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Brain structure and synaptic protein expression alterations after antidepressant treatment in a Wistar-Kyoto rat model of depression. J Affect Disord 2022; 314:293-302. [PMID: 35878834 DOI: 10.1016/j.jad.2022.07.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/20/2022] [Accepted: 07/17/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Structural MRI has demonstrated brain alterations in depression pathology and antidepressants treatment. While synaptic plasticity has been previously proposed as the potential underlying mechanism of MRI findings at a cellular and molecular scale, there is still insufficient evidence to link the MRI findings and synaptic plasticity mechanisms in depression pathology. METHODS In this study, a Wistar-Kyoto (WKY) depression rat model was treated with antidepressants (citalopram or Jie-Yu Pills) and tested in a series of behavioral tests and a 7.0 MRI scanner. We then measured dendritic spine density within altered brain regions. We also examined expression of synaptic marker proteins (PSD-95 and SYP). RESULTS WKY rats exhibited depression-like behaviors in the sucrose preference test (SPT) and forced swim test (FST), and anxiety-like behaviors in the open field test (OFT). Both antidepressants reversed behavioral changes in SPT and OFT but not in FST. We found a correlation between SPT performance and brain volumes as detected by MRI. All structural changes were consistent with alterations of the corpus callosum (white matter), dendritic spine density, as well as PSD95 and SYP expression at different levels. Two antidepressants similarly reversed these macro- and micro-changes. LIMITATIONS The single dose of antidepressants was the major limitation of this study. Further studies should focus on the white matter microstructure changes and myelin-related protein alterations, in addition to comparing the effects of ketamine. CONCLUSION Translational evidence links structural MRI changes and synaptic plasticity alterations, which promote our understanding of SPT mechanisms and antidepressant response in WKY rats.
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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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Kuhl U, Sobotta S, Skeide MA. Mathematical learning deficits originate in early childhood from atypical development of a frontoparietal brain network. PLoS Biol 2021; 19:e3001407. [PMID: 34591838 PMCID: PMC8509954 DOI: 10.1371/journal.pbio.3001407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 10/12/2021] [Accepted: 09/06/2021] [Indexed: 11/19/2022] Open
Abstract
Mathematical learning deficits are defined as a neurodevelopmental disorder (dyscalculia) in the International Classification of Diseases. It is not known, however, how such deficits emerge in the course of early brain development. Here, we conducted functional and structural magnetic resonance imaging (MRI) experiments in 3- to 6-year-old children without formal mathematical learning experience. We followed this sample until the age of 7 to 9 years, identified individuals who developed deficits, and matched them to a typically developing control group using comprehensive behavioral assessments. Multivariate pattern classification distinguished future cases from controls with up to 87% accuracy based on the regional functional activity of the right posterior parietal cortex (PPC), the network-level functional activity of the right dorsolateral prefrontal cortex (DLPFC), and the effective functional and structural connectivity of these regions. Our results indicate that mathematical learning deficits originate from atypical development of a frontoparietal network that is already detectable in early childhood.
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Affiliation(s)
- Ulrike Kuhl
- Research Group Learning in Early Childhood, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Machine Learning Group, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Sarah Sobotta
- Research Group Learning in Early Childhood, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | | | - Michael A. Skeide
- Research Group Learning in Early Childhood, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- * E-mail:
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4
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Abstract
Developmental dyslexia, a severe deficit in literacy learning, is a neurodevelopmental learning disorder. Yet, it is not clear whether existing neurobiological accounts of dyslexia capture potential predispositions of the deficit or consequences of reduced reading experience. Here, we longitudinally followed 32 children from preliterate to school age using functional and structural magnetic resonance imaging techniques. Based on standardised and age-normed reading and spelling tests administered at school age, children were classified as 16 dyslexic participants and 16 controls. This longitudinal design allowed us to disentangle possible neurobiological predispositions for developing dyslexia from effects of individual differences in literacy experience. In our sample, the disorder can be predicted already before literacy learning from auditory cortex gyrification and aberrant downstream connectivity within the speech processing system. These results provide evidence for the notion that dyslexia may originate from an atypical maturation of the speech network that precedes literacy instruction.
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5
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Jeon HA, Kuhl U, Friederici AD. Mathematical expertise modulates the architecture of dorsal and cortico-thalamic white matter tracts. Sci Rep 2019; 9:6825. [PMID: 31048754 PMCID: PMC6497695 DOI: 10.1038/s41598-019-43400-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/23/2019] [Indexed: 01/24/2023] Open
Abstract
To what extent are levels of cognitive expertise reflected in differential structural connectivity of the brain? We addressed this question by analyzing the white matter brain structure of experts (mathematicians) versus non-experts (non-mathematicians) using probabilistic tractography. Having mathematicians and non-mathematicians as participant groups enabled us to directly compare profiles of structural connectivity arising from individual levels of expertise in mathematics. Tracking from functional seed regions activated during the processing of complex arithmetic formulas revealed an involvement of various fiber bundles such the inferior fronto-occipital fascicle, arcuate fasciculus/superior longitudinal fasciculus (AF/SLF), cross-hemispheric connections of frontal lobe areas through the corpus callosum and cortico-subcortical connectivity via the bilateral thalamic radiation. With the aim of investigating expertise-dependent structural connectivity, the streamline density was correlated with the level of expertise, defined by automaticity of processing complex mathematics. The results showed that structural integrity of the AF/SLF was higher in individuals with higher automaticity, while stronger cortico-thalamic connectivity was associated with lower levels of automaticity. Therefore, we suggest that expertise in the domain of mathematics is reflected in plastic changes of the brain's white matter structure, possibly reflecting a general principle of cognitive expertise.
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Affiliation(s)
- Hyeon-Ae Jeon
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea.
- Partner Group of the Max Planck Institute for Human Cognitive and Brain Sciences at the Department for Brain and Cognitive Sciences, DGIST, Daegu, 42988, Korea.
| | - Ulrike Kuhl
- Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, 04103, Germany
| | - Angela D Friederici
- Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, 04103, Germany
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6
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Caspers S, Axer M. Decoding the microstructural correlate of diffusion MRI. NMR IN BIOMEDICINE 2019; 32:e3779. [PMID: 28858413 DOI: 10.1002/nbm.3779] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 06/28/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
Diffusion imaging has evolved considerably over the past decade. While it provides valuable information about the structural connectivity at the macro- and mesoscopic scale, bridging the gap to the microstructure at the level of single nerve fibers poses an enormous challenge. This is particularly true for the human brain with its large size, its large white-matter volume and availability of histological techniques for studying human whole-brain sections and subsequent 3D reconstruction. Classic post-mortem techniques for studying the fiber architecture of the brain, such as myeloarchitectonic staining or dye tracing, are complemented by novel histological approaches, such as 3D polarized light imaging or optical coherence tomography, enabling unique insight into the fiber architecture from large fiber bundles within deep white matter to single nerve fibers in the cortex. The present review discusses the benefits and challenges of these latest developments in comparison with the classic techniques, with particular focus on the mutual exchange between in vivo and post-mortem diffusion imaging and post-mortem microstructural approaches for understanding the wiring of the brain across different scales.
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Affiliation(s)
- Svenja Caspers
- C. and O. Vogt Institute for Brain Research, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- JARA-BRAIN, Jülich-Aachen Research Alliance, Jülich, Germany
| | - Markus Axer
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
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7
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Grinberg F, Maximov II, Farrher E, Shah NJ. Microstructure-informed slow diffusion tractography in humans enhances visualisation of fibre pathways. Magn Reson Imaging 2017; 45:7-17. [PMID: 28870514 DOI: 10.1016/j.mri.2017.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 08/15/2017] [Accepted: 08/30/2017] [Indexed: 11/26/2022]
Abstract
Conventional fibre tractography methods based on diffusion tensor imaging exploit diffusion anisotropy and directionality in the range of low diffusion weightings (b-values). High b-value Biexponential Diffusion Tensor Analysis reported previously has demonstrated that fractional anisotropy of the slow diffusion component is essentially higher than that of conventional diffusion tensor imaging whereas popular compartment models associate this slow diffusion component with axonal water fraction. One of the primary aims of this study is to elucidate the feasibility and potential benefits of "microstructure-informed" whole-brain slow-diffusion fibre tracking (SDIFT) in humans. In vivo diffusion-weighted images in humans were acquired in the extended range of diffusion weightings≤6000smm-2 at 3T. Fast and slow diffusion tensors were reconstructed using the bi-exponential tensor decomposition, and a detailed statistical analysis of the relevant whole-brain tensor metrics was performed. We visualised three-dimensional fibre tracts in in vivo human brains using deterministic streamlining via the major eigenvector of the slow diffusion tensor. In particular, we demonstrated that slow-diffusion fibre tracking provided considerably higher fibre counts of long association fibres and allowed one to reconstruct more short association fibres than conventional diffusion tensor imaging. SDIFT is suggested to be useful as a complimentary method capable to enhance reliability and visualisation of the evaluated fibre pathways. It is especially informative in precortical areas where the uncertainty of the mono-exponential tensor evaluation becomes too high due to decreased anisotropy of low b-value diffusion in these areas. Benefits can be expected in assessment of the residual axonal integrity in tissues affected by various pathological conditions, in surgical planning, and in evaluation of cortical connectivity, in particular, between Brodmann's areas.
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Affiliation(s)
- Farida Grinberg
- Institute of Neuroscience and Medicine - 4, Forschungszentrum Juelich GmbH, Juelich, Germany,; Department of Neurology, Faculty of Medicine, RWTH Aachen University, JARA, Aachen, Germany.
| | - Ivan I Maximov
- Institute of Neuroscience and Medicine - 4, Forschungszentrum Juelich GmbH, Juelich, Germany
| | - Ezequiel Farrher
- Institute of Neuroscience and Medicine - 4, Forschungszentrum Juelich GmbH, Juelich, Germany
| | - N Jon Shah
- Institute of Neuroscience and Medicine - 4, Forschungszentrum Juelich GmbH, Juelich, Germany,; Department of Neurology, Faculty of Medicine, RWTH Aachen University, JARA, Aachen, Germany
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8
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Güllmar D, Seeliger T, Gudziol H, Teichgräber UK, Reichenbach JR, Guntinas-Lichius O, Bitter T. Improvement of olfactory function after sinus surgery correlates with white matter properties measured by diffusion tensor imaging. Neuroscience 2017; 360:190-196. [DOI: 10.1016/j.neuroscience.2017.07.070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 11/17/2022]
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9
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Rheault F, Houde JC, Descoteaux M. Visualization, Interaction and Tractometry: Dealing with Millions of Streamlines from Diffusion MRI Tractography. Front Neuroinform 2017; 11:42. [PMID: 28694776 PMCID: PMC5483435 DOI: 10.3389/fninf.2017.00042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 06/07/2017] [Indexed: 01/06/2023] Open
Abstract
Recently proposed tractography and connectomics approaches often require a very large number of streamlines, in the order of millions. Generating, storing and interacting with these datasets is currently quite difficult, since they require a lot of space in memory and processing time. Compression is a common approach to reduce data size. Recently such an approach has been proposed consisting in removing collinear points in the streamlines. Removing points from streamlines results in files that cannot be robustly post-processed and interacted with existing tools, which are for the most part point-based. The aim of this work is to improve visualization, interaction and tractometry algorithms to robustly handle compressed tractography datasets. Our proposed improvements are threefold: (i) An efficient loading procedure to improve visualization (reduce memory usage up to 95% for a 0.2 mm step size); (ii) interaction techniques robust to compressed tractograms; (iii) tractometry techniques robust to compressed tractograms to eliminate biased in tract-based statistics. The present work demonstrates the need of correctly handling compressed streamlines to avoid biases in future tractometry and connectomics studies.
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Affiliation(s)
- Francois Rheault
- Sherbrooke Connectivity Imaging Lab, Computer Science Department, University of SherbrookeSherbrooke, QC, Canada.,Sherbrooke Molecular Imaging Center, University of SherbrookeSherbrooke, QC, Canada.,Centre de Recherche, Centre Hospitalier Universitaire de Sherbrooke (CHUS), University of SherbrookeSherbrooke, QC, Canada
| | - Jean-Christophe Houde
- Sherbrooke Connectivity Imaging Lab, Computer Science Department, University of SherbrookeSherbrooke, QC, Canada.,Sherbrooke Molecular Imaging Center, University of SherbrookeSherbrooke, QC, Canada.,Centre de Recherche, Centre Hospitalier Universitaire de Sherbrooke (CHUS), University of SherbrookeSherbrooke, QC, Canada
| | - Maxime Descoteaux
- Sherbrooke Connectivity Imaging Lab, Computer Science Department, University of SherbrookeSherbrooke, QC, Canada.,Sherbrooke Molecular Imaging Center, University of SherbrookeSherbrooke, QC, Canada.,Centre de Recherche, Centre Hospitalier Universitaire de Sherbrooke (CHUS), University of SherbrookeSherbrooke, QC, Canada
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Grosse Wiesmann C, Schreiber J, Singer T, Steinbeis N, Friederici AD. White matter maturation is associated with the emergence of Theory of Mind in early childhood. Nat Commun 2017; 8:14692. [PMID: 28322222 PMCID: PMC5364393 DOI: 10.1038/ncomms14692] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 01/24/2017] [Indexed: 01/16/2023] Open
Abstract
The ability to attribute mental states to other individuals is crucial for human cognition. A milestone of this ability is reached around the age of 4, when children start understanding that others can have false beliefs about the world. The neural basis supporting this critical step is currently unknown. Here, we relate this behavioural change to the maturation of white matter structure in 3- and 4-year-old children. Tract-based spatial statistics and probabilistic tractography show that the developmental breakthrough in false belief understanding is associated with age-related changes in local white matter structure in temporoparietal regions, the precuneus and medial prefrontal cortex, and with increased dorsal white matter connectivity between temporoparietal and inferior frontal regions. These effects are independent of co-developing cognitive abilities. Our findings show that the emergence of mental state representation is related to the maturation of core belief processing regions and their connection to the prefrontal cortex.
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Affiliation(s)
- Charlotte Grosse Wiesmann
- Max Planck Institute for Human Cognitive and Brain Sciences, Department of Neuropsychology, Stephanstrasse 1a, Leipzig 04103, Germany
- Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Jan Schreiber
- Max Planck Institute for Human Cognitive and Brain Sciences, Department of Neuropsychology, Stephanstrasse 1a, Leipzig 04103, Germany
| | - Tania Singer
- Max Planck Institute for Human Cognitive and Brain Sciences, Department of Social Neuroscience, Stephanstrasse 1a, Leipzig 04103, Germany
| | - Nikolaus Steinbeis
- Max Planck Institute for Human Cognitive and Brain Sciences, Department of Social Neuroscience, Stephanstrasse 1a, Leipzig 04103, Germany
- Developmental and Educational Psychology, Institute of Psychology, Leiden University, P.O. Box 9555, 2300 RB Leiden, Netherlands
| | - Angela D. Friederici
- Max Planck Institute for Human Cognitive and Brain Sciences, Department of Neuropsychology, Stephanstrasse 1a, Leipzig 04103, Germany
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Predicting early signs of dyslexia at a preliterate age by combining behavioral assessment with structural MRI. Neuroimage 2016; 143:378-386. [PMID: 27608602 DOI: 10.1016/j.neuroimage.2016.09.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 08/23/2016] [Accepted: 09/02/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Recent studies suggest that neurobiological anomalies are already detectable in pre-school children with a family history of developmental dyslexia (DD). However, there is a lack of longitudinal studies showing a direct link between those differences at a preliterate age and the subsequent literacy difficulties seen in school. It is also not clear whether the prediction of DD in pre-school children can be significantly improved when considering neurobiological predictors, compared to models based on behavioral literacy precursors only. METHODS We recruited 53 pre-reading children either with (N=25) or without a family risk of DD (N=28). Quantitative T1 MNI data and literacy precursor abilities were assessed at kindergarten age. A subsample of 35 children was tested for literacy skills either one or two years later, that is, either in first or second grade. RESULTS The group comparison of quantitative T1 measures revealed significantly higher T1 intensities in the left anterior arcuate fascicle (AF), suggesting reduced myelin concentration in preliterate children at risk of DD. A logistic regression showed that DD can be predicted significantly better (p=.024) when neuroanatomical differences between groups are used as predictors (80%) compared to a model based on behavioral predictors only (63%). The Wald statistic confirmed that the T1 intensity of the left AF is a statistically significant predictor of DD (p<.05). CONCLUSIONS Our longitudinal results provide evidence for the hypothesis that neuroanatomical anomalies in children with a family risk of DD are related to subsequent problems in acquiring literacy. Particularly, solid white matter organization in the left anterior arcuate fascicle seems to play a pivotal role.
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Tardif CL, Gauthier CJ, Steele CJ, Bazin PL, Schäfer A, Schaefer A, Turner R, Villringer A. Advanced MRI techniques to improve our understanding of experience-induced neuroplasticity. Neuroimage 2016; 131:55-72. [DOI: 10.1016/j.neuroimage.2015.08.047] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/18/2015] [Accepted: 08/20/2015] [Indexed: 12/13/2022] Open
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Abstract
Progress in magnetic resonance imaging (MRI) now makes it possible to identify the major white matter tracts in the living human brain. These tracts are important because they carry many of the signals communicated between different brain regions. MRI methods coupled with biophysical modeling can measure the tissue properties and structural features of the tracts that impact our ability to think, feel, and perceive. This review describes the fundamental ideas of the MRI methods used to identify the major white matter tracts in the living human brain.
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Affiliation(s)
- Brian A Wandell
- Department of Psychology and Stanford Neurosciences Institute, Stanford University, Stanford, California 94305;
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Takemura H, Caiafa CF, Wandell BA, Pestilli F. Ensemble Tractography. PLoS Comput Biol 2016; 12:e1004692. [PMID: 26845558 PMCID: PMC4742469 DOI: 10.1371/journal.pcbi.1004692] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 12/03/2015] [Indexed: 01/02/2023] Open
Abstract
Tractography uses diffusion MRI to estimate the trajectory and cortical projection zones of white matter fascicles in the living human brain. There are many different tractography algorithms and each requires the user to set several parameters, such as curvature threshold. Choosing a single algorithm with specific parameters poses two challenges. First, different algorithms and parameter values produce different results. Second, the optimal choice of algorithm and parameter value may differ between different white matter regions or different fascicles, subjects, and acquisition parameters. We propose using ensemble methods to reduce algorithm and parameter dependencies. To do so we separate the processes of fascicle generation and evaluation. Specifically, we analyze the value of creating optimized connectomes by systematically combining candidate streamlines from an ensemble of algorithms (deterministic and probabilistic) and systematically varying parameters (curvature and stopping criterion). The ensemble approach leads to optimized connectomes that provide better cross-validated prediction error of the diffusion MRI data than optimized connectomes generated using a single-algorithm or parameter set. Furthermore, the ensemble approach produces connectomes that contain both short- and long-range fascicles, whereas single-parameter connectomes are biased towards one or the other. In summary, a systematic ensemble tractography approach can produce connectomes that are superior to standard single parameter estimates both for predicting the diffusion measurements and estimating white matter fascicles. Diffusion MRI and tractography opened a new avenue for studying white matter fascicles and their tissue properties in the living human brain. There are many different tractography methods, and each requires the user to set several parameters. A limitation of tractography is that the results depend on the selection of algorithms and parameters. Here, we analyze an ensemble method, Ensemble Tractography (ET), that reduces the effect of algorithm and parameter selection. ET creates a large set of candidate streamlines using an ensemble of algorithms and parameter values and then selects the streamlines with strong support from the data using a global fascicle evaluation method. Compared to single parameter connectomes, ET connectomes predict diffusion MRI signals better and cover a wider range of white matter volume. Importantly, ET connectomes include both short- and long-association fascicles, which are not typically found together in single-parameter connectomes.
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Affiliation(s)
- Hiromasa Takemura
- Center for Information and Neural Networks (CiNet), National Institute of Information and Communications Technology, and Osaka University, Suita, Japan
- The Japan Society for the Promotion of Science, Tokyo, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Department of Psychology, Stanford University, Stanford, California, United States of America
- * E-mail: (HT); (FP)
| | - Cesar F. Caiafa
- Instituto Argentino de Radioastronomía (IAR)—CCT La Plata—CONICET, Villa Elisa, Buenos Aires, Argentina
| | - Brian A. Wandell
- Department of Psychology, Stanford University, Stanford, California, United States of America
| | - Franco Pestilli
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, Indiana, United States of America
- Programs in Neuroscience and Cognitive Science, Indiana University Network Science Institute, Indiana University, Bloomington, Indiana, United States of America
- * E-mail: (HT); (FP)
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Close TG, Tournier JD, Johnston LA, Calamante F, Mareels I, Connelly A. Fourier Tract Sampling (FouTS): A framework for improved inference of white matter tracts from diffusion MRI by explicitly modelling tract volume. Neuroimage 2015; 120:412-27. [DOI: 10.1016/j.neuroimage.2015.05.090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 04/06/2015] [Accepted: 05/22/2015] [Indexed: 10/23/2022] Open
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16
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Knösche TR, Anwander A, Liptrot M, Dyrby TB. Validation of tractography: Comparison with manganese tracing. Hum Brain Mapp 2015; 36:4116-34. [PMID: 26178765 PMCID: PMC5034837 DOI: 10.1002/hbm.22902] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 05/22/2015] [Accepted: 07/01/2015] [Indexed: 01/01/2023] Open
Abstract
In this study, we used invasive tracing to evaluate white matter tractography methods based on ex vivo diffusion-weighted magnetic resonance imaging (dwMRI) data. A representative selection of tractography methods were compared to manganese tracing on a voxel-wise basis, and a more qualitative assessment examined whether, and to what extent, certain fiber tracts and gray matter targets were reached. While the voxel-wise agreement was very limited, qualitative assessment revealed that tractography is capable of finding the major fiber tracts, although there were some differences between the methods. However, false positive connections were very common and, in particular, we discovered that it is not possible to achieve high sensitivity (i.e., few false negatives) and high specificity (i.e., few false positives) at the same time. Closer inspection of the results led to the conclusion that these problems mainly originate from regions with complex fiber arrangements or high curvature and are not easily resolved by sophisticated local models alone. Instead, the crucial challenge in making tractography a truly useful and reliable tool in brain research and neurology lies in the acquisition of better data. In particular, the increase of spatial resolution, under preservation of the signal-to-noise-ratio, is key.
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Affiliation(s)
- Thomas R. Knösche
- Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
| | - Alfred Anwander
- Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
| | - Matthew Liptrot
- Danish Research Centre for Magnetic ResonanceCentre for Functional and Diagnostic Imaging and ResearchCopenhagen University Hospital HvidovreHvidovreDenmark
- Department of Computer ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Tim B. Dyrby
- Danish Research Centre for Magnetic ResonanceCentre for Functional and Diagnostic Imaging and ResearchCopenhagen University Hospital HvidovreHvidovreDenmark
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Martínez-Heras E, Varriano F, Prčkovska V, Laredo C, Andorrà M, Martínez-Lapiscina EH, Calvo A, Lampert E, Villoslada P, Saiz A, Prats-Galino A, Llufriu S. Improved Framework for Tractography Reconstruction of the Optic Radiation. PLoS One 2015; 10:e0137064. [PMID: 26376179 PMCID: PMC4573981 DOI: 10.1371/journal.pone.0137064] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 08/12/2015] [Indexed: 01/21/2023] Open
Abstract
The optic radiation (OR) is one of the major components of the visual system and a key structure at risk in white matter diseases such as multiple sclerosis (MS). However, it is challenging to perform track reconstruction of the OR using diffusion MRI due to a sharp change of direction in the Meyer's loop and the presence of kissing and crossing fibers along the pathway. As such, we aimed to provide a highly precise and reproducible framework for tracking the OR from thalamic and visual cortex masks. The framework combined the generation of probabilistic streamlines by high order fiber orientation distributions estimated with constrained spherical deconvolution and an automatic post-processing based on anatomical exclusion criteria (AEC) to compensate for the presence of anatomically implausible streamlines. Specifically, those ending in the contralateral hemisphere, cerebrospinal fluid or grey matter outside the visual cortex were automatically excluded. We applied the framework to two distinct high angular resolution diffusion-weighted imaging (HARDI) acquisition protocols on one cohort, comprised of ten healthy volunteers and five MS patients. The OR was successfully delineated in both HARDI acquisitions in the healthy volunteers and MS patients. Quantitative evaluation of the OR position was done by comparing the results with histological reference data. Compared with histological mask, the OR reconstruction into a template (OR-TCT) was highly precise (percentage of voxels within the OR-TCT correctly defined as OR), ranging from 0.71 to 0.83. The sensitivity (percentage of voxels in histological reference mask correctly defined as OR in OR-TCT) ranged from 0.65 to 0.81 and the accuracy (measured by F1 score) was 0.73 to 0.77 in healthy volunteers. When AEC was not applied the precision and accuracy decreased. The absolute agreement between both HARDI datasets measured by the intraclass correlation coefficient was 0.73. This improved framework allowed us to reconstruct the OR with high reliability and accuracy independently of the acquisition parameters. Moreover, the reconstruction was possible even in the presence of tissue damage due to MS. This framework could also be applied to other tracts with complex configuration.
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Affiliation(s)
- Eloy Martínez-Heras
- Center of Neuroimmunology, Service of Neurology, Hospital Clinic and Institut d′Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Federico Varriano
- Laboratory of Surgical NeuroAnatomy (LSNA). Facultat de Medicina. Universitat de Barcelona, Barcelona, Spain
| | - Vesna Prčkovska
- Center of Neuroimmunology, Service of Neurology, Hospital Clinic and Institut d′Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Carlos Laredo
- Comprehensive Stroke Center, Department of Neuroscience. Hospital Clinic and Institut d′Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Magí Andorrà
- Center of Neuroimmunology, Service of Neurology, Hospital Clinic and Institut d′Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Elena H. Martínez-Lapiscina
- Center of Neuroimmunology, Service of Neurology, Hospital Clinic and Institut d′Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Anna Calvo
- Medical Imaging Platform, Institut d′Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Erika Lampert
- Center of Neuroimmunology, Service of Neurology, Hospital Clinic and Institut d′Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Pablo Villoslada
- Center of Neuroimmunology, Service of Neurology, Hospital Clinic and Institut d′Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Albert Saiz
- Center of Neuroimmunology, Service of Neurology, Hospital Clinic and Institut d′Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Alberto Prats-Galino
- Laboratory of Surgical NeuroAnatomy (LSNA). Facultat de Medicina. Universitat de Barcelona, Barcelona, Spain
| | - Sara Llufriu
- Center of Neuroimmunology, Service of Neurology, Hospital Clinic and Institut d′Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
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18
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Neef NE, Anwander A, Friederici AD. The Neurobiological Grounding of Persistent Stuttering: from Structure to Function. Curr Neurol Neurosci Rep 2015; 15:63. [PMID: 26228377 DOI: 10.1007/s11910-015-0579-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Nicole E Neef
- Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstr. 1a, 04103, Leipzig, Germany,
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19
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Schirner M, Rothmeier S, Jirsa VK, McIntosh AR, Ritter P. An automated pipeline for constructing personalized virtual brains from multimodal neuroimaging data. Neuroimage 2015; 117:343-57. [PMID: 25837600 DOI: 10.1016/j.neuroimage.2015.03.055] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 03/17/2015] [Accepted: 03/19/2015] [Indexed: 01/19/2023] Open
Abstract
Large amounts of multimodal neuroimaging data are acquired every year worldwide. In order to extract high-dimensional information for computational neuroscience applications standardized data fusion and efficient reduction into integrative data structures are required. Such self-consistent multimodal data sets can be used for computational brain modeling to constrain models with individual measurable features of the brain, such as done with The Virtual Brain (TVB). TVB is a simulation platform that uses empirical structural and functional data to build full brain models of individual humans. For convenient model construction, we developed a processing pipeline for structural, functional and diffusion-weighted magnetic resonance imaging (MRI) and optionally electroencephalography (EEG) data. The pipeline combines several state-of-the-art neuroinformatics tools to generate subject-specific cortical and subcortical parcellations, surface-tessellations, structural and functional connectomes, lead field matrices, electrical source activity estimates and region-wise aggregated blood oxygen level dependent (BOLD) functional MRI (fMRI) time-series. The output files of the pipeline can be directly uploaded to TVB to create and simulate individualized large-scale network models that incorporate intra- and intercortical interaction on the basis of cortical surface triangulations and white matter tractograpy. We detail the pitfalls of the individual processing streams and discuss ways of validation. With the pipeline we also introduce novel ways of estimating the transmission strengths of fiber tracts in whole-brain structural connectivity (SC) networks and compare the outcomes of different tractography or parcellation approaches. We tested the functionality of the pipeline on 50 multimodal data sets. In order to quantify the robustness of the connectome extraction part of the pipeline we computed several metrics that quantify its rescan reliability and compared them to other tractography approaches. Together with the pipeline we present several principles to guide future efforts to standardize brain model construction. The code of the pipeline and the fully processed data sets are made available to the public via The Virtual Brain website (thevirtualbrain.org) and via github (https://github.com/BrainModes/TVB-empirical-data-pipeline). Furthermore, the pipeline can be directly used with High Performance Computing (HPC) resources on the Neuroscience Gateway Portal (http://www.nsgportal.org) through a convenient web-interface.
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Affiliation(s)
- Michael Schirner
- Dept. Neurology, Charité - University Medicine, Berlin, Germany; Bernstein Focus State Dependencies of Learning, Bernstein Center for Computational Neuroscience, Berlin, Germany
| | - Simon Rothmeier
- Dept. Neurology, Charité - University Medicine, Berlin, Germany; Bernstein Focus State Dependencies of Learning, Bernstein Center for Computational Neuroscience, Berlin, Germany
| | - Viktor K Jirsa
- Institut de Neurosciences des Systèmes UMR INSERM 1106, Aix-Marseille Université Faculté de Médecine, Marseille, France
| | | | - Petra Ritter
- Dept. Neurology, Charité - University Medicine, Berlin, Germany; Bernstein Focus State Dependencies of Learning, Bernstein Center for Computational Neuroscience, Berlin, Germany; Minerva Research Group BrainModes, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; Berlin School of Mind and Brain, Mind and Brain Institute, Humboldt University, Berlin, Germany.
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20
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Pestilli F, Yeatman JD, Rokem A, Kay KN, Wandell BA. Evaluation and statistical inference for human connectomes. Nat Methods 2014; 11:1058-63. [PMID: 25194848 PMCID: PMC4180802 DOI: 10.1038/nmeth.3098] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 08/08/2014] [Indexed: 11/09/2022]
Abstract
Diffusion-weighted imaging coupled with tractography is the only method for in vivo mapping of human white-matter fascicles. Tractography takes diffusion measurements as input and produces a large collection of white-matter fascicles as output; the connectome. We introduce a method to evaluate the evidence supporting connectomes. Linear Fascicle Evaluation (LiFE) takes any connectome as input and predicts diffusion measurements as output, using the difference between the measured and predicted diffusion signals to measure prediction error. Finally, we introduce two metrics that use the prediction error to evaluate the evidence supporting properties of the connectome. One metric compares the mean prediction error between alternative hypotheses, and the second metric compares full distributions of prediction error. We use these metrics to (1) compare tractography algorithms, and (2) test hypotheses about tracts and connections.
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Affiliation(s)
- Franco Pestilli
- Department of Psychology, Stanford University, Stanford, California, USA
| | - Jason D Yeatman
- Department of Psychology, Stanford University, Stanford, California, USA
| | - Ariel Rokem
- Department of Psychology, Stanford University, Stanford, California, USA
| | - Kendrick N Kay
- 1] Department of Psychology, Stanford University, Stanford, California, USA. [2] Department of Psychology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Brian A Wandell
- Department of Psychology, Stanford University, Stanford, California, USA
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21
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Beyond fractional anisotropy: extraction of bundle-specific structural metrics from crossing fiber models. Neuroimage 2014; 100:176-91. [PMID: 24936681 DOI: 10.1016/j.neuroimage.2014.06.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 06/03/2014] [Accepted: 06/06/2014] [Indexed: 12/13/2022] Open
Abstract
Diffusion MRI (dMRI) measurements are used for inferring the microstructural properties of white matter and to reconstruct fiber pathways. Very often voxels contain complex fiber configurations comprising multiple bundles, rendering the simple diffusion tensor model unsuitable. Multi-compartment models deliver a convenient parameterization of the underlying complex fiber architecture, but pose challenges for fitting and model selection. Spherical deconvolution, in contrast, very economically produces a fiber orientation density function (fODF) without any explicit model assumptions. Since, however, the fODF is represented by spherical harmonics, a direct interpretation of the model parameters is impossible. Based on the fact that the fODF can often be interpreted as superposition of multiple peaks, each associated to one relatively coherent fiber population (bundle), we offer a solution that seeks to combine the advantages of both approaches: first the fiber configuration is modeled as fODF represented by spherical harmonics and then each of the peaks is parameterized separately in order to characterize the underlying bundle. In this work, the fODF peaks are approximated by Bingham distributions, capturing first and second-order statistics of the fiber orientations, from which we derive metrics for the parametric quantification of fiber bundles. We propose meaningful relationships between these measures and the underlying microstructural properties. We focus on metrics derived directly from properties of the Bingham distribution, such as peak length, peak direction, peak spread, integral over the peak, as well as a metric derived from the comparison of the largest peaks, which probes the complexity of the underlying microstructure. We compare these metrics to the conventionally used fractional anisotropy (FA) and show how they may help to increase the specificity of the characterization of microstructural properties. While metrics relying on the first moments of the Bingham distributions provide relatively robust results, second-order metrics representing the peak spread are only meaningful, if the SNR is very high and no fiber crossings are present in the voxel.
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22
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Moreno-Dominguez D, Anwander A, Knösche TR. A hierarchical method for whole-brain connectivity-based parcellation. Hum Brain Mapp 2014; 35:5000-25. [PMID: 24740833 DOI: 10.1002/hbm.22528] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/01/2014] [Accepted: 04/03/2014] [Indexed: 11/08/2022] Open
Abstract
In modern neuroscience there is general agreement that brain function relies on networks and that connectivity is therefore of paramount importance for brain function. Accordingly, the delineation of functional brain areas on the basis of diffusion magnetic resonance imaging (dMRI) and tractography may lead to highly relevant brain maps. Existing methods typically aim to find a predefined number of areas and/or are limited to small regions of grey matter. However, it is in general not likely that a single parcellation dividing the brain into a finite number of areas is an adequate representation of the function-anatomical organization of the brain. In this work, we propose hierarchical clustering as a solution to overcome these limitations and achieve whole-brain parcellation. We demonstrate that this method encodes the information of the underlying structure at all granularity levels in a hierarchical tree or dendrogram. We develop an optimal tree building and processing pipeline that reduces the complexity of the tree with minimal information loss. We show how these trees can be used to compare the similarity structure of different subjects or recordings and how to extract parcellations from them. Our novel approach yields a more exhaustive representation of the real underlying structure and successfully tackles the challenge of whole-brain parcellation.
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Affiliation(s)
- David Moreno-Dominguez
- Research Group "Cortical Networks and Cognitive Functions," Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
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