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Reliability of MRI-derived cortical and subcortical morphometric measures: Effects of pulse sequence, voxel geometry, and parallel imaging

2009 NeuroImage  
We examined how MRI-derived neurostructural measures are affected by three technological advancements: parallel acceleration, increased spatial resolution, and the use of a high bandwidth multiecho sequence  ...  on the reliability of downstream morphometric measures has not been extensively studied.  ...  Martinos Imaging Center at the McGovern Institute is supported in part by a generous gift from Pat and Lore McGovern. The Athinoula A.  ... 
doi:10.1016/j.neuroimage.2008.10.037 pmid:19038349 pmcid:PMC2739882 fatcat:f6f4md3mqnfyjgij2k4paa5nbm

Structural Brain Correlates Associated with Professional Handball Playing

Jürgen Hänggi, Nicolas Langer, Kai Lutz, Karin Birrer, Susan Mérillat, Lutz Jäncke, Yong He
2015 PLoS ONE  
Subcortical structures tended to be PLOS ONE | larger in handball players.  ...  The anatomical measures of the brain regions associated with handball playing were positively correlated in handball players, but not interrelated in control women.  ...  The Architecture of the Handball Player's Brain  ... 
doi:10.1371/journal.pone.0124222 pmid:25915906 pmcid:PMC4411074 fatcat:or7atodd3fctrmhhmccqfnd24i

Precision Brain Morphometry: Feasibility and Opportunities of Extreme Rapid Scans [article]

Jared A. Nielsen, Ross W. Mair, Justin T. Baker, Randy L. Buckner
2019 bioRxiv   pre-print
Effects of sequence, resolution, acceleration, and number of scans within- and between-sessions were varied across six studies that included 1,025 scans.  ...  Single ~1-min magnetization-prepared rapid gradient echo (MP-RAGE) scans that use wave-controlled aliasing in parallel imaging (Wave-CAIPI) encoding yield morphometric estimates nearly as accurate as those  ...  Acknowledgments We thank the Harvard Center for Brain Science neuroimaging facility and FAS Division of Research Computing.  ... 
doi:10.1101/530436 fatcat:ve5nbxxwvrcjhjeeetq2lotsbq

Population based MRI and DTI templates of the adult ferret brain and tools for voxelwise analysis

E.B. Hutchinson, S.C. Schwerin, K.L. Radomski, N. Sadeghi, J. Jenkins, M.E. Komlosh, M.O. Irfanoglu, S.L. Juliano, C. Pierpaoli
2017 NeuroImage  
The purpose of this study was to build and make available MRI and DTI templates and analysis tools for the ferret brain as the ferret is a well-suited species for pre-clinical MRI studies with folded cortical  ...  Four ferret brain templates were built in this study - in-vivo MRI and DTI and ex-vivo MRI and DTI - using brain images across many ferrets and region of interest (ROI) masks corresponding to established  ...  for in-vivo MRI support.  ... 
doi:10.1016/j.neuroimage.2017.03.009 pmid:28315740 pmcid:PMC6409125 fatcat:et6owo45abao5lg3qn2xs6eqt4

Cortical Surface-Based Analysis

Anders M. Dale, Bruce Fischl, Martin I. Sereno
1999 NeuroImage  
These procedures allow for the routine use of cortical surface-based analysis and visualization methods in functional brain imaging. 1999 Academic Press  ...  Several properties of the cerebral cortex, including its columnar and laminar organization, as well as the topographic organization of cortical areas, can only be properly understood in the context of  ...  ACKNOWLEDGMENTS Thanks to Christophe Destrieux for helping with the validation of the surface reconstruction, to Kevin Hall for generating most of the surfaces shown in the document (and many more!)  ... 
doi:10.1006/nimg.1998.0395 pmid:9931268 fatcat:znjzqec4fvg75i5idduwb2y644

Studying neuroanatomy using MRI

Jason P Lerch, André J W van der Kouwe, Armin Raznahan, Tomáš Paus, Heidi Johansen-Berg, Karla L Miller, Stephen M Smith, Bruce Fischl, Stamatios N Sotiropoulos
2017 Nature Neuroscience  
Developments in MRI acquisition, image processing, and data modelling have been key to these advances. However, MRI provides an indirect measurement of the biological signals we aim to investigate.  ...  The study of neuroanatomy using imaging enables key insights into how our brains function, are shaped by genes and environment, and change with development, aging, and disease.  ...  Since MRI is not a direct picture of the underlying anatomy the outcomes of derived measures, such as cortical thickness or VBM, depend on sequence and hardware choices 24, 25 .  ... 
doi:10.1038/nn.4501 pmid:28230838 fatcat:coxs7fvuxneifo5sh2yoos2nf4

Quantitative multi-parameter mapping of R1, PD*, MT, and R2* at 3T: a multi-center validation

Nikolaus Weiskopf, John Suckling, Guy Williams, Marta M. Correia, Becky Inkster, Roger Tait, Cinly Ooi, Edward T. Bullmore, Antoine Lutti
2013 Frontiers in Neuroscience  
We determined the inter-site bias, inter-site and intra-site coefficient of variation (CoV) for typical morphometric measures [i.e., gray matter (GM) probability maps used in voxel-based morphometry] and  ...  The reliability and sensitivity of these multi-center studies crucially depend on the comparability of the data generated at different sites and time points.  ...  We thank the volunteers for their time and effort participating in this study and travelling from site to site.  ... 
doi:10.3389/fnins.2013.00095 pmid:23772204 pmcid:PMC3677134 fatcat:oiczqdijxvbedbiy3mbvfsnlom

Automatic cortical surface reconstruction of high-resolution T 1 echo planar imaging data

Ville Renvall, Thomas Witzel, Lawrence L. Wald, Jonathan R. Polimeni
2016 NeuroImage  
Echo planar imaging (EPI) is the method of choice for the majority of functional magnetic resonance imaging (fMRI), yet EPI is prone to geometric distortions and thus misaligns with conventional anatomical  ...  when using cortical surface reconstructions derived directly from the MI-EPI reference.  ...  and Dagmar Välimaa Fund, Swedish Cultural Foundation in Finland (11/7793-1166), Instrumentarium Science Foundation, and the Academy of Finland (grant #265917), and was made possible  ... 
doi:10.1016/j.neuroimage.2016.04.004 pmid:27079529 pmcid:PMC5234090 fatcat:m6xd66gnp5hmxh6h2gihc5p6de

Diffusion Tensor Imaging and Its Application to Traumatic Brain Injury: Basic Principles and Recent Advances

Ping-Hong Yeh, Terrence R. Oakes, Gerard Riedy
2012 Open Journal of Medical Imaging  
Diffusion MRI tractography is an extension of diffusion weighted imaging, and can provide additional information about white matter pathways and the integrity of brain neural networks.  ...  Diffusion weighted imaging is an advanced magnetic resonance imaging (MRI) technique that is sensitive to the movement of water molecules, providing additional information on the micro-structural arrangement  ...  Derived DTI Measures Diffusivity Measures A number of related but distinct values can be derived from the DTI measurement.  ... 
doi:10.4236/ojmi.2012.24025 fatcat:h55evmhkkndapaczqmptddpguu

Focal cortical damage parallels cognitive impairment in minimal hepatic encephalopathy

Carmina Montoliu, Gabriel Gonzalez-Escamilla, Mercedes Atienza, Amparo Urios, Olga Gonzalez, Abdallah Wassel, Roberto Aliaga, Remedios Giner-Duran, Miguel A. Serra, Jose M. Rodrigo, Vicente Belloch, Vicente Felipo (+1 others)
2012 NeuroImage  
To aim this goal, cortical thickness obtained from high-resolution 3T magnetic resonance imaging (MRI) was measured in patients with no MHE (NMHE), MHE, and healthy controls.  ...  Finally, we assessed group differences in volume of different subcortical regions and their potential relationships with CFF scores/blood ammonia levels.  ...  Acknowledgments This work was supported by grants from the Spanish Ministry of Science and Innovation (SAF2008-03300 and SAF2011-25463 to JLC; SAF2008-00062, CSD2008-00005 to VF, FIS 06/0065 and PS09/00806  ... 
doi:10.1016/j.neuroimage.2012.03.041 pmid:22465844 fatcat:vuer3nwfqzg2hecfq5qrxvfaba

Pathomechanisms of HIV-Associated Cerebral Small Vessel Disease: A Comprehensive Clinical and Neuroimaging Protocol and Analysis Pipeline

Kyle D Murray, Meera V Singh, Yuchuan Zhuang, Md Nasir Uddin, Xing Qiu, Miriam T Weber, Madalina E Tivarus, Henry Z Wang, Bogachan Sahin, Jianhui Zhong, Sanjay B Maggirwar, Giovanni Schifitto
2020 Frontiers in Neurology  
MRI imaging follows the recommended clinical small vessel imaging standards and adds several advanced sequences to obtain quantitative assessments of brain tissues including white matter microstructure  ...  The effects on the neurovascular unit are evaluated by a novel combination of imaging biomarkers.  ...  ACKNOWLEDGMENTS We would like to acknowledge the contributions of additional team members to the efforts of this study, including study coordination, statistical support, image processing assistance, and  ... 
doi:10.3389/fneur.2020.595463 pmid:33384655 pmcid:PMC7769815 fatcat:mdxpzurd7zazbbq77x5zbhadxu

Automated brain tissue assessment in the elderly and demented population: Construction and validation of a sub-volume probabilistic brain atlas

Michael S. Mega, Ivo D. Dinov, John C. Mazziotta, Mario Manese, Paul M. Thompson, Chris Lindshield, Jacob Moussai, Nah Tran, Kirsten Olsen, Chris I. Zoumalan, Roger P. Woods, Arthur W. Toga
2005 NeuroImage  
Methods: 20 subjects with Alzheimer's disease (AD), mild cognitive impairment, or normal cognition underwent MRI brain imaging and had their 3D volumetric datasets manually partitioned into 68 regions  ...  Gray matter (GM), white matter (WM), and cerebral spinal fluid (CSF) voxel counts were then made in the subject's native space for comparison against automated volumetric measures within three subvolume  ...  This requires correction of the morphometric measurements by the magnitude of the Jacobian of the affine spatial transformation.  ... 
doi:10.1016/j.neuroimage.2005.03.031 pmid:15908234 fatcat:ryjc624pmbarrnbzaaco3xoeuy

The ENIGMA Stroke Recovery Working Group: Big data neuroimaging to study brain-behavior relationships after stroke

Sook-Lei Liew, Artemis Zavaliangos-Petropulu, Neda Jahanshad, Catherine E Lang, Kathryn S Hayward, Keith R Lohse, Julia M Juliano, Francesca Assogna, Lee A Baugh, Anup K Bhattacharya, Bavrina Bigjahan, Michael R Borich (+55 others)
2020 Human Brain Mapping  
Specifically, the processes for scalable data intake and preprocessing, multisite data harmonization, and large-scale stroke lesion analysis are described, and challenges unique to this type of big data  ...  The goal of the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) Stroke Recovery working group is to understand brain and behavior relationships using well-powered meta- and mega-analytic  ...  to extract standard measures of subcortical volume (from eight subcortical regions of interest, bilaterally), and cortical thickness and cortical surface area (from 34 cortical regions of interest, bilaterally  ... 
doi:10.1002/hbm.25015 pmid:32310331 pmcid:PMC8675421 fatcat:lvelmlkkzrf2nemyl6jqbdqsqq

The minimal preprocessing pipelines for the Human Connectome Project

Matthew F. Glasser, Stamatios N. Sotiropoulos, J. Anthony Wilson, Timothy S. Coalson, Bruce Fischl, Jesper L. Andersson, Junqian Xu, Saad Jbabdi, Matthew Webster, Jonathan R. Polimeni, David C. Van Essen, Mark Jenkinson
2013 NeuroImage  
This allows for combined cortical surface and subcortical volume analyses while reducing the storage and processing requirements for high  ...  The Human Connectome Project (HCP) faces the challenging task of bringing multiple magnetic resonance imaging (MRI) modalities together in a common automated preprocessing framework across a large cohort  ...  BF was supported in part by the National Center for Research Resources (P41-RR14075, and the NCRR BIRN Morphometric Project BIRN002, U24 RR021382), the National Institute for Biomedical Imaging and Bioengineering  ... 
doi:10.1016/j.neuroimage.2013.04.127 pmid:23668970 pmcid:PMC3720813 fatcat:odadekdvwzakxlxc4u24smozp4

Accurate prediction of V1 location from cortical folds in a surface coordinate system

Oliver P. Hinds, Niranjini Rajendran, Jonathan R. Polimeni, Jean C. Augustinack, Graham Wiggins, Lawrence L. Wald, H. Diana Rosas, Andreas Potthast, Eric L. Schwartz, Bruce Fischl
2008 NeuroImage  
quality of this atlas provides direct evidence that surface-based intersubject registration methods are superior to volume-based methods at superimposing functional areas of cortex and therefore are better  ...  suited to support multisubject averaging for functional imaging experiments targeting the cerebral cortex.  ...  and Stroke (R01 NS052585), as well as the Mental Illness and Neuroscience Discovery (MIND) Institute and is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes  ... 
doi:10.1016/j.neuroimage.2007.10.033 pmid:18055222 pmcid:PMC2258215 fatcat:aljlwjfsxngjnek4ybateybczi
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