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Li Y, Zhang W, Wu Y, Yin L, Zhu C, Chen Y, Cetin-Karayumak S, Cho KIK, Zekelman LR, Rushmore J, Rathi Y, Makris N, O'Donnell LJ, Zhang F. A diffusion MRI tractography atlas for concurrent white matter mapping across Eastern and Western populations. Sci Data 2024; 11:787. [PMID: 39019877 PMCID: PMC11255335 DOI: 10.1038/s41597-024-03624-2] [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: 04/09/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
The study of brain differences across Eastern and Western populations provides vital insights for understanding potential cultural and genetic influences on cognition and mental health. Diffusion MRI (dMRI) tractography is an important tool in assessing white matter (WM) connectivity and brain tissue microstructure across different populations. However, a comprehensive investigation into WM fiber tracts between Eastern and Western populations is challenged due to the lack of a cross-population WM atlas and the large site-specific variability of dMRI data. This study presents a dMRI tractography atlas, namely the East-West WM Atlas, for concurrent WM mapping between Eastern and Western populations and creates a large, harmonized dMRI dataset (n=306) based on the Human Connectome Project and the Chinese Human Connectome Project. The curated WM atlas, as well as subject-specific data including the harmonized dMRI data, the whole brain tractography data, and parcellated WM fiber tracts and their diffusion measures, are publicly released. This resource is a valuable addition to facilitating the exploration of brain commonalities and differences across diverse cultural backgrounds.
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Affiliation(s)
- Yijie Li
- School of Information and Communication Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Wei Zhang
- School of Information and Communication Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Ye Wu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Li Yin
- West China Hospital of Medical Science, Sichuan University, Chengdu, China
| | - Ce Zhu
- School of Information and Communication Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuqian Chen
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | | | - Kang Ik K Cho
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Leo R Zekelman
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Jarrett Rushmore
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, USA
| | - Yogesh Rathi
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Nikos Makris
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Lauren J O'Donnell
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA.
| | - Fan Zhang
- School of Information and Communication Engineering, University of Electronic Science and Technology of China, Chengdu, China.
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2
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Zhang D, Zong F, Zhang Q, Yue Y, Zhang F, Zhao K, Wang D, Wang P, Zhang X, Liu Y. Anat-SFSeg: Anatomically-guided superficial fiber segmentation with point-cloud deep learning. Med Image Anal 2024; 95:103165. [PMID: 38608510 DOI: 10.1016/j.media.2024.103165] [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: 09/29/2023] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024]
Abstract
Diffusion magnetic resonance imaging (dMRI) tractography is a critical technique to map the brain's structural connectivity. Accurate segmentation of white matter, particularly the superficial white matter (SWM), is essential for neuroscience and clinical research. However, it is challenging to segment SWM due to the short adjacent gyri connection in a U-shaped pattern. In this work, we propose an Anatomically-guided Superficial Fiber Segmentation (Anat-SFSeg) framework to improve the performance on SWM segmentation. The framework consists of a unique fiber anatomical descriptor (named FiberAnatMap) and a deep learning network based on point-cloud data. The spatial coordinates of fibers represented as point clouds, as well as the anatomical features at both the individual and group levels, are fed into a neural network. The network is trained on Human Connectome Project (HCP) datasets and tested on the subjects with a range of cognitive impairment levels. One new metric named fiber anatomical region proportion (FARP), quantifies the ratio of fibers in the defined brain regions and enables the comparison with other methods. Another metric named anatomical region fiber count (ARFC), represents the average fiber number in each cluster for the assessment of inter-subject differences. The experimental results demonstrate that Anat-SFSeg achieves the highest accuracy on HCP datasets and exhibits great generalization on clinical datasets. Diffusion tensor metrics and ARFC show disorder severity associated alterations in patients with Alzheimer's disease (AD) and mild cognitive impairments (MCI). Correlations with cognitive grades show that these metrics are potential neuroimaging biomarkers for AD. Furthermore, Anat-SFSeg could be utilized to explore other neurodegenerative, neurodevelopmental or psychiatric disorders.
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Affiliation(s)
- Di Zhang
- School of Airtificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Fangrong Zong
- School of Airtificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China.
| | - Qichen Zhang
- School of Airtificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Yunhui Yue
- School of Airtificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Fan Zhang
- School of Information and Communication Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Kun Zhao
- School of Airtificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Dawei Wang
- Department of Radiology, Qilu Hospital of Shandong University, Jinan, China; Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, China; Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
| | - Pan Wang
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Xi Zhang
- Department of Neurology, the Second Medical Centre, National Clinical Research Centre for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Yong Liu
- School of Airtificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
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3
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Li T, Guo Y, Jin X, Liu T, Wu G, Huang W, Chen F. Dynamic monitoring of radiation-induced white matter microstructure injury in nasopharyngeal carcinoma via high-angular resolution diffusion imaging. Brain Res 2024; 1833:148851. [PMID: 38479491 DOI: 10.1016/j.brainres.2024.148851] [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: 11/23/2023] [Revised: 02/22/2024] [Accepted: 03/05/2024] [Indexed: 03/24/2024]
Abstract
PURPOSE To investigate white matter microstructural abnormalities caused by radiotherapy in nasopharyngeal carcinoma (NPC) patients using MRI high-angular resolution diffusion imaging (HARDI). METHODS We included 127 patients with pathologically confirmed NPC: 36 in the pre-radiotherapy group, 29 in the acute response period (post-RT-AP), 23 in the early delayed period (post-RT-ED) group, and 39 in the late-delayed period (post-RT-LD) group. HARDI data were acquired for each patient, and dispersion parameters were calculated to compare the differences in specific fibre bundles among the groups. The Montreal Neurocognitive Assessment (MoCA) was used to evaluate neurocognitive function, and the correlations between dispersion parameters and MoCA were analysed. RESULTS In the right cingulum frontal parietal bundles, the fractional anisotropy value decreased to the lowest level post-RT-AP and then reversed and increased post-RT-ED and post-RT-LD. The mean, axial, and radial diffusivity were significantly increased in the post-RT-AP (p < 0.05) and decreased in the post-RT-ED and post-RT-LD groups to varying degrees. MoCA scores were decreased post-radiotherapy than those before radiotherapy (p = 0.005). MoCA and mean diffusivity exhibited a mild correlation in the left cingulum frontal parahippocampal bundle. CONCLUSIONS White matter tract changes detected by HARDI are potential biomarkers for monitoring radiotherapy-related brain damage in NPC patients.
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Affiliation(s)
- Tiansheng Li
- Department of Radiology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), NO. 19, Xiuhua St, Xiuying Dic, Haikou, Hainan, 570311, PR China
| | - Yihao Guo
- Department of Radiology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), NO. 19, Xiuhua St, Xiuying Dic, Haikou, Hainan, 570311, PR China
| | - Xin Jin
- Department of Radiology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), NO. 19, Xiuhua St, Xiuying Dic, Haikou, Hainan, 570311, PR China
| | - Tao Liu
- Department of Geriatric Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), NO. 19, Xiuhua St, Xiuying Dic, Haikou, Hainan, 570311, PR China
| | - Gang Wu
- Department of Radiotherapy, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), NO. 19, Xiuhua St, Xiuying Dic, Haikou, Hainan, 570311, PR China
| | - Weiyuan Huang
- Department of Radiology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), NO. 19, Xiuhua St, Xiuying Dic, Haikou, Hainan, 570311, PR China.
| | - Feng Chen
- Department of Radiology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), NO. 19, Xiuhua St, Xiuying Dic, Haikou, Hainan, 570311, PR China.
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4
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Poo E, Mangin JF, Poupon C, Hernández C, Guevara P. PhyberSIM: a tool for the generation of ground truth to evaluate brain fiber clustering algorithms. Front Neurosci 2024; 18:1396518. [PMID: 38872943 PMCID: PMC11169570 DOI: 10.3389/fnins.2024.1396518] [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: 03/05/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024] Open
Abstract
Diffusion Magnetic Resonance Imaging tractography is a non-invasive technique that produces a collection of streamlines representing the main white matter bundle trajectories. Methods, such as fiber clustering algorithms, are important in computational neuroscience and have been the basis of several white matter analysis methods and studies. Nevertheless, these clustering methods face the challenge of the absence of ground truth of white matter fibers, making their evaluation difficult. As an alternative solution, we present an innovative brain fiber bundle simulator that uses spline curves for fiber representation. The methodology uses a tubular model for the bundle simulation based on a bundle centroid and five radii along the bundle. The algorithm was tested by simulating 28 Deep White Matter atlas bundles, leading to low inter-bundle distances and high intersection percentages between the original and simulated bundles. To prove the utility of the simulator, we created three whole-brain datasets containing different numbers of fiber bundles to assess the quality performance of QuickBundles and Fast Fiber Clustering algorithms using five clustering metrics. Our results indicate that QuickBundles tends to split less and Fast Fiber Clustering tends to merge less, which is consistent with their expected behavior. The performance of both algorithms decreases when the number of bundles is increased due to higher bundle crossings. Additionally, the two algorithms exhibit robust behavior with input data permutation. To our knowledge, this is the first whole-brain fiber bundle simulator capable of assessing fiber clustering algorithms with realistic data.
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Affiliation(s)
- Elida Poo
- Department of Electrical Engineering, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
| | | | - Cyril Poupon
- CEA, CNRS, Baobab, Neurospin, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cecilia Hernández
- Department of Computer Science, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
- Center for Biotechnology and Bioengineering (CeBiB), Santiago, Chile
| | - Pamela Guevara
- Department of Electrical Engineering, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
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5
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Joshi A, Li H, Parikh NA, He L. A systematic review of automated methods to perform white matter tract segmentation. Front Neurosci 2024; 18:1376570. [PMID: 38567281 PMCID: PMC10985163 DOI: 10.3389/fnins.2024.1376570] [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: 01/25/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
White matter tract segmentation is a pivotal research area that leverages diffusion-weighted magnetic resonance imaging (dMRI) for the identification and mapping of individual white matter tracts and their trajectories. This study aims to provide a comprehensive systematic literature review on automated methods for white matter tract segmentation in brain dMRI scans. Articles on PubMed, ScienceDirect [NeuroImage, NeuroImage (Clinical), Medical Image Analysis], Scopus and IEEEXplore databases and Conference proceedings of Medical Imaging Computing and Computer Assisted Intervention Society (MICCAI) and International Symposium on Biomedical Imaging (ISBI), were searched in the range from January 2013 until September 2023. This systematic search and review identified 619 articles. Adhering to the specified search criteria using the query, "white matter tract segmentation OR fiber tract identification OR fiber bundle segmentation OR tractography dissection OR white matter parcellation OR tract segmentation," 59 published studies were selected. Among these, 27% employed direct voxel-based methods, 25% applied streamline-based clustering methods, 20% used streamline-based classification methods, 14% implemented atlas-based methods, and 14% utilized hybrid approaches. The paper delves into the research gaps and challenges associated with each of these categories. Additionally, this review paper illuminates the most frequently utilized public datasets for tract segmentation along with their specific characteristics. Furthermore, it presents evaluation strategies and their key attributes. The review concludes with a detailed discussion of the challenges and future directions in this field.
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Affiliation(s)
- Ankita Joshi
- Imaging Research Center, Department of Radiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Neurodevelopmental Disorders Prevention Center, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Hailong Li
- Imaging Research Center, Department of Radiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Neurodevelopmental Disorders Prevention Center, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Department of Radiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Nehal A. Parikh
- Neurodevelopmental Disorders Prevention Center, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Lili He
- Imaging Research Center, Department of Radiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Neurodevelopmental Disorders Prevention Center, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Department of Radiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Computer Science, Biomedical Informatics, and Biomedical Engineering, University of Cincinnati, Cincinnati, OH, United States
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González Rodríguez LL, Osorio I, Cofre G. A, Hernandez Larzabal H, Román C, Poupon C, Mangin JF, Hernández C, Guevara P. Phybers: a package for brain tractography analysis. Front Neurosci 2024; 18:1333243. [PMID: 38529266 PMCID: PMC10962387 DOI: 10.3389/fnins.2024.1333243] [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: 11/04/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024] Open
Abstract
We present a Python library (Phybers) for analyzing brain tractography data. Tractography datasets contain streamlines (also called fibers) composed of 3D points representing the main white matter pathways. Several algorithms have been proposed to analyze this data, including clustering, segmentation, and visualization methods. The manipulation of tractography data is not straightforward due to the geometrical complexity of the streamlines, the file format, and the size of the datasets, which may contain millions of fibers. Hence, we collected and structured state-of-the-art methods for the analysis of tractography and packed them into a Python library, to integrate and share tools for tractography analysis. Due to the high computational requirements, the most demanding modules were implemented in C/C++. Available functions include brain Bundle Segmentation (FiberSeg), Hierarchical Fiber Clustering (HClust), Fast Fiber Clustering (FFClust), normalization to a reference coordinate system, fiber sampling, calculation of intersection between sets of brain fibers, tools for cluster filtering, calculation of measures from clusters, and fiber visualization. The library tools were structured into four principal modules: Segmentation, Clustering, Utils, and Visualization (Fibervis). Phybers is freely available on a GitHub repository under the GNU public license for non-commercial use and open-source development, which provides sample data and extensive documentation. In addition, the library can be easily installed on both Windows and Ubuntu operating systems through the pip library.
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Affiliation(s)
| | - Ignacio Osorio
- Department of Electrical Engineering, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
| | - Alejandro Cofre G.
- Department of Electrical Engineering, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
| | - Hernan Hernandez Larzabal
- Department of Electrical Engineering, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
- Latin American Brain Health Institute (BrainLat), Universidad Adolfo Ibañez, Santiago, Chile
| | - Claudio Román
- Centro de Investigación y Desarrollo en Ingeniería en Salud, Universidad de Valparaíso, Valparaíso, Chile
| | - Cyril Poupon
- CEA, CNRS, Baobab, Neurospin, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Cecilia Hernández
- Department of Computer Science, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
- Center for Biotechnology and Bioengineering (CeBiB), Santiago, Chile
| | - Pamela Guevara
- Department of Electrical Engineering, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
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7
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Nie X, Ruan J, Otaduy MCG, Grinberg LT, Ringman J, Shi Y. Surface-Based Probabilistic Fiber Tracking in Superficial White Matter. IEEE TRANSACTIONS ON MEDICAL IMAGING 2024; 43:1113-1124. [PMID: 37917515 PMCID: PMC10917128 DOI: 10.1109/tmi.2023.3329451] [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] [Indexed: 11/04/2023]
Abstract
The short association fibers or U-fibers travel in the superficial white matter (SWM) beneath the cortical layer. While the U-fibers play a crucial role in various brain disorders, there is a lack of effective tools to reconstruct their highly curved trajectory from diffusion MRI (dMRI). In this work, we propose a novel surface-based framework for the probabilistic tracking of fibers on the triangular mesh representation of the SWM. By deriving a closed-form solution to transform the spherical harmonics (SPHARM) coefficients of 3D fiber orientation distributions (FODs) to local coordinate systems on each triangle, we develop a novel approach to project the FODs onto the tangent space of the SWM. After that, we utilize parallel transport to realize the intrinsic propagation of streamlines on SWM following probabilistically sampled fiber directions. Our intrinsic and surface-based method eliminates the need to perform the necessary but challenging sharp turns in 3D compared with conventional volume-based tractography methods. Using data from the Human Connectome Project (HCP), we performed quantitative comparisons to demonstrate the proposed algorithm can more effectively reconstruct the U-fibers connecting the precentral and postcentral gyrus than previous methods. Quantitative validations were then performed on post-mortem MRIs to show the reconstructed U-fibers from our method more faithfully follow the SWM than volume-based tractography. Finally, we applied our algorithm to study the parietal U-fiber connectivity changes in autosomal dominant Alzheimer's disease (ADAD) patients and successfully detected significant associations between U-fiber connectivity and disease severity.
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8
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Li Y, Nie X, Fu Y, Shi Y. FASSt : Filtering via Symmetric Autoencoder for Spherical Superficial White Matter Tractography. COMPUTATIONAL DIFFUSION MRI : MICCAI WORKSHOP 2023; 14328:129-139. [PMID: 38500570 PMCID: PMC10948089 DOI: 10.1007/978-3-031-47292-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Superficial white matter (SWM) plays an important role in functioning of the human brain, and it contains a large amount of cortico-cortical connections. However, the difficulties of generating complete and reliable U-fibers make SWM-related analysis lag behind relatively matured Deep white matter (DWM) analysis. With the aid of some newly proposed surface-based SWM tractography algorithms, we have developed a specialized SWM filtering method based on a symmetric variational autoencoder (VAE). In this work, we first demonstrate the advantage of the spherical representation and generate these spherical tracts using the triangular mesh and the registered spherical surface. We then introduce the Filtering via symmetric Autoencoder for Spherical Superficial White Matter tractography (FASSt) framework with a novel symmetric weights module to perform the filtering task in a latent space. We evaluate and compare our method with the state-of-the-art clustering-based method on diffusion MRI data from Human Connectome Project (HCP). The results show that our proposed method outperform these clustering methods and achieves excellent performance in groupwise consistency and topographic regularity.
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Affiliation(s)
- Yuan Li
- Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- Ming Hsieh Department of Electrical and Computer Engineering, Viterbi School of Engineering, University of Southern California (USC), Los Angeles, CA 90089, USA
| | - Xinyu Nie
- Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- Ming Hsieh Department of Electrical and Computer Engineering, Viterbi School of Engineering, University of Southern California (USC), Los Angeles, CA 90089, USA
| | - Yao Fu
- Department of Computer and Data Sciences, Case School of Engineering, Case Western Reserve University (CWRU), Cleveland, OH 44106, USA
| | - Yonggang Shi
- Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- Ming Hsieh Department of Electrical and Computer Engineering, Viterbi School of Engineering, University of Southern California (USC), Los Angeles, CA 90089, USA
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9
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Chen Y, Zhang C, Xue T, Song Y, Makris N, Rathi Y, Cai W, Zhang F, O'Donnell LJ. Deep fiber clustering: Anatomically informed fiber clustering with self-supervised deep learning for fast and effective tractography parcellation. Neuroimage 2023; 273:120086. [PMID: 37019346 PMCID: PMC10958986 DOI: 10.1016/j.neuroimage.2023.120086] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/02/2023] [Indexed: 04/05/2023] Open
Abstract
White matter fiber clustering is an important strategy for white matter parcellation, which enables quantitative analysis of brain connections in health and disease. In combination with expert neuroanatomical labeling, data-driven white matter fiber clustering is a powerful tool for creating atlases that can model white matter anatomy across individuals. While widely used fiber clustering approaches have shown good performance using classical unsupervised machine learning techniques, recent advances in deep learning reveal a promising direction toward fast and effective fiber clustering. In this work, we propose a novel deep learning framework for white matter fiber clustering, Deep Fiber Clustering (DFC), which solves the unsupervised clustering problem as a self-supervised learning task with a domain-specific pretext task to predict pairwise fiber distances. This process learns a high-dimensional embedding feature representation for each fiber, regardless of the order of fiber points reconstructed during tractography. We design a novel network architecture that represents input fibers as point clouds and allows the incorporation of additional sources of input information from gray matter parcellation. Thus, DFC makes use of combined information about white matter fiber geometry and gray matter anatomy to improve the anatomical coherence of fiber clusters. In addition, DFC conducts outlier removal naturally by rejecting fibers with low cluster assignment probability. We evaluate DFC on three independently acquired cohorts, including data from 220 individuals across genders, ages (young and elderly adults), and different health conditions (healthy control and multiple neuropsychiatric disorders). We compare DFC to several state-of-the-art white matter fiber clustering algorithms. Experimental results demonstrate superior performance of DFC in terms of cluster compactness, generalization ability, anatomical coherence, and computational efficiency.
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Affiliation(s)
- Yuqian Chen
- Harvard Medical School, MA, USA; The University of Sydney, NSW, Australia
| | | | - Tengfei Xue
- Harvard Medical School, MA, USA; The University of Sydney, NSW, Australia
| | - Yang Song
- The University of New South Wales, NSW, Australia
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10
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Schilling KG, Archer D, Rheault F, Lyu I, Huo Y, Cai LY, Bunge SA, Weiner KS, Gore JC, Anderson AW, Landman BA. Superficial white matter across development, young adulthood, and aging: volume, thickness, and relationship with cortical features. Brain Struct Funct 2023; 228:1019-1031. [PMID: 37074446 PMCID: PMC10320929 DOI: 10.1007/s00429-023-02642-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 04/08/2023] [Indexed: 04/20/2023]
Abstract
Superficial white matter (SWM) represents a significantly understudied part of the human brain, despite comprising a large portion of brain volume and making up a majority of cortico-cortical white matter connections. Using multiple, high-quality datasets with large sample sizes (N = 2421, age range 5-100) in combination with methodological advances in tractography, we quantified features of SWM volume and thickness across the brain and across development, young adulthood, and aging. We had four primary aims: (1) characterize SWM thickness across brain regions (2) describe associations between SWM volume and age (3) describe associations between SWM thickness and age, and (4) quantify relationships between SWM thickness and cortical features. Our main findings are that (1) SWM thickness varies across the brain, with patterns robust across individuals and across the population at the region-level and vertex-level; (2) SWM volume shows unique volumetric trajectories with age that are distinct from gray matter and other white matter trajectories; (3) SWM thickness shows nonlinear cross-sectional changes across the lifespan that vary across regions; and (4) SWM thickness is associated with features of cortical thickness and curvature. For the first time, we show that SWM volume follows a similar trend as overall white matter volume, peaking at a similar time in adolescence, leveling off throughout adulthood, and decreasing with age thereafter. Notably, the relative fraction of total brain volume of SWM continuously increases with age, and consequently takes up a larger proportion of total white matter volume, unlike the other tissue types that decrease with respect to total brain volume. This study represents the first characterization of SWM features across the large portion of the lifespan and provides the background for characterizing normal aging and insight into the mechanisms associated with SWM development and decline.
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Affiliation(s)
- Kurt G Schilling
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.
| | - Derek Archer
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Francois Rheault
- Department of Electrical Engineering and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Ilwoo Lyu
- Computer Science and Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Yuankai Huo
- Department of Electrical Engineering and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Leon Y Cai
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Silvia A Bunge
- Department of Psychology, University of California at Berkeley, Berkeley, USA
| | - Kevin S Weiner
- Department of Psychology, University of California at Berkeley, Berkeley, USA
- Helen Wills Neuroscience Institute, University of California at Berkeley, Berkeley, USA
| | - John C Gore
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
| | - Adam W Anderson
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
- Computer Science and Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
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11
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Xue T, Zhang F, Zhang C, Chen Y, Song Y, Golby AJ, Makris N, Rathi Y, Cai W, O'Donnell LJ. Superficial white matter analysis: An efficient point-cloud-based deep learning framework with supervised contrastive learning for consistent tractography parcellation across populations and dMRI acquisitions. Med Image Anal 2023; 85:102759. [PMID: 36706638 PMCID: PMC9975054 DOI: 10.1016/j.media.2023.102759] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/05/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023]
Abstract
Diffusion MRI tractography is an advanced imaging technique that enables in vivo mapping of the brain's white matter connections. White matter parcellation classifies tractography streamlines into clusters or anatomically meaningful tracts. It enables quantification and visualization of whole-brain tractography. Currently, most parcellation methods focus on the deep white matter (DWM), whereas fewer methods address the superficial white matter (SWM) due to its complexity. We propose a novel two-stage deep-learning-based framework, Superficial White Matter Analysis (SupWMA), that performs an efficient and consistent parcellation of 198 SWM clusters from whole-brain tractography. A point-cloud-based network is adapted to our SWM parcellation task, and supervised contrastive learning enables more discriminative representations between plausible streamlines and outliers for SWM. We train our model on a large-scale tractography dataset including streamline samples from labeled long- and medium-range (over 40 mm) SWM clusters and anatomically implausible streamline samples, and we perform testing on six independently acquired datasets of different ages and health conditions (including neonates and patients with space-occupying brain tumors). Compared to several state-of-the-art methods, SupWMA obtains highly consistent and accurate SWM parcellation results on all datasets, showing good generalization across the lifespan in health and disease. In addition, the computational speed of SupWMA is much faster than other methods.
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Affiliation(s)
- Tengfei Xue
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA; School of Computer Science, University of Sydney, Sydney, Australia
| | - Fan Zhang
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA.
| | - Chaoyi Zhang
- School of Computer Science, University of Sydney, Sydney, Australia
| | - Yuqian Chen
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA; School of Computer Science, University of Sydney, Sydney, Australia
| | - Yang Song
- School of Computer Science and Engineering, University of New South Wales, Sydney, Australia
| | | | - Nikos Makris
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Center for Morphometric Analysis, Massachusetts General Hospital, Boston, USA
| | - Yogesh Rathi
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Weidong Cai
- School of Computer Science, University of Sydney, Sydney, Australia
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12
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Schilling KG, Archer D, Yeh FC, Rheault F, Cai LY, Shafer A, Resnick SM, Hohman T, Jefferson A, Anderson AW, Kang H, Landman BA. Short superficial white matter and aging: a longitudinal multi-site study of 1293 subjects and 2711 sessions. AGING BRAIN 2023; 3:100067. [PMID: 36817413 PMCID: PMC9937516 DOI: 10.1016/j.nbas.2023.100067] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
It is estimated that short association fibers running immediately beneath the cortex may make up as much as 60% of the total white matter volume. However, these have been understudied relative to the long-range association, projection, and commissural fibers of the brain. This is largely because of limitations of diffusion MRI fiber tractography, which is the primary methodology used to non-invasively study the white matter connections. Inspired by recent anatomical considerations and methodological improvements in superficial white matter (SWM) tractography, we aim to characterize changes in these fiber systems in cognitively normal aging, which provide insight into the biological foundation of age-related cognitive changes, and a better understanding of how age-related pathology differs from healthy aging. To do this, we used three large, longitudinal and cross-sectional datasets (N = 1293 subjects, 2711 sessions) to quantify microstructural features and length/volume features of several SWM systems. We find that axial, radial, and mean diffusivities show positive associations with age, while fractional anisotropy has negative associations with age in SWM throughout the entire brain. These associations were most pronounced in the frontal, temporal, and temporoparietal regions. Moreover, measures of SWM volume and length decrease with age in a heterogenous manner across the brain, with different rates of change in inter-gyri and intra-gyri SWM, and at slower rates than well-studied long-range white matter pathways. These features, and their variations with age, provide the background for characterizing normal aging, and, in combination with larger association pathways and gray matter microstructural features, may provide insight into fundamental mechanisms associated with aging and cognition.
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Affiliation(s)
- Kurt G Schilling
- Department of Radiology & Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Derek Archer
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA,Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA,Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN
| | - Fang-Cheng Yeh
- Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Francois Rheault
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, United States
| | - Leon Y Cai
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, United States
| | - Andrea Shafer
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Timothy Hohman
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA,Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA,Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN
| | - Angela Jefferson
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA,Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adam W Anderson
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States
| | - Hakmook Kang
- Department of Biostatistics, Vanderbilt University, Nashville, TN, United States
| | - Bennett A Landman
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, United States
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13
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Shastin D, Genc S, Parker GD, Koller K, Tax CMW, Evans J, Hamandi K, Gray WP, Jones DK, Chamberland M. Surface-based tracking for short association fibre tractography. Neuroimage 2022; 260:119423. [PMID: 35809886 PMCID: PMC10009610 DOI: 10.1016/j.neuroimage.2022.119423] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/30/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
It is estimated that in the human brain, short association fibres (SAF) represent more than half of the total white matter volume and their involvement has been implicated in a range of neurological and psychiatric conditions. This population of fibres, however, remains relatively understudied in the neuroimaging literature. Some of the challenges pertinent to the mapping of SAF include their variable anatomical course and proximity to the cortical mantle, leading to partial volume effects and potentially affecting streamline trajectory estimation. This work considers the impact of seeding and filtering strategies and choice of scanner, acquisition, data resampling to propose a whole-brain, surface-based short (≤30-40 mm) SAF tractography approach. The framework is shown to produce longer streamlines with a predilection for connecting gyri as well as high cortical coverage. We further demonstrate that certain areas of subcortical white matter become disproportionally underrepresented in diffusion-weighted MRI data with lower angular and spatial resolution and weaker diffusion weighting; however, collecting data with stronger gradients than are usually available clinically has minimal impact, making our framework translatable to data collected on commonly available hardware. Finally, the tractograms are examined using voxel- and surface-based measures of consistency, demonstrating moderate reliability, low repeatability and high between-subject variability, urging caution when streamline count-based analyses of SAF are performed.
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Affiliation(s)
- Dmitri Shastin
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Maindy Rd, Cardiff CF24 4HQ, United Kingdom; Department of Neurosurgery, University Hospital of Wales, Cardiff, United Kingdom; BRAIN Biomedical Research Unit, Health & Care Research Wales, Cardiff, United Kingdom.
| | - Sila Genc
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Maindy Rd, Cardiff CF24 4HQ, United Kingdom
| | - Greg D Parker
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Maindy Rd, Cardiff CF24 4HQ, United Kingdom
| | - Kristin Koller
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Maindy Rd, Cardiff CF24 4HQ, United Kingdom
| | - Chantal M W Tax
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Maindy Rd, Cardiff CF24 4HQ, United Kingdom; Image Sciences Institute, University Medical Center Utrecht, Utrecht, Netherlands
| | - John Evans
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Maindy Rd, Cardiff CF24 4HQ, United Kingdom
| | - Khalid Hamandi
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Maindy Rd, Cardiff CF24 4HQ, United Kingdom; BRAIN Biomedical Research Unit, Health & Care Research Wales, Cardiff, United Kingdom; Department of Neurology, University Hospital of Wales, Cardiff, United Kingdom
| | - William P Gray
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Maindy Rd, Cardiff CF24 4HQ, United Kingdom; Department of Neurosurgery, University Hospital of Wales, Cardiff, United Kingdom; BRAIN Biomedical Research Unit, Health & Care Research Wales, Cardiff, United Kingdom
| | - Derek K Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Maindy Rd, Cardiff CF24 4HQ, United Kingdom; BRAIN Biomedical Research Unit, Health & Care Research Wales, Cardiff, United Kingdom
| | - Maxime Chamberland
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Maindy Rd, Cardiff CF24 4HQ, United Kingdom; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
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14
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Superficial white matter bundle atlas based on hierarchical fiber clustering over probabilistic tractography data. Neuroimage 2022; 262:119550. [DOI: 10.1016/j.neuroimage.2022.119550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 11/20/2022] Open
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15
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Disentangling the variability of the superficial white matter organization using regional-tractogram-based population stratification. Neuroimage 2022; 255:119197. [PMID: 35417753 DOI: 10.1016/j.neuroimage.2022.119197] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 03/10/2022] [Accepted: 04/07/2022] [Indexed: 11/22/2022] Open
Abstract
Each variation of the cortical folding pattern implies a particular rearrangement of the geometry of the fibers of the underlying white matter. While this rearrangement only impacts the ends of the long pathways, it may affect most of the trajectory of the short bundles. Therefore, mapping the short fibers of the human brain using diffusion-based tractography requires a dedicated strategy to overcome the variability of the folding patterns. In this paper, we propose a fiber-based stratification strategy splitting the population into homogeneous groups for disentangling the superficial white matter bundle organization. This strategy introduces a new refined fiber distance which includes angular considerations for inferring fine-grained atlases of the short bundles surrounding a specific sulcus and a subtractogram distance that quantifies the similitude between fiber sets of two different subjects. The stratification splits the population into groups with similar regional fiber organization using manifold learning. We first successfully test the hypothesis that the main source of variability of the regional fiber organization is the variability of the regional folding pattern. Then, in each group, we proceed with the automatic identification of the most stable bundles, at a higher granularity level than what can be achieved with the non-stratified whole population, enabling the disentanglement of the very variable configuration of the short fibers. Finally, the method searches for bundle correspondence across groups to build a population level atlas. As a proof of concept, the atlas refinement achieved by this strategy is illustrated for the fibers that surround the central sulcus and the superior temporal sulcus using the HCP dataset.
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16
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Zhang F, Daducci A, He Y, Schiavi S, Seguin C, Smith RE, Yeh CH, Zhao T, O'Donnell LJ. Quantitative mapping of the brain's structural connectivity using diffusion MRI tractography: A review. Neuroimage 2022; 249:118870. [PMID: 34979249 PMCID: PMC9257891 DOI: 10.1016/j.neuroimage.2021.118870] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/03/2021] [Accepted: 12/31/2021] [Indexed: 12/13/2022] Open
Abstract
Diffusion magnetic resonance imaging (dMRI) tractography is an advanced imaging technique that enables in vivo reconstruction of the brain's white matter connections at macro scale. It provides an important tool for quantitative mapping of the brain's structural connectivity using measures of connectivity or tissue microstructure. Over the last two decades, the study of brain connectivity using dMRI tractography has played a prominent role in the neuroimaging research landscape. In this paper, we provide a high-level overview of how tractography is used to enable quantitative analysis of the brain's structural connectivity in health and disease. We focus on two types of quantitative analyses of tractography, including: 1) tract-specific analysis that refers to research that is typically hypothesis-driven and studies particular anatomical fiber tracts, and 2) connectome-based analysis that refers to research that is more data-driven and generally studies the structural connectivity of the entire brain. We first provide a review of methodology involved in three main processing steps that are common across most approaches for quantitative analysis of tractography, including methods for tractography correction, segmentation and quantification. For each step, we aim to describe methodological choices, their popularity, and potential pros and cons. We then review studies that have used quantitative tractography approaches to study the brain's white matter, focusing on applications in neurodevelopment, aging, neurological disorders, mental disorders, and neurosurgery. We conclude that, while there have been considerable advancements in methodological technologies and breadth of applications, there nevertheless remains no consensus about the "best" methodology in quantitative analysis of tractography, and researchers should remain cautious when interpreting results in research and clinical applications.
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Affiliation(s)
- Fan Zhang
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA.
| | | | - Yong He
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China; Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China; IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China; Chinese Institute for Brain Research, Beijing, China
| | - Simona Schiavi
- Department of Computer Science, University of Verona, Verona, Italy
| | - Caio Seguin
- Melbourne Neuropsychiatry Centre, University of Melbourne and Melbourne Health, Melbourne, Australia; The University of Sydney, School of Biomedical Engineering, Sydney, Australia
| | - Robert E Smith
- The Florey Institute of Neuroscience and Mental Health, Melbourne, Australia; Florey Department of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Australia
| | - Chun-Hung Yeh
- Institute for Radiological Research, Chang Gung University, Taoyuan, Taiwan; Department of Psychiatry, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Tengda Zhao
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China; Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China; IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
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17
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Kai J, Khan AR. Assessing the Reliability of Template-Based Clustering for Tractography in Healthy Human Adults. Front Neuroinform 2022; 16:777853. [PMID: 35250526 PMCID: PMC8891507 DOI: 10.3389/fninf.2022.777853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/06/2022] [Indexed: 11/21/2022] Open
Abstract
Tractography is a non-invasive technique to investigate the brain’s structural pathways (also referred to as tracts) that connect different brain regions. A commonly used approach for identifying tracts is with template-based clustering, where unsupervised clustering is first performed on a template in order to label corresponding tracts in unseen data. However, the reliability of this approach has not been extensively studied. Here, an investigation into template-based clustering reliability was performed, assessing the output from two datasets: Human Connectome Project (HCP) and MyConnectome project. The effect of intersubject variability on template-based clustering reliability was investigated, as well as the reliability of both deep and superficial white matter tracts. Identified tracts were evaluated by assessing Euclidean distances from a dataset-specific tract average centroid, the volumetric overlap across corresponding tracts, and along-tract agreement of quantitative values. Further, two template-based techniques were employed to evaluate the reliability of different clustering approaches. Reliability assessment can increase the confidence of a tract identifying technique in future applications to study pathways of interest. The two different template-based approaches exhibited similar reliability for identifying both deep white matter tracts and the superficial white matter.
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Affiliation(s)
- Jason Kai
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, ON, Canada
| | - Ali R. Khan
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, ON, Canada
- *Correspondence: Ali R. Khan,
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18
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Vergara C, Silva F, Huerta I, Lopez-Lopez N, Vazquez A, Houenou J, Poupon C, Mangin JF, Hernandez C, Guevara P. Group-Wise Cortical Surface Parcellation Based on Inter-Subject Fiber Clustering . ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2021; 2021:2655-2659. [PMID: 34891798 DOI: 10.1109/embc46164.2021.9631099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We present an automatic algorithm for the group-wise parcellation of the cortical surface. The method is based on the structural connectivity obtained from representative brain fiber clusters, calculated via an inter-subject clustering scheme. Preliminary regions were defined from cluster-cortical mesh intersection points. The final parcellation was obtained using parcel probability maps to model and integrate the connectivity information of all subjects, and graphs to represent the overlap between parcels. Two inter-subject clustering schemes were tested, generating a total of 171 and 109 parcels, respectively. The resulting parcels were quantitatively compared with three state-of-the-art atlases. The best parcellation returned 69 parcels with a Dice similarity coefficient greater than 0.5. To the best of our knowledge, this is the first diffusion-based cortex parcellation method based on whole-brain inter-subject fiber clustering.
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19
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Goicovich I, Olivares P, Román C, Vázquez A, Poupon C, Mangin JF, Guevara P, Hernández C. Fiber Clustering Acceleration With a Modified Kmeans++ Algorithm Using Data Parallelism. Front Neuroinform 2021; 15:727859. [PMID: 34539370 PMCID: PMC8445177 DOI: 10.3389/fninf.2021.727859] [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: 06/19/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Abstract
Fiber clustering methods are typically used in brain research to study the organization of white matter bundles from large diffusion MRI tractography datasets. These methods enable exploratory bundle inspection using visualization and other methods that require identifying brain white matter structures in individuals or a population. Some applications, such as real-time visualization and inter-subject clustering, need fast and high-quality intra-subject clustering algorithms. This work proposes a parallel algorithm using a General Purpose Graphics Processing Unit (GPGPU) for fiber clustering based on the FFClust algorithm. The proposed GPGPU implementation exploits data parallelism using both multicore and GPU fine-grained parallelism present in commodity architectures, including current laptops and desktop computers. Our approach implements all FFClust steps in parallel, improving execution times in all of them. In addition, our parallel approach includes a parallel Kmeans++ algorithm implementation and defines a new variant of Kmeans++ to reduce the impact of choosing outliers as initial centroids. The results show that our approach provides clustering quality results very similar to FFClust, and it requires an execution time of 3.5 s for processing about a million fibers, achieving a speedup of 11.5 times compared to FFClust.
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Affiliation(s)
- Isaac Goicovich
- Department of Electrical Engineering, Universidad de Concepción, Concepción, Chile
| | - Paulo Olivares
- Department of Computer Science, Universidad de Concepción, Concepción, Chile
| | - Claudio Román
- Department of Electrical Engineering, Universidad de Concepción, Concepción, Chile
| | - Andrea Vázquez
- Department of Computer Science, Universidad de Concepción, Concepción, Chile
| | - Cyril Poupon
- Université Paris-Saclay, CEA, CNRS, Neurospin, Baobab, Gif-sur-Yvette, France
| | | | - Pamela Guevara
- Department of Electrical Engineering, Universidad de Concepción, Concepción, Chile
| | - Cecilia Hernández
- Department of Computer Science, Universidad de Concepción, Concepción, Chile.,Center for Biotechnology and Bioengineering, Santiago, Chile
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20
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Zhang J, Xu Z, Zhou Y, Wang P, Fu P, Xu X, Zhang D. An Empirical Comparative Study on the Two Methods of Eliciting Singers' Emotions in Singing: Self-Imagination and VR Training. Front Neurosci 2021; 15:693468. [PMID: 34456670 PMCID: PMC8387635 DOI: 10.3389/fnins.2021.693468] [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: 04/11/2021] [Accepted: 07/27/2021] [Indexed: 12/04/2022] Open
Abstract
Emotional singing can affect vocal performance and the audience's engagement. Chinese universities use traditional training techniques for teaching theoretical and applied knowledge. Self-imagination is the predominant training method for emotional singing. Recently, virtual reality (VR) technologies have been applied in several fields for training purposes. In this empirical comparative study, a VR training task was implemented to elicit emotions from singers and further assist them with improving their emotional singing performance. The VR training method was compared against the traditional self-imagination method. By conducting a two-stage experiment, the two methods were compared in terms of emotions' elicitation and emotional singing performance. In the first stage, electroencephalographic (EEG) data were collected from the subjects. In the second stage, self-rating reports and third-party teachers' evaluations were collected. The EEG data were analyzed by adopting the max-relevance and min-redundancy algorithm for feature selection and the support vector machine (SVM) for emotion recognition. Based on the results of EEG emotion classification and subjective scale, VR can better elicit the positive, neutral, and negative emotional states from the singers than not using this technology (i.e., self-imagination). Furthermore, due to the improvement of emotional activation, VR brings the improvement of singing performance. The VR hence appears to be an effective approach that may improve and complement the available vocal music teaching methods.
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Affiliation(s)
- Jin Zhang
- College of Arts, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Ziming Xu
- MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Yueying Zhou
- MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Pengpai Wang
- MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Ping Fu
- Department of Library Services, Central Washington University, Ellensburg, WA, United States
| | - Xijia Xu
- Department of Psychiatry, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China
| | - Daoqiang Zhang
- MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
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21
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Hansen CB, Yang Q, Lyu I, Rheault F, Kerley C, Chandio BQ, Fadnavis S, Williams O, Shafer AT, Resnick SM, Zald DH, Cutting LE, Taylor WD, Boyd B, Garyfallidis E, Anderson AW, Descoteaux M, Landman BA, Schilling KG. Pandora: 4-D White Matter Bundle Population-Based Atlases Derived from Diffusion MRI Fiber Tractography. Neuroinformatics 2021; 19:447-460. [PMID: 33196967 PMCID: PMC8124084 DOI: 10.1007/s12021-020-09497-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 12/21/2022]
Abstract
Brain atlases have proven to be valuable neuroscience tools for localizing regions of interest and performing statistical inferences on populations. Although many human brain atlases exist, most do not contain information about white matter structures, often neglecting them completely or labelling all white matter as a single homogenous substrate. While few white matter atlases do exist based on diffusion MRI fiber tractography, they are often limited to descriptions of white matter as spatially separate "regions" rather than as white matter "bundles" or fascicles, which are well-known to overlap throughout the brain. Additional limitations include small sample sizes, few white matter pathways, and the use of outdated diffusion models and techniques. Here, we present a new population-based collection of white matter atlases represented in both volumetric and surface coordinates in a standard space. These atlases are based on 2443 subjects, and include 216 white matter bundles derived from 6 different automated state-of-the-art tractography techniques. This atlas is freely available and will be a useful resource for parcellation and segmentation.
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Affiliation(s)
- Colin B Hansen
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Qi Yang
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Ilwoo Lyu
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Francois Rheault
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Université de Sherbrooke, Sherbrooke, Canada
| | - Cailey Kerley
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Bramsh Qamar Chandio
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Shreyas Fadnavis
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Owen Williams
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - Andrea T Shafer
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - David H Zald
- Center for Advanced Human Brain Imaging Research, Rutgers University, Piscataway, NJ, USA
| | - Laurie E Cutting
- Vanderbilt Kennedy Center, Vanderbilt University, Nashville, TN, USA
| | - Warren D Taylor
- Vanderbilt Kennedy Center, Vanderbilt University, Nashville, TN, USA
| | - Brian Boyd
- Vanderbilt Kennedy Center, Vanderbilt University, Nashville, TN, USA
| | - Eleftherios Garyfallidis
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
- Program of Neuroscience, Indiana University, Bloomington, IN, USA
| | - Adam W Anderson
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Maxime Descoteaux
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Université de Sherbrooke, Sherbrooke, Canada
| | - Bennett A Landman
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kurt G Schilling
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.
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22
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Bugain M, Dimech Y, Torzhenskaya N, Thiebaut de Schotten M, Caspers S, Muscat R, Bajada CJ. Occipital Intralobar fasciculi: a description, through tractography, of three forgotten tracts. Commun Biol 2021; 4:433. [PMID: 33785859 PMCID: PMC8010026 DOI: 10.1038/s42003-021-01935-3] [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: 07/17/2020] [Accepted: 03/03/2021] [Indexed: 02/01/2023] Open
Abstract
Diffusion MRI paired with tractography has facilitated a non-invasive exploration of many association, projection, and commissural fiber tracts. However, there is still a scarcity of research studies related to intralobar association fibers. The Dejerines' (two of the most notable neurologists of 19th century France) gave an in-depth description of the intralobar fibers of the occipital lobe. Unfortunately, their exquisite work has since been sparsely cited in the modern literature. This work gives a modern description of many of the occipital intralobar lobe fibers described by the Dejerines. We perform a virtual dissection and reconstruct the tracts using diffusion MRI tractography. The dissection is guided by the Dejerines' treatise, Anatomie des Centres Nerveux. As an accompaniment to this article, we provided a French-to-English translation of the treatise portion concerning five intra-occipital tracts, namely: the stratum calcarinum, the stratum proprium cunei, the vertical occipital fasciculus of Wernicke, the transverse fasciculus of the cuneus and the transverse fasciculus of the lingual lobule of Vialet. It was possible to reconstruct all but one of these tracts. For completeness, the recently described sledge runner fasciculus, although not one of the Dejerines' tracts, was identified and successfully reconstructed.
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Affiliation(s)
- Maeva Bugain
- grid.4462.40000 0001 2176 9482Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, The University of Malta, Msida, Malta
| | - Yana Dimech
- grid.4462.40000 0001 2176 9482Department of Cognitive Sciences, Faculty of Media and Knowledge Sciences, The University of Malta, Msida, Malta
| | - Natalia Torzhenskaya
- grid.4462.40000 0001 2176 9482Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, The University of Malta, Msida, Malta
| | - Michel Thiebaut de Schotten
- grid.462844.80000 0001 2308 1657Brain Connectivity and Behaviour Laboratory, Sorbonne Universities, Paris, France ,grid.4444.00000 0001 2112 9282Groupe d’Imagerie Neurofonctionnelle, Institut des Maladies Neurodégénératives -UMR 5293, CNRS, CEA University of Bordeaux, Bordeaux, France
| | - Svenja Caspers
- grid.8385.60000 0001 2297 375XInstitute of Neuroscience and Medicine (INM-1), Research Centre Juelich, Juelich, Germany ,grid.411327.20000 0001 2176 9917Institute for Anatomy I, Medical Faculty, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Richard Muscat
- grid.4462.40000 0001 2176 9482Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, The University of Malta, Msida, Malta
| | - Claude J. Bajada
- grid.4462.40000 0001 2176 9482Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, The University of Malta, Msida, Malta ,grid.8385.60000 0001 2297 375XInstitute of Neuroscience and Medicine (INM-1), Research Centre Juelich, Juelich, Germany
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Liang X, Zhao C, Jin X, Jiang Y, Yang L, Chen Y, Gong G. Sex-related human brain asymmetry in hemispheric functional gradients. Neuroimage 2021; 229:117761. [PMID: 33454413 DOI: 10.1016/j.neuroimage.2021.117761] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/16/2020] [Accepted: 01/07/2021] [Indexed: 01/25/2023] Open
Abstract
The left and right hemispheres of the human brain are two connected but relatively independent functional modules; they show multidimensional asymmetries ranging from particular local brain unit properties to entire hemispheric connectome topology. To date, however, it remains largely unknown whether and how hemispheric functional hierarchical structures differ between hemispheres. In the present study, we adopted a newly developed resting-state (rs) functional connectivity (FC)-based gradient approach to evaluate hemispheric functional hierarchical structures and their asymmetries in right-handed healthy young adults. Our results showed an overall mirrored principal functional gradient between hemispheres, with the sensory cortex and the default-mode network (DMN) anchored at the two opposite ends of the gradient. Interestingly, the left hemisphere showed a significantly larger full range of the principal gradient in both males and females, with males exhibiting greater leftward asymmetry. Similarly, the principal gradient component scores of two regions around the middle temporal gyrus and posterior orbitofrontal cortex exhibited similar hemisphere × sex interaction effects: a greater degree of leftward asymmetry in males than in females. Moreover, we observed significant main hemisphere and sex effects in distributed regions across the entire hemisphere. All these results are reproducible and robust between test-retest rs-fMRI sessions. Our findings provide evidence of functional gradients that enhance the present understanding of human brain asymmetries in functional organization and highlight the impact of sex on hemispheric functional gradients and their asymmetries.
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Affiliation(s)
- Xinyu Liang
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Chenxi Zhao
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China; School of Systems Science, Beijing Normal University, Beijing, China
| | - Xinhu Jin
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Yaya Jiang
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Liyuan Yang
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Yijun Chen
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Gaolang Gong
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China; Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China; Chinese Institute for Brain Research, Beijing, China.
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24
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Xu C, Sun G, Liang R, Xu X. Vector Field Streamline Clustering Framework for Brain Fiber Tract Segmentation. IEEE Trans Cogn Dev Syst 2021. [DOI: 10.1109/tcds.2021.3094555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Pron A, Deruelle C, Coulon O. U-shape short-range extrinsic connectivity organisation around the human central sulcus. Brain Struct Funct 2020; 226:179-193. [PMID: 33245395 DOI: 10.1007/s00429-020-02177-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022]
Abstract
The central sulcus is probably one of the most studied folds in the human brain, owing to its clear relationship with primary sensory-motor functional areas. However, due to the difficulty of estimating the trajectories of the U-shape fibres from diffusion MRI, the short structural connectivity of this sulcus remains relatively unknown. In this context, we studied the spatial organization of these U-shape fibres along the central sulcus. Based on high quality diffusion MRI data of 100 right-handed subjects and state-of-the-art pre-processing pipeline, we first define a connectivity space that provides a comprehensive and continuous description of the short-range anatomical connectivity around the central sulcus at both the individual and group levels. We then infer the presence of five major U-shape fibre bundles at the group level in both hemispheres by applying unsupervised clustering in the connectivity space. We propose a quantitative investigation of their position and number of streamlines as a function of hemisphere, sex and functional scores such as handedness and manual dexterity. Main findings of this study are twofold: a description of U-shape short-range connectivity along the central sulcus at group level and the evidence of a significant relationship between the position of three hand related U-shape fibre bundles and the handedness score of subjects.
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Affiliation(s)
- Alexandre Pron
- Institut de Neurosciences de La Timone, Aix-Marseille Université, CNRS, UMR 7289, Marseille, France
| | - Christine Deruelle
- Institut de Neurosciences de La Timone, Aix-Marseille Université, CNRS, UMR 7289, Marseille, France
| | - Olivier Coulon
- Institut de Neurosciences de La Timone, Aix-Marseille Université, CNRS, UMR 7289, Marseille, France.
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26
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Disruption of Conscious Access in Psychosis Is Associated with Altered Structural Brain Connectivity. J Neurosci 2020; 41:513-523. [PMID: 33229501 DOI: 10.1523/jneurosci.0945-20.2020] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/10/2020] [Accepted: 09/20/2020] [Indexed: 11/21/2022] Open
Abstract
According to global neuronal workspace (GNW) theory, conscious access relies on long-distance cerebral connectivity to allow a global neuronal ignition coding for conscious content. In patients with schizophrenia and bipolar disorder, both alterations in cerebral connectivity and an increased threshold for conscious perception have been reported. The implications of abnormal structural connectivity for disrupted conscious access and the relationship between these two deficits and psychopathology remain unclear. The aim of this study was to determine the extent to which structural connectivity is correlated with consciousness threshold, particularly in psychosis. We used a visual masking paradigm to measure consciousness threshold, and diffusion MRI tractography to assess structural connectivity in 97 humans of either sex with varying degrees of psychosis: healthy control subjects (n = 46), schizophrenia patients (n = 25), and bipolar disorder patients with (n = 17) and without (n = 9) a history of psychosis. Patients with psychosis (schizophrenia and bipolar disorder with psychotic features) had an elevated masking threshold compared with control subjects and bipolar disorder patients without psychotic features. Masking threshold correlated negatively with the mean general fractional anisotropy of white matter tracts exclusively within the GNW network (inferior frontal-occipital fasciculus, cingulum, and corpus callosum). Mediation analysis demonstrated that alterations in long-distance connectivity were associated with an increased masking threshold, which in turn was linked to psychotic symptoms. Our findings support the hypothesis that long-distance structural connectivity within the GNW plays a crucial role in conscious access, and that conscious access may mediate the association between impaired structural connectivity and psychosis.
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27
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Bodin C, Pron A, Le Mao M, Régis J, Belin P, Coulon O. Plis de passage in the superior temporal sulcus: Morphology and local connectivity. Neuroimage 2020; 225:117513. [PMID: 33130271 DOI: 10.1016/j.neuroimage.2020.117513] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/31/2022] Open
Abstract
While there is a profusion of functional investigations involving the superior temporal sulcus (STS), our knowledge of the anatomy of this sulcus is still limited by a large individual variability. In particular, an accurate characterization of the "plis de passage" (PPs), annectant gyri inside the fold, is lacking to explain this variability. Performed on 90 subjects of the HCP database, our study revealed that PPs constitute landmarks that can be identified from the geometry of the STS walls. They were found associated with a specific U-shape white-matter connectivity between the two banks of the sulcus, the amount of connectivity being related to the depth of the PPs. These findings raise new hypotheses regarding the spatial organization of PPs, the relation between cortical anatomy and structural connectivity, as well as the possible role of PPs in the regional functional organization.
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Affiliation(s)
- C Bodin
- CNRS, UMR 7289, Institut de Neurosciences de la Timone, Aix-Marseille Université, Marseille, France; Institute for Language, Communication, and the Brain, Aix-Marseille University, Marseille, France.
| | - A Pron
- CNRS, UMR 7289, Institut de Neurosciences de la Timone, Aix-Marseille Université, Marseille, France
| | - M Le Mao
- CNRS, UMR 7289, Institut de Neurosciences de la Timone, Aix-Marseille Université, Marseille, France
| | - J Régis
- INSERM U1106, Institut de Neurosciences des Systèmes, Aix-Marseille Université, Marseille, France
| | - P Belin
- CNRS, UMR 7289, Institut de Neurosciences de la Timone, Aix-Marseille Université, Marseille, France; Département de Psychologie, Université de Montréal, Montréal, Canada; Institute for Language, Communication, and the Brain, Aix-Marseille University, Marseille, France
| | - O Coulon
- CNRS, UMR 7289, Institut de Neurosciences de la Timone, Aix-Marseille Université, Marseille, France; Institute for Language, Communication, and the Brain, Aix-Marseille University, Marseille, France
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28
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López-López N, Vázquez A, Houenou J, Poupon C, Mangin JF, Ladra S, Guevara P. From Coarse to Fine-Grained Parcellation of the Cortical Surface Using a Fiber-Bundle Atlas. Front Neuroinform 2020; 14:32. [PMID: 33071768 PMCID: PMC7533645 DOI: 10.3389/fninf.2020.00032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
In this article, we present a hybrid method to create fine-grained parcellations of the cortical surface, from a coarse-grained parcellation according to an anatomical atlas, based on cortico-cortical connectivity. The connectivity information is obtained from segmented superficial and deep white matter bundles, according to bundle atlases, instead of the whole tractography. Thus, a direct matching between the fiber bundles and the cortical regions is obtained, avoiding the problem of finding the correspondence of the cortical parcels among subjects. Generating parcels from segmented fiber bundles can provide a good representation of the human brain connectome since they are based on bundle atlases that contain the most reproducible short and long connections found on a population of subjects. The method first processes the tractography of each subject and extracts the bundles of the atlas, based on a segmentation algorithm. Next, the intersection between the fiber bundles and the cortical mesh is calculated, to define the initial and final intersection points of each fiber. A fiber filtering is then applied to eliminate misclassified fibers, based on the anatomical definition of each bundle and the labels of Desikan-Killiany anatomical parcellation. A parcellation algorithm is then performed to create a subdivision of the anatomical regions of the cortex, which is reproducible across subjects. This step resolves the overlapping of the fiber bundle extremities over the cortical mesh within each anatomical region. For the analysis, the density of the connections and the degree of overlapping, is considered and represented with a graph. One of our parcellations, an atlas composed of 160 parcels, achieves a reproducibility across subjects of ≈0.74, based on the average Dice's coefficient between subject's connectivity matrices, rather than ≈0.73 obtained for a macro anatomical parcellation of 150 parcels. Moreover, we compared two of our parcellations with state-of-the-art atlases, finding a degree of similarity with dMRI, functional, anatomical, and multi-modal atlases. The higher similarity was found for our parcellation composed of 185 sub-parcels with another parcellation based on dMRI data from the same database, but created with a different approach, leading to 130 parcels in common based on a Dice's coefficient ≥0.5.
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Affiliation(s)
- Narciso López-López
- Faculty of Engineering, Universidad de Concepción, Concepción, Chile.,Universidade da Coruña, CITIC, Department of Computer Science and Information Technologies, A Coruña, Spain
| | - Andrea Vázquez
- Faculty of Engineering, Universidad de Concepción, Concepción, Chile
| | - Josselin Houenou
- Université Paris-Saclay, CEA, CNRS, Baobab, Neurospin, Gif-sur-Yvette, France.,INSERM U955 Unit, Mondor Institute for Biomedical Research, Team 15 "Translational Psychiatry", Paris, France.,Fondation Fondamental, Paris, France.,AP-HP, Department of Psychiatry and Addictology, School of Medicine, Mondor University Hospitals, DHU PePsy, Paris, France
| | - Cyril Poupon
- Université Paris-Saclay, CEA, CNRS, Baobab, Neurospin, Gif-sur-Yvette, France
| | | | - Susana Ladra
- Universidade da Coruña, CITIC, Department of Computer Science and Information Technologies, A Coruña, Spain
| | - Pamela Guevara
- Faculty of Engineering, Universidad de Concepción, Concepción, Chile
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29
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Zhang F, Xie G, Leung L, Mooney MA, Epprecht L, Norton I, Rathi Y, Kikinis R, Al-Mefty O, Makris N, Golby AJ, O'Donnell LJ. Creation of a novel trigeminal tractography atlas for automated trigeminal nerve identification. Neuroimage 2020; 220:117063. [PMID: 32574805 PMCID: PMC7572753 DOI: 10.1016/j.neuroimage.2020.117063] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/07/2020] [Accepted: 06/14/2020] [Indexed: 12/29/2022] Open
Abstract
Diffusion MRI (dMRI) tractography has been successfully used to study the trigeminal nerves (TGNs) in many clinical and research applications. Currently, identification of the TGN in tractography data requires expert nerve selection using manually drawn regions of interest (ROIs), which is prone to inter-observer variability, time-consuming and carries high clinical and labor costs. To overcome these issues, we propose to create a novel anatomically curated TGN tractography atlas that enables automated identification of the TGN from dMRI tractography. In this paper, we first illustrate the creation of a trigeminal tractography atlas. Leveraging a well-established computational pipeline and expert neuroanatomical knowledge, we generate a data-driven TGN fiber clustering atlas using tractography data from 50 subjects from the Human Connectome Project. Then, we demonstrate the application of the proposed atlas for automated TGN identification in new subjects, without relying on expert ROI placement. Quantitative and visual experiments are performed with comparison to expert TGN identification using dMRI data from two different acquisition sites. We show highly comparable results between the automatically and manually identified TGNs in terms of spatial overlap and visualization, while our proposed method has several advantages. First, our method performs automated TGN identification, and thus it provides an efficient tool to reduce expert labor costs and inter-operator bias relative to expert manual selection. Second, our method is robust to potential imaging artifacts and/or noise that can prevent successful manual ROI placement for TGN selection and hence yields a higher successful TGN identification rate.
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Affiliation(s)
- Fan Zhang
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA.
| | - Guoqiang Xie
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Neurosurgery, Nuclear Industry 215 Hospital of Shaanxi Province, Xianyang, China
| | - Laura Leung
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Michael A Mooney
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Lorenz Epprecht
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Zurich, Zurich, Switzerland
| | - Isaiah Norton
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Yogesh Rathi
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Ron Kikinis
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Ossama Al-Mefty
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Nikos Makris
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Departments of Psychiatry, Neurology and Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Alexandra J Golby
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Lauren J O'Donnell
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
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30
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Vázquez A, López-López N, Sánchez A, Houenou J, Poupon C, Mangin JF, Hernández C, Guevara P. FFClust: Fast fiber clustering for large tractography datasets for a detailed study of brain connectivity. Neuroimage 2020; 220:117070. [PMID: 32599269 DOI: 10.1016/j.neuroimage.2020.117070] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/19/2020] [Accepted: 06/16/2020] [Indexed: 01/31/2023] Open
Abstract
Automated methods that can identify white matter bundles from large tractography datasets have several applications in neuroscience research. In these applications, clustering algorithms have shown to play an important role in the analysis and visualization of white matter structure, generating useful data which can be the basis for further studies. This work proposes FFClust, an efficient fiber clustering method for large tractography datasets containing millions of fibers. Resulting clusters describe the whole set of main white matter fascicles present on an individual brain. The method aims to identify compact and homogeneous clusters, which enables several applications. In individuals, the clusters can be used to study the local connectivity in pathological brains, while at population level, the processing and analysis of reproducible bundles, and other post-processing algorithms can be carried out to study the brain connectivity and create new white matter bundle atlases. The proposed method was evaluated in terms of quality and execution time performance versus the state-of-the-art clustering techniques used in the area. Results show that FFClust is effective in the creation of compact clusters, with a low intra-cluster distance, while keeping a good quality Davies-Bouldin index, which is a metric that quantifies the quality of clustering approaches. Furthermore, it is about 8.6 times faster than the most efficient state-of-the-art method for one million fibers dataset. In addition, we show that FFClust is able to correctly identify atlas bundles connecting different brain regions, as an example of application and the utility of compact clusters.
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Affiliation(s)
- Andrea Vázquez
- Universidad de Concepción, Department of Computer Science, Concepción, Chile
| | - Narciso López-López
- Universidad de Concepción, Department of Computer Science, Concepción, Chile; Universidade da Coruña, Centro de investigación CITIC, A Coruña, Spain
| | - Alexis Sánchez
- Universidad de Concepción, Department of Computer Science, Concepción, Chile
| | - Josselin Houenou
- Université Paris-Saclay, CEA, CNRS, Baobab, Neurospin, Gif-sur-Yvette, France; INSERM U955 Unit, Mondor Institute for Biomedical Research, Team 15 "Translational Psychiatry", Créteil, France; Fondation Fondamental, Créteil, France; AP-HP, Department of Psychiatry and Addictology, Mondor University Hospitals, School of Medicine, DHU PePsy, Créteil, France
| | - Cyril Poupon
- Université Paris-Saclay, CEA, CNRS, Baobab, Neurospin, Gif-sur-Yvette, France
| | | | - Cecilia Hernández
- Universidad de Concepción, Department of Computer Science, Concepción, Chile; Center for Biotechnology and Bioengineering (CeBiB), Santiago, Chile
| | - Pamela Guevara
- Universidad de Concepción, Department of Electrical Engineering, Concepción, Chile.
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31
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Vázquez A, López-López N, Houenou J, Poupon C, Mangin JF, Ladra S, Guevara P. Automatic group-wise whole-brain short association fiber bundle labeling based on clustering and cortical surface information. Biomed Eng Online 2020; 19:42. [PMID: 32493483 PMCID: PMC7268230 DOI: 10.1186/s12938-020-00786-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/23/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Diffusion MRI is the preferred non-invasive in vivo modality for the study of brain white matter connections. Tractography datasets contain 3D streamlines that can be analyzed to study the main brain white matter tracts. Fiber clustering methods have been used to automatically group similar fibers into clusters. However, due to inter-subject variability and artifacts, the resulting clusters are difficult to process for finding common connections across subjects, specially for superficial white matter. METHODS We present an automatic method for labeling of short association bundles on a group of subjects. The method is based on an intra-subject fiber clustering that generates compact fiber clusters. Posteriorly, the clusters are labeled based on the cortical connectivity of the fibers, taking as reference the Desikan-Killiany atlas, and named according to their relative position along one axis. Finally, two different strategies were applied and compared for the labeling of inter-subject bundles: a matching with the Hungarian algorithm, and a well-known fiber clustering algorithm, called QuickBundles. RESULTS Individual labeling was executed over four subjects, with an execution time of 3.6 min. An inspection of individual labeling based on a distance measure showed good correspondence among the four tested subjects. Two inter-subject labeling were successfully implemented and applied to 20 subjects and compared using a set of distance thresholds, ranging from a conservative value of 10 mm to a moderate value of 21 mm. Hungarian algorithm led to a high correspondence, but low reproducibility for all the thresholds, with 96 s of execution time. QuickBundles led to better correspondence, reproducibility and short execution time of 9 s. Hence, the whole processing for the inter-subject labeling over 20 subjects takes 1.17 h. CONCLUSION We implemented a method for the automatic labeling of short bundles in individuals, based on an intra-subject clustering and the connectivity of the clusters with the cortex. The labels provide useful information for the visualization and analysis of individual connections, which is very difficult without any additional information. Furthermore, we provide two fast inter-subject bundle labeling methods. The obtained clusters could be used for performing manual or automatic connectivity analysis in individuals or across subjects.
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Affiliation(s)
- Andrea Vázquez
- Faculty of Engineering, Universidad de Concepción, Concepción, Chile
| | - Narciso López-López
- Faculty of Engineering, Universidad de Concepción, Concepción, Chile
- Centro de investigación CITIC, Universidade da Coruña, A Coruña, Spain
| | - Josselin Houenou
- NeuroSpin, CEA, Paris-Saclay University, Gif-sur-Yvette, France
- INSERM U955 Unit, Mondor Institute for Biomedical Research, Team 15 “Translational Psychiatry”, Créteil, France
- Fondation Fondamental, Créteil, France
- AP-HP, Department of Psychiatry and Addictology, Mondor University Hospitals, School of Medicine, DHU PePsy, Créteil, France
| | - Cyril Poupon
- NeuroSpin, CEA, Paris-Saclay University, Gif-sur-Yvette, France
| | | | - Susana Ladra
- Centro de investigación CITIC, Universidade da Coruña, A Coruña, Spain
| | - Pamela Guevara
- Faculty of Engineering, Universidad de Concepción, Concepción, Chile
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32
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Guevara M, Guevara P, Román C, Mangin JF. Superficial white matter: A review on the dMRI analysis methods and applications. Neuroimage 2020; 212:116673. [DOI: 10.1016/j.neuroimage.2020.116673] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/12/2022] Open
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33
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Wang Y, Metoki A, Smith DV, Medaglia JD, Zang Y, Benear S, Popal H, Lin Y, Olson IR. Multimodal mapping of the face connectome. Nat Hum Behav 2020; 4:397-411. [PMID: 31988441 PMCID: PMC7167350 DOI: 10.1038/s41562-019-0811-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 12/09/2019] [Indexed: 01/13/2023]
Abstract
Face processing supports our ability to recognize friend from foe, form tribes and understand the emotional implications of changes in facial musculature. This skill relies on a distributed network of brain regions, but how these regions interact is poorly understood. Here we integrate anatomical and functional connectivity measurements with behavioural assays to create a global model of the face connectome. We dissect key features, such as the network topology and fibre composition. We propose a neurocognitive model with three core streams; face processing along these streams occurs in a parallel and reciprocal manner. Although long-range fibre paths are important, the face network is dominated by short-range fibres. Finally, we provide evidence that the well-known right lateralization of face processing arises from imbalanced intra- and interhemispheric connections. In summary, the face network relies on dynamic communication across highly structured fibre tracts, enabling coherent face processing that underpins behaviour and cognition.
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Affiliation(s)
- Yin Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, and IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China.
| | - Athanasia Metoki
- Department of Psychology, Temple University, Philadelphia, PA, USA
| | - David V Smith
- Department of Psychology, Temple University, Philadelphia, PA, USA
| | - John D Medaglia
- Department of Psychology, Drexel University, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yinyin Zang
- School of Psychological and Cognitive Sciences and Beijing Key Laboratory of Behavior and Mental Health, Peking University, Beijing, China
| | - Susan Benear
- Department of Psychology, Temple University, Philadelphia, PA, USA
| | - Haroon Popal
- Department of Psychology, Temple University, Philadelphia, PA, USA
| | - Ying Lin
- Department of Psychology, Temple University, Philadelphia, PA, USA
| | - Ingrid R Olson
- Department of Psychology, Temple University, Philadelphia, PA, USA.
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Registration-free analysis of diffusion MRI tractography data across subjects through the human lifespan. Neuroimage 2020; 214:116703. [PMID: 32151759 PMCID: PMC8482444 DOI: 10.1016/j.neuroimage.2020.116703] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 01/21/2020] [Accepted: 03/02/2020] [Indexed: 02/05/2023] Open
Abstract
Diffusion MRI tractography produces massive sets of streamlines that need to be clustered into anatomically meaningful white-matter bundles. Conventional clustering techniques group streamlines based on their proximity in Euclidean space. We have developed AnatomiCuts, an unsupervised method for clustering tractography streamlines based on their neighboring anatomical structures, rather than their coordinates in Euclidean space. In this work, we show that the anatomical similarity metric used in AnatomiCuts can be extended to find corresponding clusters across subjects and across hemispheres, without inter-subject or inter-hemispheric registration. Our proposed approach enables group-wise tract cluster analysis, as well as studies of hemispheric asymmetry. We evaluate our approach on data from the pilot MGH-Harvard-USC Lifespan Human Connectome project, showing improved correspondence in tract clusters across 184 subjects aged 8-90. Our method shows up to 38% improvement in the overlap of corresponding clusters when comparing subjects with large age differences. The techniques presented here do not require registration to a template and can thus be applied to populations with large inter-subject variability, e.g., due to brain development, aging, or neurological disorders.
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Roman C, Cardenas N, Poupon C, Mangin JF, Guevara P. The effect of the number of fibers in tractography reconstruction of white matter bundles. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020; 2019:2825-2829. [PMID: 31946481 DOI: 10.1109/embc.2019.8856379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The study of white matter (WM) through diffusion Magnetic Resonance Imaging (dMRI) is crucial to obtain a better understanding of human brain connections and functions, at a macroscopic level. A large number of works have focused on long range brain connections, while recently, several studies have also analyzed superficial WM connectivity. In recent years, with the massive use of HCP database, and its processing with known softwares like DSI Studio and MRtrix, it is necessary to evaluate the influence of tractography parameters on the reconstruction of fiber bundles and further analyses. We study the effect of the number of fibers, for whole brain tractography, on the reconstruction of deep and superficial WM bundles based on their segmentation using multi-subject bundle atlases. For DSI Studio (deterministic algorithm), a value of 1M fibers could reconstruct most of deep white matter (DWM) bundles, while a value of 1.5M was required for superficial white matter (SWM) bundles. In the case of MRtrix (probabilistic algorithm), a value of 3M fibers was found to be suitable for the study of both kinds of fibers. Furthermore, we found the tracking of SWM bundles to be more sensitive to several parameters than DWM, for DSI Studio.
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36
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Pinto D, Roman C, Guevara M, Poupon C, Mangin JF, Guevara P. A stringent fiber distance measure for dMRI tractography clustering and segmentation. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2018; 2018:1-4. [PMID: 30440248 DOI: 10.1109/embc.2018.8512333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most analysis and segmentation methods for diffusion MRI tractography datasets require a fiber distance measure able to determine the similarity between a pair of fibers. We present a stringent fiber distance measure able to perform a good discrimination between fiber shapes and lengths. It uses three terms: (i) a fiber maximum Euclidean distance, (ii) a fiber shape distance, and (iii) a fiber length distance. The distance was evaluated applying a hierarchical clustering of fibers connecting the pre-and post-central gyri of a subject. Results where compared with other known fiber distance measures. A better sensitivity to differences in fiber shape and length was found for the proposed distance. This will be very useful for the detailed study and description of white matter bundles. Known bundles will be better decomposed into sub-bundles, with more precision on the bundle shape and on the regions connected by the fibers. For short association bundles, this distance will be a real improvement, as even the most stringent distance used until now shows some limitations when evaluating the similarity of these fibers.
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37
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Wu Y, Zhang F, Makris N, Ning Y, Norton I, She S, Peng H, Rathi Y, Feng Y, Wu H, O'Donnell LJ. Investigation into local white matter abnormality in emotional processing and sensorimotor areas using an automatically annotated fiber clustering in major depressive disorder. Neuroimage 2018; 181:16-29. [PMID: 29890329 PMCID: PMC6415925 DOI: 10.1016/j.neuroimage.2018.06.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/02/2018] [Accepted: 06/05/2018] [Indexed: 01/17/2023] Open
Abstract
This work presents an automatically annotated fiber cluster (AAFC) method to enable identification of anatomically meaningful white matter structures from the whole brain tractography. The proposed method consists of 1) a study-specific whole brain white matter parcellation using a well-established data-driven groupwise fiber clustering pipeline to segment tractography into multiple fiber clusters, and 2) a novel cluster annotation method to automatically assign an anatomical tract annotation to each fiber cluster by employing cortical parcellation information across multiple subjects. The novelty of the AAFC method is that it leverages group-wise information about the fiber clusters, including their fiber geometry and cortical terminations, to compute a tract anatomical label for each cluster in an automated fashion. We demonstrate the proposed AAFC method in an application of investigating white matter abnormality in emotional processing and sensorimotor areas in major depressive disorder (MDD). Seven tracts of interest related to emotional processing and sensorimotor functions are automatically identified using the proposed AAFC method as well as a comparable method that uses a cortical parcellation alone. Experimental results indicate that our proposed method is more consistent in identifying the tracts across subjects and across hemispheres in terms of the number of fibers. In addition, we perform a between-group statistical analysis in 31 MDD patients and 62 healthy subjects on the identified tracts using our AAFC method. We find statistical differences in diffusion measures in local regions within a fiber tract (e.g. 4 fiber clusters within the identified left hemisphere cingulum bundle (consisting of 14 clusters) are significantly different between the two groups), suggesting the ability of our method in identifying potential abnormality specific to subdivisions of a white matter structure.
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Affiliation(s)
- Ye Wu
- Institution of Information Processing and Automation, Zhejiang University of Technology, Hangzhou, China; Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikos Makris
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuping Ning
- Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Hui'ai Hospital), Guangzhou, China
| | - Isaiah Norton
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shenglin She
- Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Hui'ai Hospital), Guangzhou, China
| | - Hongjun Peng
- Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Hui'ai Hospital), Guangzhou, China
| | - Yogesh Rathi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuanjing Feng
- Institution of Information Processing and Automation, Zhejiang University of Technology, Hangzhou, China
| | - Huawang Wu
- Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Hui'ai Hospital), Guangzhou, China.
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Zhang F, Wu Y, Norton I, Rigolo L, Rathi Y, Makris N, O'Donnell LJ. An anatomically curated fiber clustering white matter atlas for consistent white matter tract parcellation across the lifespan. Neuroimage 2018; 179:429-447. [PMID: 29920375 PMCID: PMC6080311 DOI: 10.1016/j.neuroimage.2018.06.027] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/01/2018] [Accepted: 06/08/2018] [Indexed: 12/15/2022] Open
Abstract
This work presents an anatomically curated white matter atlas to enable consistent white matter tract parcellation across different populations. Leveraging a well-established computational pipeline for fiber clustering, we create a tract-based white matter atlas including information from 100 subjects. A novel anatomical annotation method is proposed that leverages population-based brain anatomical information and expert neuroanatomical knowledge to annotate and categorize the fiber clusters. A total of 256 white matter structures are annotated in the proposed atlas, which provides one of the most comprehensive tract-based white matter atlases covering the entire brain to date. These structures are composed of 58 deep white matter tracts including major long range association and projection tracts, commissural tracts, and tracts related to the brainstem and cerebellar connections, plus 198 short and medium range superficial fiber clusters organized into 16 categories according to the brain lobes they connect. Potential false positive connections are annotated in the atlas to enable their exclusion from analysis or visualization. In addition, the proposed atlas allows for a whole brain white matter parcellation into 800 fiber clusters to enable whole brain connectivity analyses. The atlas and related computational tools are open-source and publicly available. We evaluate the proposed atlas using a testing dataset of 584 diffusion MRI scans from multiple independently acquired populations, across genders, the lifespan (1 day-82 years), and different health conditions (healthy control, neuropsychiatric disorders, and brain tumor patients). Experimental results show successful white matter parcellation across subjects from different populations acquired on multiple scanners, irrespective of age, gender or disease indications. Over 99% of the fiber tracts annotated in the atlas were detected in all subjects on average. One advantage in terms of robustness is that the tract-based pipeline does not require any cortical or subcortical segmentations, which can have limited success in young children and patients with brain tumors or other structural lesions. We believe this is the first demonstration of consistent automated white matter tract parcellation across the full lifespan from birth to advanced age.
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Affiliation(s)
- Fan Zhang
- Harvard Medical School, Boston, USA.
| | - Ye Wu
- Harvard Medical School, Boston, USA
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