, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Feng-Lei Zhou
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London (UCL), London, UK
- MicroPhantoms Limited, Cambridge, UK
| | - Muhamed Barakovic
- Translational Imaging in Neurology (ThINk) Basel, Department of Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Jean-Philippe Thiran
- Signal Processing Laboratory 5 (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
- Centre d'Imagerie Biomédicale (CIBM), EPFL, Lausanne, Switzerland
| | - Derek K Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Cardiff, UK
| | - Geoffrey J M Parker
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London (UCL), London, UK
- Department of Neuroinflammation, Queen Square Institute of Neurology, University College London (UCL), London, UK
- Bioxydyn Limited, Manchester, UK
| | - Tim B Dyrby
- Danish Research Centre for Magnetic Resonance (DRCMR), Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
- Department of Applied Mathematics and Computer Science, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
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2
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Lee HH, Tian Q, Sheft M, Coronado-Leija R, Ramos-Llorden G, Abdollahzadeh A, Fieremans E, Novikov DS, Huang SY. The effects of axonal beading and undulation on axonal diameter estimation from diffusion MRI: Insights from simulations in human axons segmented from three-dimensional electron microscopy. NMR IN BIOMEDICINE 2024; 37:e5087. [PMID: 38168082 PMCID: PMC10942763 DOI: 10.1002/nbm.5087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 01/05/2024]
Abstract
The increasing availability of high-performance gradient systems in human MRI scanners has generated great interest in diffusion microstructural imaging applications such as axonal diameter mapping. Practically, sensitivity to axon diameter in diffusion MRI is attained at strong diffusion weightings b , where the deviation from the expected 1 / b scaling in white matter yields a finite transverse diffusivity, which is then translated into an axon diameter estimate. While axons are usually modeled as perfectly straight, impermeable cylinders, local variations in diameter (caliber variation or beading) and direction (undulation) are known to influence axonal diameter estimates and have been observed in microscopy data of human axons. In this study, we performed Monte Carlo simulations of diffusion in axons reconstructed from three-dimensional electron microscopy of a human temporal lobe specimen using simulated sequence parameters matched to the maximal gradient strength of the next-generation Connectome 2.0 human MRI scanner ( ≲ 500 mT/m). We show that axon diameter estimation is accurate for nonbeaded, nonundulating fibers; however, in fibers with caliber variations and undulations, the axon diameter is heavily underestimated due to caliber variations, and this effect overshadows the known overestimation of the axon diameter due to undulations. This unexpected underestimation may originate from variations in the coarse-grained axial diffusivity due to caliber variations. Given that increased axonal beading and undulations have been observed in pathological tissues, such as traumatic brain injury and ischemia, the interpretation of axon diameter alterations in pathology may be significantly confounded.
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Affiliation(s)
- Hong-Hsi Lee
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Qiyuan Tian
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Maxina Sheft
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Harvard–MIT Health Sciences and Technology, Cambridge, Massachusetts, USA
| | - Ricardo Coronado-Leija
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, USA
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, USA
| | - Gabriel Ramos-Llorden
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Ali Abdollahzadeh
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, USA
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, USA
| | - Els Fieremans
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, USA
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, USA
| | - Dmitry S. Novikov
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, USA
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, USA
| | - Susie Y. Huang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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3
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Chakwizira A, Zhu A, Foo T, Westin CF, Szczepankiewicz F, Nilsson M. Diffusion MRI with free gradient waveforms on a high-performance gradient system: Probing restriction and exchange in the human brain. Neuroimage 2023; 283:120409. [PMID: 37839729 DOI: 10.1016/j.neuroimage.2023.120409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/29/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023] Open
Abstract
The dependence of the diffusion MRI signal on the diffusion time carries signatures of restricted diffusion and exchange. Here we seek to highlight these signatures in the human brain by performing experiments using free gradient waveforms designed to be selectively sensitive to the two effects. We examine six healthy volunteers using both strong and ultra-strong gradients (80, 200 and 300 mT/m). In an experiment featuring a large set of 150 gradient waveforms with different sensitivities to restricted diffusion and exchange, our results reveal unique and different time-dependence signatures in grey and white matter. Grey matter was characterised by both restricted diffusion and exchange and white matter predominantly by restricted diffusion. Exchange in grey matter was at least twice as fast as in white matter, across all subjects and all gradient strengths. The cerebellar cortex featured relatively short exchange times (115 ms). Furthermore, we show that gradient waveforms with tailored designs can be used to map exchange in the human brain. We also assessed the feasibility of clinical applications of the method used in this work and found that the exchange-related contrast obtained with a 25-minute protocol at 300 mT/m was preserved in a 4-minute protocol at 300 mT/m and a 10-minute protocol at 80 mT/m. Our work underlines the utility of free waveforms for detecting time dependence signatures due to restricted diffusion and exchange in vivo, which may potentially serve as a tool for studying diseased tissue.
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Affiliation(s)
- Arthur Chakwizira
- Department of Medical Radiation Physics, Clinical Sciences Lund, Lund University, Lund, Sweden.
| | - Ante Zhu
- GE Research, Niskayuna, New York, United States
| | - Thomas Foo
- GE Research, Niskayuna, New York, United States
| | - Carl-Fredrik Westin
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Filip Szczepankiewicz
- Department of Medical Radiation Physics, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Markus Nilsson
- Department of Clinical Sciences Lund, Radiology, Lund University, Lund, Sweden; Department of Radiology, Skåne University Hospital, Lund, Sweden
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Villarreal-Haro JL, Gardier R, Canales-Rodríguez EJ, Fischi-Gomez E, Girard G, Thiran JP, Rafael-Patiño J. CACTUS: a computational framework for generating realistic white matter microstructure substrates. Front Neuroinform 2023; 17:1208073. [PMID: 37603781 PMCID: PMC10434236 DOI: 10.3389/fninf.2023.1208073] [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: 04/18/2023] [Accepted: 07/13/2023] [Indexed: 08/23/2023] Open
Abstract
Monte-Carlo diffusion simulations are a powerful tool for validating tissue microstructure models by generating synthetic diffusion-weighted magnetic resonance images (DW-MRI) in controlled environments. This is fundamental for understanding the link between micrometre-scale tissue properties and DW-MRI signals measured at the millimetre-scale, optimizing acquisition protocols to target microstructure properties of interest, and exploring the robustness and accuracy of estimation methods. However, accurate simulations require substrates that reflect the main microstructural features of the studied tissue. To address this challenge, we introduce a novel computational workflow, CACTUS (Computational Axonal Configurator for Tailored and Ultradense Substrates), for generating synthetic white matter substrates. Our approach allows constructing substrates with higher packing density than existing methods, up to 95% intra-axonal volume fraction, and larger voxel sizes of up to 500μm3 with rich fibre complexity. CACTUS generates bundles with angular dispersion, bundle crossings, and variations along the fibres of their inner and outer radii and g-ratio. We achieve this by introducing a novel global cost function and a fibre radial growth approach that allows substrates to match predefined targeted characteristics and mirror those reported in histological studies. CACTUS improves the development of complex synthetic substrates, paving the way for future applications in microstructure imaging.
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Affiliation(s)
- Juan Luis Villarreal-Haro
- Signal Processing Laboratory (LTS5), École Polytechnique Frale de Lausanne (EPFL), Lausanne, Switzerland
| | - Remy Gardier
- Signal Processing Laboratory (LTS5), École Polytechnique Frale de Lausanne (EPFL), Lausanne, Switzerland
| | - Erick J. Canales-Rodríguez
- Signal Processing Laboratory (LTS5), École Polytechnique Frale de Lausanne (EPFL), Lausanne, Switzerland
| | - Elda Fischi-Gomez
- Signal Processing Laboratory (LTS5), École Polytechnique Frale de Lausanne (EPFL), Lausanne, Switzerland
- CIBM Center for Biomedical Imaging, Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Gabriel Girard
- Signal Processing Laboratory (LTS5), École Polytechnique Frale de Lausanne (EPFL), Lausanne, Switzerland
- CIBM Center for Biomedical Imaging, Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
- Department of Computer Science, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Philippe Thiran
- Signal Processing Laboratory (LTS5), École Polytechnique Frale de Lausanne (EPFL), Lausanne, Switzerland
- CIBM Center for Biomedical Imaging, Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Jonathan Rafael-Patiño
- Signal Processing Laboratory (LTS5), École Polytechnique Frale de Lausanne (EPFL), Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
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5
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Lee HH, Tian Q, Sheft M, Coronado-Leija R, Ramos-Llorden G, Abdollahzadeh A, Fieremans E, Novikov DS, Huang SY. The influence of axonal beading and undulation on axonal diameter mapping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537494. [PMID: 37131702 PMCID: PMC10153226 DOI: 10.1101/2023.04.19.537494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We consider the effect of non-cylindrical axonal shape on axonal diameter mapping with diffusion MRI. Practical sensitivity to axon diameter is attained at strong diffusion weightings b , where the deviation from the 1 / b scaling yields the finite transverse diffusivity, which is then translated into axon diameter. While axons are usually modeled as perfectly straight, impermeable cylinders, the local variations in diameter (caliber variation or beading) and direction (undulation) have been observed in microscopy data of human axons. Here we quantify the influence of cellular-level features such as caliber variation and undulation on axon diameter estimation. For that, we simulate the diffusion MRI signal in realistic axons segmented from 3-dimensional electron microscopy of a human brain sample. We then create artificial fibers with the same features and tune the amplitude of their caliber variations and undulations. Numerical simulations of diffusion in fibers with such tunable features show that caliber variations and undulations result in under- and over-estimation of axon diameters, correspondingly; this bias can be as large as 100%. Given that increased axonal beading and undulations have been observed in pathological tissues, such as traumatic brain injury and ischemia, the interpretation of axon diameter alterations in pathology may be significantly confounded.
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Affiliation(s)
- Hong-Hsi Lee
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA 02129,USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Qiyuan Tian
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA 02129,USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Maxina Sheft
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA 02129,USA
- Harvard-MIT Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Ricardo Coronado-Leija
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY 10016, USA
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY 10016, USA
| | - Gabriel Ramos-Llorden
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA 02129,USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Ali Abdollahzadeh
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY 10016, USA
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY 10016, USA
| | - Els Fieremans
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY 10016, USA
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY 10016, USA
| | - Dmitry S. Novikov
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY 10016, USA
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY 10016, USA
| | - Susie Y. Huang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA 02129,USA
- Harvard Medical School, Boston, MA 02115, USA
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6
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Chakwizira A, Zhu A, Foo T, Westin CF, Szczepankiewicz F, Nilsson M. Diffusion MRI with free gradient waveforms on a high-performance gradient system: Probing restriction and exchange in the human brain. ARXIV 2023:arXiv:2304.02764v1. [PMID: 37064535 PMCID: PMC10104199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The dependence of the diffusion MRI signal on the diffusion time carries signatures of restricted diffusion and exchange. Here we seek to highlight these signatures in the human brain by performing experiments using free gradient waveforms that are selectively sensitive to the two effects. We examine six healthy volunteers using both strong and ultra-strong gradients (80, 200 and 300 mT/m). In an experiment featuring a large set of gradient waveforms with different sensitivities to restricted diffusion and exchange (150 samples), our results reveal unique time-dependence signatures in grey and white matter, where the former is characterised by both restricted diffusion and exchange and the latter predominantly exhibits restricted diffusion. Furthermore, we show that gradient waveforms with independently varying sensitivities to restricted diffusion and exchange can be used to map exchange in the human brain. We consistently find that exchange in grey matter is at least twice as fast as in white matter, across all subjects and all gradient strengths. The shortest exchange times observed in this study were in the cerebellar cortex (115 ms). We also assess the feasibility of future clinical applications of the method used in this work, where we find that the grey-white matter exchange contrast obtained with a 25-minute 300 mT/m protocol is preserved by a 4-minute 300 mT/m and a 10-minute 80 mT/m protocol. Our work underlines the utility of free waveforms for detecting time-dependence signatures due to restricted diffusion and exchange in vivo, which may potentially serve as a tool for studying diseased tissue.
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Affiliation(s)
- Arthur Chakwizira
- Medical Radiation Physics, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Ante Zhu
- GE Research, Niskayuna, New York, USA
| | | | - Carl-Fredrik Westin
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | | | - Markus Nilsson
- Department of Clinical Sciences Lund, Radiology, Lund University, Lund, Sweden
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7
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Warner W, Palombo M, Cruz R, Callaghan R, Shemesh N, Jones DK, Dell'Acqua F, Ianus A, Drobnjak I. Temporal Diffusion Ratio (TDR) for imaging restricted diffusion: Optimisation and pre-clinical demonstration. Neuroimage 2023; 269:119930. [PMID: 36750150 PMCID: PMC7615244 DOI: 10.1016/j.neuroimage.2023.119930] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 01/12/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023] Open
Abstract
Temporal Diffusion Ratio (TDR) is a recently proposed dMRI technique (Dell'Acqua et al., proc. ISMRM 2019) which provides contrast between areas with restricted diffusion and areas either without restricted diffusion or with length scales too small for characterisation. Hence, it has a potential for informing on pore sizes, in particular the presence of large axon diameters or other cellular structures. TDR employs the signal from two dMRI acquisitions obtained with the same, large, b-value but with different diffusion gradient waveforms. TDR is advantageous as it employs standard acquisition sequences, does not make any assumptions on the underlying tissue structure and does not require any model fitting, avoiding issues related to model degeneracy. This work for the first time introduces and optimises the TDR method in simulation for a range of different tissues and scanner constraints and validates it in a pre-clinical demonstration. We consider both substrates containing cylinders and spherical structures, representing cell soma in tissue. Our results show that contrasting an acquisition with short gradient duration, short diffusion time and high gradient strength with an acquisition with long gradient duration, long diffusion time and low gradient strength, maximises the TDR contrast for a wide range of pore configurations. Additionally, in the presence of Rician noise, computing TDR from a subset (50% or fewer) of the acquired diffusion gradients rather than the entire shell as proposed originally further improves the contrast. In the last part of the work the results are demonstrated experimentally on rat spinal cord. In line with simulations, the experimental data shows that optimised TDR improves the contrast compared to non-optimised TDR. Furthermore, we find a strong correlation between TDR and histology measurements of axon diameter. In conclusion, we find that TDR has great potential and is a very promising alternative (or potentially complement) to model-based approaches for informing on pore sizes and restricted diffusion in general.
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Affiliation(s)
- William Warner
- Centre for Medical Image Computing (CMIC), Computer Science Department, University College London, United Kingdom
| | - Marco Palombo
- Cardiff University Brain Research Imaging Centre, School of Psychology, Cardiff University, Cardiff, United Kingdom; School of Computer Science and Informatics, Cardiff University, Cardiff, United Kingdom
| | - Renata Cruz
- Champalimaud Research, Champalimaud Foundation, Lisbon, Portugal
| | | | - Noam Shemesh
- Champalimaud Research, Champalimaud Foundation, Lisbon, Portugal
| | - Derek K Jones
- Cardiff University Brain Research Imaging Centre, School of Psychology, Cardiff University, Cardiff, United Kingdom
| | - Flavio Dell'Acqua
- NatBrainLab, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Andrada Ianus
- Champalimaud Research, Champalimaud Foundation, Lisbon, Portugal.
| | - Ivana Drobnjak
- Centre for Medical Image Computing (CMIC), Computer Science Department, University College London, United Kingdom.
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8
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Pizzolato M, Canales-Rodríguez EJ, Andersson M, Dyrby TB. Axial and radial axonal diffusivities and radii from single encoding strongly diffusion-weighted MRI. Med Image Anal 2023; 86:102767. [PMID: 36867913 DOI: 10.1016/j.media.2023.102767] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/13/2022] [Accepted: 02/08/2023] [Indexed: 02/18/2023]
Abstract
We enable the estimation of the per-axon axial diffusivity from single encoding, strongly diffusion-weighted, pulsed gradient spin echo data. Additionally, we improve the estimation of the per-axon radial diffusivity compared to estimates based on spherical averaging. The use of strong diffusion weightings in magnetic resonance imaging (MRI) allows to approximate the signal in white matter as the sum of the contributions from only axons. At the same time, spherical averaging leads to a major simplification of the modeling by removing the need to explicitly account for the unknown distribution of axonal orientations. However, the spherically averaged signal acquired at strong diffusion weightings is not sensitive to the axial diffusivity, which cannot therefore be estimated although needed for modeling axons - especially in the context of multi-compartmental modeling. We introduce a new general method for the estimation of both the axial and radial axonal diffusivities at strong diffusion weightings based on kernel zonal modeling. The method could lead to estimates that are free from partial volume bias with gray matter or other isotropic compartments. The method is tested on publicly available data from the MGH Adult Diffusion Human Connectome project. We report reference values of axonal diffusivities based on 34 subjects, and derive estimates of axonal radii from only two shells. The estimation problem is also addressed from the angle of the required data preprocessing, the presence of biases related to modeling assumptions, current limitations, and future possibilities.
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Affiliation(s)
- Marco Pizzolato
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark; Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark.
| | | | - Mariam Andersson
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
| | - Tim B Dyrby
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark; Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
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9
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Chakwizira A, Westin C, Brabec J, Lasič S, Knutsson L, Szczepankiewicz F, Nilsson M. Diffusion MRI with pulsed and free gradient waveforms: Effects of restricted diffusion and exchange. NMR IN BIOMEDICINE 2023; 36:e4827. [PMID: 36075110 PMCID: PMC10078514 DOI: 10.1002/nbm.4827] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 08/27/2022] [Accepted: 09/06/2022] [Indexed: 05/06/2023]
Abstract
Monitoring time dependence with diffusion MRI yields observables sensitive to compartment sizes (restricted diffusion) and membrane permeability (water exchange). However, restricted diffusion and exchange have opposite effects on the diffusion-weighted signal, which can lead to errors in parameter estimates. In this work, we propose a signal representation that incorporates the effects of both restricted diffusion and exchange up to second order in b-value and is compatible with gradient waveforms of arbitrary shape. The representation features mappings from a gradient waveform to two scalars that separately control the sensitivity to restriction and exchange. We demonstrate that these scalars span a two-dimensional space that can be used to choose waveforms that selectively probe restricted diffusion or exchange, eliminating the correlation between the two phenomena. We found that waveforms with specific but unconventional shapes provide an advantage over conventional pulsed and oscillating gradient acquisitions. We also show that parametrization of waveforms into a two-dimensional space can be used to understand protocols from other approaches that probe restricted diffusion and exchange. For example, we found that the variation of mixing time in filter-exchange imaging corresponds to variation of our exchange-weighting scalar at a fixed value of the restriction-weighting scalar. The proposed signal representation was evaluated using Monte Carlo simulations in identical parallel cylinders with hexagonal and random packing as well as parallel cylinders with gamma-distributed radii. Results showed that the approach is sensitive to sizes in the interval 4-12 μm and exchange rates in the simulated range of 0 to 20 s - 1 , but also that there is a sensitivity to the extracellular geometry. The presented theory constitutes a simple and intuitive description of how restricted diffusion and exchange influence the signal as well as a guide to protocol design capable of separating the two effects.
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Affiliation(s)
- Arthur Chakwizira
- Department of Medical Radiation Physics, LundLund UniversityLundSweden
| | - Carl‐Fredrik Westin
- Department of Radiology, Brigham and Women's HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Jan Brabec
- Department of Medical Radiation Physics, LundLund UniversityLundSweden
| | - Samo Lasič
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and ResearchCopenhagen University Hospital ‐ Amager and HvidovreCopenhagenDenmark
- Random Walk Imaging ABLundSweden
| | - Linda Knutsson
- Department of Medical Radiation Physics, LundLund UniversityLundSweden
- Russell H. Morgan Department of Radiology and Radiological ScienceJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- F. M. Kirby Research Center for Functional Brain ImagingKennedy Krieger InstituteBaltimoreMarylandUSA
| | | | - Markus Nilsson
- Department of Clinical Sciences Lund, RadiologyLund UniversityLundSweden
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10
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Yendiki A, Aggarwal M, Axer M, Howard AF, van Cappellen van Walsum AM, Haber SN. Post mortem mapping of connectional anatomy for the validation of diffusion MRI. Neuroimage 2022; 256:119146. [PMID: 35346838 PMCID: PMC9832921 DOI: 10.1016/j.neuroimage.2022.119146] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 03/02/2022] [Accepted: 03/23/2022] [Indexed: 01/13/2023] Open
Abstract
Diffusion MRI (dMRI) is a unique tool for the study of brain circuitry, as it allows us to image both the macroscopic trajectories and the microstructural properties of axon bundles in vivo. The Human Connectome Project ushered in an era of impressive advances in dMRI acquisition and analysis. As a result of these efforts, the quality of dMRI data that could be acquired in vivo improved substantially, and large collections of such data became widely available. Despite this progress, the main limitation of dMRI remains: it does not image axons directly, but only provides indirect measurements based on the diffusion of water molecules. Thus, it must be validated by methods that allow direct visualization of axons but that can only be performed in post mortem brain tissue. In this review, we discuss methods for validating the various features of connectional anatomy that are extracted from dMRI, both at the macro-scale (trajectories of axon bundles), and at micro-scale (axonal orientations and other microstructural properties). We present a range of validation tools, including anatomic tracer studies, Klingler's dissection, myelin stains, label-free optical imaging techniques, and others. We provide an overview of the basic principles of each technique, its limitations, and what it has taught us so far about the accuracy of different dMRI acquisition and analysis approaches.
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Affiliation(s)
- Anastasia Yendiki
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States,Corresponding author (A. Yendiki)
| | - Manisha Aggarwal
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Markus Axer
- Forschungszentrum Jülich, Institute of Neuroscience and Medicine, Jülich, Germany,Department of Physics, University of Wuppertal Germany
| | - Amy F.D. Howard
- Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Anne-Marie van Cappellen van Walsum
- Department of Medical Imaging, Anatomy, Radboud University Medical Center, Nijmegen, the Netherland,Cognition and Behaviour, Donders Institute for Brain, Nijmegen, the Netherland
| | - Suzanne N. Haber
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY, United States,McLean Hospital, Belmont, MA, United States
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11
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Schiavi S, Lu PJ, Weigel M, Lutti A, Jones DK, Kappos L, Granziera C, Daducci A. Bundle myelin fraction (BMF) mapping of different white matter connections using microstructure informed tractography. Neuroimage 2022; 249:118922. [PMID: 35063648 PMCID: PMC7615247 DOI: 10.1016/j.neuroimage.2022.118922] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/13/2022] Open
Abstract
To date, we have scarce information about the relative myelination level of different fiber bundles in the human brain. Indirect evidence comes from postmortem histology data but histological stainings are unable to follow a specific bundle and determine its intrinsic myelination. In this context, quantitative MRI, and diffusion MRI tractography may offer a viable solution by providing, respectively, voxel-wise myelin sensitive maps and the pathways of the major tracts of the brain. Then, "tractometry" can be used to combine these two pieces of information by averaging tissue features (obtained from any voxel-wise map) along the streamlines recovered with diffusion tractography. Although this method has been widely used in the literature, in cases of voxels containing multiple fiber populations (each with different levels of myelination), tractometry provides biased results because the same value will be attributed to any bundle passing through the voxel. To overcome this bias, we propose a new method - named "myelin streamline decomposition" (MySD) - which extends convex optimization modeling for microstructure informed tractography (COMMIT) allowing the actual value measured by a microstructural map to be deconvolved on each individual streamline, thereby recovering unique bundle-specific myelin fractions (BMFs). We demonstrate the advantage of our method with respect to tractometry in well-studied bundles and compare the cortical projection of the obtained bundle-wise myelin values of both methods. We also prove the stability of our approach across different subjects and different MRI sensitive myelin mapping approaches. This work provides a proof-of-concept of in vivo investigations of entire neuronal pathways that, to date, are not possible.
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Affiliation(s)
- Simona Schiavi
- Department of Computer Science, University of Verona, Italy; Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Italy.
| | - Po-Jui Lu
- Departments of Medicine, Clinical Research and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland; Translational Imaging in Neurology (ThINk) Basel, Department of Medicine and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Matthias Weigel
- Departments of Medicine, Clinical Research and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland; Translational Imaging in Neurology (ThINk) Basel, Department of Medicine and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland; Radiological Physics, Department of Radiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Antoine Lutti
- Laboratory for Research in Neuroimaging, Department of Clinical Neuroscience, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Derek K Jones
- Cardiff University Brain Research Imaging Centre, Cardiff University, United Kingdom; Neuroscience and Mental Health Research Institute, Cardiff University, United Kingdom
| | - Ludwig Kappos
- Departments of Medicine, Clinical Research and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland; Translational Imaging in Neurology (ThINk) Basel, Department of Medicine and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Cristina Granziera
- Departments of Medicine, Clinical Research and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland; Translational Imaging in Neurology (ThINk) Basel, Department of Medicine and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
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12
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Fan Q, Eichner C, Afzali M, Mueller L, Tax CMW, Davids M, Mahmutovic M, Keil B, Bilgic B, Setsompop K, Lee HH, Tian Q, Maffei C, Ramos-Llordén G, Nummenmaa A, Witzel T, Yendiki A, Song YQ, Huang CC, Lin CP, Weiskopf N, Anwander A, Jones DK, Rosen BR, Wald LL, Huang SY. Mapping the Human Connectome using Diffusion MRI at 300 mT/m Gradient Strength: Methodological Advances and Scientific Impact. Neuroimage 2022; 254:118958. [PMID: 35217204 DOI: 10.1016/j.neuroimage.2022.118958] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 12/20/2022] Open
Abstract
Tremendous efforts have been made in the last decade to advance cutting-edge MRI technology in pursuit of mapping structural connectivity in the living human brain with unprecedented sensitivity and speed. The first Connectom 3T MRI scanner equipped with a 300 mT/m whole-body gradient system was installed at the Massachusetts General Hospital in 2011 and was specifically constructed as part of the Human Connectome Project. Since that time, numerous technological advances have been made to enable the broader use of the Connectom high gradient system for diffusion tractography and tissue microstructure studies and leverage its unique advantages and sensitivity to resolving macroscopic and microscopic structural information in neural tissue for clinical and neuroscientific studies. The goal of this review article is to summarize the technical developments that have emerged in the last decade to support and promote large-scale and scientific studies of the human brain using the Connectom scanner. We provide a brief historical perspective on the development of Connectom gradient technology and the efforts that led to the installation of three other Connectom 3T MRI scanners worldwide - one in the United Kingdom in Cardiff, Wales, another in Continental Europe in Leipzig, Germany, and the latest in Asia in Shanghai, China. We summarize the key developments in gradient hardware and image acquisition technology that have formed the backbone of Connectom-related research efforts, including the rich array of high-sensitivity receiver coils, pulse sequences, image artifact correction strategies and data preprocessing methods needed to optimize the quality of high-gradient strength dMRI data for subsequent analyses. Finally, we review the scientific impact of the Connectom MRI scanner, including advances in diffusion tractography, tissue microstructural imaging, ex vivo validation, and clinical investigations that have been enabled by Connectom technology. We conclude with brief insights into the unique value of strong gradients for dMRI and where the field is headed in the coming years.
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Affiliation(s)
- Qiuyun Fan
- Department of Biomedical Engineering, College of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin, China; Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; Harvard Medical School, Boston, MA, USA
| | - Cornelius Eichner
- Max Planck Institute for Human Cognitive and Brain Sciences, Department of Neuropsychology, Leipzig, Germany
| | - Maryam Afzali
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Cardiff, Wales, UK; Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Lars Mueller
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Chantal M W Tax
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Cardiff, Wales, UK; Image Sciences Institute, University Medical Center (UMC) Utrecht, Utrecht, Netherlands
| | - Mathias Davids
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; Harvard Medical School, Boston, MA, USA; Computer Assisted Clinical Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Mirsad Mahmutovic
- Institute of Medical Physics and Radiation Protection (IMPS), TH-Mittelhessen University of Applied Sciences (THM), Giessen, Germany
| | - Boris Keil
- Institute of Medical Physics and Radiation Protection (IMPS), TH-Mittelhessen University of Applied Sciences (THM), Giessen, Germany
| | - Berkin Bilgic
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; Harvard Medical School, Boston, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Kawin Setsompop
- Department of Radiology, Stanford University, Stanford, CA, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Hong-Hsi Lee
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; Harvard Medical School, Boston, MA, USA
| | - Qiyuan Tian
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; Harvard Medical School, Boston, MA, USA
| | - Chiara Maffei
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; Harvard Medical School, Boston, MA, USA
| | - Gabriel Ramos-Llordén
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; Harvard Medical School, Boston, MA, USA
| | - Aapo Nummenmaa
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; Harvard Medical School, Boston, MA, USA
| | | | - Anastasia Yendiki
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; Harvard Medical School, Boston, MA, USA
| | - Yi-Qiao Song
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA USA
| | - Chu-Chung Huang
- Key Laboratory of Brain Functional Genomics (MOE & STCSM), Affiliated Mental Health Center (ECNU), School of Psychology and Cognitive Science, East China Normal University, Shanghai, China; Shanghai Changning Mental Health Center, Shanghai, China
| | - Ching-Po Lin
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Nikolaus Weiskopf
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.; Felix Bloch Institute for Solid State Physics, Faculty of Physics and Earth Sciences, Leipzig University, Leipzig, Germany
| | - Alfred Anwander
- Max Planck Institute for Human Cognitive and Brain Sciences, Department of Neuropsychology, Leipzig, Germany
| | - Derek K Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Cardiff, Wales, UK
| | - Bruce R Rosen
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; Harvard Medical School, Boston, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Lawrence L Wald
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; Harvard Medical School, Boston, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Susie Y Huang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States; Harvard Medical School, Boston, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States.
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13
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Grussu F, Bernatowicz K, Casanova-Salas I, Castro N, Nuciforo P, Mateo J, Barba I, Perez-Lopez R. Diffusion MRI signal cumulants and hepatocyte microstructure at fixed diffusion time: Insights from simulations, 9.4T imaging, and histology. Magn Reson Med 2022; 88:365-379. [PMID: 35181943 PMCID: PMC9303340 DOI: 10.1002/mrm.29174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/21/2021] [Accepted: 01/07/2022] [Indexed: 11/09/2022]
Abstract
Purpose Relationships between diffusion‐weighted MRI signals and hepatocyte microstructure were investigated to inform liver diffusion MRI modeling, focusing on the following question: Can cell size and diffusivity be estimated at fixed diffusion time, realistic SNR, and negligible contribution from extracellular/extravascular water and exchange? Methods Monte Carlo simulations were performed within synthetic hepatocytes for varying cell size/diffusivity L/D0, and clinical protocols (single diffusion encoding; maximum b‐value: {1000, 1500, 2000} s/mm2; 5 unique gradient duration/separation pairs; SNR = {∞, 100, 80, 40, 20}), accounting for heterogeneity in (D0,L) and perfusion contamination. Diffusion (D) and kurtosis (K) coefficients were calculated, and relationships between (D0,L) and (D,K) were visualized. Functions mapping (D,K) to (D0,L) were computed to predict unseen (D0,L) values, tested for their ability to classify discrete cell‐size contrasts, and deployed on 9.4T ex vivo MRI‐histology data of fixed mouse livers Results Relationships between (D,K) and (D0,L) are complex and depend on the diffusion encoding. Functions mapping D,K to (D0,L) captures salient characteristics of D0(D,K) and L(D,K) dependencies. Mappings are not always accurate, but they enable just under 70% accuracy in a three‐class cell‐size classification task (for SNR = 20, bmax = 1500 s/mm2, δ = 20 ms, and Δ = 75 ms). MRI detects cell‐size contrasts in the mouse livers that are confirmed by histology, but overestimates the largest cell sizes. Conclusion Salient information about liver cell size and diffusivity may be retrieved from minimal diffusion encodings at fixed diffusion time, in experimental conditions and pathological scenarios for which extracellular, extravascular water and exchange are negligible.
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Affiliation(s)
- Francesco Grussu
- Radiomics Group, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Kinga Bernatowicz
- Radiomics Group, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Irene Casanova-Salas
- Prostate Cancer Translational Research Group, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Natalia Castro
- Prostate Cancer Translational Research Group, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Paolo Nuciforo
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Joaquin Mateo
- Prostate Cancer Translational Research Group, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Ignasi Barba
- NMR Lab, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Raquel Perez-Lopez
- Radiomics Group, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Department of Radiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
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14
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Connecting macroscopic diffusion metrics of cardiac diffusion tensor imaging and microscopic myocardial structures based on simulation. Med Image Anal 2022; 77:102325. [DOI: 10.1016/j.media.2021.102325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/20/2022]
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15
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Andersson M, Pizzolato M, Kjer HM, Skodborg KF, Lundell H, Dyrby TB. Does powder averaging remove dispersion bias in diffusion MRI diameter estimates within real 3D axonal architectures? Neuroimage 2021; 248:118718. [PMID: 34767939 DOI: 10.1016/j.neuroimage.2021.118718] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/26/2021] [Accepted: 11/08/2021] [Indexed: 11/26/2022] Open
Abstract
Noninvasive estimation of axon diameter with diffusion MRI holds the potential to investigate the dynamic properties of the brain network and pathology of neurodegenerative diseases. Recent studies use powder averaging to account for complex white matter architectures, but these have not been validated for real axonal geometries from regions that contain fibre crossings. Here, we present 120-304μm long segmented axons from X-ray nano-holotomography volumes of a splenium and crossing fibre region of a vervet monkey brain. We show that the axons in the complex crossing fibre region, which contains callosal, association, and corticospinal connections, are larger and exhibit a wider distribution than those of the splenium region. To accurately estimate the axon diameter in these regions, therefore, sensitivity to a wide range of diameters is required. We demonstrate how the q-value, b-value, signal-to-noise ratio and the assumed intra-axonal parallel diffusivity influence the range of measurable diameters with powder average approaches. Furthermore, we show how Gaussian distributed noise results in a wider range of measurable diameter at high b-values than Rician distributed noise, even at high signal-to-noise ratios of 100. The number of gradient directions is also shown to impose a lower bound on measurable diameter. Our results indicate that axon diameter estimation can be performed with only few b-shells, and that additional shells do not improve the accuracy of the estimate. For strong gradients available on human Connectom and preclinical scanners, Monte Carlo simulations of diffusion confirm that powder averaging techniques succeed in providing accurate estimates of axon diameter across a range of sequence parameters and diffusion times, even in complex white matter architectures. At relatively low b-values, the diameter estimate becomes sensitive to axonal microdispersion and the intra-axonal parallel diffusivity shows time dependency at both in vivo and ex vivo intrinsic diffusivities.
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Affiliation(s)
- Mariam Andersson
- Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre 2650, Denmark; Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Marco Pizzolato
- Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre 2650, Denmark; Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark; Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Hans Martin Kjer
- Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre 2650, Denmark; Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Katrine Forum Skodborg
- Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre 2650, Denmark; Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Henrik Lundell
- Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre 2650, Denmark; Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Tim B Dyrby
- Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre 2650, Denmark; Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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16
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Huang SY, Witzel T, Keil B, Scholz A, Davids M, Dietz P, Rummert E, Ramb R, Kirsch JE, Yendiki A, Fan Q, Tian Q, Ramos-Llordén G, Lee HH, Nummenmaa A, Bilgic B, Setsompop K, Wang F, Avram AV, Komlosh M, Benjamini D, Magdoom KN, Pathak S, Schneider W, Novikov DS, Fieremans E, Tounekti S, Mekkaoui C, Augustinack J, Berger D, Shapson-Coe A, Lichtman J, Basser PJ, Wald LL, Rosen BR. Connectome 2.0: Developing the next-generation ultra-high gradient strength human MRI scanner for bridging studies of the micro-, meso- and macro-connectome. Neuroimage 2021; 243:118530. [PMID: 34464739 PMCID: PMC8863543 DOI: 10.1016/j.neuroimage.2021.118530] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/10/2021] [Accepted: 08/27/2021] [Indexed: 11/26/2022] Open
Abstract
The first phase of the Human Connectome Project pioneered advances in MRI technology for mapping the macroscopic structural connections of the living human brain through the engineering of a whole-body human MRI scanner equipped with maximum gradient strength of 300 mT/m, the highest ever achieved for human imaging. While this instrument has made important contributions to the understanding of macroscale connectional topology, it has also demonstrated the potential of dedicated high-gradient performance scanners to provide unparalleled in vivo assessment of neural tissue microstructure. Building on the initial groundwork laid by the original Connectome scanner, we have now embarked on an international, multi-site effort to build the next-generation human 3T Connectome scanner (Connectome 2.0) optimized for the study of neural tissue microstructure and connectional anatomy across multiple length scales. In order to maximize the resolution of this in vivo microscope for studies of the living human brain, we will push the diffusion resolution limit to unprecedented levels by (1) nearly doubling the current maximum gradient strength from 300 mT/m to 500 mT/m and tripling the maximum slew rate from 200 T/m/s to 600 T/m/s through the design of a one-of-a-kind head gradient coil optimized to minimize peripheral nerve stimulation; (2) developing high-sensitivity multi-channel radiofrequency receive coils for in vivo and ex vivo human brain imaging; (3) incorporating dynamic field monitoring to minimize image distortions and artifacts; (4) developing new pulse sequences to integrate the strongest diffusion encoding and highest spatial resolution ever achieved in the living human brain; and (5) calibrating the measurements obtained from this next-generation instrument through systematic validation of diffusion microstructural metrics in high-fidelity phantoms and ex vivo brain tissue at progressively finer scales with accompanying diffusion simulations in histology-based micro-geometries. We envision creating the ultimate diffusion MRI instrument capable of capturing the complex multi-scale organization of the living human brain - from the microscopic scale needed to probe cellular geometry, heterogeneity and plasticity, to the mesoscopic scale for quantifying the distinctions in cortical structure and connectivity that define cyto- and myeloarchitectonic boundaries, to improvements in estimates of macroscopic connectivity.
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Affiliation(s)
- Susie Y Huang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | | | - Boris Keil
- Institute of Medical Physics and Radiation Protection (IMPS), TH-Mittelhessen University of Applied Sciences (THM), Giessen, Germany
| | - Alina Scholz
- Institute of Medical Physics and Radiation Protection (IMPS), TH-Mittelhessen University of Applied Sciences (THM), Giessen, Germany
| | - Mathias Davids
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | - John E Kirsch
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Anastasia Yendiki
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Qiuyun Fan
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Qiyuan Tian
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Gabriel Ramos-Llordén
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hong-Hsi Lee
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Aapo Nummenmaa
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Berkin Bilgic
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kawin Setsompop
- Radiological Sciences Laboratory, Department of Radiology, Stanford University, Stanford, CA, USA
| | - Fuyixue Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexandru V Avram
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Michal Komlosh
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Dan Benjamini
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Kulam Najmudeen Magdoom
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Sudhir Pathak
- Learning Research and Development Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Walter Schneider
- Learning Research and Development Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dmitry S Novikov
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA; Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY, USA
| | - Els Fieremans
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA; Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY, USA
| | - Slimane Tounekti
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Choukri Mekkaoui
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jean Augustinack
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel Berger
- Department of Molecular and Cell Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Alexander Shapson-Coe
- Department of Molecular and Cell Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jeff Lichtman
- Department of Molecular and Cell Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Peter J Basser
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Lawrence L Wald
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bruce R Rosen
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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17
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Grisot G, Haber SN, Yendiki A. Diffusion MRI and anatomic tracing in the same brain reveal common failure modes of tractography. Neuroimage 2021; 239:118300. [PMID: 34171498 PMCID: PMC8475636 DOI: 10.1016/j.neuroimage.2021.118300] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/29/2021] [Accepted: 06/21/2021] [Indexed: 12/15/2022] Open
Abstract
Anatomic tracing is recognized as a critical source of knowledge on brain circuitry that can be used to assess the accuracy of diffusion MRI (dMRI) tractography. However, most prior studies that have performed such assessments have used dMRI and tracer data from different brains and/or have been limited in the scope of dMRI analysis methods allowed by the data. In this work, we perform a quantitative, voxel-wise comparison of dMRI tractography and anatomic tracing data in the same macaque brain. An ex vivo dMRI acquisition with high angular resolution and high maximum b-value allows us to compare a range of q-space sampling, orientation reconstruction, and tractography strategies. The availability of tracing in the same brain allows us to localize the sources of tractography errors and to identify axonal configurations that lead to such errors consistently, across dMRI acquisition and analysis strategies. We find that these common failure modes involve geometries such as branching or turning, which cannot be modeled well by crossing fibers. We also find that the default thresholds that are commonly used in tractography correspond to rather conservative, low-sensitivity operating points. While deterministic tractography tends to have higher sensitivity than probabilistic tractography in that very conservative threshold regime, the latter outperforms the former as the threshold is relaxed to avoid missing true anatomical connections. On the other hand, the q-space sampling scheme and maximum b-value have less of an impact on accuracy. Finally, using scans from a set of additional macaque brains, we show that there is enough inter-individual variability to warrant caution when dMRI and tracer data come from different animals, as is often the case in the tractography validation literature. Taken together, our results provide insights on the limitations of current tractography methods and on the critical role that anatomic tracing can play in identifying potential avenues for improvement.
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Affiliation(s)
| | - Suzanne N Haber
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY, United States; McLean Hospital, Belmont, MA, United States
| | - Anastasia Yendiki
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States.
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18
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Kerkelä L, Nery F, Callaghan R, Zhou F, Gyori NG, Szczepankiewicz F, Palombo M, Parker GJM, Zhang H, Hall MG, Clark CA. Comparative analysis of signal models for microscopic fractional anisotropy estimation using q-space trajectory encoding. Neuroimage 2021; 242:118445. [PMID: 34375753 DOI: 10.1016/j.neuroimage.2021.118445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/06/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Microscopic diffusion anisotropy imaging using diffusion-weighted MRI and multidimensional diffusion encoding is a promising method for quantifying clinically and scientifically relevant microstructural properties of neural tissue. Several methods for estimating microscopic fractional anisotropy (µFA), a normalized measure of microscopic diffusion anisotropy, have been introduced but the differences between the methods have received little attention thus far. In this study, the accuracy and precision of µFA estimation using q-space trajectory encoding and different signal models were assessed using imaging experiments and simulations. Three healthy volunteers and a microfibre phantom were imaged with five non-zero b-values and gradient waveforms encoding linear and spherical b-tensors. Since the ground-truth µFA was unknown in the imaging experiments, Monte Carlo random walk simulations were performed using axon-mimicking fibres for which the ground truth was known. Furthermore, parameter bias due to time-dependent diffusion was quantified by repeating the simulations with tuned waveforms, which have similar power spectra, and with triple diffusion encoding, which, unlike q-space trajectory encoding, is not based on the assumption of time-independent diffusion. The truncated cumulant expansion of the powder-averaged signal, gamma-distributed diffusivities assumption, and q-space trajectory imaging, a generalization of the truncated cumulant expansion to individual signals, were used to estimate µFA. The gamma-distributed diffusivities assumption consistently resulted in greater µFA values than the second order cumulant expansion, 0.1 greater when averaged over the whole brain. In the simulations, the generalized cumulant expansion provided the most accurate estimates. Importantly, although time-dependent diffusion caused significant overestimation of µFA using all the studied methods, the simulations suggest that the resulting bias in µFA is less than 0.1 in human white matter.
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Affiliation(s)
- Leevi Kerkelä
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK.
| | - Fabio Nery
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Ross Callaghan
- UCL Centre for Medical Image Computing, University College London, London, UK
| | - Fenglei Zhou
- UCL Centre for Medical Image Computing, University College London, London, UK; UCL School of Pharmacy, University College London, London, UK
| | - Noemi G Gyori
- UCL Centre for Medical Image Computing, University College London, London, UK; UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Filip Szczepankiewicz
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts, US; Harvard Medical School, Boston, Massachusetts, US; Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Marco Palombo
- UCL Centre for Medical Image Computing, University College London, London, UK
| | - Geoff J M Parker
- UCL Centre for Medical Image Computing, University College London, London, UK; Bioxydyn Limited, Manchester, UK; UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Hui Zhang
- UCL Centre for Medical Image Computing, University College London, London, UK
| | - Matt G Hall
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK; National Physical Laboratory, Teddington, UK
| | - Chris A Clark
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
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19
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Ianus A, Alexander DC, Zhang H, Palombo M. Mapping complex cell morphology in the grey matter with double diffusion encoding MR: A simulation study. Neuroimage 2021; 241:118424. [PMID: 34311067 PMCID: PMC8961003 DOI: 10.1016/j.neuroimage.2021.118424] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 07/13/2021] [Accepted: 07/21/2021] [Indexed: 01/18/2023] Open
Abstract
This paper investigates the impact of cell body (namely soma) size and branching of cellular projections on diffusion MR imaging (dMRI) and spectroscopy (dMRS) signals for both standard single diffusion encoding (SDE) and more advanced double diffusion encoding (DDE) measurements using numerical simulations. The aim is to investigate the ability of dMRI/dMRS to characterize the complex morphology of brain cells focusing on these two distinctive features of brain grey matter. To this end, we employ a recently developed computational framework to create three dimensional meshes of neuron-like structures for Monte Carlo simulations, using diffusion coefficients typical of water and brain metabolites. Modelling the cellular structure as realistically connected spherical soma and cylindrical cellular projections, we cover a wide range of combinations of sphere radii and branching order of cellular projections, characteristic of various grey matter cells. We assess the impact of spherical soma size and branching order on the b-value dependence of the SDE signal as well as the time dependence of the mean diffusivity (MD) and mean kurtosis (MK). Moreover, we also assess the impact of spherical soma size and branching order on the angular modulation of DDE signal at different mixing times, together with the mixing time dependence of the apparent microscopic anisotropy (μA), a promising contrast derived from DDE measurements. The SDE results show that spherical soma size has a measurable impact on both the b-value dependence of the SDE signal and the MD and MK diffusion time dependence for both water and metabolites. On the other hand, we show that branching order has little impact on either, especially for water. In contrast, the DDE results show that spherical soma size has a measurable impact on the DDE signal's angular modulation at short mixing times and the branching order of cellular projections significantly impacts the mixing time dependence of the DDE signal's angular modulation as well as of the derived μA, for both water and metabolites. Our results confirm that SDE based techniques may be sensitive to spherical soma size, and most importantly, show for the first time that DDE measurements may be more sensitive to the dendritic tree complexity (as parametrized by the branching order of cellular projections), paving the way for new ways of characterizing grey matter morphology, non-invasively using dMRS and potentially dMRI.
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Affiliation(s)
- A Ianus
- Centre for Medical Image Computing and Department of Computer Science, University College London, London, United Kingdom; Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - D C Alexander
- Centre for Medical Image Computing and Department of Computer Science, University College London, London, United Kingdom
| | - H Zhang
- Centre for Medical Image Computing and Department of Computer Science, University College London, London, United Kingdom
| | - M Palombo
- Centre for Medical Image Computing and Department of Computer Science, University College London, London, United Kingdom.
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20
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Scan-rescan repeatability of axonal imaging metrics using high-gradient diffusion MRI and statistical implications for study design. Neuroimage 2021; 240:118323. [PMID: 34216774 PMCID: PMC8646020 DOI: 10.1016/j.neuroimage.2021.118323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/12/2021] [Accepted: 06/26/2021] [Indexed: 11/29/2022] Open
Abstract
Axon diameter mapping using diffusion MRI in the living human brain has attracted growing interests with the increasing availability of high gradient strength MRI systems. A systematic assessment of the consistency of axon diameter estimates within and between individuals is needed to gain a comprehensive understanding of how such methods extend to quantifying differences in axon diameter index between groups and facilitate the design of neurobiological studies using such measures. We examined the scan-rescan repeatability of axon diameter index estimation based on the spherical mean technique (SMT) approach using diffusion MRI data acquired with gradient strengths up to 300 mT/m on a 3T Connectom system in 7 healthy volunteers. We performed statistical power analyses using data acquired with the same protocol in a larger cohort consisting of 15 healthy adults to investigate the implications for study design. Results revealed a high degree of repeatability in voxel-wise restricted volume fraction estimates and tract-wise estimates of axon diameter index derived from high-gradient diffusion MRI data. On the region of interest (ROI) level, across white matter tracts in the whole brain, the Pearson’s correlation coefficient of the axon diameter index estimated between scan and rescan experiments was r = 0.72 with an absolute deviation of 0.18 μm. For an anticipated 10% effect size in studies of axon diameter index, most white matter regions required a sample size of less than 15 people to observe a measurable difference between groups using an ROI-based approach. To facilitate the use of high-gradient strength diffusion MRI data for neuroscientific studies of axonal microstructure, the comprehensive multi-gradient strength, multi-diffusion time data used in this work will be made publicly available, in support of open science and increasing the accessibility of such data to the greater scientific community.
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21
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Barakovic M, Girard G, Schiavi S, Romascano D, Descoteaux M, Granziera C, Jones DK, Innocenti GM, Thiran JP, Daducci A. Bundle-Specific Axon Diameter Index as a New Contrast to Differentiate White Matter Tracts. Front Neurosci 2021; 15:646034. [PMID: 34211362 PMCID: PMC8239216 DOI: 10.3389/fnins.2021.646034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/17/2021] [Indexed: 12/30/2022] Open
Abstract
In the central nervous system of primates, several pathways are characterized by different spectra of axon diameters. In vivo methods, based on diffusion-weighted magnetic resonance imaging, can provide axon diameter index estimates non-invasively. However, such methods report voxel-wise estimates, which vary from voxel-to-voxel for the same white matter bundle due to partial volume contributions from other pathways having different microstructure properties. Here, we propose a novel microstructure-informed tractography approach, COMMITAxSize, to resolve axon diameter index estimates at the streamline level, thus making the estimates invariant along trajectories. Compared to previously proposed voxel-wise methods, our formulation allows the estimation of a distinct axon diameter index value for each streamline, directly, furnishing a complementary measure to the existing calculation of the mean value along the bundle. We demonstrate the favourable performance of our approach comparing our estimates with existing histologically-derived measurements performed in the corpus callosum and the posterior limb of the internal capsule. Overall, our method provides a more robust estimation of the axon diameter index of pathways by jointly estimating the microstructure properties of the tissue and the macroscopic organisation of the white matter connectivity.
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Affiliation(s)
- Muhamed Barakovic
- Signal Processing Lab 5, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, United Kingdom
- Translational Imaging in Neurology (ThINk) Basel, Department of Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
- Neurologic Clinic and Policlinic, Departments of Medicine, Clinical Research and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Gabriel Girard
- Signal Processing Lab 5, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- CIBM Center for BioMedical Imaging, Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Simona Schiavi
- Signal Processing Lab 5, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Computer Science, University of Verona, Verona, Italy
| | - David Romascano
- Signal Processing Lab 5, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Maxime Descoteaux
- Sherbrooke Connectivity Imaging Lab, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Cristina Granziera
- Translational Imaging in Neurology (ThINk) Basel, Department of Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
- Neurologic Clinic and Policlinic, Departments of Medicine, Clinical Research and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Derek K. Jones
- Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, United Kingdom
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, Australia
| | - Giorgio M. Innocenti
- Signal Processing Lab 5, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Brain and Mind Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jean-Philippe Thiran
- Signal Processing Lab 5, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- CIBM Center for BioMedical Imaging, Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
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22
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Masutani Y. Recent Advances in Parameter Inference for Diffusion MRI Signal Models. Magn Reson Med Sci 2021; 21:132-147. [PMID: 34024863 PMCID: PMC9199979 DOI: 10.2463/mrms.rev.2021-0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In this paper, fundamentals and recent progress for obtaining biological features quantitatively by using diffusion MRI are reviewed. First, a brief description of diffusion MRI history, application, and development was presented. Then, well-known parametric models including diffusion tensor imaging (DTI), diffusional kurtosis imaging (DKI), and neurite orientation dispersion diffusion imaging (NODDI) are introduced with several classifications in various viewpoints with other modeling schemes. In addition, this review covers mathematical generalization and examples of methodologies for the model parameter inference from conventional fitting to recent machine learning approaches, which is called Q-space learning (QSL). Finally, future perspectives on diffusion MRI parameter inference are discussed with the aspects of imaging modeling and simulation.
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23
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Veraart J, Raven EP, Edwards LJ, Weiskopf N, Jones DK. The variability of MR axon radii estimates in the human white matter. Hum Brain Mapp 2021; 42:2201-2213. [PMID: 33576105 PMCID: PMC8046139 DOI: 10.1002/hbm.25359] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/07/2021] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
The noninvasive quantification of axonal morphology is an exciting avenue for gaining understanding of the function and structure of the central nervous system. Accurate non-invasive mapping of micron-sized axon radii using commonly applied neuroimaging techniques, that is, diffusion-weighted MRI, has been bolstered by recent hardware developments, specifically MR gradient design. Here the whole brain characterization of the effective MR axon radius is presented and the inter- and intra-scanner test-retest repeatability and reproducibility are evaluated to promote the further development of the effective MR axon radius as a neuroimaging biomarker. A coefficient-of-variability of approximately 10% in the voxelwise estimation of the effective MR radius is observed in the test-retest analysis, but it is shown that the performance can be improved fourfold using a customized along-tract analysis.
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Affiliation(s)
- Jelle Veraart
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of RadiologyNew York University Grossman School of MedicineNew YorkNew YorkUSA
| | - Erika P. Raven
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of RadiologyNew York University Grossman School of MedicineNew YorkNew YorkUSA
- CUBRIC, School of PsychologyCardiff UniversityCardiffUK
| | - Luke J. Edwards
- Department of NeurophysicsMax Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
| | - Nikolaus Weiskopf
- Department of NeurophysicsMax Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
- Felix Bloch Institute for Solid State Physics, Faculty of Physics and Earth SciencesLeipzig UniversityLeipzigGermany
| | - Derek K. Jones
- CUBRIC, School of PsychologyCardiff UniversityCardiffUK
- Mary MacKillop Institute for Health ResearchAustralian Catholic UniversityMelbourneVictoriaAustralia
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24
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In vivo tensor-valued diffusion MRI of focal demyelination in white and deep grey matter of rodents. NEUROIMAGE-CLINICAL 2021; 30:102675. [PMID: 34215146 PMCID: PMC8100629 DOI: 10.1016/j.nicl.2021.102675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 02/02/2023]
Abstract
We performed in-vivo tensor-valued diffusion MRI in demyelinating rodents. Lysolecithin was injected in white and deep grey matter to cause focal demyelination. Focal demyelination reduced microscopic fractional anisotropy (µFA). Isotropic kurtosis may be particularly sensitive to deep grey matter lesions.
Background Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease leading to damage of white matter (WM) and grey matter (GM). Magnetic resonance imaging (MRI) is the modality of choice to assess brain damage in MS, but there is an unmet need in MRI for achieving higher sensitivity and specificity to MS-related microstructural alterations in WM and GM. Objective To explore whether tensor-valued diffusion MRI (dMRI) can yield sensitive microstructural read-outs for focal demyelination in cerebral WM and deep GM (DGM). Methods Eight rats underwent L-α-Lysophosphatidylcholine (LPC) injections in the WM and striatum to introduce focal demyelination. Multimodal MRI was performed at 7 Tesla after 7 days. Tensor-valued dMRI was complemented by diffusion tensor imaging, quantitative MRI and proton magnetic resonance spectroscopy (MRS). Results Quantitative MRI and MRS confirmed that LPC injections caused inflammatory demyelinating lesions in WM and DGM. Tensor-valued dMRI illustrated a significant decline of microscopic fractional anisotropy (µFA) in both LPC-treated WM and DGM (P < 0.005) along with a marked increase of isotropic kurtosis (MKI) in DGM (P < 0.0001). Conclusion Tensor-valued dMRI bears considerable potential for microstructural imaging in MS, suggesting a regional µFA decrease may be a sensitive indicator of MS lesions, while a regional MKI increase may be particularly sensitive in detecting DGM lesions of MS.
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25
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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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26
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Lee HH, Fieremans E, Novikov DS. Realistic Microstructure Simulator (RMS): Monte Carlo simulations of diffusion in three-dimensional cell segmentations of microscopy images. J Neurosci Methods 2020; 350:109018. [PMID: 33279478 DOI: 10.1016/j.jneumeth.2020.109018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/16/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Monte Carlo simulations of diffusion are commonly used as a model validation tool as they are especially suitable for generating the diffusion MRI signal in complicated tissue microgeometries. NEW METHOD Here we describe the details of implementing Monte Carlo simulations in three-dimensional (3d) voxelized segmentations of cells in microscopy images. Using the concept of the corner reflector, we largely reduce the computational load of simulating diffusion within and exchange between multiple cells. Precision is further achieved by GPU-based parallel computations. RESULTS Our simulation of diffusion in white matter axons segmented from a mouse brain demonstrates its value in validating biophysical models. Furthermore, we provide the theoretical background for implementing a discretized diffusion process, and consider the finite-step effects of the particle-membrane reflection and permeation events, needed for efficient simulation of interactions with irregular boundaries, spatially variable diffusion coefficient, and exchange. COMPARISON WITH EXISTING METHODS To our knowledge, this is the first Monte Carlo pipeline for MR signal simulations in a substrate composed of numerous realistic cells, accounting for their permeable and irregularly-shaped membranes. CONCLUSIONS The proposed RMS pipeline makes it possible to achieve fast and accurate simulations of diffusion in realistic tissue microgeometry, as well as the interplay with other MR contrasts. Presently, RMS focuses on simulations of diffusion, exchange, and T1 and T2 NMR relaxation in static tissues, with a possibility to straightforwardly account for susceptibility-induced T2* effects and flow.
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Affiliation(s)
- Hong-Hsi Lee
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA; Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY, USA.
| | - Els Fieremans
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA; Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY, USA
| | - Dmitry S Novikov
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA; Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY, USA
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27
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Novikov DS. The present and the future of microstructure MRI: From a paradigm shift to normal science. J Neurosci Methods 2020; 351:108947. [PMID: 33096152 DOI: 10.1016/j.jneumeth.2020.108947] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/29/2020] [Accepted: 09/10/2020] [Indexed: 12/29/2022]
Abstract
The aspiration of imaging tissue microstructure with MRI is to uncover micrometer-scale tissue features within millimeter-scale imaging voxels, in vivo. This kind of super-resolution has fueled a paradigm shift within the biomedical imaging community. However, what feels like an ongoing revolution in MRI, has been conceptually experienced in physics decades ago; from this point of view, our current developments can be seen as Thomas Kuhn's "normal science" stage of progress. While the concept of model-based quantification below the nominal imaging resolution is not new, its possibilities in neuroscience and neuroradiology are only beginning to be widely appreciated. This disconnect calls for communicating the progress of tissue microstructure MR imaging to its potential users. Here, a number of recent research developments are outlined in terms of the overarching concept of coarse-graining the tissue structure over an increasing diffusion length. A variety of diffusion models and phenomena are summarized on the phase diagram of diffusion MRI, with the unresolved problems and future directions corresponding to its unexplored domains.
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Affiliation(s)
- Dmitry S Novikov
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA.
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