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BIC Defacing Algorithm [article]

Vladimir Fonov, D. Louis Collins
2018 bioRxiv   pre-print
The algorithm is implemented using the MINC library and source code is publicly available.  ...  Public distribution of imaging information from several MRI data processing projects at the BIC has lead to the development of this DEFACING algorithm that is used as part of anonymisation process.  ...  Currently there are a number of research projects that are making MRI data publicly available, including but not limited to the NIH pediatric database project [2] , the Biomedical Informatics Research  ... 
doi:10.1101/275453 fatcat:wp3nnrfjvbbx3gucrtfm5cluwm

Unbiased average age-appropriate atlases for pediatric studies

Vladimir Fonov, Alan C. Evans, Kelly Botteron, C. Robert Almli, Robert C. McKinstry, D. Louis Collins
2011 NeuroImage  
The public availability of these atlases will facilitate analysis of pediatric MRI data and enable comparison of results between studies in a common standardized space specific to pediatric research.  ...  Spatial normalization, registration, and segmentation techniques for Magnetic Resonance Imaging (MRI) often use a target or template volume to facilitate processing, take advantage of prior information  ...  maps, and mincaverage to calculate intensity averages, all of which are publicly available (packages.bic.mni.mcgill.ca).  ... 
doi:10.1016/j.neuroimage.2010.07.033 pmid:20656036 pmcid:PMC2962759 fatcat:ubrovmf5lvckfblejg42bfrrwy

In vivo Population Averaged Stereotaxic T2w MRI Brain Template for the Adult Yucatan Micropig

Stephano J. Chang, Andrea J. Santamaria, Francisco J. Sanchez, Luz M. Villamil, Pedro Pinheiro Saraiva, Jose Rodriguez, Yohjans Nunez-Gomez, Ioan Opris, Juan P. Solano, James D. Guest, Brian R. Noga
2020 Frontiers in Neuroanatomy  
Many different templates have been created to represent specific study populations and made publicly available for human and animal research.  ...  This allows for a standardized comparison of neuroimaging data between subjects and provides neuroimaging software with a probabilistic framework upon which further processing and analysis can be based  ...  Finally, Watanabe et al. (2001) created a population averaged T1 template from 22 male adult Göttingen minipigs (9-11 months); however, this template was limited to linear registration methods available  ... 
doi:10.3389/fnana.2020.599701 pmid:33281567 pmcid:PMC7691581 fatcat:2lfj5rhmxzc3znmqs2z4z6snrq

Comparison of different methods for average anatomical templates creation: do we really gain anything from a diffeomorphic framework? [article]

Vladimir Fonov, D. Louis Collins
2018 bioRxiv   pre-print
(AAT) construction - a common technique used in large population studies.  ...  In this work, we evaluated several state-of-the-art non-diffeomorphic and diffeomorphic non-linear registration frameworks in terms of their ability to build AATs.  ...  In the spirit of reproducible research, the source code for these comparisons is made publicly available for at the url: http://anonymous.web.site [note: anonymous only during review].  ... 
doi:10.1101/277087 fatcat:sv4uk2y7d5frvi3ilpbjet3rnq

3D Reconstructed Cyto-, Muscarinic M2 Receptor, and Fiber Architecture of the Rat Brain Registered to the Waxholm Space Atlas

Nicole Schubert, Markus Axer, Martin Schober, Anh-Minh Huynh, Marcel Huysegoms, Nicola Palomero-Gallagher, Jan G. Bjaalie, Trygve B. Leergaard, Mehmet E. Kirlangic, Katrin Amunts, Karl Zilles
2016 Frontiers in Neuroanatomy  
The Waxholm Space (http://software.incf.org/software/waxholm-space) is a publicly available 3D coordinate-based standard reference space for the mapping and registration of neuroanatomical data in rodent  ...  The registration of the brain sections into the atlas is performed by using both linear and non-linear transformations.  ...  Darine for valuable assistance with the use of neuroinformatics tools and infrastructures.  ... 
doi:10.3389/fnana.2016.00051 pmid:27199682 pmcid:PMC4853377 fatcat:vcqja46h2zbbvcljeuqcfbloky

Spatio-Temporal Regularization for Longitudinal Registration to Subject-Specific 3d Template

Nicolas Guizard, Vladimir S. Fonov, Daniel García-Lorenzo, Kunio Nakamura, Bérengère Aubert-Broche, D. Louis Collins, Arrate Muñoz-Barrutia
2015 PLoS ONE  
We propose to use 4D non-linear registration with spatio-temporal regularization to correct for potential longitudinal inconsistencies in the context of structure segmentation.  ...  We validate our method with different sets of real MRI data, compare it to available longitudinal methods such as FreeSurfer, SPM12, QUARC, TBM, and KNBSI, and demonstrate that spatially local temporal  ...  Evans) [66] , a Canada-wide platform for distributed processing, for computation.  ... 
doi:10.1371/journal.pone.0133352 pmid:26301716 pmcid:PMC4547713 fatcat:l2o7ooqmg5fmdk7drwibl3bxli

Neurodevelopmental MRI brain templates for children from 2 weeks to 4 years of age

Carmen E. Sanchez, John E. Richards, C. Robert Almli
2011 Developmental Psychobiology  
To remedy this issue, we created a single database made up of a series of pediatric, age-specific MRI average brain templates.  ...  A listing of the participating sites and a complete listing of the study investigators can be found at  ...  linear registration techniques.  ... 
doi:10.1002/dev.20579 pmid:21688258 pmcid:PMC3184192 fatcat:ikbwco4obrcpfliv4jmsa433w4

BEaST: Brain extraction based on nonlocal segmentation technique

Simon F. Eskildsen, Pierrick Coupé, Vladimir Fonov, José V. Manjón, Kelvin K. Leung, Nicolas Guizard, Shafik N. Wassef, Lasse Riis Østergaard, D. Louis Collins
2012 NeuroImage  
The segmentation accuracy of the method is better than two widely used publicly available methods and recent state-of-the-art hybrid approaches.  ...  A library of 80 priors is semi-automatically constructed from the NIH-sponsored MRI study of normal brain development, the International Consortium for Brain Mapping, and the Alzheimer's Disease Neuroimaging  ...  Acknowledgements The authors would like to thank Professor Nick Fox, Dementia Research Centre, Institute of Neurology, London, for contributing with the ADNI semi-automatic brain segmentations. This  ... 
doi:10.1016/j.neuroimage.2011.09.012 pmid:21945694 fatcat:qbd3t6xtbjhvzimkbobr3teqxy

The construction of MRI brain/head templates for Chinese children from 7 to 16 years of age

Wanze Xie, John E. Richards, Du Lei, Hongyan Zhu, Kang Lee, Qiyong Gong
2015 Developmental Cognitive Neuroscience  
A total of 138 Chinese children (51 F/87 M) were included in this study.  ...  image analysis techniques.  ...  Template availability The Chinese average head and brain MRI templates are publicly available for research including clinical and experimental studies of brain development.  ... 
doi:10.1016/j.dcn.2015.08.008 pmid:26343862 pmcid:PMC4714595 fatcat:lp435w6wzzbbrprcxi45cr3nou

Windows on the brain: the emerging role of atlases and databases in neuroscience

David C. Van Essen
2002 Current Opinion in Neurobiology  
Brain atlases and associated databases have great potential as gateways for navigating, accessing, and visualizing a wide range of neuroscientific data.  ...  Recent progress towards realizing this potential includes the establishment of probabilistic atlases, surface-based atlases and associated databases, combined with improvements in visualization capabilities  ...  Institute, the National Library of Medicine and the National Aeronautics and Space Administration, and by the National Partnership for Advanced Computational Infrastructure.  ... 
doi:10.1016/s0959-4388(02)00361-6 pmid:12367638 fatcat:kzvgy5fwefcstbz7bahdyubnzm

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  
comparison to a book atlas.  ...  Numerous image processing techniques are available for transforming images into a common coordinate system (Zuk and Atkins, 1996) .  ...  A P P E N D I X .  ... 
doi:10.1016/j.jneumeth.2014.11.005 pmid:25445058 fatcat:efd2c5rysjhm5au7zgwim3gt2e

Software Tools for the Analysis of Functional Magnetic Resonance Imaging

Mehdi Behroozi, Mohammad Reza Daliri
2012 Basic and Clinical Neuroscience  
Currently, there is a large variety of software packages for the analysis of fMRI data, each providing many features for users.  ...  In this paper, several software tools have been introduced and they have been evaluated for comparison of their functionality and their features.  ...  A number of publicly available packages have functions for most of the necessary processing steps: SPM, FSL, AFNI, DPTools, BrainVoyager, VoxBo and etc. (see Table 1 ).  ... 
doaj:c89ba4d7eff64c98a07aaed975573b3d fatcat:lfm4knddyrdmhctgskjdtlagy4

Huntington's Disease Mouse Models Online: High-Resolution MRI Images with Stereotaxic Templates for Computational Neuroanatomy

Stephen J. Sawiak, Nigel I. Wood, T. Adrian Carpenter, A. Jennifer Morton, Grainne M. McAlonan
2012 PLoS ONE  
We are making the whole dataset (399 transgenic HD and wildtype (WT) brains, from mice aged 9-80 weeks) publicly available.  ...  Here we used MRI to make a dataset of ex vivo brains from two different rodent models of Huntington's disease (HD), the R6/2 line and the YAC 128 mouse.  ...  A linear fit to the WT brains (solid line) showing two standard deviations above and below (dashed lines) is repeated on each graph to aid comparison.  ... 
doi:10.1371/journal.pone.0053361 pmid:23300918 pmcid:PMC3534048 fatcat:hb6c3cw66bggbpy6miqwfjhipa

MRI Brain Templates of the Male Yucatan Minipig

Carly Norris, Jonathan Lisinski, Elizabeth McNeil, John W VanMeter, Pamela VandeVord, Stephen LaConte
2021 NeuroImage  
In addition, several aspects of this study are unique, including the comparison of linear and non-linear template generation, the characterization of a large and homogeneous cohort, an analysis of effective  ...  resolution after averaging, and the evaluation of potential in-template bias as well as a comparison with a template from another minipig species using a "left-out" validation set.  ...  MRI scans provided by Office of Naval Research award N0001414-C-0254.  ... 
doi:10.1016/j.neuroimage.2021.118015 pmid:33798725 fatcat:5sis7zfvozca5htp3memt6w6ge

MRI Brain Templates of the Male Yucatan Minipig [article]

Carly Norris, Jonathan Lisinski, Elizabeth Fievisohn, John W. VanMeter, Pam VandeVord, Stephen M LaConte
2020 biorxiv/medrxiv   pre-print
In addition, several aspects of this study are unique, including the comparison of linear and non-linear template generation, the characterization of a large and homogeneous cohort, an analysis of effective  ...  resolution after averaging, and the evaluation of potential within template bias as well as a comparison with a template from another minipig species using a "left-out" validation set.  ...  MRI scans provided by Office of Naval Research award N0001414-C-0254.  ... 
doi:10.1101/2020.07.17.209064 fatcat:xroyc7fzmjep3muwyub5uylx5y
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