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Clustering of Whole-Brain White Matter Short Association Bundles Using HARDI Data

Claudio Román, Miguel Guevara, Ronald Valenzuela, Miguel Figueroa, Josselin Houenou, Delphine Duclap, Cyril Poupon, Jean-François Mangin, Pamela Guevara
2017 Frontiers in Neuroinformatics  
The database can be requested from cyril.poupon@cea. fr and will be available from the Human Brain Project in a near future.  ...  The first attempt of clustering short association fibers was done by Guevara et al. (2012) , leading to the creation of an atlas of short association fibers of the left hemisphere.  ...  For the atlas creation, the robust atlas creation method uses two independent groups of subjects.  ... 
doi:10.3389/fninf.2017.00073 pmid:29311886 pmcid:PMC5744462 fatcat:xf3ehgs2hncjbklmkqyc372rki

Superficial white matter: A review on the dMRI analysis methods and applications

Miguel Guevara, Pamela Guevara, Claudio Román, Jean-François Mangin
2020 NeuroImage  
The shape and localization of these short bundles present a high variability across subjects.  ...  Therefore, the mapping of SWM bundles and the use of the resulting atlases for clinical studies requiere dedicated methodologies that are reviewed in this paper.  ...  This was the first work using a fully automatic approach describing well-defined bundles in the whole brain, based on HARDI data.  ... 
doi:10.1016/j.neuroimage.2020.116673 pmid:32114152 fatcat:onw3cxzkvzau7lng54dtgzlwga

From Coarse to Fine-Grained Parcellation of the Cortical Surface Using a Fiber-Bundle Atlas

Narciso López-López, Andrea Vázquez, Josselin Houenou, Cyril Poupon, Jean-François Mangin, Susana Ladra, Pamela Guevara
2020 Frontiers in Neuroinformatics  
Generating parcels from segmented fiber bundles can provide a good representation of the human brain connectome since they are based on bundle atlases that contain the most reproducible short and long  ...  The connectivity information is obtained from segmented superficial and deep white matter bundles, according to bundle atlases, instead of the whole tractography.  ...  A different strategy for creating a parcellation is to use a hybrid method involving the use of bundles segmented from a bundle atlas.  ... 
doi:10.3389/fninf.2020.00032 pmid:33071768 pmcid:PMC7533645 fatcat:zqa3xfyu65gc7mzq4hzt6fcgli

Robust and efficient linear registration of white-matter fascicles in the space of streamlines

Eleftherios Garyfallidis, Omar Ocegueda, Demian Wassermann, Maxime Descoteaux
2015 NeuroImage  
We also show how our novel method can be used to create bundle-specific atlases in a straightforward manner and we give an example of a probabilistic atlas construction of the optic radiation.  ...  We first show that this method can be used successfully to align individual bundles as well as whole brain streamlines.  ...  Finally, we thank Alfred Anwander and Thomas Knösche of the Leipzig Max Planck Institute for Human Cognitive and Brain Sciences, Germany, for sharing the MPI dataset.  ... 
doi:10.1016/j.neuroimage.2015.05.016 pmid:25987367 fatcat:vhgox4r22je4rahevlrt7vfsqi

FFClust: Fast fiber clustering for large tractography datasets for a detailed study of brain connectivity

Andrea Vázquez, Narciso López-López, Alexis Sánchez, Josselin Houenou, Cyril Poupon, Jean-François Mangin, Cecilia Hernández, Pamela Guevara
2020 NeuroImage  
algorithms can be carried out to study the brain connectivity and create new white matter bundle atlases.  ...  In addition, we show that FFClust is able to correctly identify atlas bundles connecting different brain regions, as an example of application and the utility of compact clusters.  ...  A special interest is its use for the study of short association bundles and their segmentation, as well as of subdivisions of long anatomical bundles. The proposed approach consists of four steps.  ... 
doi:10.1016/j.neuroimage.2020.117070 pmid:32599269 fatcat:6p4htw5exbep7d2owg4aupdg7q

Automatic Atlas-Based Segmentation of Brain White Matter in Neonates at Risk for Neurodevelopmental Disorders [chapter]

L. Fonseca, C. van Pul, N. Lori, R. van den Boom, P. Andriessen, J. Buijs, A. Vilanova
2017 Mathematics and Visualization  
Therefore, we propose a new in-vivo and non-invasive global analysis of the WM patterns at the brain: we perform an  ...  3 This work was developed in collaboration with: ABSTRACT Maturation degree of anatomical white matter (WM) structures at the brain can constitute a biomarker for prediction of neurodevelopmental disorders  ...  Atlas Creation A brain atlas is a map of the brain that consists of pictures and/or tables and charts that label the anatomical structures, i.e., the atlas labels.  ... 
doi:10.1007/978-3-319-61358-1_15 fatcat:2k46uyhudvfm7aq3fan3eog5r4

Optimization of macaque brain DMRI connectome by neuron tracing and myelin stain data

Tuo Zhang, Jun Kong, Ke Jing, Hanbo Chen, Xi Jiang, Longchuan Li, Lei Guo, Jianfeng Lu, Xiaoping Hu, Tianming Liu
2018 Computerized Medical Imaging and Graphics  
The FVE brain map, the optimal brain map (out of the three brain maps in the present work) for global connectome, was used to construct connective matrices.  ...  a large-scale connectome on living primate brains.  ...  References Anderson JC, Binzegger T, Martin KA, Rockland KS. 1998 The connection from cortical area V1 to V5: a light and electron microscopic study. J Neurosci 18 (24)  ... 
doi:10.1016/j.compmedimag.2018.06.001 pmid:30170273 pmcid:PMC6176488 fatcat:qqauh2vupzejdahskssdth24rm

Computer-aided diagnostic reporting of FDG PET for the diagnosis of Alzheimer's disease

A. Prestia, C. Muscio, A. Caroli, G. B. Frisoni
2013 Clinical and translational imaging  
Standardization of readouts is a key factor for the use of markers in the clinic. Automated tools have been developed aimed at aiding diagnostic reporting and making it more reliable.  ...  Some involve the statistical voxelby-voxel comparison of 18 F-FDG uptake compared to a normative dataset, which provides a statistical map of difference of metabolism and requires expert judgement.  ...  needed for use in clinical practice [60] Provide whole-brain assessment [44] Expert judgment, user training or a neuroanatomical atlas required [65] Normative database not unanimously identified  ... 
doi:10.1007/s40336-013-0031-1 fatcat:z4en5ou6mzau7nvrqdo2szshpq

Principles and open questions in functional brain network reconstruction

Onerva Korhonen, Massimiliano Zanin, David Papo
2021 Human Brain Mapping  
of brain function.  ...  Here, we review some fundamental conceptual underpinnings and technical issues associated with brain network reconstruction, and discuss how their mutual influence concurs in clarifying the organization  ...  Atlas-based approaches use a local projection of function on anatomy, whereas data-driven approaches typically use bare dynamics.  ... 
doi:10.1002/hbm.25462 pmid:34013636 pmcid:PMC8249902 fatcat:57mynxqhwjgxjgn7g7rzzlib34

Biomarker identification in neurologic diseases: improving diagnostics and therapeutics

Keith D Coon, Travis Dunckley, Dietrich A Stephan
2004 Expert Review of Molecular Diagnostics  
Among them are the availability of tissue at the site of pathology, poor clinical diagnostics, the complexity of the brain and a general dearth of functional end points and models for validation.  ...  These challenges and ways to overcome them are presented here in the context of a disease known to be a robust model for biomarker identification, Alzheimer's disease.  ...  The creation of a standardized protocol for brain banking guidelines used for collection, dissection and preservation of tissue samples is the key to achieving the level of tissue availability that is  ... 
doi:10.1586/14737159.4.3.361 pmid:15137903 fatcat:pbxp3tkigjd5tmgr2pgmp3azye

Hundreds of brain maps in one atlas: Registering coordinate-independent primate neuro-anatomical data to a standard brain

Gleb Bezgin, Vasily A. Vakorin, A. John van Opstal, Anthony R. McIntosh, Rembrandt Bakker
2012 NeuroImage  
Brain regions from 9 different brain maps were directly mapped to a standard macaque cortex using the tool A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT 2 Caret (Van Essen and Dierker, 2007)  ...  Here we describe an approach to spatially register all cortical brain regions from the macaque structural connectivity database CoCoMac, which contains the combined tracing study results from 459 publications  ...  Note that the words 'atlas' and 'parcellation' are often used instead of 'map'; here, we prefer to use the term 'map', particularly if the parcellation only covers a part of the brain (or a part of the  ... 
doi:10.1016/j.neuroimage.2012.04.013 pmid:22521477 fatcat:f2mueabtsnfdpetym3dbtsjqei

A Structural Atlas of the Developing Zebrafish Telencephalon Based on Spatially-Restricted Transgene Expression

Katherine J. Turner, Thomas A. Hawkins, Pedro M. Henriques, Leonardo E. Valdivia, Isaac H. Bianco, Stephen W. Wilson, Mónica Folgueira
2022 Frontiers in Neuroanatomy  
These datasets were registered to reference brains to form an atlas of telencephalic development at key stages of the eversion process (1dpf, 2dpf, and 5dpf) and compared to expression in adulthood.  ...  Finally, we registered gata2:EGFPbi105 expression to the Zebrafish Brain Browser 6dpf reference brain (ZBB, see Marquart et al., 2015, 2017; Tabor et al., 2019), to allow comparison of this expression  ...  , Thomas Auer for his advice and sharing of reagents for the single cell labeling using Crispr, and Tom Becker for the Et(gata2:GFP) bi105 line.  ... 
doi:10.3389/fnana.2022.840924 pmid:35721460 pmcid:PMC9198225 fatcat:h3szuus4fzea5frkx7eurxv5pu

HiDiver: A Suite of Methods to Merge Magnetic Resonance Histology, Light Sheet Microscopy, and Complete Brain Delineations [article]

G. Allan Johnson, Yuqi Tian, Gary P. Cofer, James C. Cook, James C. Gee, Adam Hall, Kathryn J Hornburg, Yi Qi, Fang-Cheng Yeh, Nian Wang, Leonard E. White, Robert W. Williams
2022 bioRxiv   pre-print
Whole brain connectomes are generated using over 100 diffusion weighted images acquired with gradients at uniformly spaced angles. Track density images are generated at a super-resolution of 5 um.  ...  Throughput is sufficiently high that HiDiver is now being used in comprehensive quantitative studies of the impact of gene variants and aging on rodent brain cytoarchitecture.  ...  Rosen for invaluable help in developing the r1CCFv3 used for the first time in this publication. Thanks to Drs. Lu Lu, Suheeta Roy, and David G.  ... 
doi:10.1101/2022.02.10.479607 fatcat:tt5f54lyivctfh7kqg3evormoy

Navigating the Murine Brain: Toward Best Practices for Determining and Documenting Neuroanatomical Locations in Experimental Studies

Ingvild E. Bjerke, Martin Øvsthus, Krister A. Andersson, Camilla H. Blixhavn, Heidi Kleven, Sharon C. Yates, Maja A. Puchades, Jan G. Bjaalie, Trygve B. Leergaard
2018 Frontiers in Neuroanatomy  
Based on these findings, we suggest a set of minimum requirements for documentation of anatomical location in experimental murine brain research.  ...  We furthermore demonstrate how these requirements have been applied in the EU Human Brain Project to optimize workflows for integration of heterogeneous data in common reference atlases.  ...  Acknowledgements The work presented in this thesis was performed between 2017 and 2020 at the Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo.  ... 
doi:10.3389/fnana.2018.00082 pmid:30450039 pmcid:PMC6224483 fatcat:gg3ph35hevfw3jxdy4h4tebqiu

MIDA: A Multimodal Imaging-Based Detailed Anatomical Model of the Human Head and Neck

Maria Ida Iacono, Esra Neufeld, Esther Akinnagbe, Kelsey Bower, Johanna Wolf, Ioannis Vogiatzis Oikonomidis, Deepika Sharma, Bryn Lloyd, Bertram J. Wilm, Michael Wyss, Klaas P. Pruessmann, Andras Jakab (+6 others)
2015 PLoS ONE  
The model offers also a detailed characterization of eyes, ears, and deep brain structures.  ...  A special automatic atlas-based segmentation procedure was adopted to include a detailed map of the nuclei of the thalamus and midbrain into the head model.  ...  The mention of commercial products, their sources, or their use in connection with material reported herein is not to be construed as either an actual or implied endorsement of such products by the Department  ... 
doi:10.1371/journal.pone.0124126 pmid:25901747 pmcid:PMC4406723 fatcat:hqm5m7h73rhchdzqpapd7b5p34
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