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Whole Brain Magnetic Resonance Image Atlases: A Systematic Review of Existing Atlases and Caveats for Use in Population Imaging

David Alexander Dickie, Susan D. Shenkin, Devasuda Anblagan, Juyoung Lee, Manuel Blesa Cabez, David Rodriguez, James P. Boardman, Adam Waldman, Dominic E. Job, Joanna M. Wardlaw
2017 Frontiers in Neuroinformatics  
2017) Whole brain magnetic resonance image atlases: a systematic review of existing atlases and caveats for use in population imaging. Front. Neuroinform. 11:1.  ...  Atlases have important applications in research, e.g., as registration and 4 segmentation targets to underpin image analysis in population imaging studies, and 5  ...  It is for this reason that we 26 undertook the following systematic review to identify, collate and describe existing 27 structural MRI brain atlases. 28 29 In this review we aim to summarise the currently  ... 
doi:10.3389/fninf.2017.00001 pmid:28154532 pmcid:PMC5244468 fatcat:axxm6m7svnduflvtdvtt7q7tkm

Processing of structural neuroimaging data in young children: Bridging the gap between current practice and state-of-the-art methods

Thanh Vân Phan, Dirk Smeets, Joel B. Talcott, Maaike Vandermosten
2017 Developmental Cognitive Neuroscience  
These methods are mainly related to the use of age-specific or 4D brain atlases, improved methods for quantifying and optimizing image quality, and provision for registration of developmental data obtained  ...  Pediatric studies based on Magnetic Resonance Imaging (MRI) over this age range have recently become more frequent, with the advantage of providing in vivo and non-invasive high-resolution images of the  ...  Other than using existing brain atlases, there are also automatic tools for building population-specific atlases.  ... 
doi:10.1016/j.dcn.2017.08.009 pmid:29033222 pmcid:PMC6969273 fatcat:nadoyjiegbajpgz23q52ihx3ry

Benchmarking functional connectome-based predictive models for resting-state fMRI

Kamalaker Dadi, Mehdi Rahim, Alexandre Abraham, Darya Chyzhyk, Michael Milham, Bertrand Thirion, Gaël Varoquaux
2019 NeuroImage  
We systematically study the prediction performances of models in 6 different cohorts and a total of 2000 individuals, encompassing neuro-degenerative (Alzheimer's, Post-traumatic stress disorder), neuro-psychiatric  ...  Our benchmarks summarize more than 240 different pipelines and outline modeling choices that show consistent prediction performances in spite of variations in the populations and sites.  ...  Introduction Resting-state functional Magnetic Resonance Imaging (rest-fMRI), based on the analysis of brain activity without specific task, has become a tool of choice to probe human brain function in  ... 
doi:10.1016/j.neuroimage.2019.02.062 pmid:30836146 fatcat:gyc6jxopp5gihn3alwgrf7zcge

A Hybrid High-Resolution Anatomical MRI Atlas with Sub-parcellation of Cortical Gyri using Resting fMRI [article]

Anand A Joshi, Soyoung Choi, Minqi Chong, Gaurav Sonkar, Jorge Gonzalez-Martinez, Dileep Nair, Jessica Wisnowski, Justin Haldar, David Shattuck, Hanna Damasio, Richard M Leahy
2020 bioRxiv   pre-print
Brain atlases provide reference parcellations of the brain that are essential for population neuroimaging studies.  ...  A single-subject, high-resolution T1-weighted image was acquired and was then processed by an expert neuroanatomist using semi-automated methods in BrainSuite.  ...  The HCP data used in this work were provided by the Human Connectome Project, WU-Minn Consortium (Principal Investigators: David Van Essen and Kamil Ugurbil; 1U54MH091657) funded by the 16 NIH Institutes  ... 
doi:10.1101/2020.09.12.294322 fatcat:llicth3vwndjrn36py2cdq7osa

Bringing Anatomical Information into Neuronal Network Models [article]

Sacha Jennifer van Albada, Aitor Morales-Gregorio, Timo Dickscheid, Alexandros Goulas, Rembrandt Bakker, Sebastian Bludau, Günther Palm, Claus-Christian Hilgetag, Markus Diesmann
2020 arXiv   pre-print
Given the still existing need for modelers to navigate a complex data landscape full of holes and stumbling blocks, it is vital that the field of neuroanatomy is moving toward increasingly systematic data  ...  It is instructive, and in certain cases necessary, to use organizational principles that link the plethora of data within a unifying framework where regularities of brain structure can be exploited to  ...  diffusion tensor imaging (DTI), a magnetic resonance imaging method that detects axon tracts.  ... 
arXiv:2007.00031v2 fatcat:lud5jok65re5rhecxjtsis3x5u

Is it time to re-prioritize neuroimaging databases and digital repositories?

John Darrell Van Horn, Arthur W. Toga
2009 NeuroImage  
In this article, we review the progress made in neuroimaging databases, their role in data sharing, data management, potential for the construction of brain atlases, recording data provenance, and value  ...  We feature the LONI IDA as an example of an archive being used as a source for brain atlas workflow construction, list several instances of other successful uses of image databases, and comment on archive  ...  Acknowledgments The authors express their gratitude to our colleagues in the Laboratory of Neuro Imaging (LONI) and those collaborators at our partner laboratories who utilize LONI database and computational  ... 
doi:10.1016/j.neuroimage.2009.03.086 pmid:19371790 pmcid:PMC2754579 fatcat:qxjviytffrexbf7wrn2xfkrns4

Resting-State Functional Connectivity in the Infant Brain: Methods, Pitfalls, and Potentiality

Chandler R. L. Mongerson, Russell W. Jennings, David Borsook, Lino Becerra, Dusica Bajic
2017 Frontiers in Pediatrics  
SCA is a model-based, hypothesis-driven approach used to measure BOLD response in an anatomically defined seed region-of-interest (ROI), ultimately generating whole-brain  ...  Despite distinct analytical approaches, both techniques result in identification of comparable RSNs (41).  ...  FIGURe 4 | 4 Registration of functional magnetic resonance imaging (fMRI) image to native space. Figure illustrates examples of poor (A and A′) 8) .  ... 
doi:10.3389/fped.2017.00159 pmid:28856131 pmcid:PMC5557740 fatcat:lzs7kc32s5a6nnvxycgi6rhege

Temporal Dynamics of Brain Anatomy

Arthur W. Toga, Paul M. Thompson
2003 Annual Review of Biomedical Engineering  
The resulting four-dimensional (4D) maps of brain anatomy are warehoused in population-based brain atlases.  ...  We review a variety of mathematical and computational approaches to detect structural brain change with unprecedented sensitivity, both spatially and temporally.  ...  ., Detection of subtle changes to the brain in infants and children using subvoxel registration and subtraction of serial magnetic resonance images. Am J Neurorad, 18, 829, 1997.  ... 
doi:10.1146/annurev.bioeng.5.040202.121611 pmid:14527311 fatcat:apd6t7esxjcqxgqkq6sphz7zcu

Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain

Kyra T. Newmaster, Fae A. Kronman, Yuan-ting Wu, Yongsoo Kim
2022 Frontiers in Neuroanatomy  
Here we review key technical considerations for implementing a brain mapping pipeline using the mouse brain as a primary model system.  ...  Remarkable advances in neuroscience techniques enable labeling and imaging of these individual cell types and their interactions throughout intact mammalian brains at a cellular resolution allowing neuroscientists  ...  High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice.  ... 
doi:10.3389/fnana.2021.787601 pmid:35095432 pmcid:PMC8794814 fatcat:mzoj2dst6nagnh2rn56ghy64zm

Multimodal population brain imaging in the UK Biobank prospective epidemiological study

Karla L Miller, Fidel Alfaro-Almagro, Neal K Bangerter, David L Thomas, Essa Yacoub, Junqian Xu, Andreas J Bartsch, Saad Jbabdi, Stamatios N Sotiropoulos, Jesper L R Andersson, Ludovica Griffanti, Gwenaëlle Douaud (+9 others)
2016 Nature Neuroscience  
For example, magnetic resonance imaging (MRI) has demonstrated altered brain activity associated with the APOE genotype decades in advance of symptoms associated with Alzheimer's disease 1 , and conversion  ...  Image-based measures of brain structure and function may evolve in a complex way throughout aging and progression of neuropathology.  ...  We are very grateful for additional input into the imaging protocol and image processing pipelines from the following:  ... 
doi:10.1038/nn.4393 pmid:27643430 pmcid:PMC5086094 fatcat:3h3qzvoptnewpewaqgkchhx3kq

A Systematic Approach to Dissection of the Equine Brain–Evaluation of a Species-Adapted Protocol for Beginners and Experts

Maya-Lena Bitschi, Zoltán Bagó, Marco Rosati, Sven Reese, Lutz S. Goehring, Kaspar Matiasek
2020 Frontiers in Neuroanatomy  
Hence, we developed a species-specific slice protocol for whole brain vs. hemispheric dissection and tested its applicability and practicability in the field, as well as its neuroanatomical accuracy and  ...  Introduction of new imaging modalities for the equine brain have refocused attention on the horse as a natural model for ethological, neuroanatomical, and neuroscientific investigations.  ...  Magnetic resonance imaging of a brain abscess in a 10-month-old filly. Vet. Radiol.  ... 
doi:10.3389/fnana.2020.614929 pmid:33390909 pmcid:PMC7775367 fatcat:74zsnxm3l5fmfde5lq67txc23a

Learning and comparing functional connectomes across subjects

Gaël Varoquaux, R. Cameron Craddock
2013 NeuroImage  
Functional connectomes capture brain interactions via synchronized fluctuations in the functional magnetic resonance imaging signal.  ...  Methods of estimating functional connectomes from the imaging signal have undergone rapid developments and the literature is full of diverse strategies for comparing them.  ...  The authors would like to thank the anonymous reviewers for their suggestions, which improved the manuscript.  ... 
doi:10.1016/j.neuroimage.2013.04.007 pmid:23583357 fatcat:aqvged4fgffclo2rzp6afzrewa

Deep learning applications for the classification of psychiatric disorders using neuroimaging data: systematic review and meta-analysis [article]

Mirjam Quaak, Laurens van de Mortel, Rajat Mani Thomas, Guido van Wingen
2020 medRxiv   pre-print
Only sixteen studies could be included in a meta-regression to quantitatively compare DL and ML performance.  ...  This review provides an overview of the different DL applications within psychiatry and compares DL model accuracy to conventional machine learning (ML).  ...  A., Sharifi, A. & Pedram, M. M. Diagnosis of Autism Spectrum Disorders in Young Children Based on Resting-State Functional Magnetic Resonance Imaging Data Using Convolutional Neural Networks. J.  ... 
doi:10.1101/2020.06.12.20129130 fatcat:4uppkakshnedhgdvdxipzepbbq

Functional connectivity MRI in infants: Exploration of the functional organization of the developing brain

Christopher D. Smyser, Abraham Z. Snyder, Jeffrey J. Neil
2011 NeuroImage  
Functional connectivity magnetic resonance imaging (fcMRI) utilizes spontaneous, low frequency (< 0.1 Hz), coherent fluctuations in blood oxygen level dependent (BOLD) signal to identify networks of functional  ...  Due to the intrinsic characteristics of its image acquisition and analysis, fcMRI offers a novel neuroimaging approach well suited to investigation of infants.  ...  The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1016/j.neuroimage.2011.02.073 pmid:21376813 pmcid:PMC3089442 fatcat:jde4ndiqwfgpfg7ivjmbvicufu

Connectome-based lesion-symptom mapping (CLSM): A novel approach to map neurological function

Ezequiel Gleichgerrcht, Julius Fridriksson, Chris Rorden, Leonardo Bonilha
2017 NeuroImage: Clinical  
Whole-brain CLSM therefore has the potential to identify key connections for behavior independently of a priori assumptions with applicability across a broad spectrum of neurological and psychiatric diseases  ...  Initial limitations with this approach were largely overcome by voxel-based lesion-symptom mapping (VLSM), a method introduced in the early 2000s, which allows for a whole-brain approach to study the association  ...  There were initially some caveats that limited the applicability of lesion studies in a more systematic fashion.  ... 
doi:10.1016/j.nicl.2017.08.018 pmid:28884073 pmcid:PMC5581860 fatcat:of6mhraefvhvldhpqdx7qnwpde
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