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Population-averaged diffusion tensor imaging atlas of the Sprague Dawley rat brain

Jelle Veraart, Trygve B. Leergaard, Bjørnar T. Antonsen, Wim Van Hecke, Ines Blockx, Ben Jeurissen, Yi Jiang, Annemie Van der Linden, G. Allan Johnson, Marleen Verhoye, Jan Sijbers
2011 NeuroImage  
To facilitate analysis and assignment of location in rat brain neuroimaging investigations, we have developed a population-averaged three-dimensional DTI atlas of the normal adult Sprague Dawley rat brain  ...  The atlas is constructed from high resolution ex vivo DTI images, which were nonlinearly warped into a population-averaged in vivo brain template.  ...  In vivo data were acquired at the bio-imaging lab (University of Antwerp).  ... 
doi:10.1016/j.neuroimage.2011.06.063 pmid:21749925 pmcid:PMC3454512 fatcat:cwtm2xte45abddig3ra2em2xxy

Automatic skull-stripping of rat MRI/DTI scans and atlas building

Ipek Oguz, Joohwi Lee, Francois Budin, Ashley Rumple, Matthew McMurray, Cindy Ehlers, Fulton Crews, Josephine Johns, Martin Styner, David R. Haynor, Benoit M. Dawant
2011 Medical Imaging 2011: Image Processing  
3D Magnetic Resonance (MR) and Diffusion Tensor Imaging (DTI) have become important noninvasive tools for the study of animal models of brain development and neuropathologies.  ...  We also demonstrate how to either modify an external atlas or to build an atlas from the population itself to present a self-contained approach.  ...  ACKNOWLEDGEMENTS This research was funded by the NIH Program Project IP01DA022446-02, the UNC Neurodevelopmental Disorders Research Center HD 03110, the NIH STTR grant R41 NS059095, the NIH grant RC1AA019211  ... 
doi:10.1117/12.878405 pmid:21909227 pmcid:PMC3168953 dblp:conf/miip/OguzLBRMECJS11 fatcat:2ixnibgz6fh2bfvgfkrhqfluoa

3-Dimensional Diffusion Tensor Imaging (DTI) Atlas of the Rat Brain

Ashley Rumple, Matthew McMurray, Josephine Johns, Jean Lauder, Pooja Makam, Marlana Radcliffe, Ipek Oguz, Allan Siegel
2013 PLoS ONE  
This project seeks to develop a set of detailed 3D anatomical atlases of the brain at postnatal day 5 (P5), 14 (P14), and adults (P72) in Sprague-Dawley rats.  ...  Having a high resolution, detailed atlas not only can expand understanding of rodent brain anatomy, but also enables automatic segmentation of new images, thus greatly increasing the efficiency of future  ...  Acknowledgments We are grateful to Hong Yuan, Hongyu An, Yu Cai, and Martin Styner for their help with image acquisition, to Francois Budin for his insightful contributions to the data processing and atlas  ... 
doi:10.1371/journal.pone.0067334 pmid:23861758 pmcid:PMC3702494 fatcat:usr3eg5njzelrb7mhkfdrm3sd4

Waxholm Space atlas of the Sprague Dawley rat brain

Eszter A. Papp, Trygve B. Leergaard, Evan Calabrese, G. Allan Johnson, Jan G. Bjaalie
2014 NeuroImage  
We have acquired a microscopic resolution isotropic MRI and DTI atlasing template for the Sprague Dawley rat brain with 39 μm isotropic voxels for the MRI volume and 78 μm isotropic voxels for the DTI.  ...  procedures in the rat brain.  ...  This work was supported by grants from the Research Council of Norway and the EC Human Brain Project to J.G.B.  ... 
doi:10.1016/j.neuroimage.2014.04.001 pmid:24726336 pmcid:PMC4160085 fatcat:7oquoulfxvaupnzfnxir77bnpa

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  
The use of structural magnetic resonance imaging (sMRI) and diffusion tensor imaging (DTI) in animal models of neuropathology is of increasing interest to the neuroscience community.  ...  Keywords: small animal imaging, neonatal neuroimaging, drug abuse, brain segmentation, white matter pathways, magnetic resonance imaging, diffusion tensor imaging  ...  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

Anatomical landmarks for registration of experimental image data to volumetric rodent brain atlasing templates

Marina Sergejeva, Eszter A. Papp, Rembrandt Bakker, Manuel A. Gaudnek, Yuko Okamura-Oho, Jyl Boline, Jan G. Bjaalie, Andreas Hess
2015 Journal of Neuroscience Methods  
Dawley rat brain (Paper I), including the MRI/DTI volumes of the atlasing template, the raw diffusion tensor data, the anatomical delineations, masks for the complete brain volume and white and gray matter  ...  We present an atlas of the adult Sprague Dawley rat brain designed along these principles.  ... 
doi:10.1016/j.jneumeth.2014.11.005 pmid:25445058 fatcat:efd2c5rysjhm5au7zgwim3gt2e

A multidimensional magnetic resonance histology atlas of the Wistar rat brain

G. Allan Johnson, Evan Calabrese, Alexandra Badea, George Paxinos, Charles Watson
2012 NeuroImage  
c) threedimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe  ...  We have produced a multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH).  ...  We are grateful to Sally Gewalt and James Cook for assistance with the imaging pipelines. We thank Dr. Yi Qi and Gary Cofer for assistance in specimen preparation and scanning.  ... 
doi:10.1016/j.neuroimage.2012.05.041 pmid:22634863 pmcid:PMC3408821 fatcat:mvghzt74ord5lpgvwo576feyli

The Translational Role of Diffusion Tensor Image Analysis in Animal Models of Developmental Pathologies

Ipek Oguz, Matthew S. McMurray, Martin Styner, Josephine M. Johns
2012 Developmental Neuroscience  
tion about the analysis of data resulting from small animal DTI studies to facilitate the translation of these studies to clinical data.  ...  In addition to an in-depth review of translational analysis techniques, we present a number of relevant clinical and animal studies using DTI to investigate developmental insults in order to further illustrate  ...  We would also like to acknowledge the financial support of the  ... 
doi:10.1159/000336825 pmid:22627095 pmcid:PMC3566876 fatcat:bxq7w2bs7faurcgxfordlot3se

Mapping sex-specific neurodevelopmental alterations in neurite density and morphology in a rat genetic model of psychiatric illness

Brian R. Barnett, Sue Y. Yi, McKenzie J. Poetzel, Keith Dodd, Nicholas A. Stowe, John-Paul J. Yu
2021 eNeuro  
NODDI has improved our ability to image neuronal microstructure over conventional techniques such as diffusion tensor imaging (DTI) and is particularly suited for studies of the developing brain as it  ...  the ability of advanced diffusion weighted imaging methods such as NODDI to examine the role of biological sex and its influence on brain microstructure in psychiatric illness.SIGNIFICANCE STATEMENT This  ...  Small Animal Imaging Facility at the University of Wisconsin Carbone Cancer Center; and bioinformatics support from the Institute for Clinical and Translational  ... 
doi:10.1523/eneuro.0426-20.2020 pmid:33441401 pmcid:PMC7986540 fatcat:kgggvtk5lffkdgpczqon7cucl4

Quantitative mapping of trimethyltin injury in the rat brain using magnetic resonance histology

G. Allan Johnson, Evan Calabrese, Peter B. Little, Laurence Hedlund, Yi Qi, Alexandra Badea
2014 Neurotoxicology  
We report for the first time diffusion tensor imagebased detection of changes in white matter regions, including fimbria and corpus callosum, in the brains of rats exposed to 8 mg/Kg and 12 mg/Kg trimethyltin  ...  In this study, deformation-based morphometry detected areas where previous studies have detected cell loss, while voxel-wise analyses of diffusion tensor parameters revealed microstructural changes due  ...  We are particularly grateful to the members of the ISLI / HESI Project Committee on Imaging for Translational Safety Assessment Index.cfm?  ... 
doi:10.1016/j.neuro.2014.02.009 pmid:24631313 pmcid:PMC4053477 fatcat:amwbo2cwwncsfkqtkbrj525kdi

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  
Cocaine-exposed (prenatal days 1-20, 30mg/kg/day) rat pups were sedated and imaged live using diffusion tensor imaging and postmortem (fixed) using magnetic resonance histology on postnatal day 14.  ...  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/ pmid:25459688 pmcid:PMC4291294 fatcat:wyfritz4gjdcln7eu5gysmqbka

Reproducibility of Neurite Orientation Dispersion and Density Imaging (NODDI) in rats at 9.4 Tesla

Patrick McCunn, Kyle M. Gilbert, Peter Zeman, Alex X. Li, Michael J. Strong, Ali R. Khan, Robert Bartha, Aaron Jon Newman
2019 PLoS ONE  
The purpose of this study was to determine the reproducibility of NODDI in the rat brain at 9.4 Tesla.  ...  Neurite Orientation Dispersion and Density Imaging (NODDI) is a diffusion MRI (dMRI) technique used to characterize tissue microstructure by compartmental modelling of neural water fractions.  ...  The Waxholm Space Atlas Sprague Dawley template includes binary masks for the relevant brain regions of interest in this study.  ... 
doi:10.1371/journal.pone.0215974 pmid:31034490 pmcid:PMC6488046 fatcat:ak5ojxvswnfwnlfrquclu7jx3a

Gut microbiome populations are associated with structure-specific changes in white matter architecture

Irene M. Ong, Jose G. Gonzalez, Sean J. McIlwain, Emily A. Sawin, Andrew J. Schoen, Nagesh Adluru, Andrew L. Alexander, John-Paul J. Yu
2018 Translational Psychiatry  
Utilizing diffusion tensor imaging, we identified global changes in white matter structural integrity occurring in a diet-dependent manner.  ...  Changes in brain structure were found to be associated with diet-dependent changes in gut microbiome populations using a machine learning classifier for quantitative assessment of the strength of microbiome-brain  ...  Rauch for outstanding imaging support through the Small Animal Imaging Supplementary information The online version of this article ( contains supplementary  ... 
doi:10.1038/s41398-017-0022-5 pmid:29317592 pmcid:PMC5802560 fatcat:6wdvh3sornhy5hxgjiesmlo7jm

Structural and Functional Brain Remodeling during Pregnancy with Diffusion Tensor MRI and Resting-State Functional MRI

Russell W. Chan, Leon C. Ho, Iris Y. Zhou, Patrick P. Gao, Kevin C. Chan, Ed X. Wu, Xi-Nian Zuo
2015 PLoS ONE  
In this study, diffusion tensor imaging (DTI) and resting-state functional MRI (rsfMRI) were employed to investigate and document the effects of pregnancy on the structure and function of the brain tissues  ...  Fifteen Sprague-Dawley female rats were longitudinally studied at three days before mating (baseline) and seventeen days after mating (G17).  ...  Performed the experiments: RWC. Analyzed the data: RWC. Contributed reagents/materials/analysis tools: RWC LCH IYZ. Wrote the paper: RWC PPG KCC EXW.  ... 
doi:10.1371/journal.pone.0144328 pmid:26658306 pmcid:PMC4675543 fatcat:uvngfzqnvfapfllognixtftr2m

Altered diffusion tensor imaging measurements in aged transgenic Huntington disease rats

Bjørnar T. Antonsen, Yi Jiang, Jelle Veraart, Hong Qu, Huu Phuc Nguyen, Jan Sijbers, Stephan von Hörsten, G. Allan Johnson, Trygve B. Leergaard
2012 Brain Structure and Function  
We confirm earlier reports that HD rats express a moderate neuropathological phenotype, and provide evidence of altered DTI measures in specific HD-related brain regions, in the absence of pronounced morphometric  ...  In this report, we contribute to the anatomical phenotyping of this model by comparing high-resolution ex vivo DTI measurements obtained in aged transgenic HD rats and wild-type controls.  ...  During the construction of the study-specific population-based DTI atlas (Veraart et al. 2011a ) the magnitude of the deformation fields needed to warp the different images to the atlas and the bias to  ... 
doi:10.1007/s00429-012-0427-0 pmid:22618438 pmcid:PMC3586769 fatcat:cxugqtsmufdr3fsxvh7mskwfra
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