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A computational atlas of the hippocampal formation using ex vivo , ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI

Juan Eugenio Iglesias, Jean C. Augustinack, Khoa Nguyen, Christopher M. Player, Allison Player, Michelle Wright, Nicole Roy, Matthew P. Frosch, Ann C. McKee, Lawrence L. Wald, Bruce Fischl, Koen Van Leemput
2015 NeuroImage  
Here we describe the construction of a statistical atlas of the hippocampal formation at the subregion level using ultra-high resolution, ex vivo MRI.  ...  The manual labels from the in vivo and ex vivo data were combined into a single computational atlas of the hippocampal formation with a novel atlas building algorithm based on Bayesian inference.  ...  The authors would also like to acknowledge Rohit Koppula and Lianne Cagnazzi for their help with the manual segmentation of the ex vivo MRI data; and Susanne Mueller and Paul Yushkevich for their help  ... 
doi:10.1016/j.neuroimage.2015.04.042 pmid:25936807 pmcid:PMC4461537 fatcat:oksmsx6wdrccbazgzvutbrjtqa

Hippocampal subfields at ultra high field MRI: An overview of segmentation and measurement methods

Alessia Giuliano, Graziella Donatelli, Mirco Cosottini, Michela Tosetti, Alessandra Retico, Maria Evelina Fantacci
2017 Hippocampus  
In the recent years, the increasing availability of Magnetic Resonance Imaging (MRI) scanners that operate at ultra-high field (UHF), that is, with static magnetic field strength !  ...  Compared to conventional high-field scanners, these systems can provide new contrasts, increased signal-to-noise ratio and higher spatial resolution, thus they may improve the visualization of very small  ...  Another important application of manual HF subfield segmentation methods is the construction of high-resolution anatomical atlases using ex vivo data.  ... 
doi:10.1002/hipo.22717 pmid:28188659 pmcid:PMC5573987 fatcat:njiutzqnrfe7ldchxeehe2fs5y

Post-mortem inference of the human hippocampal connectivity and microstructure using ultra-high field diffusion MRI at 11.7 T

Justine Beaujoin, Nicola Palomero-Gallagher, Fawzi Boumezbeur, Markus Axer, Jeremy Bernard, Fabrice Poupon, Daniel Schmitz, Jean-François Mangin, Cyril Poupon
2018 Brain Structure and Function  
These results demonstrate that ex vivo ultra-high field/ultra-high gradients diffusion-weighted MRI allows the mapping of the inner connectivity of the human hippocampus, its microstructure, and to accurately  ...  A major target of this paper is the demonstration of diffusion MRI potential, using ultra-high field (11.7 T) and strong gradients (750 mT/m), to reveal the extra-and intrahippocampal connectivity in addition  ...  distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were  ... 
doi:10.1007/s00429-018-1617-1 pmid:29387938 pmcid:PMC5968081 fatcat:4cttfy7ienhrxex4ra43xngsly

Analysis of Hippocampal Subfields in Sickle Cell Disease Using Ultrahigh Field MRI [article]

Tales Santini, Minseok Koo, Nadim Farhat, Vinicius P. Campos, Salem Alkhateeb, Marcelo A. C. Vieira, Meryl A. Butters, Caterina Rosano, Howard J. Aizenstein, Joseph Mettenburg, Enrico M. Novelli, Tamer S Ibrahim
2020 bioRxiv   pre-print
Both T1 and T2 weighted images were used for automatic segmentation of the hippocampus subfields.  ...  Other hippocampal subregions also showed a trend towards smaller volumes in the SCD group. These findings support previous reports of reduced volume in the temporal lobe in SCD patients.  ...  A 345 computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: 346 application to adaptive segmentation of in vivo MRI. Neuroimage. 2015;115:117-37. 347 32.  ... 
doi:10.1101/2020.11.10.377564 fatcat:om4nh6c2mfclzav3bedm7oztey

Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI

Maged Goubran, Christoph Leuze, Brian Hsueh, Markus Aswendt, Li Ye, Qiyuan Tian, Michelle Y. Cheng, Ailey Crow, Gary K. Steinberg, Jennifer A. McNab, Karl Deisseroth, Michael Zeineh
2019 Nature Communications  
, and their correlation with in-vivo biomarkers.  ...  to the ischemic core.  ...  Acknowledgements The authors thank Newton Cho, Jordan Squair, Vanessa Sochat, Masaki Ito, Stéphane Pagès, and Yu Wang for their help with pipeline optimization, testing, and validation experiments.  ... 
doi:10.1038/s41467-019-13374-0 pmid:31796741 pmcid:PMC6890789 fatcat:6amqk6fsojcgzjalhqvxp7wqym

MRI Techniques and New Animal Models for Imaging the Brain [chapter]

Elodie Chaillou, Yves Tillet, Frdric Andersso
2012 When Things Go Wrong - Diseases and Disorders of the Human Brain  
The same researchers also built a 3D probabilistic pig brain atlas of the deep brain structures using ex vivo adult Large White pig brains.  ...  As mentioned above, a high-resolution atlas of the pig brain has been constructed (Saikali et al. 2010) .  ...  of disease but also the prediction of a huge increase in the number of people becoming afflicted.  ... 
doi:10.5772/35834 fatcat:hqdqiirinvbaraxafxbazxg2gu

Exposure to ultrafine particles, intracellular production of reactive oxygen species in leukocytes and altered levels of endothelial progenitor cells

Kim Jantzen, Peter Møller, Dorina Gabriela Karottki, Yulia Olsen, Gabriel Bekö, Geo Clausen, Lars-Georg Hersoug, Steffen Loft
2016 Toxicology  
Thanks to the increasing resolution of MR images and computational atlases, automatic segmentation of hippocampal subregions is becoming feasible in MRI scans.  ...  A B S T R A C T The hippocampal formation is a complex, heterogeneous structure that consists of a number of distinct, interacting subregions.  ...  Support for this research was also provided in part by the National Cancer Institute (1K25-CA181632-01), the Genentech Foundation (G-40819) and the Nvidia corporation, which donated a Titan X GPU.  ... 
doi:10.1016/j.tox.2016.06.007 pmid:27311922 fatcat:kgjbdmo6ybbyzapmxrwl5bmtpa

SYSTEMATIC COMPARISON OF DIFFERENT TECHNIQUES TO MEASURE HIPPOCAMPAL SUBFIELD VOLUMES IN ADNI2

Susanne G. Mueller, Paul A. Yushkevich, Lei Wang, Koen van Leemput, Kate Alpert, Katrina Paz, Sandhitsu Das, Eugenio Iglesias, Michael W. Weiner
2016 Alzheimer's & Dementia  
Model-based subfield segmentation using ex-vivo atlas (FreeSurfer 6.0). 2. T2-based automated multi-atlas segmentation combined with similarity-weighted voting (ASHS). 3.  ...  Methods: The high resolution T2 weighted hippocampal images (T2-HighRes) and the corresponding T1 images from 106 ADNI2 subjects (41 controls, 57 MCI, 8 AD) were processed as follows. A. T1-based: 1.  ...  Acknowledgment The project was supported by a grant of the Alzheimer's Association (ADNI 2-12-233036) to MWW and SGM. None of the authors has a conflict of interest to declare.  ... 
doi:10.1016/j.jalz.2016.06.1399 fatcat:byhrkp5quzgpvc6gk3mxntnvee

Systematic comparison of different techniques to measure hippocampal subfield volumes in ADNI2

Susanne G. Mueller, Paul A. Yushkevich, Sandhitsu Das, Lei Wang, Koen Van Leemput, Juan Eugenio Iglesias, Kate Alpert, Adam Mezher, Peter Ng, Katrina Paz, Michael W. Weiner
2018 NeuroImage: Clinical  
Model-based subfield segmentation using ex-vivo atlas (FreeSurfer 6.0). 2. T2-based automated multi-atlas segmentation combined with similarity-weighted voting (ASHS). 3.  ...  Methods: The high resolution T2 weighted hippocampal images (T2-HighRes) and the corresponding T1 images from 106 ADNI2 subjects (41 controls, 57 MCI, 8 AD) were processed as follows. A. T1-based: 1.  ...  Acknowledgment The project was supported by a grant of the Alzheimer's Association (ADNI 2-12-233036) to MWW and SGM. None of the authors has a conflict of interest to declare.  ... 
doi:10.1016/j.nicl.2017.12.036 pmid:29527502 pmcid:PMC5842756 fatcat:sgtkjzsplrfdpebyvy744zgsce

Using diffusion MRI data acquired with ultra-high gradients to improve tractography in routine-quality data [article]

C. Maffei, C. Lee, M. Planich, M. Ramprasad, N. Ravi, D. Trainor, Z. Urban, M. Kim, R.J. Jones, A. Henin, S.G. Hofmann, D.A. Pizzagalli (+6 others)
2021 bioRxiv   pre-print
AbstractThe development of scanners with ultra-high gradients, spearheaded by the Human Connectome Project, has led to dramatic improvements in the spatial, angular, and diffusion resolution that is feasible  ...  for in vivo diffusion MRI acquisitions.  ...  “A probabilistic atlas of the human thalamic nuclei 1142 combining ex vivo MRI and histology.”  ... 
doi:10.1101/2021.06.28.450265 fatcat:laud55hjqzg6rhpd3cdqxsgyoa

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  
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  ...  macaque and marmoset monkeys using protocols and methods adapted from the HCP; (ii) acquire quantitative invasive tract-tracing data for cortical and subcortical projections to cortical areas; and (iii  ...  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
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  ...  macaque and marmoset monkeys using protocols and methods adapted from the HCP; (ii) acquire quantitative invasive tract-tracing data for cortical and subcortical projections to cortical areas; and (iii  ...  These atlas sections will be aligned to high-resolution structural MRI (spatial resolution of 0.5mm) obtained in vivo from the same animal that will in turn be aligned to the Yerkes19 atlas.  ... 
arXiv:2010.00308v3 fatcat:xqccnaz2hzcs7pqedcutkvktea

Minimal Specifications for Non-Human Primate MRI: Challenges in Standardizing and Harmonizing Data Collection

Joonas A. Autio, Qi Zhu, Xiaolian Li, Matthew F. Glasser, Caspar M. Schwiedrzik, Damien A. Fair, Jan Zimmermann, Essa Yacoub, Ravi S. Menon, David C. Van Essen, Takuya Hayashi, Brian Russ (+1 others)
2021 NeuroImage  
Recent methodological advances in MRI have enabled substantial growth in neuroimaging studies of non-human primates (NHPs), while open data-sharing through the PRIME-DE initiative has increased the availability  ...  of NHP MRI data and the need for robust multi-subject multi-center analyses.  ...  Acknowledgements We express gratitude to the Primate Neuroimaging Data-Exchange (PRIME-DE) initiative and to all institutions that contributed to the PRIME-DE dataset.  ... 
doi:10.1016/j.neuroimage.2021.118082 pmid:33882349 pmcid:PMC8594288 fatcat:rcy2qe2o75gybigrak6hyigupa

Using diffusion MRI data acquired with ultra-high gradient strength to improve tractography in routine-quality data

C. Maffei, C. Lee, M. Planich, M. Ramprasad, N. Ravi, D. Trainor, Z. Urban, M. Kim, R.J. Jones, A. Henin, S.G. Hofmann, D.A. Pizzagalli (+6 others)
2021 NeuroImage  
The development of scanners with ultra-high gradient strength, spearheaded by the Human Connectome Project, has led to dramatic improvements in the spatial, angular, and diffusion resolution that is feasible  ...  for in vivo diffusion MRI acquisitions.  ...  Introduction Diffusion MRI (dMRI) tractography allows us to investigate the connectional anatomy of the human brain in vivo and non-invasively.  ... 
doi:10.1016/j.neuroimage.2021.118706 pmid:34780916 pmcid:PMC8835483 fatcat:sqjn4ezcgja23awguib3se3qjy

No evidence for morphometric associations of the amygdala and hippocampus with the five-factor model personality traits in relatively healthy young adults

Joshua C. Gray, Max M. Owens, Courtland S. Hyatt, Joshua D. Miller, Hengyi Rao
2018 PLoS ONE  
Additionally, recent advances in MRI analysis methods provide unprecedented accuracy in measuring these structures and enable segmentation into their substructures.  ...  is associated with the five-factor model (FFM) personality traits in a sample of relatively healthy young adults.  ...  A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI.  ... 
doi:10.1371/journal.pone.0204011 pmid:30235257 pmcid:PMC6147458 fatcat:3wa5g6kwpnadlpgzfzbh3ood2i
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