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Data on the test-retest reproducibility of streamline counts as a measure of structural connectivity

Lena V. Schumacher, Marco Reisert, Kai Nitschke, Karl Egger, Horst Urbach, Jürgen Hennig, Cornelius Weiller, Christoph P. Kaller
2018 Data in Brief  
These data are related to the research article entitled 'Probing the reproducibility of quantitative estimates of structural connectivity derived from global tractography ' (Schumacher et al., Neuroimage  ...  These data provide estimations of test-retest reproducibility of streamline counts based on diffusion weighted imaging (DWI) data using a global tractography algorithm in a sample of young healthy adults  ...  Acknowledgements The authors of this article (LVS, MR, KN, KE, HU, JH, CW, CPK) report no conflicts of interest. The Transparency document.  ... 
doi:10.1016/j.dib.2018.05.145 pmid:30229011 pmcid:PMC6140827 fatcat:zxyn6jz325czba6r4vgypracaq

Mapping remodeling of thalamocortical projections in the living reeler mouse brain by diffusion tractography

L.-A. Harsan, C. David, M. Reisert, S. Schnell, J. Hennig, D. von Elverfeldt, J. F. Staiger
2013 Proceedings of the National Academy of Sciences of the United States of America  
Currently, the only methodology providing a global noninvasive window into structural brain connectivity is diffusion tractography.  ...  We quantitatively validated the TC projections inferred from in vivo tractography with correlative histological axonal tracing in the same wild-type and reeler mutant mice.  ...  Valerij Kiselev for very helpful discussions regarding the global tracking algorithm.  ... 
doi:10.1073/pnas.1218330110 pmid:23610438 pmcid:PMC3651497 fatcat:ewcfpopx3vgfbgss5ltvz4dlja

Quantitative assessment of a framework for creating anatomical brain networks via global tractography

Longchuan Li, James K. Rilling, Todd M. Preuss, Matthew F. Glasser, Frederick W. Damen, Xiaoping Hu
2012 NeuroImage  
Interregional connections of the brain measured with diffusion tractography can be used to infer valuable information regarding both brain structure and function.  ...  different than that of local tractography, possibly resulting from the increased fiber complexity of real tissues.  ...  Acknowledgments We thank the reviewers for their valuable suggestions, which significantly improved the quality of the manuscript. We thank Dr.  ... 
doi:10.1016/j.neuroimage.2012.03.071 pmid:22484406 pmcid:PMC3407566 fatcat:276hxq4rj5fj7hbiorot5huxim

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

On the cortical connectivity in the macaque brain: a comparison of diffusion tractography and histological tracing data

Gabriel Girard, Roberto Caminiti, Alexandra Battaglia-Mayer, Etienne St-Onge, Karen S. Ambrosen, Simon F. Eskildsen, Kristine Krug, Tim B. Dyrby, Maxime Descoteaux, Jean-Philippe Thiran, Giorgio M. Innocenti
2020 NeuroImage  
Diffusion-weighted magnetic resonance imaging (DW-MRI) tractography is a non-invasive tool to probe neural connections and the structure of the white matter.  ...  The rich literature in histological connectivity analysis studies in the macaque monkey enables quantitative evaluation of the performance of tractography algorithms.  ...  derived binary connectivity estimation of the studied network.  ... 
doi:10.1016/j.neuroimage.2020.117201 pmid:32739552 fatcat:mdz4pgcrenbclg5sotewd76iae

Building connectomes using diffusion MRI: why, how and but

Stamatios N. Sotiropoulos, Andrew Zalesky
2017 NMR in Biomedicine  
than chemical tracers and microscopic techniques and they cannot estimate the directionality of connections.  ...  However, in vivo mapping of connections in humans offers the potential of considerable advantages 6 : (i) many connections in many subjects can be studied simultaneously; (ii) structural connections can  ...  AZ is supported by a fellowship from the National Health and Medical Research Council of Australia (APP1047648). We would also like to thank Alfred Anwander and Saad Jbabdi for useful discussions.  ... 
doi:10.1002/nbm.3752 pmid:28654718 fatcat:2adafayqyzbgbdr6n3vlj2kcwi

Processing and Visualization of Diffusion MRI [chapter]

James G. Malcolm, Yogesh Rathi, Carl-Fredrik Westin
2010 Biomedical Image Processing  
We describe various approaches to modeling the local diffusion structure from scanner measurements. We then look at techniques to trace out neural pathways and infer global tissue structure.  ...  Last, we draw upon these as building blocks for the visualization and analysis of the neural architecture of individuals and groups.  ...  Further, scalar measures derived from these models similarly benefit from incorporating neighborhood information [114] . Next we outlined various methods of tractography to infer connectivity.  ... 
doi:10.1007/978-3-642-15816-2_16 fatcat:uqcj676gbzc3fkqlk6vwep3mfm

Tractography: Where Do We Go from Here?

Saad Jbabdi, Heidi Johansen-Berg
2011 Brain Connectivity  
However, as a method to study brain connectivity, tractography suffers from limitations, as it is indirect, inaccurate, and difficult to quantify.  ...  Diffusion tractography offers enormous potential for the study of human brain anatomy.  ...  The authors are funded by the Medical Research Council (S.J.) and the Wellcome Trust (H.J.B.). Author Disclosure Statement No competing financial interests exist.  ... 
doi:10.1089/brain.2011.0033 pmid:22433046 pmcid:PMC3677805 fatcat:6lfmoed2vfcfbk6b6zpq2bj7xu

Assessing White Matter Pathology in Early-Stage Parkinson Disease Using Diffusion MRI: A Systematic Review

Maurizio Bergamino, Elizabeth G. Keeling, Virendra R. Mishra, Ashley M. Stokes, Ryan R. Walsh
2020 Frontiers in Neurology  
Structural brain white matter (WM) changes such as axonal caliber, density, myelination, and orientation, along with WM-dependent structural connectivity, may be impacted early in Parkinson disease (PD  ...  Diffusion tensor imaging (DTI) is the most commonly utilized method to probe WM pathological changes.  ...  Although the combination of different dMRI acquisitions and analyses may yield new and more accurate information related to dMRI-derived WM structural disorganization and global connectivity changes in  ... 
doi:10.3389/fneur.2020.00314 pmid:32477235 pmcid:PMC7240075 fatcat:mmsi3dv2mbbyhkw7lf3diirxau

The R1-weighted connectome: complementing brain networks with a myelin-sensitive measure

Tommy Boshkovski, Ljupco Kocarev, Julien Cohen-Adad, Bratislav Mišić, Stéphane Lehéricy, Nikola Stikov, Matteo Mancini
2020 Network Neuroscience  
Complementing the structural connectome, obtained with diffusion MRI tractography, with a myelin-sensitive measure could result in a more complete model of structural brain connectivity and give better  ...  Overall, the R1-weighted connectome provides a different perspective on structural connectivity taking into account white matter myeloarchitecture.  ...  The R1-weighted connectome  ... 
doi:10.1162/netn_a_00179 pmid:34189369 pmcid:PMC8233108 fatcat:mpypkv4yl5ds7o4t35i7kqhhti

Diffusion magnetic resonance imaging for Brainnetome: A critical review

Nianming Zuo, Jian Cheng, Tianzi Jiang
2012 Neuroscience Bulletin  
The term "human connectome" was proposed to emphasize "a comprehensive structural description of the network of elements and connections forming the human brain" [3, 10, 11] .  ...  Extending the connectome, the Brainnetome was conceived to reveal not only physical structural connectivities but also functional connectivities by various levels of in-vivo imaging methods and ex-vivo  ...  The estimated EAP and two kinds of ODFs estimated using SPFI from monkey data, where the crossing angles of fibers are almost 90° are shown in Fig. 4.  ... 
doi:10.1007/s12264-012-1245-3 pmid:22833036 pmcid:PMC5560260 fatcat:7zsg3b4hsfbypjqgtdeq66ar6y

Genetics of Path Lengths in Brain Connectivity Networks: HARDI-Based Maps in 457 Adults [chapter]

Neda Jahanshad, Gautam Prasad, Arthur W. Toga, Katie L. McMahon, Greig I. de Zubicaray, Nicholas G. Martin, Margaret J. Wright, Paul M. Thompson
2012 Lecture Notes in Computer Science  
Here we combined genotyping, anatomical MRI and HARDI to understand how our genes influence the cortical connections, using whole-brain tractography.  ...  Many connectivity measures including path lengths are generally defined as the number of nodes traversed to connect a node in a graph to the others.  ...  Acknowledgments This study was supported by the National Institute of Child Health and Human Development (R01 HD050735), and the National Health and Medical Research Council (NHMRC 486682), Australia.  ... 
doi:10.1007/978-3-642-33530-3_3 pmid:25584366 pmcid:PMC4288784 fatcat:tk4hg5uzjzh2zf46jprizdsxfm

Tract Specific Reproducibility of Tractography Based Morphology and Diffusion Metrics

René M. H. Besseling, Jacobus F. A. Jansen, Geke M. Overvliet, Maarten J. Vaessen, Hilde M. H. Braakman, Paul A. M. Hofman, Albert P. Aldenkamp, Walter H. Backes, Yong He
2012 PLoS ONE  
The reproducibility of tractography is important to determine its sensitivity to pathological abnormalities.  ...  The reproducibility of tract morphology has not yet been systematically studied and the recently developed tractography contrast Tract Density Imaging (TDI) has not yet been assessed at the tract specific  ...  Acknowledgments We would like to thank Donald Tournier, Alexander Leemans and Ben Jeurissen for useful discussions and Kerstin Pannek for her advice on normalization of the whole brain tractograms.  ... 
doi:10.1371/journal.pone.0034125 pmid:22485157 pmcid:PMC3317780 fatcat:l6ahjz2g4bbkjl5mx2fs2w2oq4

An automated pipeline for constructing personalized virtual brains from multimodal neuroimaging data

Michael Schirner, Simon Rothmeier, Viktor K. Jirsa, Anthony Randal McIntosh, Petra Ritter
2015 NeuroImage  
With the pipeline we also introduce novel ways of estimating the transmission strengths of fiber tracts in whole-brain structural connectivity (SC) networks and compare the outcomes of different tractography  ...  In order to quantify the robustness of the connectome extraction part of the pipeline we computed several metrics that quantify its rescan reliability and compared them to other tractography approaches  ...  Acknowledgments The authors acknowledge the support of the German Ministry of Education and Research (Bernstein Focus State Dependencies of Learning 01GQ0971) to PR, the James S.  ... 
doi:10.1016/j.neuroimage.2015.03.055 pmid:25837600 fatcat:lfpdxcvh7ndwld4synfmbqvsym

Kernel regression estimation of fiber orientation mixtures in diffusion MRI

Ryan P. Cabeen, Mark E. Bastin, David H. Laidlaw
2016 NeuroImage  
We then demonstrate the creation of a multi-fiber tractography atlas from a population of 80 human subjects.  ...  fronto-parietal connections of the superior longitudinal fasciculus I, II, and III.  ...  Acknowledgments We would like to thank the anonymous reviewers for their constructive feedback.  ... 
doi:10.1016/j.neuroimage.2015.11.061 pmid:26691524 pmcid:PMC4870009 fatcat:eaqwn6vipjb6df4piaeuv37kdq
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