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Vidal JP, Danet L, Péran P, Pariente J, Bach Cuadra M, Zahr NM, Barbeau EJ, Saranathan M. Robust thalamic nuclei segmentation from T1-weighted MRI using polynomial intensity transformation. Brain Struct Funct 2024; 229:1087-1101. [PMID: 38546872 PMCID: PMC11147736 DOI: 10.1007/s00429-024-02777-5] [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: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 04/09/2024]
Abstract
Accurate segmentation of thalamic nuclei, crucial for understanding their role in healthy cognition and in pathologies, is challenging to achieve on standard T1-weighted (T1w) magnetic resonance imaging (MRI) due to poor image contrast. White-matter-nulled (WMn) MRI sequences improve intrathalamic contrast but are not part of clinical protocols or extant databases. In this study, we introduce histogram-based polynomial synthesis (HIPS), a fast preprocessing transform step that synthesizes WMn-like image contrast from standard T1w MRI using a polynomial approximation for intensity transformation. HIPS was incorporated into THalamus Optimized Multi-Atlas Segmentation (THOMAS) pipeline, a method developed and optimized for WMn MRI. HIPS-THOMAS was compared to a convolutional neural network (CNN)-based segmentation method and THOMAS modified for the use of T1w images (T1w-THOMAS). The robustness and accuracy of the three methods were tested across different image contrasts (MPRAGE, SPGR, and MP2RAGE), scanner manufacturers (PHILIPS, GE, and Siemens), and field strengths (3 T and 7 T). HIPS-transformed images improved intra-thalamic contrast and thalamic boundaries, and HIPS-THOMAS yielded significantly higher mean Dice coefficients and reduced volume errors compared to both the CNN method and T1w-THOMAS. Finally, all three methods were compared using the frequently travelling human phantom MRI dataset for inter- and intra-scanner variability, with HIPS displaying the least inter-scanner variability and performing comparably with T1w-THOMAS for intra-scanner variability. In conclusion, our findings highlight the efficacy and robustness of HIPS in enhancing thalamic nuclei segmentation from standard T1w MRI.
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Affiliation(s)
- Julie P Vidal
- CNRS, CerCo (Brain and Cognition Research Center), Paul Sabatier University, Toulouse, France
- INSERM, ToNiC (Toulouse NeuroImaging Center), Paul Sabatier University, Toulouse, France
| | - Lola Danet
- INSERM, ToNiC (Toulouse NeuroImaging Center), Paul Sabatier University, Toulouse, France
- Neurology Department, Purpan Hospital, Toulouse University Hospital Center, Toulouse, France
| | - Patrice Péran
- INSERM, ToNiC (Toulouse NeuroImaging Center), Paul Sabatier University, Toulouse, France
| | - Jérémie Pariente
- INSERM, ToNiC (Toulouse NeuroImaging Center), Paul Sabatier University, Toulouse, France
- Neurology Department, Purpan Hospital, Toulouse University Hospital Center, Toulouse, France
| | - Meritxell Bach Cuadra
- CIBM Center for Biomedical Imaging, Radiology Department, Lausanne University and University Hospital, Lausanne, Switzerland
| | - Natalie M Zahr
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Emmanuel J Barbeau
- CNRS, CerCo (Brain and Cognition Research Center), Paul Sabatier University, Toulouse, France
| | - Manojkumar Saranathan
- Department of Radiology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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2
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Vidal JP, Danet L, Péran P, Pariente J, Cuadra MB, Zahr NM, Barbeau EJ, Saranathan M. Robust thalamic nuclei segmentation from T1-weighted MRI using polynomial intensity transformation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.30.24301606. [PMID: 38352493 PMCID: PMC10862991 DOI: 10.1101/2024.01.30.24301606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Accurate segmentation of thalamic nuclei, crucial for understanding their role in healthy cognition and in pathologies, is challenging to achieve on standard T1-weighted (T1w) magnetic resonance imaging (MRI) due to poor image contrast. White-matter-nulled (WMn) MRI sequences improve intrathalamic contrast but are not part of clinical protocols or extant databases. In this study, we introduce histogram-based polynomial synthesis (HIPS), a fast preprocessing transform step that synthesizes WMn-like image contrast from standard T1w MRI using a polynomial approximation for intensity transformation. HIPS was incorporated into THalamus Optimized Multi-Atlas Segmentation (THOMAS) pipeline, a method developed and optimized for WMn MRI. HIPS-THOMAS was compared to a convolutional neural network (CNN)-based segmentation method and THOMAS modified for T1w images (T1w-THOMAS). The robustness and accuracy of the three methods were tested across different image contrasts (MPRAGE, SPGR, and MP2RAGE), scanner manufacturers (PHILIPS, GE, and Siemens), and field strengths (3T and 7T). HIPS-transformed images improved intra-thalamic contrast and thalamic boundaries, and HIPS-THOMAS yielded significantly higher mean Dice coefficients and reduced volume errors compared to both the CNN method and T1w-THOMAS. Finally, all three methods were compared using the frequently travelling human phantom MRI dataset for inter- and intra-scanner variability, with HIPS displaying the least inter-scanner variability and performing comparably with T1w-THOMAS for intra-scanner variability. In conclusion, our findings highlight the efficacy and robustness of HIPS in enhancing thalamic nuclei segmentation from standard T1w MRI.
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3
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Li Y, Li R, Gu J, Yi H, He J, Lu F, Gao J. Enhanced group-level dorsolateral prefrontal cortex subregion parcellation through functional connectivity-based distance-constrained spectral clustering with application to autism spectrum disorder. Cereb Cortex 2024; 34:bhae020. [PMID: 38300216 DOI: 10.1093/cercor/bhae020] [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: 11/24/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/02/2024] Open
Abstract
The dorsolateral prefrontal cortex (DLPFC) assumes a central role in cognitive and behavioral control, emerging as a crucial target region for interventions in autism spectrum disorder neuroregulation. Consequently, we endeavor to unravel the functional subregions within the DLPFC to shed light on the intricate functions of the brain. We introduce a distance-constrained spectral clustering (SC-DW) methodology that leverages functional connection to identify distinctive functional subregions within the DLPFC. Furthermore, we verify the relationship between the functional characteristics of these subregions and their clinical implications. Our methodology begins with principal component analysis to extract the salient features. Subsequently, we construct an adjacency matrix, which is constrained by the spatial properties of the brain, by linearly combining the distance matrix and a similarity matrix. The quality of spectral clustering is further optimized through multiple cluster evaluation coefficient. The results from SC-DW revealed four uniform and contiguous subregions within the bilateral DLPFC. Notably, we observe a substantial positive correlation between the functional characteristics of the third and fourth subregions in the left DLPFC with clinical manifestations. These findings underscore the unique insights offered by our proposed methodology in the realms of brain subregion delineation and therapeutic targeting.
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Affiliation(s)
- Yanling Li
- School of Electrical Engineering and Electronic Information, Xihua University, 9999 Hongguang Avenue, Pixian District, Chengdu City, Sichuan Province, Chengdu 610039, China
| | - Rui Li
- School of Electrical Engineering and Electronic Information, Xihua University, 9999 Hongguang Avenue, Pixian District, Chengdu City, Sichuan Province, Chengdu 610039, China
| | - Jiahe Gu
- School of Electrical Engineering and Electronic Information, Xihua University, 9999 Hongguang Avenue, Pixian District, Chengdu City, Sichuan Province, Chengdu 610039, China
| | - Hongtao Yi
- School of Electrical Engineering and Electronic Information, Xihua University, 9999 Hongguang Avenue, Pixian District, Chengdu City, Sichuan Province, Chengdu 610039, China
| | - Junbiao He
- School of Electrical Engineering and Electronic Information, Xihua University, 9999 Hongguang Avenue, Pixian District, Chengdu City, Sichuan Province, Chengdu 610039, China
| | - Fengmei Lu
- The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China, 2006 Xiyuan Avenue, High-tech Zone (West Zone), Chengdu City, Sichuan Province, Chengdu 610054, China
| | - Jingjing Gao
- School of Information and Communication Engineering, University of Electronic Science and Technology of China, 2006 Xiyuan Avenue, High-tech Zone (West Zone), Chengdu City, Sichuan Province, Chengdu 611731, China
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4
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Betzel RF, Faskowitz J, Sporns O. Living on the edge: network neuroscience beyond nodes. Trends Cogn Sci 2023; 27:1068-1084. [PMID: 37716895 PMCID: PMC10592364 DOI: 10.1016/j.tics.2023.08.009] [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: 05/15/2023] [Revised: 07/14/2023] [Accepted: 08/10/2023] [Indexed: 09/18/2023]
Abstract
Network neuroscience has emphasized the connectional properties of neural elements - cells, populations, and regions. This has come at the expense of the anatomical and functional connections that link these elements to one another. A new perspective - namely one that emphasizes 'edges' - may prove fruitful in addressing outstanding questions in network neuroscience. We highlight one recently proposed 'edge-centric' method and review its current applications, merits, and limitations. We also seek to establish conceptual and mathematical links between this method and previously proposed approaches in the network science and neuroimaging literature. We conclude by presenting several avenues for future work to extend and refine existing edge-centric analysis.
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Affiliation(s)
- Richard F Betzel
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA; Cognitive Science Program, Indiana University, Bloomington, IN 47405, USA; Program in Neuroscience, Indiana University, Bloomington, IN 47405, USA; Network Science Institute, Indiana University, Bloomington, IN 47405, USA.
| | - Joshua Faskowitz
- Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD, USA
| | - Olaf Sporns
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA; Cognitive Science Program, Indiana University, Bloomington, IN 47405, USA; Program in Neuroscience, Indiana University, Bloomington, IN 47405, USA; Network Science Institute, Indiana University, Bloomington, IN 47405, USA
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5
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Kulkarni M, Kent JS, Park K, Guell X, Anteraper S. Resting-state functional connectivity-based parcellation of the human dentate nucleus: new findings and clinical relevance. Brain Struct Funct 2023; 228:1799-1810. [PMID: 37439862 DOI: 10.1007/s00429-023-02665-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/11/2023] [Indexed: 07/14/2023]
Abstract
For years, the cerebellum was left out of functional magnetic resonance imaging (fMRI) studies due to technological limitations. The advent of novel data acquisition and reconstruction strategies (e.g., whole-brain simultaneous multi-slice imaging) employing multi-channel array coils has overcome such limitations, ushering unprecedented improvements in temporal signal-to-noise ratio and spatiotemporal resolution. Here, we aim to provide a brief report on the deep cerebellar nuclei, specifically focusing on the dentate nuclei, the primary output nuclei, situated within both cognitive and motor cerebello-cerebral circuits. We highlight the importance of functional parcellation in refining our understanding of broad resting-state functional connectivity (RSFC) in both health and disease. First, we review work relevant to the functional topography of the dentate nuclei, including recent advances in functional parcellation. Next, we review RSFC studies using the dentate nuclei as seed regions of interest in neurological and psychiatric populations and discuss the potential benefits of applying functionally defined subdivisions. Finally, we discuss recent technological advances and underscore ultrahigh-field neuroimaging as a tool to potentiate functionally parcellated RSFC analyses in clinical populations.
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Affiliation(s)
- Maitreyee Kulkarni
- Department of Psychology, School of Behavioral and Brain Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Jerillyn S Kent
- Department of Psychology, School of Behavioral and Brain Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Katie Park
- University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Xavier Guell
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sheeba Anteraper
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, 2201 Inwood Road, Dallas, TX, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, United States.
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6
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Zhao Y, Gao Y, Li M, Anderson AW, Ding Z, Gore JC. Functional Parcellation of Human Brain Using Localized Topo-Connectivity Mapping. IEEE TRANSACTIONS ON MEDICAL IMAGING 2022; 41:2670-2680. [PMID: 35442885 PMCID: PMC9844109 DOI: 10.1109/tmi.2022.3168888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The analysis of connectivity between parcellated regions of cortex provides insights into the functional architecture of the brain at a systems level. However, the derivation of functional structures from voxel-wise analyses at finer scales remains a challenge. We propose a novel method, called localized topo-connectivity mapping with singular-value-decomposition-informed filtering (or filtered LTM), to identify and characterize voxel-wise functional structures in the human brain from resting-state fMRI data. Here we describe its mathematical formulation and provide a proof-of-concept using simulated data that allow an intuitive interpretation of the results of filtered LTM. The algorithm has also been applied to 7T fMRI data acquired as part of the Human Connectome Project to generate group-average LTM images. Generally, most of the functional structures revealed by LTM images agree in the boundaries with anatomical structures identified by T1-weighted images and fractional anisotropy maps derived from diffusion MRI. In addition, the LTM images also reveal subtle functional variations that are not apparent in the anatomical structures. To assess the performance of LTM images, the subcortical region and occipital white matter were separately parcellated. Statistical tests were performed to demonstrate that the synchronies of fMRI signals in LTM-derived functional parcels are significantly larger than those with geometric perturbations. Overall, the filtered LTM approach can serve as a tool to investigate the functional organization of the brain at the scale of individual voxels as measured in fMRI.
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7
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Peng L, Luo Z, Zeng LL, Hou C, Shen H, Zhou Z, Hu D. Parcellating the human brain using resting-state dynamic functional connectivity. Cereb Cortex 2022; 33:3575-3590. [PMID: 35965076 DOI: 10.1093/cercor/bhac293] [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: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/14/2022] Open
Abstract
Brain cartography has expanded substantially over the past decade. In this regard, resting-state functional connectivity (FC) plays a key role in identifying the locations of putative functional borders. However, scant attention has been paid to the dynamic nature of functional interactions in the human brain. Indeed, FC is typically assumed to be stationary across time, which may obscure potential or subtle functional boundaries, particularly in regions with high flexibility and adaptability. In this study, we developed a dynamic FC (dFC)-based parcellation framework, established a new functional human brain atlas termed D-BFA (DFC-based Brain Functional Atlas), and verified its neurophysiological plausibility by stereo-EEG data. As the first dFC-based whole-brain atlas, the proposed D-BFA delineates finer functional boundaries that cannot be captured by static FC, and is further supported by good correspondence with cytoarchitectonic areas and task activation maps. Moreover, the D-BFA reveals the spatial distribution of dynamic variability across the brain and generates more homogenous parcels compared with most alternative parcellations. Our results demonstrate the superiority and practicability of dFC in brain parcellation, providing a new template to exploit brain topographic organization from a dynamic perspective. The D-BFA will be publicly available for download at https://github.com/sliderplm/D-BFA-618.
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Affiliation(s)
- Limin Peng
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha 410073, China
| | - Zhiguo Luo
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha 410073, China
| | - Ling-Li Zeng
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha 410073, China
| | - Chenping Hou
- College of Science, National University of Defense Technology, Changsha 410073, China
| | - Hui Shen
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha 410073, China
| | - Zongtan Zhou
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha 410073, China
| | - Dewen Hu
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha 410073, China
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8
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Idesis S, Faskowitz J, Betzel RF, Corbetta M, Sporns O, Deco G. Edge-centric analysis of stroke patients: An alternative approach for biomarkers of lesion recovery. Neuroimage Clin 2022; 35:103055. [PMID: 35661469 PMCID: PMC9163596 DOI: 10.1016/j.nicl.2022.103055] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 11/17/2022]
Abstract
Most neuroimaging studies of post-stroke recovery rely on analyses derived from standard node-centric functional connectivity to map the distributed effects in stroke patients. Here, given the importance of nonlocal and diffuse damage, we use an edge-centric approach to functional connectivity in order to provide an alternative description of the effects of this disorder. These techniques allow for the rendering of metrics such as normalized entropy, which describes the diversity of edge communities at each node. Moreover, the approach enables the identification of high amplitude co-fluctuations in fMRI time series. We found that normalized entropy is associated with stroke lesion severity and continually increases across the time of patients' recovery. Furthermore, high amplitude co-fluctuations not only relate to the lesion severity but are also associated with patients' level of recovery. The current study is the first edge-centric application for a clinical population in a longitudinal dataset and demonstrates how a different perspective for functional data analysis can further characterize topographic modulations of brain dynamics.
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Affiliation(s)
- Sebastian Idesis
- Center for Brain and Cognition (CBC), Department of Information Technologies and Communications (DTIC), Pompeu Fabra University, Edifici Mercè Rodoreda, Carrer Trias i Fargas 25-27, 08005 Barcelona, Catalonia, Spain.
| | - Joshua Faskowitz
- Department of Psychological and Brain Science, Indiana University, Bloomington, IN 47405, United States; Program in Neuroscience, Indiana University, Bloomington, IN 47405, United States
| | - Richard F Betzel
- Department of Psychological and Brain Science, Indiana University, Bloomington, IN 47405, United States; Program in Neuroscience, Indiana University, Bloomington, IN 47405, United States; Cognitive Science Program, Indiana University, Bloomington, IN 47405, United States; Network Science Institute, Indiana University, Bloomington, IN 47405, United States
| | - Maurizio Corbetta
- Padova Neuroscience Center (PNC), University of Padova, via Orus 2/B, 35129 Padova, Italy; Department of Neuroscience (DNS), University of Padova, via Giustiniani 2, 35128 Padova, Italy; Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110, United States; Department of Radiology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110, United States; VIMM, Venetian Institute of Molecular Medicine (VIMM), Biomedical Foundation, via Orus 2, 35129 Padova, Italy
| | - Olaf Sporns
- Department of Psychological and Brain Science, Indiana University, Bloomington, IN 47405, United States; Program in Neuroscience, Indiana University, Bloomington, IN 47405, United States; Cognitive Science Program, Indiana University, Bloomington, IN 47405, United States; Network Science Institute, Indiana University, Bloomington, IN 47405, United States
| | - Gustavo Deco
- Center for Brain and Cognition (CBC), Department of Information Technologies and Communications (DTIC), Pompeu Fabra University, Edifici Mercè Rodoreda, Carrer Trias i Fargas 25-27, 08005 Barcelona, Catalonia, Spain; Institució Catalana de Recerca I Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Catalonia, Spain
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9
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Williams B, Roesch E, Christakou A. Systematic validation of an automated thalamic parcellation technique using anatomical data at 3T. Neuroimage 2022; 258:119340. [DOI: 10.1016/j.neuroimage.2022.119340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/20/2022] [Accepted: 05/28/2022] [Indexed: 11/24/2022] Open
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10
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Kumar VJ, Scheffler K, Hagberg GE, Grodd W. Quantitative Susceptibility Mapping of the Basal Ganglia and Thalamus at 9.4 Tesla. Front Neuroanat 2021; 15:725731. [PMID: 34602986 PMCID: PMC8483181 DOI: 10.3389/fnana.2021.725731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/23/2021] [Indexed: 12/15/2022] Open
Abstract
The thalamus (Th) and basal ganglia (BG) are central subcortical connectivity hubs of the human brain, whose functional anatomy is still under intense investigation. Nevertheless, both substructures contain a robust and reproducible functional anatomy. The quantitative susceptibility mapping (QSM) at ultra-high field may facilitate an improved characterization of the underlying functional anatomy in vivo. We acquired high-resolution QSM data at 9.4 Tesla in 21 subjects, and analyzed the thalamic and BG by using a prior defined functional parcellation. We found a more substantial contribution of paramagnetic susceptibility sources such as iron in the pallidum in contrast to the caudate, putamen, and Th in descending order. The diamagnetic susceptibility sources such as myelin and calcium revealed significant contributions in the Th parcels compared with the BG. This study presents a detailed nuclei-specific delineation of QSM-provided diamagnetic and paramagnetic susceptibility sources pronounced in the BG and the Th. We also found a reasonable interindividual variability as well as slight hemispheric differences. The results presented here contribute to the microstructural knowledge of the Th and the BG. In specific, the study illustrates QSM values (myelin, calcium, and iron) in functionally similar subregions of the Th and the BG.
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Affiliation(s)
| | - Klaus Scheffler
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,Biomedical Magnetic Resonance, University Hospital and Eberhard-Karl's University, Tübingen, Germany
| | - Gisela E Hagberg
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,Biomedical Magnetic Resonance, University Hospital and Eberhard-Karl's University, Tübingen, Germany
| | - Wolfgang Grodd
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
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Boelens Keun JT, van Heese EM, Laansma MA, Weeland CJ, de Joode NT, van den Heuvel OA, Gool JK, Kasprzak S, Bright JK, Vriend C, van der Werf YD. Structural assessment of thalamus morphology in brain disorders: A review and recommendation of thalamic nucleus segmentation and shape analysis. Neurosci Biobehav Rev 2021; 131:466-478. [PMID: 34587501 DOI: 10.1016/j.neubiorev.2021.09.044] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 08/25/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022]
Abstract
The thalamus is a central brain structure crucially involved in cognitive, emotional, sensory, and motor functions and is often reported to be involved in the pathophysiology of neurological and psychiatric disorders. The functional subdivision of the thalamus warrants morphological investigation on the level of individual subnuclei. In addition to volumetric measures, the investigation of other morphological features may give additional insights into thalamic morphology. For instance, shape features offer a higher spatial resolution by revealing small, regional differences that are left undetected in volumetric analyses. In this review, we discuss the benefits and limitations of recent advances in neuroimaging techniques to investigate thalamic morphology in vivo, leading to our proposed methodology. This methodology consists of available pipelines for volume and shape analysis, focussing on the morphological features of volume, thickness, and surface area. We demonstrate this combined approach in a Parkinson's disease cohort to illustrate their complementarity. Considering our findings, we recommend a combined methodology as it allows for more sensitive investigation of thalamic morphology in clinical populations.
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Affiliation(s)
- Jikke T Boelens Keun
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Eva M van Heese
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Max A Laansma
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Cees J Weeland
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Niels T de Joode
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Odile A van den Heuvel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Jari K Gool
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands; SEIN, Heemstede, the Netherlands; Department of Neurology, LUMC, Leiden, the Netherlands
| | - Selina Kasprzak
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Joanna K Bright
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Chris Vriend
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Ysbrand D van der Werf
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands.
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12
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The specificity of thalamic alterations in Korsakoff's syndrome: Implications for the study of amnesia. Neurosci Biobehav Rev 2021; 130:292-300. [PMID: 34454914 DOI: 10.1016/j.neubiorev.2021.07.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 04/01/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
The pathophysiological mechanisms behind amnesia are still unknown. Recent literature, through the study of patients with Alcohol Use Disorder with and without Korsakoff's syndrome, increasingly shows that physiological alterations to the thalamus have an important role in the development of amnesia. This review gives an overview of neuropsychological, neuropathological and neuroimaging contributions to the understanding of Korsakoff's syndrome, highlighting the central role of the thalamus in this amnesia. The thalamus being a multi-nucleus structure, the limitations regarding the loci, nature and alterations to specific nuclei are discussed, along with potential solutions. Finally, future directions for clinical research are laid out to unravel the intricacies inherent to amnesia. They consider the need to evaluate the physiological role of the thalamus, not only as an entity but also as part of a brain circuit through a more integrative approach.
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13
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Cooper RA, Kurkela KA, Davis SW, Ritchey M. Mapping the organization and dynamics of the posterior medial network during movie watching. Neuroimage 2021; 236:118075. [PMID: 33910099 PMCID: PMC8290580 DOI: 10.1016/j.neuroimage.2021.118075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/06/2021] [Indexed: 11/18/2022] Open
Abstract
Brain regions within a posterior medial network (PMN) are characterized by sensitivity to episodic tasks, and they also demonstrate strong functional connectivity as part of the default network. Despite its cohesive structure, delineating the intranetwork organization and functional diversity of the PMN is crucial for understanding its contributions to multidimensional event cognition. Here, we probed functional connectivity of the PMN during movie watching to identify its pattern of connections and subnetwork functions in a split-sample replication of 136 participants. Consistent with prior findings of default network fractionation, we identified distinct PMN subsystems: a Ventral PM subsystem (retrosplenial cortex, parahippocampal cortex, posterior angular gyrus) and a Dorsal PM subsystem (medial prefrontal cortex, hippocampus, precuneus, posterior cingulate cortex, anterior angular gyrus). Ventral and Dorsal PM subsystems were differentiated by functional connectivity with parahippocampal cortex and precuneus and integrated by retrosplenial cortex and posterior cingulate cortex, respectively. Finally, the distinction between PMN subsystems is functionally relevant: whereas both Dorsal and Ventral PM connectivity tracked the movie content, only Ventral PM connections increased in strength at event transitions and appeared sensitive to episodic memory. Overall, these findings reveal PMN functional pathways and the distinct functional roles of intranetwork subsystems during event cognition.
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Affiliation(s)
- Rose A Cooper
- Department of Psychology and Neuroscience, Boston College, United States.
| | - Kyle A Kurkela
- Department of Psychology and Neuroscience, Boston College, United States
| | - Simon W Davis
- Department of Neurology, Duke University School of Medicine, United States
| | - Maureen Ritchey
- Department of Psychology and Neuroscience, Boston College, United States
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14
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Basile GA, Bertino S, Bramanti A, Ciurleo R, Anastasi GP, Milardi D, Cacciola A. In Vivo Super-Resolution Track-Density Imaging for Thalamic Nuclei Identification. Cereb Cortex 2021; 31:5613-5636. [PMID: 34296740 DOI: 10.1093/cercor/bhab184] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 11/12/2022] Open
Abstract
The development of novel techniques for the in vivo, non-invasive visualization and identification of thalamic nuclei has represented a major challenge for human neuroimaging research in the last decades. Thalamic nuclei have important implications in various key aspects of brain physiology and many of them show selective alterations in various neurologic and psychiatric disorders. In addition, both surgical stimulation and ablation of specific thalamic nuclei have been proven to be useful for the treatment of different neuropsychiatric diseases. The present work aimed at describing a novel protocol for histologically guided delineation of thalamic nuclei based on short-tracks track-density imaging (stTDI), which is an advanced imaging technique exploiting high angular resolution diffusion tractography to obtain super-resolved white matter maps. We demonstrated that this approach can identify up to 13 distinct thalamic nuclei bilaterally with very high inter-subject (ICC: 0.996, 95% CI: 0.993-0.998) and inter-rater (ICC:0.981; 95% CI:0.963-0.989) reliability, and that both subject-based and group-level thalamic parcellation show a fair share of similarity to a recent standard-space histological thalamic atlas. Finally, we showed that stTDI-derived thalamic maps can be successfully employed to study structural and functional connectivity of the thalamus and may have potential implications both for basic and translational research, as well as for presurgical planning purposes.
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Affiliation(s)
- Gianpaolo Antonio Basile
- Brain Mapping Lab, Department of Biomedical, Dental Sciences and Morphological and Functional Images, University of Messina, 98124 Messina, Italy
| | - Salvatore Bertino
- Brain Mapping Lab, Department of Biomedical, Dental Sciences and Morphological and Functional Images, University of Messina, 98124 Messina, Italy
| | - Alessia Bramanti
- Department of Medicine, Surgery and Dentistry "Medical School of Salerno", University of Salerno, 84084 Baronissi, Italy
| | - Rosella Ciurleo
- IRCCS Centro Neurolesi "Bonino Pulejo", 98124 Messina, Italy
| | - Giuseppe Pio Anastasi
- Brain Mapping Lab, Department of Biomedical, Dental Sciences and Morphological and Functional Images, University of Messina, 98124 Messina, Italy
| | - Demetrio Milardi
- Brain Mapping Lab, Department of Biomedical, Dental Sciences and Morphological and Functional Images, University of Messina, 98124 Messina, Italy
| | - Alberto Cacciola
- Brain Mapping Lab, Department of Biomedical, Dental Sciences and Morphological and Functional Images, University of Messina, 98124 Messina, Italy
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15
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Chauvin RJ, Buitelaar JK, Sprooten E, Oldehinkel M, Franke B, Hartman C, Heslenfeld DJ, Hoekstra PJ, Oosterlaan J, Beckmann CF, Mennes M. Task-generic and task-specific connectivity modulations in the ADHD brain: an integrated analysis across multiple tasks. Transl Psychiatry 2021; 11:159. [PMID: 33750765 PMCID: PMC7943764 DOI: 10.1038/s41398-021-01284-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 11/23/2022] Open
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is associated with altered functioning in multiple cognitive domains and neural networks. This paper offers an overarching biological perspective across these. We applied a novel strategy that extracts functional connectivity modulations in the brain across one (Psingle), two (Pmix) or three (Pall) cognitive tasks and compared the pattern of modulations between participants with ADHD (n-89), unaffected siblings (n = 93) and controls (n = 84; total N = 266; age range = 8-27 years). Participants with ADHD had significantly fewer Pall connections (modulated regardless of task), but significantly more task-specific (Psingle) connectivity modulations than the other groups. The amplitude of these Psingle modulations was significantly higher in ADHD. Unaffected siblings showed a similar degree of Pall connectivity modulation as controls but a similar degree of Psingle connectivity modulation as ADHD probands. Pall connections were strongly reproducible at the individual level in controls, but showed marked heterogeneity in both participants with ADHD and unaffected siblings. The pattern of reduced task-generic and increased task-specific connectivity modulations in ADHD may be interpreted as reflecting a less efficient functional brain architecture due to a reduction in the ability to generalise processing pathways across multiple cognitive domains. The higher amplitude of unique task-specific connectivity modulations in ADHD may index a more "effortful" coping strategy. Unaffected siblings displayed a task connectivity profile in between that of controls and ADHD probands, supporting an endophenotype view. Our approach provides a new perspective on the core neural underpinnings of ADHD.
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Affiliation(s)
- Roselyne J. Chauvin
- grid.10417.330000 0004 0444 9382Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.5590.90000000122931605Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands ,grid.4367.60000 0001 2355 7002Department of Neurology, Washington University School of Medicine, St Louis, USA
| | - Jan K. Buitelaar
- grid.10417.330000 0004 0444 9382Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.5590.90000000122931605Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands ,grid.461871.d0000 0004 0624 8031Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
| | - Emma Sprooten
- grid.10417.330000 0004 0444 9382Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.5590.90000000122931605Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Marianne Oldehinkel
- grid.10417.330000 0004 0444 9382Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.5590.90000000122931605Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands ,grid.1002.30000 0004 1936 7857School of Psychological Sciences, Monash Institute of Cognitive and Clinical Neurosciences, Monash University, Melbourne, VIC Australia
| | - Barbara Franke
- grid.5590.90000000122931605Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Departments of Human Genetics and Psychiatry, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Catharina Hartman
- grid.4494.d0000 0000 9558 4598University of Groningen, University Medical Center Groningen, Department of Psychiatry, Groningen, The Netherlands
| | - Dirk J. Heslenfeld
- Amsterdam UMC, University of Amsterdam & Vrije Universiteit Amsterdam, Emma Neuroscience Group at Emma Children’s Hospital, department of Pediatrics, Amsterdam Reproduction & Development, Amsterdam, The Netherlands
| | - Pieter J. Hoekstra
- grid.4494.d0000 0000 9558 4598University of Groningen, University Medical Center Groningen, Department of Psychiatry, Groningen, The Netherlands
| | - Jaap Oosterlaan
- Amsterdam UMC, University of Amsterdam & Vrije Universiteit Amsterdam, Emma Neuroscience Group at Emma Children’s Hospital, department of Pediatrics, Amsterdam Reproduction & Development, Amsterdam, The Netherlands ,grid.12380.380000 0004 1754 9227Clinical Neuropsychology section, Vrije Universiteit, Van der Boechortstraat 7, 1081 BT Amsterdam, The Netherlands
| | - Christian F. Beckmann
- grid.10417.330000 0004 0444 9382Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.5590.90000000122931605Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands ,grid.4991.50000 0004 1936 8948Centre for Functional MRI of the Brain (FMRIB), University of Oxford, Oxford, UK
| | - Maarten Mennes
- grid.5590.90000000122931605Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
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16
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Bielski K, Adamus S, Kolada E, Rączaszek-Leonardi J, Szatkowska I. Parcellation of the human amygdala using recurrence quantification analysis. Neuroimage 2020; 227:117644. [PMID: 33338610 DOI: 10.1016/j.neuroimage.2020.117644] [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: 08/26/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 01/05/2023] Open
Abstract
Several previous attempts have been made to divide the human amygdala into smaller subregions based on the unique functional properties of the subregions. Although these attempts have provided valuable insight into the functional heterogeneity in this structure, the possibility that spatial patterns of functional characteristics can quickly change over time has rarely been considered in previous studies. In the present study, we explicitly account for the dynamic nature of amygdala activity. Our goal was not only to develop another parcellation method but also to augment existing methods with novel information about amygdala subdivisions. We performed state-specific amygdala parcellation using resting-state fMRI (rsfMRI) data and recurrence quantification analysis (RQA). RsfMRI data from 102 subjects were acquired with a 3T Trio Siemens scanner. We analyzed values of several RQA measures across all voxels in the amygdala and found two amygdala subdivisions, the ventrolateral (VL) and dorsomedial (DM) subdivisions, that differ with respect to one of the RQA measures, Shannon's entropy of diagonal lines. Compared to the DM subdivision, the VL subdivision can be characterized by a higher value of entropy. The results suggest that VL activity is determined and influenced by more brain structures than is DM activity. To assess the biological validity of the obtained subdivisions, we compared them with histological atlases and currently available parcellations based on structural connectivity patterns (Anatomy Probability Maps) and cytoarchitectonic features (SPM Anatomy toolbox). Moreover, we examined their cortical and subcortical functional connectivity. The obtained results are similar to those previously reported on parcellation performed on the basis of structural connectivity patterns. Functional connectivity analysis revealed that the VL subdivision has strong connections to several cortical areas, whereas the DM subdivision is mainly connected to subcortical regions. This finding suggests that the VL subdivision corresponds to the basolateral subdivision of the amygdala (BLA), while the DM subdivision has some characteristics typical of the centromedial amygdala (CMA). The similarity in functional connectivity patterns between the VL subdivision and BLA, as well as between the DM subdivision and CMA, confirm the utility of our parcellation method. Overall, the study shows that parcellation based on BOLD signal dynamics is a powerful tool for identifying distinct functional systems within the amygdala. This tool might be useful for future research on functional brain organization.
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Affiliation(s)
- Krzysztof Bielski
- Laboratory of Emotions Neurobiology, BRAINCITY - Centre of Excellence for Neural Plasticity and Brain Disorders, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Sylwia Adamus
- Laboratory of Emotions Neurobiology, BRAINCITY - Centre of Excellence for Neural Plasticity and Brain Disorders, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Emilia Kolada
- Laboratory of Emotions Neurobiology, BRAINCITY - Centre of Excellence for Neural Plasticity and Brain Disorders, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | - Iwona Szatkowska
- Laboratory of Emotions Neurobiology, BRAINCITY - Centre of Excellence for Neural Plasticity and Brain Disorders, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
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17
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Fan L, Zhong Q, Qin J, Li N, Su J, Zeng LL, Hu D, Shen H. Brain parcellation driven by dynamic functional connectivity better capture intrinsic network dynamics. Hum Brain Mapp 2020; 42:1416-1433. [PMID: 33283954 PMCID: PMC7927310 DOI: 10.1002/hbm.25303] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 01/04/2023] Open
Abstract
Until now, dynamic functional connectivity (dFC) based on functional magnetic resonance imaging is typically estimated on a set of predefined regions of interest (ROIs) derived from an anatomical or static functional atlas which follows an implicit assumption of functional homogeneity within ROIs underlying temporal fluctuation of functional coupling, potentially leading to biases or underestimation of brain network dynamics. Here, we presented a novel computational method based on dynamic functional connectivity degree (dFCD) to derive meaningful brain parcellations that can capture functional homogeneous regions in temporal variance of functional connectivity. Several spatially distributed but functionally meaningful areas that are well consistent with known intrinsic connectivity networks were identified through independent component analysis (ICA) of time‐varying dFCD maps. Furthermore, a systematical comparison with commonly used brain atlases, including the Anatomical Automatic Labeling template, static ICA‐driven parcellation and random parcellation, demonstrated that the ROI‐definition strategy based on the proposed dFC‐driven parcellation could better capture the interindividual variability in dFC and predict observed individual cognitive performance (e.g., fluid intelligence, cognitive flexibility, and sustained attention) based on chronnectome. Together, our findings shed new light on the functional organization of resting brains at the timescale of seconds and emphasized the significance of a dFC‐driven and voxel‐wise functional homogeneous parcellation for network dynamics analyses in neuroscience.
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Affiliation(s)
- Liangwei Fan
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
| | - Qi Zhong
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
| | - Jian Qin
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
| | - Na Li
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jianpo Su
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
| | - Ling-Li Zeng
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
| | - Dewen Hu
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
| | - Hui Shen
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
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18
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Datta R, Bacchus MK, Kumar D, Elliott MA, Rao A, Dolui S, Reddy R, Banwell BL, Saranathan M. Fast automatic segmentation of thalamic nuclei from MP2RAGE acquisition at 7 Tesla. Magn Reson Med 2020; 85:2781-2790. [PMID: 33270943 DOI: 10.1002/mrm.28608] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/29/2020] [Accepted: 10/30/2020] [Indexed: 12/26/2022]
Abstract
PURPOSE Thalamic nuclei are largely invisible in conventional MRI due to poor contrast. Thalamus Optimized Multi-Atlas Segmentation (THOMAS) provides automatic segmentation of 12 thalamic nuclei using white-matter-nulled (WMn) Magnetization Prepared Rapid Gradient Echo (MPRAGE) sequence at 7T, but increases overall scan duration. Routinely acquired, bias-corrected Magnetization Prepared 2 Rapid Gradient Echo (MP2RAGE) sequence yields superior tissue contrast and quantitative T1 maps. Application of THOMAS to MP2RAGE has been investigated in this study. METHODS Eight healthy volunteers and five pediatric-onset multiple sclerosis patients were recruited at Children's Hospital of Philadelphia and scanned at Siemens 7T with WMn-MPRAGE and multi-echo-MP2RAGE (ME-MP2RAGE) sequences. White-matter-nulled contrast was synthesized (MP2-SYN) from T1 maps from ME-MP2RAGE sequence. Thalamic nuclei were segmented using THOMAS joint label fusion algorithm from WMn-MPRAGE and MP2-SYN datasets. THOMAS pipeline was modified to use majority voting to segment bias corrected T1-weighted uniform (MP2-UNI) images. Thalamic nuclei from MP2-SYN and MP2-UNI images were evaluated against corresponding nuclei obtained from WMn-MPRAGE images using dice coefficients, volume similarity indices (VSIs) and distance between centroids. RESULTS For MP2-SYN, dice > 0.85 and VSI > 0.95 was achieved for five larger nuclei and dice > 0.6 and VSI > 0.7 was achieved for seven smaller nuclei. The dice and VSI were slightly higher, whereas the distance between centroids were smaller for MP2-SYN compared to MP2-UNI, indicating improved performance using the MP2-SYN image. CONCLUSIONS THOMAS algorithm can successfully segment thalamic nuclei in MP2RAGE images with essentially equivalent quality as WMn-MPRAGE, widening its applicability in studies focused on thalamic involvement in aging and disease.
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Affiliation(s)
- Ritobrato Datta
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Micky K Bacchus
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Dushyant Kumar
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mark A Elliott
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aditya Rao
- Biological Basis of Behavior Program, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sudipto Dolui
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ravinder Reddy
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brenda L Banwell
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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19
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Zamani Esfahlani F, Jo Y, Faskowitz J, Byrge L, Kennedy DP, Sporns O, Betzel RF. High-amplitude cofluctuations in cortical activity drive functional connectivity. Proc Natl Acad Sci U S A 2020; 117:28393-28401. [PMID: 33093200 PMCID: PMC7668041 DOI: 10.1073/pnas.2005531117] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Resting-state functional connectivity is used throughout neuroscience to study brain organization and to generate biomarkers of development, disease, and cognition. The processes that give rise to correlated activity are, however, poorly understood. Here we decompose resting-state functional connectivity using a temporal unwrapping procedure to assess the contributions of moment-to-moment activity cofluctuations to the overall connectivity pattern. This approach temporally resolves functional connectivity at a timescale of single frames, which enables us to make direct comparisons of cofluctuations of network organization with fluctuations in the blood oxygen level-dependent (BOLD) time series. We show that surprisingly, only a small fraction of frames exhibiting the strongest cofluctuation amplitude are required to explain a significant fraction of variance in the overall pattern of connection weights as well as the network's modular structure. These frames coincide with frames of high BOLD activity amplitude, corresponding to activity patterns that are remarkably consistent across individuals and identify fluctuations in default mode and control network activity as the primary driver of resting-state functional connectivity. Finally, we demonstrate that cofluctuation amplitude synchronizes across subjects during movie watching and that high-amplitude frames carry detailed information about individual subjects (whereas low-amplitude frames carry little). Our approach reveals fine-scale temporal structure of resting-state functional connectivity and discloses that frame-wise contributions vary across time. These observations illuminate the relation of brain activity to functional connectivity and open a number of directions for future research.
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Affiliation(s)
| | - Youngheun Jo
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405
| | - Joshua Faskowitz
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405
- Program in Neuroscience, Indiana University, Bloomington, IN 47405
| | - Lisa Byrge
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405
| | - Daniel P Kennedy
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405
- Program in Neuroscience, Indiana University, Bloomington, IN 47405
- Cognitive Science Program, Indiana University, Bloomington, IN 47405
| | - Olaf Sporns
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405
- Program in Neuroscience, Indiana University, Bloomington, IN 47405
- Cognitive Science Program, Indiana University, Bloomington, IN 47405
- Network Science Institute, Indiana University, Bloomington, IN 47405
| | - Richard F Betzel
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405;
- Program in Neuroscience, Indiana University, Bloomington, IN 47405
- Cognitive Science Program, Indiana University, Bloomington, IN 47405
- Network Science Institute, Indiana University, Bloomington, IN 47405
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20
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Lake EMR, Ge X, Shen X, Herman P, Hyder F, Cardin JA, Higley MJ, Scheinost D, Papademetris X, Crair MC, Constable RT. Simultaneous cortex-wide fluorescence Ca 2+ imaging and whole-brain fMRI. Nat Methods 2020; 17:1262-1271. [PMID: 33139894 PMCID: PMC7704940 DOI: 10.1038/s41592-020-00984-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 09/21/2020] [Indexed: 12/31/2022]
Abstract
Achieving a comprehensive understanding of brain function requires multiple imaging modalities with complementary strengths. We present an approach for concurrent widefield optical and functional magnetic resonance imaging. By merging these modalities, we can simultaneously acquire whole-brain blood-oxygen-level-dependent (BOLD) and whole-cortex calcium-sensitive fluorescent measures of brain activity. In a transgenic murine model, we show that calcium predicts the BOLD signal, using a model that optimizes a gamma-variant transfer function. We find consistent predictions across the cortex, which are best at low frequency (0.009-0.08 Hz). Furthermore, we show that the relationship between modality connectivity strengths varies by region. Our approach links cell-type-specific optical measurements of activity to the most widely used method for assessing human brain function.
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Affiliation(s)
- Evelyn M R Lake
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA.
| | - Xinxin Ge
- Department of Neurobiology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Xilin Shen
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Peter Herman
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Fahmeed Hyder
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Jessica A Cardin
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Michael J Higley
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT, USA
| | - Dustin Scheinost
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Xenophon Papademetris
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Michael C Crair
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA. .,Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA. .,Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, USA.
| | - R Todd Constable
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA. .,Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, USA. .,Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.
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21
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Edge-centric functional network representations of human cerebral cortex reveal overlapping system-level architecture. Nat Neurosci 2020; 23:1644-1654. [PMID: 33077948 DOI: 10.1038/s41593-020-00719-y] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/03/2020] [Indexed: 12/18/2022]
Abstract
Network neuroscience has relied on a node-centric network model in which cells, populations and regions are linked to one another via anatomical or functional connections. This model cannot account for interactions of edges with one another. In this study, we developed an edge-centric network model that generates constructs 'edge time series' and 'edge functional connectivity' (eFC). Using network analysis, we show that, at rest, eFC is consistent across datasets and reproducible within the same individual over multiple scan sessions. We demonstrate that clustering eFC yields communities of edges that naturally divide the brain into overlapping clusters, with regions in sensorimotor and attentional networks exhibiting the greatest levels of overlap. We show that eFC is systematically modulated by variation in sensory input. In future work, the edge-centric approach could be useful for identifying novel biomarkers of disease, characterizing individual variation and mapping the architecture of highly resolved neural circuits.
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22
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A systematic comparison of structural-, structural connectivity-, and functional connectivity-based thalamus parcellation techniques. Brain Struct Funct 2020; 225:1631-1642. [PMID: 32440784 DOI: 10.1007/s00429-020-02085-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 05/09/2020] [Indexed: 12/14/2022]
Abstract
The thalamus consists of several histologically and functionally distinct nuclei increasingly implicated in brain pathology and important for treatment, motivating the need for development of fast and accurate thalamic parcellation. The contrast between thalamic nuclei as well as between the thalamus and surrounding tissues is poor in T1- and T2-weighted magnetic resonance imaging (MRI), inhibiting efforts to date to segment the thalamus using standard clinical MRI. Automatic parcellation techniques have been developed to leverage thalamic features better captured by advanced MRI methods, including magnetization prepared rapid acquisition gradient echo (MP-RAGE), diffusion tensor imaging (DTI), and resting-state functional MRI (fMRI). Despite operating on fundamentally different image contrasts, these methods claim a high degree of agreement with the Morel stereotactic atlas of the thalamus. However, no comparison has been undertaken to compare the results of these disparate parcellation methods. We have implemented state-of-the-art structural-, diffusion-, and functional imaging-based thalamus parcellation techniques and used them on a single set of subjects. We present the first systematic qualitative and quantitative comparison of these methods. The results show that DTI parcellation agrees more with structural parcellation in the larger thalamic nuclei, while rsfMRI parcellation agrees more with structural parcellation in the smaller nuclei. Structural parcellation is the most accurate in the delineation of small structures such as the habenular, antero-ventral, and medial geniculate nuclei.
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Przeździk I, Faber M, Fernández G, Beckmann CF, Haak KV. Gradient mapping in the human hippocampus: Reply to Poppenk. Cortex 2020; 128:318-321. [PMID: 32402493 DOI: 10.1016/j.cortex.2020.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/05/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Izabela Przeździk
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Myrthe Faber
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Communication and Cognition, Tilburg Center for Cognition and Communication, Tilburg University, the Netherlands
| | - Guillén Fernández
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian F Beckmann
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Oxford Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), University of Oxford, Nuffield Department of Clinical Neurosciences, Oxford, United Kingdom
| | - Koen V Haak
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.
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24
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Gravbrot N, Saranathan M, Pouratian N, Kasoff W. Advanced Imaging and Direct Targeting of the Motor Thalamus and Dentato-Rubro-Thalamic Tract for Tremor: A Systematic Review. Stereotact Funct Neurosurg 2020; 98:220-240. [DOI: 10.1159/000507030] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 02/27/2020] [Indexed: 11/19/2022]
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25
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Pinter D, Beckmann CF, Fazekas F, Khalil M, Pichler A, Gattringer T, Ropele S, Fuchs S, Enzinger C. Morphological MRI phenotypes of multiple sclerosis differ in resting-state brain function. Sci Rep 2019; 9:16221. [PMID: 31700126 PMCID: PMC6838050 DOI: 10.1038/s41598-019-52757-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/29/2019] [Indexed: 11/09/2022] Open
Abstract
We aimed to assess differences in resting-state functional connectivity (FC) between distinct morphological MRI-phenotypes in multiple sclerosis (MS). Out of 180 MS patients, we identified those with high T2-hyperintense lesion load (T2-LL) and high normalized brain volume (NBV; a predominately white matter damage group, WMD; N = 37) and patients with low T2-LL and low NBV (N = 37; a predominately grey matter damage group; GMD). Independent component analysis of resting-state fMRI was used to test for differences in the sensorimotor network (SMN) between MS MRI-phenotypes and compared to 37 age-matched healthy controls (HC). The two MS groups did not differ regarding EDSS scores, disease duration and distribution of clinical phenotypes. WMD compared to GMD patients showed increased FC in all sub-units of the SMN (sex- and age-corrected). WMD patients had increased FC compared to HC and GMD patients in the central SMN (leg area). Only in the WMD group, higher EDSS scores and T2-LL correlated with decreased connectivity in SMN sub-units. MS patients with distinct morphological MRI-phenotypes also differ in brain function. The amount of focal white matter pathology but not global brain atrophy affects connectivity in the central SMN (leg area) of the SMN, consistent with the notion of a disconnection syndrome.
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Affiliation(s)
- Daniela Pinter
- Department of Neurology, Medical University of Graz, Auenbruggerplatz 22, Graz, Austria
- Research Unit for Neuronal Plasticity and Repair, Medical University of Graz, Auenbruggerplatz 22, Graz, Austria
| | - Christian F Beckmann
- Donders Institute, Cognitive Neuroscience Department and Centre for Cognitive Neuroimaging, Radboud University Nijmegen, Kapittelweg 29, Nijmegen, The Netherlands
| | - Franz Fazekas
- Department of Neurology, Medical University of Graz, Auenbruggerplatz 22, Graz, Austria
| | - Michael Khalil
- Department of Neurology, Medical University of Graz, Auenbruggerplatz 22, Graz, Austria
| | - Alexander Pichler
- Department of Neurology, Medical University of Graz, Auenbruggerplatz 22, Graz, Austria
| | - Thomas Gattringer
- Department of Neurology, Medical University of Graz, Auenbruggerplatz 22, Graz, Austria
| | - Stefan Ropele
- Department of Neurology, Medical University of Graz, Auenbruggerplatz 22, Graz, Austria
| | - Siegrid Fuchs
- Department of Neurology, Medical University of Graz, Auenbruggerplatz 22, Graz, Austria
| | - Christian Enzinger
- Department of Neurology, Medical University of Graz, Auenbruggerplatz 22, Graz, Austria.
- Research Unit for Neuronal Plasticity and Repair, Medical University of Graz, Auenbruggerplatz 22, Graz, Austria.
- Division of Neuroradiology, Vascular and Interventional Radiology, Department of Radiology, Medical University of Graz, Auenbruggerplatz 9, Graz, Austria.
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26
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Yang Y, Wang L, Lei Y, Zhu Y, Shen H. Manifold Learning of Dynamic Functional Connectivity Reliably Identifies Functionally Consistent Coupling Patterns in Human Brains. Brain Sci 2019; 9:E309. [PMID: 31689958 PMCID: PMC6895885 DOI: 10.3390/brainsci9110309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 12/21/2022] Open
Abstract
Most previous work on dynamic functional connectivity (dFC) has focused on analyzing temporal traits of functional connectivity (similar coupling patterns at different timepoints), dividing them into functional connectivity states and detecting their between-group differences. However, the coherent functional connectivity of brain activity among the temporal dynamics of functional connectivity remains unknown. In the study, we applied manifold learning of local linear embedding to explore the consistent coupling patterns (CCPs) that reflect functionally homogeneous regions underlying dFC throughout the entire scanning period. By embedding the whole-brain functional connectivity in a low-dimensional manifold space based on the Human Connectome Project (HCP) resting-state data, we identified ten stable patterns of functional coupling across regions that underpin the temporal evolution of dFC. Moreover, some of these CCPs exhibited significant neurophysiological meaning. Furthermore, we apply this method to HCP rsfMR and tfMRI data as well as sleep-deprivation data and found that the topological organization of these low-dimensional structures has high potential for predicting sleep-deprivation states (classification accuracy of 92.3%) and task types (100% identification for all seven tasks).In summary, this work provides a methodology for distilling coherent low-dimensional functional connectivity structures in complex brain dynamics that play an important role in performing tasks or characterizing specific states of the brain.
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Affiliation(s)
- Yuyuan Yang
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha 410073, China.
| | - Lubin Wang
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China.
| | - Yu Lei
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China.
| | - Yuyang Zhu
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China.
| | - Hui Shen
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha 410073, China.
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27
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Abstract
A defining aspect of brain organization is its spatial heterogeneity, which gives rise to multiple topographies at different scales. Brain parcellation - defining distinct partitions in the brain, be they areas or networks that comprise multiple discontinuous but closely interacting regions - is thus fundamental for understanding brain organization and function. The past decade has seen an explosion of in vivo MRI-based approaches to identify and parcellate the brain on the basis of a wealth of different features, ranging from local properties of brain tissue to long-range connectivity patterns, in addition to structural and functional markers. Given the high diversity of these various approaches, assessing the convergence and divergence among these ensuing maps is a challenge. Inter-individual variability adds to this challenge but also provides new opportunities when coupled with cross-species and developmental parcellation studies.
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28
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Qian S, Wang X, Qu X, Zhang P, Li Q, Wang R, Liu DQ. Links Between the Amplitude Modulation of Low-Frequency Spontaneous Fluctuation Across Resting State Conditions and Thalamic Functional Connectivity. Front Hum Neurosci 2019; 13:199. [PMID: 31263405 PMCID: PMC6584839 DOI: 10.3389/fnhum.2019.00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/28/2019] [Indexed: 11/13/2022] Open
Abstract
A comparison of the different types of resting state reveals some interesting characteristics of spontaneous brain activity that cannot be found in a single condition. Differences in the amplitude of low-frequency fluctuation (ALFF) between the eyes open (EO) and the eyes closed (EC) almost have a spatially distinct pattern with traditional EO-EC activation within sensory systems, suggesting the divergent functional roles of ALFF and activation. However, the underlying mechanism is far from clear. Since the thalamus plays an essential role in sensory processing, one critical step toward understanding the divergences is to depict the relationships between the thalamus and the ALFF modulation in sensory regions. In this preliminary study, we examined the association between the changes of ALFF and the changes of thalamic functional connectivity (FC) between EO and EC. We focused on two visual thalamic nuclei, the lateral geniculate nucleus (LGN) and the pulvinar (Pu). FC results showed that LGN had stronger synchronization with regions in lateral but not in medial visual networks, while Pu had a weaker synchronization with auditory and sensorimotor areas during EO compared with EC. Moreover, the patterns of FC modulation exhibited considerable overlaps with the ALFF modulation, and there were significant correlations between them across subjects. Our findings support the crucial role of the thalamus in amplitude modulation of low-frequency spontaneous activity in sensory systems, and may pave the way to elucidate the mechanisms governing distinction between evoked activation and modulation of low-frequency spontaneous brain activity.
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Affiliation(s)
- Shufang Qian
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, China
| | - Xinbo Wang
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, China
| | - Xiujuan Qu
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, China
| | - Peiwen Zhang
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, China
| | - Qiuyue Li
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, China
| | - Ruidi Wang
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, China
| | - Dong-Qiang Liu
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, China
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29
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Bielczyk NZ, Uithol S, van Mourik T, Anderson P, Glennon JC, Buitelaar JK. Disentangling causal webs in the brain using functional magnetic resonance imaging: A review of current approaches. Netw Neurosci 2019; 3:237-273. [PMID: 30793082 PMCID: PMC6370462 DOI: 10.1162/netn_a_00062] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/08/2018] [Indexed: 01/05/2023] Open
Abstract
In the past two decades, functional Magnetic Resonance Imaging (fMRI) has been used to relate neuronal network activity to cognitive processing and behavior. Recently this approach has been augmented by algorithms that allow us to infer causal links between component populations of neuronal networks. Multiple inference procedures have been proposed to approach this research question but so far, each method has limitations when it comes to establishing whole-brain connectivity patterns. In this paper, we discuss eight ways to infer causality in fMRI research: Bayesian Nets, Dynamical Causal Modelling, Granger Causality, Likelihood Ratios, Linear Non-Gaussian Acyclic Models, Patel's Tau, Structural Equation Modelling, and Transfer Entropy. We finish with formulating some recommendations for the future directions in this area.
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Affiliation(s)
- Natalia Z. Bielczyk
- Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Sebo Uithol
- Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
- Bernstein Centre for Computational Neuroscience, Charité Universitätsmedizin, Berlin, Germany
| | - Tim van Mourik
- Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Paul Anderson
- Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
- Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Jeffrey C. Glennon
- Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Jan K. Buitelaar
- Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
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30
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Pergola G, Danet L, Pitel AL, Carlesimo GA, Segobin S, Pariente J, Suchan B, Mitchell AS, Barbeau EJ. The Regulatory Role of the Human Mediodorsal Thalamus. Trends Cogn Sci 2018; 22:1011-1025. [PMID: 30236489 PMCID: PMC6198112 DOI: 10.1016/j.tics.2018.08.006] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/31/2018] [Accepted: 08/17/2018] [Indexed: 12/17/2022]
Abstract
The function of the human mediodorsal thalamic nucleus (MD) has so far eluded a clear definition in terms of specific cognitive processes and tasks. Although it was at first proposed to play a role in long-term memory, a set of recent studies in animals and humans has revealed a more complex, and broader, role in several cognitive functions. The MD seems to play a multifaceted role in higher cognitive functions together with the prefrontal cortex and other cortical and subcortical brain areas. Specifically, we propose that the MD is involved in the regulation of cortical networks especially when the maintenance and temporal extension of persistent activity patterns in the frontal lobe areas are required.
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Affiliation(s)
- Giulio Pergola
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari 70124, Italy.
| | - Lola Danet
- Toulouse NeuroImaging Center, Université de Toulouse, Inserm, UPS 31024, France; CHU Toulouse Purpan, Neurology Department, Toulouse 31059, France
| | - Anne-Lise Pitel
- Normandie University, UNICAEN, PSL Research University, EPHE, INSERM, U1077, CHU de Caen, Neuropsychologie et Imagerie de la Mémoire Humaine, 14000 Caen, France
| | - Giovanni A Carlesimo
- Department of Systems Medicine, Tor Vergata University and S. Lucia Foundation, Rome, Italy
| | - Shailendra Segobin
- Normandie University, UNICAEN, PSL Research University, EPHE, INSERM, U1077, CHU de Caen, Neuropsychologie et Imagerie de la Mémoire Humaine, 14000 Caen, France
| | - Jérémie Pariente
- Toulouse NeuroImaging Center, Université de Toulouse, Inserm, UPS 31024, France; CHU Toulouse Purpan, Neurology Department, Toulouse 31059, France
| | - Boris Suchan
- Clinical Neuropsychology, Ruhr University Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Anna S Mitchell
- Department of Experimental Psychology, University of Oxford, The Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK; Equivalent contribution as last authors.
| | - Emmanuel J Barbeau
- Centre de recherche Cerveau et Cognition, UMR5549, Université de Toulouse - CNRS, Toulouse 31000, France; Equivalent contribution as last authors
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31
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Liu A, Lin SJ, Mi T, Chen X, Chan P, Wang ZJ, McKeown MJ. Decreased subregional specificity of the putamen in Parkinson's Disease revealed by dynamic connectivity-derived parcellation. Neuroimage Clin 2018; 20:1163-1175. [PMID: 30388599 PMCID: PMC6214880 DOI: 10.1016/j.nicl.2018.10.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 10/08/2018] [Accepted: 10/21/2018] [Indexed: 12/16/2022]
Abstract
Parkinson's Disease (PD) is associated with decreased ability to perform habitual tasks, relying instead on goal-directed behaviour subserved by different cortical/subcortical circuits, including parts of the putamen. We explored the functional subunits in the putamen in PD using novel dynamic connectivity features derived from resting state fMRI recorded from thirty PD subjects and twenty-eight age-matched healthy controls (HC). Dynamic functional segmentation of the putamina was obtained by determining the correlation between each voxel in each putamen along a moving window and applying a joint temporal clustering algorithm to establish cluster membership of each voxel at each window. Contiguous voxels that had consistent cluster membership across all windows were then considered to be part of a homogeneous functional subunit. As PD subjects robustly had two homogenous clusters in the putamina, we also segmented the putamina in HC into two dynamic clusters for a fair comparison. We then estimated the dynamic connectivity using sliding windowed correlation between the mean signal from the identified homogenous subunits and 56 other predefined cortical and subcortical ROIs. Specifically, the mean dynamic connectivity strength and connectivity deviation were then compared to evaluate subregional differences. HC subjects had significant differences in mean dynamic connectivity and connectivity deviation between the two putaminal subunits. The posterior subunit connected strongly to sensorimotor areas, the cerebellum, as well as the middle frontal gyrus. The anterior subunit had strong mean dynamic connectivity to the nucleus accumbens, hippocampus, amygdala, caudate and cingulate. In contrast, PD subjects had fewer differences in mean dynamic connectivity between subunits, indicating a degradation of subregional specificity. Overall UPDRS III and MoCA scores could be predicted using mean dynamic connectivity strength and connectivity deviation. Side of onset of the disease was also jointly related with functional connectivity features. Our results suggest a robust loss of specificity of mean dynamic connectivity and connectivity deviation in putaminal subunits in PD that is sensitive to disease severity. In addition, altered mean dynamic connectivity and connectivity deviation features in PD suggest that looking at connectivity dynamics offers an additional dimension for assessment of neurodegenerative disorders.
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Affiliation(s)
- Aiping Liu
- Pacific Parkinson's Research Centre, Vancouver, Canada; Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, Canada.
| | - Sue-Jin Lin
- Pacific Parkinson's Research Centre, Vancouver, Canada; Graduate Program in Neuroscience, University of British Columbia, Vancouver, Canada
| | - Taomian Mi
- Department of Neurology, Neurobiology and Geriatrics, Xuanwu Hospital of Capital Medical University, Beijing Institute of Brain Disorders, Beijing, China
| | - Xun Chen
- Department of Electronic Science and Technology, University of Science and Technology of China, Hefei, China.
| | - Piu Chan
- Department of Neurology, Neurobiology and Geriatrics, Xuanwu Hospital of Capital Medical University, Beijing Institute of Brain Disorders, Beijing, China
| | - Z Jane Wang
- Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, Canada
| | - Martin J McKeown
- Pacific Parkinson's Research Centre, Vancouver, Canada; Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, Canada; Graduate Program in Neuroscience, University of British Columbia, Vancouver, Canada; Department of Medicine (Neurology), University of British Columbia, Vancouver, Canada
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32
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New approaches in psychiatric drug development. Eur Neuropsychopharmacol 2018; 28:983-993. [PMID: 30056086 DOI: 10.1016/j.euroneuro.2018.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 06/18/2018] [Accepted: 06/25/2018] [Indexed: 02/03/2023]
Abstract
Numerous novel neuroscience-based drug targets have been identified in recent years. However, it remains unclear how these targets relate to the expression of symptoms in central nervous system (CNS) disorders in general and psychiatric disorders in particular. To discuss this issue, a New Frontiers Meetings of European College of Neuropsychopharmacology (ECNP) was organized to address the challenges in translational neuroscience research that are impeding the effective development of new treatments. The main aim of this meeting was to discuss scientific insights, concepts and methodologies in order to improve drug development for psychiatric disorders. The meeting was designed to bring together stakeholders from academia, pharmaceutical industry, and regulatory agencies. Here we provide a synopsis of the proceedings from the meeting entitled 'New approaches to psychiatric drug development'. New views on psychiatric drug development were presented to address the challenges and pitfalls as identified by the different stakeholders. The general conclusion of the meeting was that drug discovery could be stimulated by designing new classification and sensitive assessment tools for psychiatric disorders, which bear closer relationships to neuropharmacological and neuroscientific developments. This is in line with the vision of precision psychiatry in which patients are clustered, not merely on symptoms, but primarily on biological phenotypes that represent pathophysiological relevant and 'drugable' processes. To achieve these goals, a closer collaboration between all stakeholders in early stages of development is essential to define the research criteria together and to reach consensus on new quantitative biological methodologies and etiology-directed treatments.
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33
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Chauvin RJ, Mennes M, Buitelaar JK, Beckmann CF. Assessing age-dependent multi-task functional co-activation changes using measures of task-potency. Dev Cogn Neurosci 2017; 33:5-16. [PMID: 29223425 PMCID: PMC6206256 DOI: 10.1016/j.dcn.2017.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 11/29/2017] [Accepted: 11/29/2017] [Indexed: 01/06/2023] Open
Abstract
It is being hypothesised that the developing adolescent brain is increasingly enlisting long-range connectivity, allowing improved communication between spatially distant brain regions. The developmental trajectories of such maturational changes remain elusive. Here, we aim to study how the brain engages in multiple tasks (working memory, reward processing, and inhibition) at the network-level and evaluate how effects of age across these tasks are related to each other. We characterise how the brain departs from its functional baseline architecture towards task-induced functional connectivity modulations using a novel measure called task potency, allowing direct comparison between tasks by defining sensitivity to one or multiple tasks. By applying this method in a sample of healthy participants (N = 218) aged 8-30 years, we demonstrate maturational changes in task-dependent functional co-activation over and above baseline connectivity maturation. Our results provide evidence for task-specific maturational windows with different cognitive systems probed by different tasks displaying specific age-range dependencies of strongest developmental change. Our results highlight the use of task potency for modelling developmental trajectories and the impact of differential maturation across tasks. This enables better characterisation of cognitive processes disrupted in neurodevelopmental disorders and may explain the increased level of heterogeneity observed in adolescent population studies.
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Affiliation(s)
- Roselyne J Chauvin
- Radboud University Medical Center, Department of Cognitive Neuroscience, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands.
| | - Maarten Mennes
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Jan K Buitelaar
- Radboud University Medical Center, Department of Cognitive Neuroscience, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Christian F Beckmann
- Radboud University Medical Center, Department of Cognitive Neuroscience, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands; Centre for Functional MRI of the Brain (FMRIB), University of Oxford, Oxford, United Kingdom
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34
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Huertas I, Oldehinkel M, van Oort ESB, Garcia-Solis D, Mir P, Beckmann CF, Marquand AF. A Bayesian spatial model for neuroimaging data based on biologically informed basis functions. Neuroimage 2017; 161:134-148. [PMID: 28782681 PMCID: PMC5692833 DOI: 10.1016/j.neuroimage.2017.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/27/2017] [Accepted: 08/02/2017] [Indexed: 01/13/2023] Open
Abstract
The dominant approach to neuroimaging data analysis employs the voxel as the unit of computation. While convenient, voxels lack biological meaning and their size is arbitrarily determined by the resolution of the image. Here, we propose a multivariate spatial model in which neuroimaging data are characterised as a linearly weighted combination of multiscale basis functions which map onto underlying brain nuclei or networks or nuclei. In this model, the elementary building blocks are derived to reflect the functional anatomy of the brain during the resting state. This model is estimated using a Bayesian framework which accurately quantifies uncertainty and automatically finds the most accurate and parsimonious combination of basis functions describing the data. We demonstrate the utility of this framework by predicting quantitative SPECT images of striatal dopamine function and we compare a variety of basis sets including generic isotropic functions, anatomical representations of the striatum derived from structural MRI, and two different soft functional parcellations of the striatum derived from resting-state fMRI (rfMRI). We found that a combination of ∼50 multiscale functional basis functions accurately represented the striatal dopamine activity, and that functional basis functions derived from an advanced parcellation technique known as Instantaneous Connectivity Parcellation (ICP) provided the most parsimonious models of dopamine function. Importantly, functional basis functions derived from resting fMRI were more accurate than both structural and generic basis sets in representing dopamine function in the striatum for a fixed model order. We demonstrate the translational validity of our framework by constructing classification models for discriminating parkinsonian disorders and their subtypes. Here, we show that ICP approach is the only basis set that performs well across all comparisons and performs better overall than the classical voxel-based approach. This spatial model constitutes an elegant alternative to voxel-based approaches in neuroimaging studies; not only are their atoms biologically informed, they are also adaptive to high resolutions, represent high dimensions efficiently, and capture long-range spatial dependencies, which are important and challenging objectives for neuroimaging data. A multivariate spatial model using brain parcellations as basis functions is proposed. Brain regions can be modeled as a superposition of multiscale basis functions. These basis functions are biologically meaningful and capture spatial dependencies. Our framework allows to develop accurate and parsimonious clinical models. The model is computationally efficient, enhances power and adapts to high resolutions.
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Affiliation(s)
- Ismael Huertas
- Unidad de Trastornos del Movimiento, Servicio de Neurología y NeurofisiologíaClínica, Instituto de Biomedicina de Sevilla (IBiS), Hospital UniversitarioVirgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Marianne Oldehinkel
- Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen, The Netherlands; Donders Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Erik S B van Oort
- Donders Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - David Garcia-Solis
- Servicio de Medicina Nuclear, UDIM, Hospital UniversitarioVirgen del Rocío, Seville, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Pablo Mir
- Unidad de Trastornos del Movimiento, Servicio de Neurología y NeurofisiologíaClínica, Instituto de Biomedicina de Sevilla (IBiS), Hospital UniversitarioVirgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Christian F Beckmann
- Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen, The Netherlands; Donders Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands; Oxford Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), University of Oxford, United Kingdom
| | - Andre F Marquand
- Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen, The Netherlands; Donders Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands; Department of Neuroimaging, Centre for Neuroimaging Sciences, Institute of Psychiatry, King's College London, United Kingdom.
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