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Does function fit structure? A ground truth for non-invasive neuroimaging

Claire Stevenson, Matthew Brookes, José David López, Luzia Troebinger, Jeremie Mattout, William Penny, Peter Morris, Arjan Hillebrand, Richard Henson, Gareth Barnes
2014 NeuroImage  
There are now a number of non-invasive methods to image human brain function in-vivo.  ...  However, the accuracy of these images remains unknown and can currently only be estimated through the use of invasive recordings to generate a functional ground truth.  ...  Acknowledgments The Wellcome Trust Centre for Neuroimaging is funded by a strategic award from the Wellcome Trust.  ... 
doi:10.1016/j.neuroimage.2014.02.033 pmid:24636880 pmcid:PMC4073649 fatcat:tjtnhcetezcxjjkjiuolzcsftq

Do We Need a Human post mortem Whole-Brain Anatomical Ground Truth in in vivo Magnetic Resonance Imaging?

Anneke Alkemade, Josephine M. Groot, Birte U. Forstmann
2018 Frontiers in Neuroanatomy  
Non-invasive in vivo neuroimaging techniques provide a wide array of possibilities to study human brain function.  ...  Its definition requires a system in which non-invasive approaches can be validated using invasive methods of investigation.  ...  Non-invasive in vivo neuroimaging techniques provide a wide array of possibilities to study human brain function.  ... 
doi:10.3389/fnana.2018.00110 pmid:30568580 pmcid:PMC6290065 fatcat:qnfyxuhk5rhl5hf6u3www3aawu

The CONNECT project: Combining macro- and micro-structure

Yaniv Assaf, Daniel C. Alexander, Derek K. Jones, Albero Bizzi, Tim E.J. Behrens, Chris A. Clark, Yoram Cohen, Tim B. Dyrby, Petra S. Huppi, Thomas R. Knoesche, Denis LeBihan, Geoff J.M. Parker (+1 others)
2013 NeuroImage  
The CONNECT (Consortium Of Neuroimagers for the Non-invasive Exploration of brain Connectivity and Tracts) project aimed to combine tractography and micro-structural measures of the living human brain  ...  In parallel to the development of tractography, additional diffusion MRI based frameworks (CHARMED, AxCaliber, ActiveAx) were developed enabling the extraction of a multitude of micro-structural parameters  ...  The EU CONNECT consortium (Consortium Of Neuroimagers for the Non-invasive Exploration of brain Connectivity and Tracts) ( set out to explore if micro-structural measures of the white  ... 
doi:10.1016/j.neuroimage.2013.05.055 pmid:23727318 fatcat:2hlmflqpmnc3piswo6mybzai64

Characterization of network structure in stereoEEG data using consensus-based partial coherence

Marije Ter Wal, Pasquale Cardellicchio, Giorgio LoRusso, Veronica Pelliccia, Pietro Avanzini, Guy A. Orban, Paul H.E. Tiesinga
2018 NeuroImage  
A B S T R A C T Coherence is a widely used measure to determine the frequency-resolved functional connectivity between pairs of recording sites, but this measure is confounded by shared inputs to the pair  ...  For instance, calculating the partial coherence using a pseudoinverse method produces a high number of false positives when it is applied to a large number of channels.  ...  Introduction A central task in neuroimaging is the identification of connections in the brain, either structural, i.e. mediated by direct axonal connections, or functional, i.e. related to the task, context  ... 
doi:10.1016/j.neuroimage.2018.06.011 pmid:29885486 fatcat:d2qomwn2wjgb5pytxf43yy2ube

Network Structure Inference, A Survey: Motivations, Methods, and Applications [article]

Ivan Brugere and Brian Gallagher and Tanya Y. Berger-Wolf
2018 arXiv   pre-print
Existing approaches for inferring networks from data are found across many application domains and use specialized knowledge to infer and measure the quality of inferred network for a specific task or  ...  In most cases, relationship between nodes are not directly observable and must be inferred: does one gene regulate the expression of another?  ...  However, the fidelity of this model in terms of fitting error, or reconstruction against a partial ground truth network does not measure the network's usefulness for answering questions on the original  ... 
arXiv:1610.00782v4 fatcat:neu7tyamijhixbjv6rasksyasu

Diffusion MRI at 25: Exploring brain tissue structure and function

Denis Le Bihan, Heidi Johansen-Berg
2012 NeuroImage  
The ability to visualize anatomical connections between different parts of the brain, non-invasively and on an individual basis, has emerged as a major breakthrough for neurosciences.  ...  It is also rapidly becoming a standard for white matter disorders, as diffusion tensor imaging (DTI) can reveal abnormalities in white matter fiber structure and provide outstanding maps of brain connectivity  ...  Acknowledgments HJB is grateful for support from the Wellcome Trust and the NIH Human Connectome Project.  ... 
doi:10.1016/j.neuroimage.2011.11.006 pmid:22120012 pmcid:PMC3683822 fatcat:khrtpjwmtbb7tfkdrcoph2o3om

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
Over the last two decades, the study of brain connectivity using dMRI tractography has played a prominent role in the neuroimaging research landscape.  ...  In this paper, we provide a high-level overview of how tractography is used to enable quantitative analysis of the brain's structural connectivity in health and disease.  ...  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

A Framework for Inter-Subject Prediction of Functional Connectivity From Structural Networks

Fani Deligianni, Gael Varoquaux, Bertrand Thirion, David J. Sharp, Christian Ledig, Robert Leech, Daniel Rueckert
2013 IEEE Transactions on Medical Imaging  
Magnetic Resonance Imaging (MRI) is central to the study of brain networks because it allows non-invasive, in-vivo measures of both functional and structural connections.  ...  Although, there is a profound lack of ground truth data, there are numerous functional studies that draw conclusions about functional and structural connectivity among regions implicated in well known  ... 
doi:10.1109/tmi.2013.2276916 pmid:23934663 fatcat:26fl7luy6refzfjywvuc3edzvu

Integrated resource for functional and structural connectivity of the marmoset brain [article]

Xiaoguang Tian, Yuyuan Chen, Piotr Majka, Diego Szczupak, Yonatan Sanz-Perl, Cecil Chern-Chyi Yen, Chuanjun Tong, Kun Song, Haiteng Jiang, Daniel Glen, Gustavo Deco, Marcello G. P. Rosa (+3 others)
2021 bioRxiv   pre-print
While resources for studying structural connectivity of non-human primate marmoset brains already exist, their integration with functional connectivity data has remained unavailable.  ...  The comprehensive integration of structural and functional connectivity data is required for the accurate modeling of brain functions.  ...  "ground truth" data from neuronal tracing (Buckner and Margulies, 2019) .  ... 
doi:10.1101/2021.11.12.468389 fatcat:vqv534qnyzewrmvvjx4zadpyfa

The NonHuman Primate Neuroimaging & Neuroanatomy Project

Takuya Hayashi, Yujie Hou, Matthew F Glasser, Joonas A Autio, Kenneth Knoblauch, Miho Inoue-Murayama, Tim Coalson, Essa Yacoub, Stephen Smith, Henry Kennedy, David C Van Essen
2021 NeuroImage  
Such efforts depend upon the accuracy of non-invasive brain imaging measures. However, 'ground truth' validation of connectivity using invasive tracers is not feasible in humans.  ...  We are acquiring high-resolution structural, functional, and diffusion MRI data together with behavioral measures from over 100 individual macaques and marmosets in order to generate non-invasive measures  ...  Acknowledgements This study is supported by a grant Brain/MINDS -beyond from References under revision of this special issue of NeuroImage Autio, J.A., Zhu, Q., Li, X., Glasser, M.F., Schwiedrzik,  ... 
doi:10.1016/j.neuroimage.2021.117726 pmid:33484849 pmcid:PMC8079967 fatcat:tfv3sm6xpjfnfj2uarpqwnyc5u

The NonHuman Primate Neuroimaging Neuroanatomy Project [article]

Takuya Hayashi, Yujie Hou, Matthew F Glasser, Joonas A Autio, Kenneth Knoblauch, Miho Inoue-Murayama, Tim Coalson, Essa Yacoub, Stephen Smith, Henry Kennedy, David C Van Essen
2021 arXiv   pre-print
However, ground truth validation of connectivity using invasive tracers is not feasible in humans.  ...  Multi-modal neuroimaging projects are advancing our understanding of human brain architecture, function, connectivity using high-quality non-invasive data from many subjects.  ...  A major opportunity for NHP research is to provide a platform for using quantitative measures of 'ground truth' tracer-based connectivity to evaluate neuroimaging-based estimates of structural connectivity  ... 
arXiv:2010.00308v3 fatcat:xqccnaz2hzcs7pqedcutkvktea

Machine Learning Methods for Diagnosing Autism Spectrum Disorder and Attention- Deficit/Hyperactivity Disorder Using Functional and Structural MRI: A Survey

Taban Eslami, Fahad Almuqhim, Joseph S. Raiker, Fahad Saeed
2021 Frontiers in Neuroinformatics  
directions for the field.  ...  We envision a future where the diagnosis of ASD, ADHD, and other mental disorders is accomplished, and quantified using imaging techniques, such as MRI, and machine-learning models.  ...  Finally, the prediction error is calculated in the output layer by applying a loss function to the predicted value and ground truth.  ... 
doi:10.3389/fninf.2020.575999 pmid:33551784 pmcid:PMC7855595 fatcat:3iqw3aeb6fhrxnoqlq3yuqj7vy

Ventralis intermedius nucleus anatomical variability assessment by MRI structural connectivity [article]

Francisca Ferreira, John Ashburner, Harith Akram, Ludvic Zrinzo, Hui Zhang, Christian Lambert
2020 biorxiv/medrxiv   pre-print
Lateralisation of cerebellar functions, such as speech, may contribute to the observed asymmetry.  ...  efficacy and reduce side-effects of thalamic surgery for tremor.  ...  Furthermore, it is possible that histological ground truth does not necessarily need to perfectly match when the aim is to generate targeting maps to optimise functional surgical outcomes.  ... 
doi:10.1101/2020.08.05.236679 fatcat:wbecofeypbbdvmuwcikvjbnvtq

Validation of structural brain connectivity networks: The impact of scanning parameters

Karen S. Ambrosen, Simon F. Eskildsen, Max Hinne, Kristine Krug, Henrik Lundell, Mikkel N. Schmidt, Marcel A.J. van Gerven, Morten Mørup, Tim B. Dyrby
2019 NeuroImage  
As gold standard we use the connectivity matrix obtained invasively with histological tracers by Markov et al. (2014).  ...  Evaluation of the structural connectivity (SC) of the brain based on tractography has mainly focused on the choice of diffusion model, tractography algorithm, and their respective parameter settings.  ...  Acknowledgement We wish to thank Thomas Kn€ osche, MPI in Leipzig for good discussions in relation to SNR and image resolution.  ... 
doi:10.1016/j.neuroimage.2019.116207 pmid:31539592 fatcat:fplus64mfbczbob6q7zulw6vta

Quantitative Evaluation of Intensity Inhomogeneity Correction Methods for Structural MR Brain Images

Marco Ganzetti, Nicole Wenderoth, Dante Mantini
2015 Neuroinformatics  
Accordingly, we used enhanced configurations for a more objective comparison between methods.  ...  Here we tackled the problem of objectively comparing INU correction techniques for T1-weighted images, which are the most commonly used in structural brain imaging.  ...  Acknowledgments DM holds a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (101253/Z/13/Z).  ... 
doi:10.1007/s12021-015-9277-2 pmid:26306865 pmcid:PMC4706843 fatcat:i7djtxasdncfhi4sbvqsvzqvoy
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