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Synergy of Image Analysis for Animal and Human Neuroimaging Supports Translational Research on Drug Abuse

Guido Gerig, Ipek Oguz, Sylvain Gouttard, Joohwi Lee, Hongyu An, Weili Lin, Matthew McMurray, Karen Grewen, Josephine Johns, Martin Andreas Styner
2011 Frontiers in Psychiatry  
For this purpose, we developed a synergistic, parallel approach to imaging and image analysis for the human and the rodent branch of our study.  ...  We propose the use of non-invasive neuroimaging to study developmental brain structural and white matter pathway abnormalities via sMRI and DTI, as advanced MR imaging technology is readily available and  ...  Furthermore, we would like to thanks Fulton Crews, Allan Johnson and Sheryl Moy for their insightful discussion on the topic of cross-species studies and small animal imaging.  ... 
doi:10.3389/fpsyt.2011.00053 pmid:22013425 pmcid:PMC3189614 fatcat:ljxxmkx6orazbivhuuclyjnchq

Multi-contrast human neonatal brain atlas: Application to normal neonate development analysis

Kenichi Oishi, Susumu Mori, Pamela K. Donohue, Thomas Ernst, Lynn Anderson, Steven Buchthal, Andreia Faria, Hangyi Jiang, Xin Li, Michael I. Miller, Peter C.M. van Zijl, Linda Chang
2011 NeuroImage  
Diffusion tensor imaging (DTI), which provides rich and quantitative anatomical contrast in neonate brains, is an ideal technology for normalization-based neonatal brain analysis.  ...  Normalization-based image analysis is one of the most effective methods for image quantification and statistical comparison.  ...  Acknowledgments The authors thank Dr. Jon Skranes of the Norwegian University of Science and Technology for helpful suggestions, and Ms. Mary McAllister for help with manuscript editing.  ... 
doi:10.1016/j.neuroimage.2011.01.051 pmid:21276861 pmcid:PMC3066278 fatcat:l46ls6c3obfkfguxvkdr3hxmsm

UNC-Emory Infant Atlases for Macaque Brain Image Analysis: Postnatal Brain Development through 12 Months

Yundi Shi, Francois Budin, Eva Yapuncich, Ashley Rumple, Jeffrey T. Young, Christa Payne, Xiaodong Zhang, Xiaoping Hu, Jodi Godfrey, Brittany Howell, Mar M. Sanchez, Martin A. Styner
2017 Frontiers in Neuroscience  
We present here a set of novel computation atlases for structural MRI and Diffusion Tensor Imaging as crucial resource for the analysis of MRI data from non-human primate rhesus monkey (Macaca mulatta)  ...  Probabilistic spatial prior definitions for the major tissue classes were trained on each atlas with expert manual segmentations.  ...  The YNPRC is fully accredited by the Association for the Assessment and Accreditation of Laboratory Care, International.  ... 
doi:10.3389/fnins.2016.00617 pmid:28119564 pmcid:PMC5222830 fatcat:36c6zddzbrhh7hscvje2bpkszi

A Bayesian approach to the creation of a study-customized neonatal brain atlas

Yajing Zhang, Linda Chang, Can Ceritoglu, Jon Skranes, Thomas Ernst, Susumu Mori, Michael I. Miller, Kenichi Oishi
2014 NeuroImage  
Atlas-based image analysis (ABA), in which an anatomical "parcellation map" is used for parcelby-parcel image quantification, is widely used to analyze anatomical and functional changes related to brain  ...  The resultant "study-customized" T1weighted and diffusion tensor imaging (DTI) template, with three-dimensional anatomical parcellation that defined 122 brain regions, was compared with the JHU-neonate-SS  ...  Steven Buchthal) who assisted with the data collection and data transfer. We also thank Ms. Mary McAllister for help with manuscript editing.  ... 
doi:10.1016/j.neuroimage.2014.07.001 pmid:25026155 pmcid:PMC4165785 fatcat:xv2w5avgmbfnlfota4mvhpfzve

Diffusion Tensor Based White Matter Tract Atlases for Pediatric Populations

Sarah J. Short, Dae Kun Jang, Rachel J. Steiner, Rebecca L. Stephens, Jessica B. Girault, Martin Styner, John H. Gilmore
2022 Frontiers in Neuroscience  
For this reason, appropriate image processing of infant MR imaging requires the use of age-specific reference atlases.  ...  Via the UNC-NAMIC DTI Fiber Analysis Framework, our pediatric atlases provide the computational templates necessary for the fully automatic analysis of infant DTI data.  ...  A total of 47 tract segments were obtained for the neonatal DTI atlas (see Lee et al., 2015) .  ... 
doi:10.3389/fnins.2022.806268 pmid:35401073 pmcid:PMC8985548 fatcat:q5qc2yamrfg43bmdhjj3zhfiyu

Spatio-temporal analysis of early brain development

Neda Sadeghi, Marcel Prastawa, John H. Gilmore, Weili Lin, Guido Gerig
2010 2010 Conference Record of the Forty Fourth Asilomar Conference on Signals, Systems and Computers  
We focus on normal brain development as is observed in the multimodal longitudinal MRI/DTI data of neonates to two years of age.  ...  Analysis of human brain development is a crucial step for improved understanding of neurodevelopmental disorders.  ...  adult brain to infant brain and at the same time to register the white matter atlas to the infant images.  ... 
doi:10.1109/acssc.2010.5757670 pmid:25328368 pmcid:PMC4199456 fatcat:o32ze72xozhwvftdhiubbpa2gu

Baby brain atlases

Kenichi Oishi, Linda Chang, Hao Huang
2018 NeuroImage  
"Brain atlas" in this review refers to a 3D-brain image with a set of reference labels, such as a parcellation map, as the anatomical reference that guides the mapping of the brain.  ...  The potential use of disease-based atlases to characterize clinically relevant information, such as clinical labels, in addition to conventional anatomical labels, is also discussed.  ...  Mary McAllister for her help with manuscript editing.  ... 
doi:10.1016/j.neuroimage.2018.04.003 pmid:29625234 pmcid:PMC6170732 fatcat:gnrvdzatbba6dmnnckjoduaigi

Computational neuroanatomy of baby brains: A review

Gang Li, Li Wang, Pew-Thian Yap, Fan Wang, Zhengwang Wu, Yu Meng, Pei Dong, Jaeil Kim, Feng Shi, Islem Rekik, Weili Lin, Dinggang Shen
2018 NeuroImage  
Consequently, the existing computational tools developed typically for adult brains are not suitable for infant brain MR image processing.  ...  The increasing availability of non-invasive infant brain MR images provides unprecedented opportunities for accurate and reliable charting of dynamic early brain developmental trajectories in understanding  ...  Atlas based approaches Most of the techniques for infant brain tissue segmentation rely on pre-segmented brain atlases (please refer to Section 3.4 for detailed introduction of atlases).  ... 
doi:10.1016/j.neuroimage.2018.03.042 pmid:29574033 pmcid:PMC6150852 fatcat:w2o27wt5afhktd7zoophmhnmi4

Fetal brain growth portrayed by a spatiotemporal diffusion tensor MRI atlas computed from in utero images

Shadab Khan, Lana Vasung, Bahram Marami, Caitlin K. Rollins, Onur Afacan, Cynthia M. Ortinau, Edward Yang, Simon K. Warfield, Ali Gholipour
2018 NeuroImage  
This paper presents the first DTI atlas of the fetal brain computed from in utero diffusion-weighted images.  ...  These results and analyses show that our DTI atlas of the fetal brain is useful for reliable detection of major neuronal fiber bundle pathways and for characterization of the fetal brain reorganization  ...  This was done through deformable registration between T2w and DTI atlases at each GA, and labels were propagated using atlas-based segmentation .  ... 
doi:10.1016/j.neuroimage.2018.08.030 pmid:30172006 pmcid:PMC6289660 fatcat:hv5wyrfqv5g7ba7xj6r4uqq564

Automatic Atlas-Based Segmentation of Brain White Matter in Neonates at Risk for Neurodevelopmental Disorders [chapter]

L. Fonseca, C. van Pul, N. Lori, R. van den Boom, P. Andriessen, J. Buijs, A. Vilanova
2017 Mathematics and Visualization  
3 This work was developed in collaboration with: ABSTRACT Maturation degree of anatomical white matter (WM) structures at the brain can constitute a biomarker for prediction of neurodevelopmental disorders  ...  Therefore, we propose a new in-vivo and non-invasive global analysis of the WM patterns at the brain: we perform an  ...  We implemented an automatic pipeline for atlas-based segmentation of WM diffusion tensor imaging (DTI) tractography.  ... 
doi:10.1007/978-3-319-61358-1_15 fatcat:2k46uyhudvfm7aq3fan3eog5r4

Advanced Neonatal NeuroMRI

Kenichi Oishi, Andreia V. Faria, Susumu Mori
2012 Magnetic Resonance Imaging Clinics of North America  
Based on the multicontrast data, a neonate brain atlas was created, which allows automated segmentation of neonate brain MR images.  ...  The accuracy, advantages, and potential pitfalls of this atlas-based segmentation approach are discussed.  ...  This publication was made possible by grants from the National Institutes of Health (R21AG033774, P41RR015241, U24RR021382, P01EB001955, R01AG20012, and R01HD065955), and from the National Center for Research  ... 
doi:10.1016/j.mric.2011.08.009 pmid:22118594 pmcid:PMC3256737 fatcat:s7kw3ccoyrexbbaunl2okb7teq

Advancing Fetal Brain MRI: Targets for the Future

Catherine Limperopoulos, Cedric Clouchoux
2009 Seminars in Perinatology  
Fetal MRI is becoming an increasingly powerful imaging tool for studying brain development in vivo.  ...  Until recently, the application of advanced magnetic resonance imaging techniques was limited by motion in the nonsedated fetus.  ...  Development of an In Vivo 3-D Fetal MRI Brain Atlas Although brain atlases are widely used for image processing in adult MRI, no such atlas is currently available for the fetal brain.  ... 
doi:10.1053/j.semperi.2009.04.002 pmid:19631089 fatcat:nwbuhdbsa5bnhbsp7m2vrpw57y

Infant Brain Atlases from Neonates to 1- and 2-Year-Olds

Feng Shi, Pew-Thian Yap, Guorong Wu, Hongjun Jia, John H. Gilmore, Weili Lin, Dinggang Shen, Hitoshi Okazawa
2011 PLoS ONE  
State-of-the-art MR image segmentation and registration techniques were employed, to construct which include the templates (grayscale average images), tissue probability maps (TPMs), and brain parcellation  ...  Experiments of typical infant applications validated that the proposed atlas outperformed other atlases and is hence very useful for infant-related studies.  ...  In response to this, population-based atlases were introduced, e.g., the MNI305 [8] and ICBM152 brain atlases [9] , which were obtained by averaging the anatomical magnetic resonance (MR) images of  ... 
doi:10.1371/journal.pone.0018746 pmid:21533194 pmcid:PMC3077403 fatcat:xuw5l6g3xfhfvafsez2cmzxamm

Mapping the critical gestational age at birth that alters brain development in preterm-born infants using multi-modal MRI

Dan Wu, Linda Chang, Kentaro Akazawa, Kumiko Oishi, Jon Skranes, Thomas Ernst, Kenichi Oishi
2017 NeuroImage  
The analysis was performed in 126 regions across the whole brain using an atlas-based image quantification approach to investigate the spatial pattern of the critical GAB.  ...  In order to investigate the critical gestational age at birth (GAB) that alters the developmental trajectory of gray and white matter structures in the brain, we investigated diffusion tensor and quantitative  ...  The contents of this paper are solely the responsibility of the authors and do not necessarily represent the official view of NIH or the Central Norway Regional Health Authority.  ... 
doi:10.1016/j.neuroimage.2017.01.046 pmid:28111189 pmcid:PMC5367973 fatcat:gubbsuffhjeqjepmw7wbkktdkm

Effects of prenatal cocaine exposure on early postnatal rodent brain structure and diffusion properties

Matthew S. McMurray, Ipek Oguz, Ashley M. Rumple, Beatriz Paniagua, Martin A. Styner, Josephine M. Johns
2015 Neurotoxicology and Teratology  
tensor imaging; and 2) to determine the feasibility of rodent in vivo neuroimaging for usage in longitudinal studies of developmental disorders.  ...  Volume and diffusion properties in whole brain as well as specific regions of interest were then assessed from the resulting images.  ...  Allan Johnson and Gary Cofey at the Duke Center for in Vivo Microscopy for their assistance in MR histology acquisition and the usage of their equipment.  ... 
doi:10.1016/j.ntt.2014.11.007 pmid:25459688 pmcid:PMC4291294 fatcat:wyfritz4gjdcln7eu5gysmqbka
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