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Pieciak T, París G, Beck D, Maximov II, Tristán-Vega A, de Luis-García R, Westlye LT, Aja-Fernández S. Spherical means-based free-water volume fraction from diffusion MRI increases non-linearly with age in the white matter of the healthy human brain. Neuroimage 2023; 279:120324. [PMID: 37574122 DOI: 10.1016/j.neuroimage.2023.120324] [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: 04/02/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023] Open
Abstract
The term free-water volume fraction (FWVF) refers to the signal fraction that could be found as the cerebrospinal fluid of the brain, which has been demonstrated as a sensitive measure that correlates with cognitive performance and various neuropathological processes. It can be quantified by properly fitting the isotropic component of the magnetic resonance (MR) signal in diffusion-sensitized sequences. Using N=287 healthy subjects (178F/109M) aged 25-94, this study examines in detail the evolution of the FWVF obtained with the spherical means technique from multi-shell acquisitions in the human brain white matter across the adult lifespan, which has been previously reported to exhibit a positive trend when estimated from single-shell data using the bi-tensor signal representation. We found evidence of a noticeably non-linear gain after the sixth decade of life, with a region-specific variate and varying change rate of the spherical means-based multi-shell FWVF parameter with age, at the same time, a heteroskedastic pattern across the adult lifespan is suggested. On the other hand, the FW corrected diffusion tensor imaging (DTI) leads to a region-dependent flattened age-related evolution of the mean diffusivity (MD) and fractional anisotropy (FA), along with a considerable reduction in their variability, as compared to the studies conducted over the standard (single-component) DTI. This way, our study provides a new perspective on the trajectory-based assessment of the brain and explains the conceivable reason for the variations observed in FA and MD parameters across the lifespan with previous studies under the standard diffusion tensor imaging.
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Affiliation(s)
- Tomasz Pieciak
- Laboratorio de Procesado de Imagen (LPI), ETSI Telecomunicación, Universidad de Valladolid, Valladolid, Spain.
| | - Guillem París
- Laboratorio de Procesado de Imagen (LPI), ETSI Telecomunicación, Universidad de Valladolid, Valladolid, Spain
| | - Dani Beck
- Department of Psychology, University of Oslo, Oslo, Norway; NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway. https://twitter.com/_DaniBeck
| | - Ivan I Maximov
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Health and Functioning, Western Norway University of Applied Sciences, Bergen, Norway
| | - Antonio Tristán-Vega
- Laboratorio de Procesado de Imagen (LPI), ETSI Telecomunicación, Universidad de Valladolid, Valladolid, Spain
| | - Rodrigo de Luis-García
- Laboratorio de Procesado de Imagen (LPI), ETSI Telecomunicación, Universidad de Valladolid, Valladolid, Spain
| | - Lars T Westlye
- Department of Psychology, University of Oslo, Oslo, Norway; NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway; KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway. https://twitter.com/larswestlye
| | - Santiago Aja-Fernández
- Laboratorio de Procesado de Imagen (LPI), ETSI Telecomunicación, Universidad de Valladolid, Valladolid, Spain. https://twitter.com/SantiagoAjaFer1
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Martín-Martín C, Planchuelo-Gómez Á, Guerrero ÁL, García-Azorín D, Tristán-Vega A, de Luis-García R, Aja-Fernández S. Viability of AMURA biomarkers from single-shell diffusion MRI in clinical studies. Front Neurosci 2023; 17:1106350. [PMID: 37234256 PMCID: PMC10208402 DOI: 10.3389/fnins.2023.1106350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/30/2023] [Indexed: 05/27/2023] Open
Abstract
Diffusion Tensor Imaging (DTI) is the most employed method to assess white matter properties using quantitative parameters derived from diffusion MRI, but it presents known limitations that restrict the evaluation of complex structures. The objective of this study was to validate the reliability and robustness of complementary diffusion measures extracted with a novel approach, Apparent Measures Using Reduced Acquisitions (AMURA), with a typical diffusion MRI acquisition from a clinical context in comparison with DTI with application to clinical studies. Fifty healthy controls, 51 episodic migraine and 56 chronic migraine patients underwent single-shell diffusion MRI. Four DTI-based and eight AMURA-based parameters were compared between groups with tract-based spatial statistics to establish reference results. On the other hand, following a region-based analysis, the measures were assessed for multiple subsamples with diverse reduced sample sizes and their stability was evaluated with the coefficient of quartile variation. To assess the discrimination power of the diffusion measures, we repeated the statistical comparisons with a region-based analysis employing reduced sample sizes with diverse subsets, decreasing 10 subjects per group for consecutive reductions, and using 5,001 different random subsamples. For each sample size, the stability of the diffusion descriptors was evaluated with the coefficient of quartile variation. AMURA measures showed a greater number of statistically significant differences in the reference comparisons between episodic migraine patients and controls compared to DTI. In contrast, a higher number of differences was found with DTI parameters compared to AMURA in the comparisons between both migraine groups. Regarding the assessments reducing the sample size, the AMURA parameters showed a more stable behavior than DTI, showing a lower decrease for each reduced sample size or a higher number of regions with significant differences. However, most AMURA parameters showed lower stability in relation to higher coefficient of quartile variation values than the DTI descriptors, although two AMURA measures showed similar values to DTI. For the synthetic signals, there were AMURA measures with similar quantification to DTI, while other showed similar behavior. These findings suggest that AMURA presents favorable characteristics to identify differences of specific microstructural properties between clinical groups in regions with complex fiber architecture and lower dependency on the sample size or assessing technique than DTI.
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Affiliation(s)
- Carmen Martín-Martín
- Laboratorio de Procesado de Imagen (LPI), Universidad de Valladolid, Valladolid, Spain
| | - Álvaro Planchuelo-Gómez
- Laboratorio de Procesado de Imagen (LPI), Universidad de Valladolid, Valladolid, Spain
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
| | - Ángel L. Guerrero
- Headache Unit, Department of Neurology, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
- Department of Medicine, Universidad de Valladolid, Valladolid, Spain
| | - David García-Azorín
- Headache Unit, Department of Neurology, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Antonio Tristán-Vega
- Laboratorio de Procesado de Imagen (LPI), Universidad de Valladolid, Valladolid, Spain
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Tristán-Vega A, Pieciak T, París G, Rodríguez-Galván JR, Aja-Fernández S. HYDI-DSI revisited: Constrained non-parametric EAP imaging without q-space re-gridding. Med Image Anal 2023; 84:102728. [PMID: 36542908 DOI: 10.1016/j.media.2022.102728] [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: 01/26/2022] [Revised: 10/20/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Hybrid Diffusion Imaging (HYDI) was one of the first attempts to use multi-shell samplings of the q-space to infer diffusion properties beyond Diffusion Tensor Imaging (DTI) or High Angular Resolution Diffusion Imaging (HARDI). HYDI was intended as a flexible protocol embedding both DTI (for lower b-values) and HARDI (for higher b-values) processing, as well as Diffusion Spectrum Imaging (DSI) when the entire data set was exploited. In the latter case, the spherical sampling of the q-space is re-gridded by interpolation to a Cartesian lattice whose extent covers the range of acquired b-values, hence being acquisition-dependent. The Discrete Fourier Transform (DFT) is afterwards used to compute the corresponding Cartesian sampling of the Ensemble Average Propagator (EAP) in an entirely non-parametric way. From this lattice, diffusion markers such as the Return To Origin Probability (RTOP) or the Mean Squared Displacement (MSD) can be numerically estimated. We aim at re-formulating this scheme by means of a Fourier Transform encoding matrix that eliminates the need for q-space re-gridding at the same time it preserves the non-parametric nature of HYDI-DSI. The encoding matrix is adaptively designed at each voxel according to the underlying DTI approximation, so that an optimal sampling of the EAP can be pursued without being conditioned by the particular acquisition protocol. The estimation of the EAP is afterwards carried out as a regularized Quadratic Programming (QP) problem, which allows to impose positivity constraints that cannot be trivially embedded within the conventional HYDI-DSI. We demonstrate that the definition of the encoding matrix in the adaptive space allows to analytically (as opposed to numerically) compute several popular descriptors of diffusion with the unique source of error being the cropping of high frequency harmonics in the Fourier analysis of the attenuation signal. They include not only RTOP and MSD, but also Return to Axis/Plane Probabilities (RTAP/RTPP), which are defined in terms of specific spatial directions and are not available with the former HYDI-DSI. We report extensive experiments that suggest the benefits of our proposal in terms of accuracy, robustness and computational efficiency, especially when only standard, non-dedicated q-space samplings are available.
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Affiliation(s)
| | - Tomasz Pieciak
- LPI, ETSI Telecomunicación, Universidad de Valladolid, Spain; AGH University of Science and Technology, Kraków, Poland
| | - Guillem París
- LPI, ETSI Telecomunicación, Universidad de Valladolid, Spain
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Rodríguez-Galván JR, París G, Tristán-Vega A, Alberola-López C. Diffusion sampling schemes: A generalized methodology with nongeometric criteria. Magn Reson Med 2023; 89:2270-2280. [PMID: 36705075 DOI: 10.1002/mrm.29605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/24/2022] [Accepted: 01/13/2023] [Indexed: 01/28/2023]
Abstract
PURPOSE The aim of this paper is to show that geometrical criteria for designing multishell q $$ q $$ -space sampling procedures do not necessarily translate into reconstruction matrices with high figures of merit commonly used in the compressed sensing theory. In addition, we show that a well-known method for visiting k-space in radial three-dimensional acquisitions, namely, the Spiral Phyllotaxis, is a competitive initialization for the optimization of our nonconvex objective function. THEORY AND METHODS We propose the gradient design method WISH (WeIghting SHells) which uses an objective function that accounts for weighted distances between gradients within M-tuples of consecutive shells, with M $$ M $$ ranging between 1 and the maximum number of shells S $$ S $$ . All the M $$ M $$ -tuples share the same weight ω M $$ {\omega}_M $$ . The objective function is optimized for a sample of these weights, using Spiral Phyllotaxis as initialization. State-of-the-art General Electrostatic Energy Minimization (GEEM) and Spherical Codes (SC) were used for comparison. For the three methods, reconstruction matrices of the attenuation signal using MAP-MRI were tested using figures of merit borrowed from the Compressed Sensing theory (namely, Restricted Isometry Property -RIP- and Coherence); we also tested the gradient design using a geometric criterion based on Voronoi cells. RESULTS For RIP and Coherence, WISH got better results in at least one combination of weights, whilst the criterion based on Voronoi cells showed an unrelated pattern. CONCLUSION The versatility provided by WISH is supported by better results. Optimization in the weight parameter space is likely to provide additional improvements. For a practical design with an intermediate number of gradients, our results recommend to carry out the methodology here used to determine the appropriate gradient table.
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Affiliation(s)
| | - Guillem París
- Laboratorio de Procesado de Imagen (LPI), Universidad de Valladolid, Valladolid, Spain
| | - Antonio Tristán-Vega
- Laboratorio de Procesado de Imagen (LPI), Universidad de Valladolid, Valladolid, Spain
| | - Carlos Alberola-López
- Laboratorio de Procesado de Imagen (LPI), Universidad de Valladolid, Valladolid, Spain
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París G, Pieciak T, Aja‐Fernández S, Tristán‐Vega A. Efficient estimation of propagator anisotropy and non-Gaussianity in multishell diffusion MRI with micro-structure adaptive convolution kernels and dual Fourier integral transforms. Magn Reson Med 2023; 89:440-453. [PMID: 36121312 PMCID: PMC9826470 DOI: 10.1002/mrm.29435] [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: 01/25/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 01/11/2023]
Abstract
PURPOSE We seek to reformulate the so-called Propagator Anisotropy (PA) and Non-Gaussianity (NG), originally conceived for the Mean Apparent Propagator diffusion MRI (MAP-MRI), to the Micro-Structure adaptive convolution kernels and dual Fourier Integral Transforms (MiSFIT). These measures describe relevant normalized features of the Ensemble Average Propagator (EAP). THEORY AND METHODS First, the indices, which are defined as the EAP's dissimilarity from an isotropic (PA) or a Gaussian (NG) one, are analytically reformulated within the MiSFIT framework. Then a comparison between the resulting maps is drawn by means of a visual analysis, a quantitative assessment via numerical simulations, a test-retest study across the MICRA dataset (6 subjects scanned five times) and, finally, a computational time evaluation. RESULTS Findings illustrate the visual similarity between the indices computed with either technique. Evaluation against synthetic ground truth data, however, demonstrates MiSFIT's improved accuracy. In addition, the test-retest study reveals MiSFIT's higher degree of reliability in most of white matter regions. Finally, the computational time evaluation shows MiSFIT's time reduction up to two orders of magnitude. CONCLUSIONS Despite being a direct development on the MAP-MRI representation, the PA and the NG can be reliably and efficiently computed within MiSFIT's framework. This, together with the previous findings in the original MiSFIT's article, could mean the difference that definitely qualifies diffusion MRI to be incorporated into regular clinical settings.
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Affiliation(s)
- Guillem París
- Laboratorio de Procesado de Imagen (LPI)Universidad de ValladolidValladolidCastilla y LeónSpain
| | - Tomasz Pieciak
- Laboratorio de Procesado de Imagen (LPI)Universidad de ValladolidValladolidCastilla y LeónSpain,AGH University of Science and TechnologyKrakowPoland
| | - Santiago Aja‐Fernández
- Laboratorio de Procesado de Imagen (LPI)Universidad de ValladolidValladolidCastilla y LeónSpain
| | - Antonio Tristán‐Vega
- Laboratorio de Procesado de Imagen (LPI)Universidad de ValladolidValladolidCastilla y LeónSpain
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The Role of Knowledge Creation-Oriented Convolutional Neural Network in Learning Interaction. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:6493311. [PMID: 35341199 PMCID: PMC8942628 DOI: 10.1155/2022/6493311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 12/11/2022]
Abstract
When convolutional neural network (CNN) applications have different tasks in the source domain and target domain, but both have labels, it is easy to ignore the difference between the source domain and target domain by using the current traditional method, and the recognition effect of image features is not ideal. This paper proposes a deep migration learning method based on improved ResNet based on existing research to avoid this problem. This method extracts high-order statistical features of images by increasing the number of network layers for classification when performing model transfer learning. The ImageNet dataset is used as the source domain, and a Deep Residual Network (DRN) is used for model transfer based on homogeneous data. Firstly, the ResNet model is pretrained. Then, the last fully connected layer of the source model is modified, and the final deep model is constructed by fine-tuning the network by adding an adjustment module. The impact of content differences between datasets on recognizing transfer learning features is reduced through model transfer and deep feature extraction. The deep transfer learning methods after improving ResNet are compared through experiments. The identification algorithm is based on Support Vector Machine (SVM), the deep transfer learning method on Visual Geometry Group (VGG)-19, and the deep transfer learning method based on Inception-V3. Four experiments are performed on MNIST and CIFAR-10 datasets. By analyzing the experimental data, ResNet's improved deep transfer learning method achieves 97.98% and 90.45% accuracy on the MNIST and CIFAR-10 datasets, and 95.33% and 85.07% on the test set. The accuracy and recognition accuracy on the training and test sets have been improved to a certain extent. The combination of CNN and transfer learning can effectively alleviate the difficulty of obtaining labeled data. Therefore, the application of a CNN in transfer learning is significant.
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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: 22] [Impact Index Per Article: 11.0] [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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8
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Tian Q, Fan Q, Witzel T, Polackal MN, Ohringer NA, Ngamsombat C, Russo AW, Machado N, Brewer K, Wang F, Setsompop K, Polimeni JR, Keil B, Wald LL, Rosen BR, Klawiter EC, Nummenmaa A, Huang SY. Comprehensive diffusion MRI dataset for in vivo human brain microstructure mapping using 300 mT/m gradients. Sci Data 2022; 9:7. [PMID: 35042861 PMCID: PMC8766594 DOI: 10.1038/s41597-021-01092-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/25/2021] [Indexed: 12/27/2022] Open
Abstract
Strong gradient systems can improve the signal-to-noise ratio of diffusion MRI measurements and enable a wider range of acquisition parameters that are beneficial for microstructural imaging. We present a comprehensive diffusion MRI dataset of 26 healthy participants acquired on the MGH-USC 3 T Connectome scanner equipped with 300 mT/m maximum gradient strength and a custom-built 64-channel head coil. For each participant, the one-hour long acquisition systematically sampled the accessible diffusion measurement space, including two diffusion times (19 and 49 ms), eight gradient strengths linearly spaced between 30 mT/m and 290 mT/m for each diffusion time, and 32 or 64 uniformly distributed directions. The diffusion MRI data were preprocessed to correct for gradient nonlinearity, eddy currents, and susceptibility induced distortions. In addition, scan/rescan data from a subset of seven individuals were also acquired and provided. The MGH Connectome Diffusion Microstructure Dataset (CDMD) may serve as a test bed for the development of new data analysis methods, such as fiber orientation estimation, tractography and microstructural modelling.
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Affiliation(s)
- Qiyuan Tian
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
- Harvard Medical School, Boston, Massachusetts, United States
| | - Qiuyun Fan
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
- Harvard Medical School, Boston, Massachusetts, United States
| | - Thomas Witzel
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
- Harvard Medical School, Boston, Massachusetts, United States
| | - Maya N Polackal
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
| | - Ned A Ohringer
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
| | - Chanon Ngamsombat
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
| | - Andrew W Russo
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Natalya Machado
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Kristina Brewer
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Fuyixue Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
| | - Kawin Setsompop
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
- Harvard Medical School, Boston, Massachusetts, United States
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
- Harvard Medical School, Boston, Massachusetts, United States
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
| | - Boris Keil
- Department of Life Science Engineering, Institute of Medical Physics and Radiation Protection, Giessen, Germany
| | - Lawrence L Wald
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
- Harvard Medical School, Boston, Massachusetts, United States
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
| | - Bruce R Rosen
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
- Harvard Medical School, Boston, Massachusetts, United States
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
| | - Eric C Klawiter
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
- Harvard Medical School, Boston, Massachusetts, United States
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Aapo Nummenmaa
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States
- Harvard Medical School, Boston, Massachusetts, United States
| | - Susie Y Huang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, United States.
- Harvard Medical School, Boston, Massachusetts, United States.
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States.
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Aja-Fernández S, Pieciak T, Martín-Martín C, Planchuelo-Gómez Á, de Luis-García R, Tristán-Vega A. Moment-based representation of the diffusion inside the brain from reduced DMRI acquisitions: generalized AMURA. Med Image Anal 2022; 77:102356. [DOI: 10.1016/j.media.2022.102356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/13/2021] [Accepted: 01/06/2022] [Indexed: 01/18/2023]
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Tristán-Vega A, París G, de Luis-García R, Aja-Fernández S. Accurate free-water estimation in white matter from fast diffusion MRI acquisitions using the spherical means technique. Magn Reson Med 2021; 87:1028-1035. [PMID: 34463395 DOI: 10.1002/mrm.28997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 01/09/2023]
Abstract
PURPOSE To accurately estimate the partial volume fraction of free water in the white matter from diffusion MRI acquisitions not demanding strong sensitizing gradients and/or large collections of different b-values. Data sets considered comprise ∼ 32-64 gradients near b = 1000 s / mm 2 plus ∼ 6 gradients near b = 500 s / mm 2 . THEORY AND METHODS The spherical means of each diffusion MRI set with the same b-value are computed. These means are related to the inherent diffusion parameters within the voxel (free- and cellular-water fractions; cellular-water diffusivity), which are solved by constrained nonlinear least squares regression. RESULTS The proposed method outperforms those based on mixtures of two Gaussians for the kind of data sets considered. W.r.t. the accuracy, the former does not introduce significant biases in the scenarios of interest, while the latter can reach a bias of 5%-7% if fiber crossings are present. W.r.t. the precision, a variance near 10 % , compared to 15%, can be attained for usual configurations. CONCLUSION It is possible to compute reliable estimates of the free-water fraction inside the white matter by complementing typical DTI acquisitions with few gradients at a lowb-value. It can be done voxel-by-voxel, without imposing spatial regularity constraints.
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Affiliation(s)
- Antonio Tristán-Vega
- Laboratorio de Procesado de Imagen (LPI), Universidad de Valladolid, Valladolid, Spain
| | - Guillem París
- Laboratorio de Procesado de Imagen (LPI), Universidad de Valladolid, Valladolid, Spain
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