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Fiber up-sampling and quality assessment of tractograms - towards quantitative brain connectivity

Stefan Sommer, Sebastian Kozerke, Erich Seifritz, Philipp Staempfli
2016 Brain and Behavior  
Nevertheless, deriving a reliable quantification of connectivity strength between different brain areas is still a challenge.  ...  Nevertheless, deriving a reliable quantification of connectivity strength between different brain areas is still a challenge.  ...  This complicates the estimation of reliable tractograms and thus the extraction of biologically meaningful connectivity measures between brain areas which are a crucial requirement for an accurate, quantitative  ... 
doi:10.1002/brb3.588 pmid:28127510 pmcid:PMC5256175 fatcat:kd5gubdhnrdctfo3jwwbdd2xim

Network analysis shows decreased ipsilesional structural connectivity in glioma patients [article]

Lucius Samo Fekonja, Ziqian Wang, Alberto Cacciola, Timo Roine, Baran D. Aydogan, Darius Mewes, Sebastian Vellmer, Peter Vajkoczy, Thomas Picht
2021 medRxiv   pre-print
Here, we used network measures to characterize gliomarelated decreases in structural connectivity by comparing the ipsi- with the contralesional hemispheres of patients and correlated findings with neurological  ...  We found that lesion location resulted in differential impairment of both short and long 30 connectivity patterns.  ...  Subsequently, the whole-brain tractograms were filtered to 10'000'000 streamlines with spherical-deconvolution .  ... 
doi:10.1101/2021.06.22.21259319 fatcat:iupa4ais5nd2dg2f54swgkwqai

Groupwise Track Filtering via Iterative Message Passing and Pruning,

Yihao Xia, Yonggang Shi
2020 NeuroImage  
Tractography is an important tool for the in vivo analysis of brain connectivity based on diffusion MRI data, but it also has well-known limitations in false positives and negatives for the faithful reconstruction  ...  We first formalize our groupwise concept with a flexible definition that characterizes the consistency of a track with respect to other group members based on three important aspects: degree, affinity,  ...  Data used in this paper were partly provided by the Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904) and DOD ADNI (Department of Defense award number  ... 
doi:10.1016/j.neuroimage.2020.117147 pmid:32673747 pmcid:PMC7780547 fatcat:wzhwhrmtendmfffywpvuicdb24

Microstructural changes in the reward system are associated with post-stroke depression

Lena KL Oestreich, Paul Wright, Michael J O'Sullivan
2020 NeuroImage: Clinical  
Subnetworks of decreased FA-weighted and increased FW-weighted connectivity were observed in patients with PSD relative to healthy controls.  ...  The study enrolled 16 healthy controls, 12 stroke patients with PSD and 34 stroke patients free of PSD. Participants underwent 3T structural and diffusion MRI.  ...  Acknowledgements The authors thank the coordinators of the King's Hyperacute Stroke Research Centre for their help with identifying and recruiting patients, and the manager and staff of the NIHR Wellcome  ... 
doi:10.1016/j.nicl.2020.102360 pmid:32795963 pmcid:PMC7426585 fatcat:zy2wiv2yonbkfm4n3ic7nvi53i

Quantitative mapping of the brain's structural connectivity using diffusion MRI tractography: a review [article]

Fan Zhang, Alessandro Daducci, Yong He, Simona Schiavi, Caio Seguin, Robert Smith, Chun-Hung Yeh, Tengda Zhao, Lauren J. O'Donnell
2021 arXiv   pre-print
In this paper, we provide a high-level overview of how tractography is used to enable quantitative analysis of the brain's structural connectivity in health and disease.  ...  Over the last two decades, the study of brain connectivity using dMRI tractography has played a prominent role in the neuroimaging research landscape.  ...  CHY is grateful to the Ministry of Science and Technology of Taiwan (MOST 109-2222-E-182-001-MY3) for the support.  ... 
arXiv:2104.11644v1 fatcat:l3ixpcwu7jb7zcqo2sm5pswmja

Diagnosis and Prognosis Using Machine Learning Trained on Brain Morphometry and White Matter Connectomes [article]

Yun Wang, Chenxiao Xu, Ji-Hwan Park, Seonjoo Lee, Yaakov Stern, Jong Hun Kim, Shinjae Yoo, Hyoung Seop Kim, Jiook Cha
2018 bioRxiv   pre-print
Here we tested the utility of structural MRI and diffusion MRI as imaging markers of AD using high-throughput brain phenotyping including morphometry and white-matter structural connectome (whole-brain  ...  This study indicates promising utility of multimodal MRI, particularly structural connectome, combined with high-throughput brain phenotyping and machine learning analytics to extract salient features  ...  This study was supported by NIMH K01 MH109836 (Cha), Brain and Behavior Research Foundation NARSAD Young Investigator award (Cha), Korean Scientists and Engineers Association Young Investigator Grant (  ... 
doi:10.1101/255141 fatcat:cfvsbvqmxnf27keulvxyt5d6pm

Subtle white matter alterations in schizophrenia identified with a new measure of fiber density

Philipp Stämpfli, Stefan Sommer, Andrei Manoliu, Achim Burrer, André Schmidt, Marcus Herdener, Erich Seifritz, Stefan Kaiser, Matthias Kirschner
2019 Scientific Reports  
Altered cerebral connectivity is one of the core pathophysiological mechanism underlying the development and progression of information-processing deficits in schizophrenia.  ...  FD and FA maps were derived from diffusion data of 25 healthy controls (HC) and 21 patients with schizophrenia (SZ).  ...  However, the reliable extraction of quantitative measures from tractograms across different populations remains challenging.  ... 
doi:10.1038/s41598-019-40070-2 pmid:30874571 pmcid:PMC6420505 fatcat:527qh2sfxza2lj423ffo7fnvda

A population-based atlas of the human pyramidal tract in 410 healthy participants

Quentin Chenot, Nathalie Tzourio-Mazoyer, François Rheault, Maxime Descoteaux, Fabrice Crivello, Laure Zago, Emmanuel Mellet, Gaël Jobard, Marc Joliot, Bernard Mazoyer, Laurent Petit
2018 Brain Structure and Function  
Introduction One of the challenges in the human brain connectomic field is to improve our knowledge about major long-range white matter (WM) connections and to link them with behavioral measurements, clinical  ...  ., 2017) , each tractogram was built using constrained-spherical deconvolution and particle-filter tractography with anatomical priors (Girard et al., 2014) .  ... 
doi:10.1007/s00429-018-1798-7 pmid:30460551 fatcat:2hcklsws5bc3jivsruhxneetw4

Diagnosis and Prognosis Using Machine Learning Trained on Brain Morphometry and White Matter Connectomes [article]

Yun Wang, Chenxiao Xu, Ji-Hwan Park, Seonjoo Lee, Yaakov Stern, Shinjae Yoo, Jong Hun Kim, Hyoung Seop Kim, Jiook Cha
2018 bioRxiv   pre-print
Here we tested the utility of commonly available multimodal MRI (T1-weighted structure and diffusion MRI), combined with high-throughput brain phenotyping-morphometry and connectomics-and machine learning  ...  Accurate, reliable prediction of risk for Alzheimers disease (AD) is essential for early, disease-modifying therapeutics.  ...  This study was supported by NIMH K01 MH109836 (Cha), Brain and Behavior Research Foundation NARSAD Young Investigator award (Cha), Korean Scientists and Engineers Association Young Investigator Grant (  ... 
doi:10.1101/407601 fatcat:bskcwpjihzg67nvdr4422vg6ve

An afferent white matter pathway from the pulvinar to the amygdala facilitates fear recognition

Jessica McFadyen, Jason B Mattingley, Marta I Garrido
2019 eLife  
Critically, individuals with greater fibre density in this pathway also had stronger dynamic coupling and enhanced fearful face recognition.  ...  Our findings provide converging evidence for the recruitment of an afferent subcortical pulvinar connection to the amygdala that facilitates fear recognition.Editorial note: This article has been through  ...  For example, a structure located deep within the brain called the amygdala is connected to other parts of the brain that regulate hormones, senses and muscles.  ... 
doi:10.7554/elife.40766 pmid:30648533 pmcid:PMC6335057 fatcat:siw4huqfxzedldl5po25vn25gm

A probabilistic atlas of the human pyramidal tract in 410 healthy participants [article]

Quentin Chenot, Nathalie Tzourio-Mazoyer, Francois Rheault, Maxime Descoteaux, Fabrice Crivello, Laure Zago, Emmanuel Mellet, Gael Jobard, Marc Joliot, Bernard Mazoyer, Laurent Petit
2018 biorxiv/medrxiv   pre-print
Here, we combined a precise manual positioning of individual subcortical regions of interest along the descending pathway of the PyT with a new bundle-specific tractography algorithm.  ...  We then extracted both left and right PyT in a large cohort of 410 healthy participants and built a probabilistic atlas of the whole-fanning PyT with a complete description of its most cortico-lateral  ...  Introduction One of the challenges in the human brain connectomic field is to improve our knowledge about major long-range white matter (WM) connections and to link them with behavioral measurements, clinical  ... 
doi:10.1101/251108 fatcat:vhujcyegx5h27ajdzn5ffjzdlm

A registration method for improving quantitative assessment in probabilistic diffusion tractography

J.L. Waugh, J.K. Kuster, M.L. Makhlouf, J.M. Levenstein, T.J. Multhaupt-Buell, S.K. Warfield, N. Sharma, A.J. Blood
2019 NeuroImage  
Diffusion MRI-based probabilistic tractography is a powerful tool for non-invasively investigating normal brain architecture and alterations in structural connectivity associated with disease states.  ...  We then developed a method for tract alignment that enhances the existing standard whole brain registration, and then tested whether this method improved the reliability of groupwise contrasts.  ...  Waugh was supported by the Clinical Research Training Fellowship, American Academy of Neurology, and the Silverman Family Fellowship, Bachmann-Strauss Dystonia and Parkinson Foundation.  ... 
doi:10.1016/j.neuroimage.2018.12.057 pmid:30611874 pmcid:PMC6790978 fatcat:7dtyicfk3bghvaixggbfvnwoiq

The ENIGMA Toolbox: Cross-disorder integration and multiscale neural contextualization of multisite neuroimaging datasets [article]

Sara Lariviere, Casey Paquola, Bo-yong Park, Jessica Royer, Yezhou Wang, Oualid Benkarim, Reinder Vos de Wael, Sofie Louise Valk, Sophia I Thomopoulos, Matthias Kirschner, Sanjay Sisodiya, Carrie McDonald (+3 others)
2020 bioRxiv   pre-print
Our Toolbox equips scientists with tutorials to explore molecular, histological, and network correlates of noninvasive neuroimaging markers of brain disorders.  ...  yielded some of the largest studies of the healthy and diseased brain.  ...  The authors would like to express their gratitude to the open science initiatives that made this work possible: (i) The ENIGMA Consortium ( DECLARATION OF INTEREST The authors declare no competing  ... 
doi:10.1101/2020.12.21.423838 fatcat:attlmrhftzhtbp4csnq4pthgni

Mapping Short Association Fibers in the Early Cortical Visual Processing Stream Using In Vivo Diffusion Tractography

2020 Cerebral Cortex  
Short association fibers (U-fibers) connect proximal cortical areas and constitute the majority of white matter connections in the human brain.  ...  This study demonstrates a robust U-fiber connectivity mapping in vivo and is an important step toward construction of a more complete human brain connectome.  ...  Conflict of Interest: The Max Planck Institute for Human Cognitive and Brain Sciences has an institutional research agreement with Siemens Healthineers.  ... 
doi:10.1093/cercor/bhaa049 pmid:32297628 pmcid:PMC7325803 fatcat:i4ha7rw6hncfbo4mf6etwox5su

Genetic influences on hub connectivity of the human connectome [article]

Aurina Arnatkeviciute, Ben D. Fulcher, Stuart Oldham, Jeggan Tiego, Casey Paquola, Zachary F Gerring, Kevin M Aquino, Ziarih Hawi, Beth Johnson, Gareth M Ball, Marieke Klein, Gustavo Deco (+3 others)
2020 bioRxiv   pre-print
Brain network hubs are both highly connected and highly inter-connected, forming a critical communication backbone for coherent neural dynamics.  ...  Together, our findings indicate that genetic influences on brain connectivity are not uniformly distributed throughout the brain, but are instead concentrated on the functionally valuable, metabolically  ...  The resulting tractogram was then combined with the cortical parcellation for each subject to produce a network map of white matter connectivity.  ... 
doi:10.1101/2020.06.21.163915 fatcat:rnsvjbqsgfclplnphiitwmxncy
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