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Tools for multiple granularity analysis of brain MRI data for individualized image analysis

Aigerim Djamanakova, Xiaoying Tang, Xin Li, Andreia V. Faria, Can Ceritoglu, Kenichi Oishi, Argye E. Hillis, Marilyn Albert, Constantine Lyketsos, Michael I. Miller, Susumu Mori
2014 NeuroImage  
Voxel-based analysis is widely used for quantitative analysis of brain MRI.  ...  The multiple atlases were then applied to T1-weighted MR images of each subject data for automated brain parcellation and five levels of ontological relationships were established, which further reduced  ...  structural relationships -Our approach examines the brain anatomy from multiple granularity levels -Our approach is suitable for phenotype analysis of individual patients Comparison of granularity reduction  ... 
doi:10.1016/j.neuroimage.2014.06.046 pmid:24981408 pmcid:PMC4165692 fatcat:tvri4jfx7nhjtjocfiqcb7hbpa

Evaluation of Cross-Protocol Stability of a Fully Automated Brain Multi-Atlas Parcellation Tool

Zifei Liang, Xiaohai He, Can Ceritoglu, Xiaoying Tang, Yue Li, Kwame S. Kutten, Kenichi Oishi, Michael I. Miller, Susumu Mori, Andreia V. Faria, Huiguang He
2015 PLoS ONE  
When dealing with data from various sources, it is crucial that these tools are robust for many different imaging protocols.  ...  The entire brain was parceled into five different levels of granularity.  ...  Conclusion We describe the use of a fully automated image parcellation tool for brain MRI, using a multiatlas approach.  ... 
doi:10.1371/journal.pone.0133533 pmid:26208327 pmcid:PMC4514626 fatcat:3esmuc5pt5dc3catxheo6sg22q

Content-based image retrieval for brain MRI: An image-searching engine and population-based analysis to utilize past clinical data for future diagnosis

Andreia V. Faria, Kenichi Oishi, Shoko Yoshida, Argye Hillis, Michael I. Miller, Susumu Mori
2015 NeuroImage: Clinical  
Brain MRI Content-based image retrieval Atlas-based analysis Radiological diagnosis is based on subjective judgment by radiologists.  ...  We explored and tested the power of individual classifications and of performing a search for images with similar anatomical features in a database using partial least squares-discriminant analysis (PLS-DA  ...  We thank NIH (grants P41RR15241, RO1AG20012, and RO1NS058299 (SM), RO1HD065955 (KO), RO3EB014357 (AVF), R01 DC011317 and R01 DC 03681 (AH)) for financial support.  ... 
doi:10.1016/j.nicl.2015.01.008 pmid:25685706 pmcid:PMC4309952 fatcat:hhel3q5e6rdb7mcoxb5uehqfyy

Atlas-Based Neuroinformatics via MRI: Harnessing Information from Past Clinical Cases and Quantitative Image Analysis for Patient Care

Susumu Mori, Kenichi Oishi, Andreia V. Faria, Michael I. Miller
2013 Annual Review of Biomedical Engineering  
Despite the rapid progress of image analysis technologies for magnetic resonance imaging of the human brain, these methods have not been widely adopted for clinical diagnoses.  ...  As these are indexed via parametric representations, we can use image retrieval tools to search for phenotypes along with their clinical metadata.  ...  The content of this Article is solely the responsibility of the authors and do not necessarily represent the official view of any of the institutes. LITERATURE CITED  ... 
doi:10.1146/annurev-bioeng-071812-152335 pmid:23642246 pmcid:PMC3719383 fatcat:t24iyi4rybalhm4y77sxapzpsi

Untapped Neuroimaging Tools for Neuro-Oncology: Connectomics and Spatial Transcriptomics

Jurgen Germann, Gelareh Zadeh, Alireza Mansouri, Walter Kucharczyk, Andres M. Lozano, Alexandre Boutet
2022 Cancers  
Magnetic resonance imaging (MRI) is instrumental for the diagnosis and treatment monitoring of patients with brain tumors.  ...  Thanks to technological advances, structural brain MRI can now be transformed into a so-called average brain accounting for individual morphological differences, which enables retrospective group analysis  ...  At present, magnetic resonance imaging (MRI) is a key tool for the diagnosis and treatment monitoring of brain tumors.  ... 
doi:10.3390/cancers14030464 pmid:35158732 pmcid:PMC8833690 fatcat:ly35atvdzvf7jft2dgzighnfti

Brain MRI Pattern Recognition Translated to Clinical Scenarios

Andreia V. Faria, Zifei Liang, Michael I. Miller, Susumu Mori
2017 Frontiers in Neuroscience  
The independent variables were the volumes of 283 anatomical areas, derived from automated segmentation of T1-high resolution brain MRIs.  ...  The segmentation based volumetric quantification reduces image dimensionality from the voxel level [on the order of O(10 6 )] to anatomical structures [O(10 2 )] for subsequent statistical analysis.  ...  ACKNOWLEDGMENTS We are grateful to the individuals who participated in this research. We thank Dr. Argye Hillis, Dr. Christopher Ross, and Dr. Sarah Ying, for data sharing.  ... 
doi:10.3389/fnins.2017.00578 pmid:29104527 pmcid:PMC5655969 fatcat:chqh4q3x7vfbxbh6wi2yhbcc6a

Cloud-Based Brain Magnetic Resonance Image Segmentation and Parcellation System for Individualized Prediction of Cognitive Worsening

Ryo Sakamoto, Christopher Marano, Michael I. Miller, Constantine G. Lyketsos, Yue Li, Susumu Mori, Kenichi Oishi, Alzheimer's Disease Neuroimaging Initiative ADNI
2019 Journal of Healthcare Engineering  
Despite multiple efforts to apply computational brain magnetic resonance image (MRI) analysis in predicting cognitive worsening, with several successes, brain MRI is not routinely quantified in clinical  ...  Each MRI was parcellated into 265 anatomical units based on the MRICloud fully automated image segmentation function, to measure the volume of each parcel.  ...  Data collection and sharing for this project was funded by the Alzheimer's  ... 
doi:10.1155/2019/9507193 pmid:30838124 pmcid:PMC6374863 fatcat:jdjoc2mq4bgnvnahvdthbwro7i

Investigating microstructural variation in the human hippocampus using non-negative matrix factorization

Raihaan Patel, Christopher J. Steele, Anthony Chen, Sejal Patel, Gabriel A. Devenyi, Jürgen Germann, Christine L. Tardif, M. Mallar Chakravarty
2019 NeuroImage  
Taken together, our work suggests non-negative matrix factorization as a spatially specific analytical approach for neuroimaging studies and advocates for the use of multiple metrics for data-driven component  ...  Finally, we related individual subject weightings to demographic and behavioural measures using a partial least squares analysis.  ...  Ragini Verma (Professor in Section of Biomedical Image Analysis, Department of Radiology, University of Pennsylvania) for her discussion and consultations regarding diffusion processing.  ... 
doi:10.1016/j.neuroimage.2019.116348 pmid:31715254 fatcat:g6o2ydjg5nc5rp26izpxjhggxu

A Framework for Cortical Layer Composition Analysis using Low Resolution T1 MRI Images [article]

Ittai Shamir, Omri Tomer, Zvi Baratz, Galia Tsarfaty, Maya Faraggi, Assaf Horowitz, Yaniv Assaf
2018 bioRxiv   pre-print
We use a low resolution echo planar imaging inversion recovery (EPI IR) MRI scan protocol that provides fast acquisition (~12 minutes) and enables extraction of multiple T1 relaxation time components per  ...  Despite technological advancements in the field of high resolution MRI, accurate estimation of whole brain layer composition has remained limited due to partial volume effects, leaving some layers far  ...  IR Decay Function Fit These data were used for multiple T1 analysis, by calculating T1 values and their corresponding partial volumes on a voxel-by-voxel basis.  ... 
doi:10.1101/390112 fatcat:733efbdwqvdkjd5dejgnv3axxa

Modelling cortical laminar connectivity in the macaque brain [article]

Ittai Shamir, Yaniv Assaf
2020 bioRxiv   pre-print
We use multi-modal ex-vivo MRI imaging of both white and grey matter, which are then integrated via our simple model of laminar connectivity.  ...  In this work, we revisit laminar-level connectivity in the macaque brain using a whole-brain MRI-based approach.  ...  IR decay function fit: The IR 3D FLASH data were used for multiple T1 analysis, by calculating T1 values and their corresponding partial volumes on a voxel-by-voxel basis.  ... 
doi:10.1101/2020.07.19.210526 fatcat:nuy7kolaqba6revo6zdhbjcmca

MR Diffusion Histology and Micro-Tractography Reveal Mesoscale Features of the Human Cerebellum

Flavio Dell'Acqua, Istvan Bodi, David Slater, Marco Catani, Michel Modo
2013 Cerebellum  
State-of-the-art in vivo magnetic resonance imaging (MRI) methods, such as diffusion tractography techniques, can reveal trajectories of the major white matter pathways, but their correspondence with underlying  ...  Current histological techniques provide powerful methods for unravelling local axonal architecture, but the relatively low volume of data that can be acquired in a reasonable amount of time limits their  ...  Po-Wah So, the manager of the preclinical imaging unit at KCL, and the British Heart Foundation for funding the 7T MRI scanner.  ... 
doi:10.1007/s12311-013-0503-x pmid:23907655 pmcid:PMC3824945 fatcat:fxexf6gfvng6vkbcyqwjl74ib4

A collaborative resource platform for non-human primate neuroimaging [article]

Adam Messinger, Nikoloz Sirmpilatze, Katja Heuer, Kep Kee Loh, Rogier Mars, Julien Sein, Ting Xu, Daniel Glen, Benjamin Jung, Jakob Seidlitz, Paul Taylor, Roberto Toro (+20 others)
2020 biorxiv/medrxiv   pre-print
PRIME-RE is a dynamic community-driven hub for the exchange of practical knowledge, specialized analytical tools, and open data repositories, specifically related to NHP neuroimaging.  ...  Resources that were primarily developed for human neuroimaging often need to be significantly adapted for use with NHPs or other animals, which has led to an abundance of custom, in-house solutions.  ...  Acknowledgements We would like to thank Patrick Markwalter for assistance with compiling references, editing and formatting.  ... 
doi:10.1101/2020.07.31.230185 fatcat:6vpogby2ezhu3jgxnpjlkbt3ai

A collaborative resource platform for non-human primate neuroimaging

Adam Messinger, Nikoloz Sirmpilatze, Katja Heuer, Kep Kee Loh, Rogier B. Mars, Julien Sein, Ting Xu, Daniel Glen, Benjamin Jung, Jakob Seidlitz, Paul Taylor, Roberto Toro (+20 others)
2021 NeuroImage  
PRIME-RE is a dynamic community-driven hub for the exchange of practical knowledge, specialized analytical tools, and open data repositories, specifically related to NHP neuroimaging.  ...  Resources that were primarily developed for human neuroimaging often need to be significantly adapted for use with NHPs or other animals, which has led to an abundance of custom, in-house solutions.  ...  Acknowledgements We would like to thank Patrick Markwalter for assistance with compiling references, editing and formatting.  ... 
doi:10.1016/j.neuroimage.2020.117519 pmid:33227425 fatcat:67ng3nt3uvbg3l4n4prlshuuwi

Imaging whole-brain cytoarchitecture of mouse with MRI-based quantitative susceptibility mapping

Hongjiang Wei, Luke Xie, Russell Dibb, Wei Li, Kyle Decker, Yuyao Zhang, G. Allan Johnson, Chunlei Liu
2016 NeuroImage  
The proper microstructural arrangement of complex neural structures is essential for establishing the functional circuitry of the brain.  ...  We present an MRI method to resolve tissue microstructure and infer brain cytoarchitecture by mapping the magnetic susceptibility in the brain at high resolution.  ...  R21HL122759, and by the National Multiple Sclerosis Society through grant RG4723.  ... 
doi:10.1016/j.neuroimage.2016.05.033 pmid:27181764 pmcid:PMC5201162 fatcat:24mkcl2sfrhpbpc7ije3jvqhwi

Construction and application of human neonatal DTI atlases

Rajiv Deshpande, Linda Chang, Kenichi Oishi
2015 Frontiers in Neuroanatomy  
Moreover, ABA can be used in high-throughput analysis to efficiently process medical images and to assess longitudinal brain changes.  ...  Future directions for this method include research designed to increase the accuracy of the image parcellation.  ...  subject brain atlas of the neonatal brain that integrates DTI-data with co-registered anatomical MRI.  ... 
doi:10.3389/fnana.2015.00138 pmid:26578899 pmcid:PMC4620146 fatcat:h3kibxisgfbunpnn2jnfawb6ci
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