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A New Cortical Surface Parcellation Model and Its Automatic Implementation [chapter]

Cédric Clouchoux, Olivier Coulon, Jean-Luc Anton, Jean-François Mangin, Jean Régis
2006 Lecture Notes in Computer Science  
The aim of our method is to exhibit a new way to describe the cortical surface organization, in both anatomical and functional terms.  ...  The parcellation is obtained using an anatomically constrained surface-based coordinate system from which we define a complete partition of the surface.  ...  In this paper, we propose a new approach to automatically define a robust gyri-based parcellation of the cortical surface.  ... 
doi:10.1007/11866763_24 fatcat:7n5ope6n5nai3fcoctw25uabi4

Automatic parcellation of cortical surfaces using random forests

Yu Meng, Gang Li, Yaozong Gao, Dinggang Shen
2015 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)  
In this paper, we propose a new method leveraging random forests and graph cuts methods to parcellate cortical surfaces into a set of gyral-based regions, using multiple surface atlases with manual labels  ...  Automatic and accurate parcellation of cortical surfaces into anatomically and functionally meaningful regions is of fundamental importance in brain mapping.  ...  INTRODUCTION Automatic and accurate parcellation of cortical surfaces into anatomically and functionally meaningful regions is of fundamental importance in human brain mapping [1] .  ... 
doi:10.1109/isbi.2015.7163995 pmid:26405505 pmcid:PMC4578305 dblp:conf/isbi/MengLGS15 fatcat:vfs6aana45bghjiusevjx6gozi

Automatically Parcellating the Human Cerebral Cortex

B. Fischl
2004 Cerebral Cortex  
We present a technique for automatically assigning a neuroanatomical label to each location on a cortical surface model based on probabilistic informatio estimated from a manually labeled training set.  ...  The result is a complete labeling of cortical sulci and gyri.  ...  Thanks also to Andrea Boehland, Bobbie Holland and Nicole Cullen for providing manual parcellations for use in this paper.  ... 
doi:10.1093/cercor/bhg087 pmid:14654453 fatcat:vcnxj2dkfbfx7aud4t5glj7m54

Automatic cortical sulcal parcellation based on surface principal direction flow field tracking

Gang Li, Lei Guo, Jingxin Nie, Tianming Liu
2009 NeuroImage  
In this paper, a novel method is proposed for automatic cortical sulcal parcellation based on the geometric characteristics of cortical surface including its principal curvatures and principal directions  ...  Automatic parcellation of the cortical surface into sulcal regions is of great importance in structural and functional mapping of the human brain.  ...  Acknowledgement G Li , J Nie and L Guo were supported by the NWPU Foundation for Fundamental Research.  ... 
doi:10.1016/j.neuroimage.2009.03.039 pmid:19328234 pmcid:PMC2756525 fatcat:outn6su4dfdulf7svwzg3xdqfy

Analyzing imaging biomarkers for traumatic brain injury using 4d modeling of longitudinal MRI

Bo Wang, Marcel Prastawa, Andrei Irimia, Micah C. Chambers, Neda Sadeghi, Paul M. Vespa, John D. van Horn, Guido Gerig
2013 2013 IEEE 10th International Symposium on Biomedical Imaging  
We propose a new methodology for computing imaging biomarkers in TBI by extending a recently proposed spatiotemporal 4D modeling approach in order to compute quantitative features of tissue change.  ...  The proposed method computes surface-based and voxel-based measurements such as cortical thickness, volume changes, and geometric deformation.  ...  CONCLUSIONS We propose a new framework for computing imaging biomarkers by extending our recently developed spatiotemporal model construction.  ... 
doi:10.1109/isbi.2013.6556793 pmid:24443697 pmcid:PMC3892715 dblp:conf/isbi/WangPICSVHG13 fatcat:m3yuipyxavdopdbesnfognof4y

Cortical surface parcellation based on intra-subject white matter fiber clustering [article]

Narciso López-López, Andrea Vázquez, Cyril Poupon, Jean-François Mangin, Pamela Guevara
2020 arXiv   pre-print
Results in five subjects from ARCHI database show a good individual cortical parcellation for each one, composed of about 200 subparcels per hemisphere and complying with these connectivity measures.  ...  The fibers that make up each cluster are then intersected with the cortical mesh and then filtered to discard outliers.  ...  In this work, we propose a new hybrid method of individual cortical parcellation based on WM connectivity and intra-subject fiber clustering, with automatic parcel labeling.  ... 
arXiv:2002.09034v1 fatcat:m5534eypkvb4zmde7rpgepftau

Parcellation Schemes and Statistical Tests to Detect Active Regions on the Cortical Surface [chapter]

Bertrand Thirion, Alan Tucholka, Jean-Baptiste Poline
2010 Proceedings of COMPSTAT'2010  
In this paper, we propose a new approach that first defines anatomical regions such as cortical gyri outlined on the cortical surface, and then segments these regions into functionally homogeneous structures  ...  using a parcellation procedure that includes an explicit between-subject variability model, i.e. random effects.  ...  data Ys, results from a spatial model, shared across subjects, that provides the probability w that each surface point belongs to a parcel, and a hierarchical model of the functional parameters, with  ... 
doi:10.1007/978-3-7908-2604-3_58 dblp:conf/compstat/ThirionTP10 fatcat:4aq2menjbfccfcvwp46mcd7fue

Fast cortical surface reconstruction from MRI using deep learning

Jianxun Ren, Qingyu Hu, Weiwei Wang, Wei Zhang, Catherine S. Hubbard, Pingjia Zhang, Ning An, Ying Zhou, Louisa Dahmani, Danhong Wang, Xiaoxuan Fu, Zhenyu Sun (+4 others)
2022 Brain Informatics  
Importantly, the model demonstrated good generalizability in previously unseen data and showed high test–retest reliability in cortical morphometrics and anatomical parcellations.  ...  AbstractReconstructing cortical surfaces from structural magnetic resonance imaging (MRI) is a prerequisite for surface-based functional and anatomical image analyses.  ...  Network implementation The network model was implemented in Python 3.8.8 using PyTorch framework 1.6.0 [40] .  ... 
doi:10.1186/s40708-022-00155-7 pmid:35262808 pmcid:PMC8907118 fatcat:z45geoz5crefrowd26oiyi55o4

Local-Global Parcellation of the Human Cerebral Cortex From Intrinsic Functional Connectivity MRI [article]

Alexander Schaefer, Ru Kong, Evan M. Gordon, Timothy O. Laumann, Xi-Nian Zuo, Avram Holmes, Simon B. Eickhoff, B. T. Thomas Yeo
2017 bioRxiv   pre-print
Here we propose a gradient-weighted Markov Random Field (gwMRF) model integrating local gradient and global similarity approaches.  ...  Furthermore, gwMRF parcellations agreed with the boundaries of certain cortical areas defined using histology and visuotopic fMRI.  ...  al., 2016) and a multimodal parcellation derived from a semi-automatic method (Glasser et al., 2016) .  ... 
doi:10.1101/135632 fatcat:nwl56qsicfexrk6xvg4glbe234

Accurate nonlinear mapping between MNI volumetric and FreeSurfer surface coordinate systems

Jianxiao Wu, Gia H. Ngo, Douglas Greve, Jingwei Li, Tong He, Bruce Fischl, Simon B. Eickhoff, B.T. Thomas Yeo
2018 Human Brain Mapping  
fsaverage and projection of fsaverage parcellations to MNI152/Colin27.  ...  resting-state fMRI parcellations from fsaverage to MNI152/Colin27 for volumetric analysis of new data.  ...  FreeSurfer constitutes a suite of automatic algorithms that extract models of most macroscopic human brain structures from T1 MRI data.  ... 
doi:10.1002/hbm.24213 pmid:29770530 fatcat:6a3mur2clvazfkgtwjyxcc32aa

Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity MRI

Alexander Schaefer, Ru Kong, Evan M Gordon, Timothy O Laumann, Xi-Nian Zuo, Avram J Holmes, Simon B Eickhoff, B T Thomas Yeo
2017 Cerebral Cortex  
Here, we propose a gradient-weighted Markov Random Field (gwMRF) model integrating local gradient and global similarity approaches.  ...  Furthermore, gwMRF parcellations agreed with the boundaries of certain cortical areas defined using histology and visuotopic fMRI.  ...  Consequently, it is unclear if there is a correct number of brain parcels or if cortical areas are necessarily the optimal resolution for cortical parcellations.  ... 
doi:10.1093/cercor/bhx179 pmid:28981612 fatcat:omaez3tu3jcxdg2kqa6rkstsgu

Algorithm to find high density EEG scalp coordinates and analysis of their correspondence to structural and functional regions of the brain

Paolo Giacometti, Katherine L. Perdue, Solomon G. Diamond
2014 Journal of Neuroscience Methods  
An algorithm is introduced for automatic calculation of the International 10-20, 10-10, and 10-5 scalp coordinates of EEG electrodes on a boundary element mesh of a human head.  ...  The parcellation method presented summarizes the EEG scalp locations with respect to brain regions without computation of a full EEG forward model solution.  ...  Acknowledgments This work was supported by the NIH National Institute of Aging R21AG033256, Dartmouth SYNERGY, and the Institute for Quantitative Biomedical Sciences (iQBS).  ... 
doi:10.1016/j.jneumeth.2014.04.020 pmid:24769168 pmcid:PMC4071772 fatcat:g2noifbnwnec7bwms7lyd5o5du

ciftiTools: A package for reading, writing, visualizing and manipulating CIFTI files in R [article]

Damon Pham, John Muschelli, Amanda Mejia
2021 arXiv   pre-print
gray matter data from the subcortex and cerebellum into a single file.  ...  Surface- and grayordinate-based analysis of MR data has well-recognized advantages, including improved whole-cortex visualization, the ability to perform surface smoothing to avoid issues associated with  ...  We use to create a mask of only that parcel, and to create a new with two measurements: the original parcellation and the masked PCC.  ... 
arXiv:2106.11338v2 fatcat:btquudjj6bhfflkpo6suxghwfe

Bayesian approach for network modeling of brain structural features

Anand A. Joshi, Shantanu H. Joshi, Richard M. Leahy, David W. Shattuck, Ivo Dinov, Arthur W. Toga, Robert C. Molthen, John B. Weaver
2010 Medical Imaging 2010: Biomedical Applications in Molecular, Structural, and Functional Imaging  
cortical surface areas.  ...  Results are presented for a population of 466 brains, where a SEM (structural equation modeling) approach is used to generate a Bayesian network model, as well as a dependency graph for the joint distribution  ...  It calculates volumes of individual grey matter parcellations in mm 3 and surface area in mm 2 .  ... 
doi:10.1117/12.844548 fatcat:jrp6ppsf3bhf5lvqx4en7ij7uy

MEG Source Localization of Spatially Extended Generators of Epileptic Activity: Comparing Entropic and Hierarchical Bayesian Approaches

Rasheda Arman Chowdhury, Jean Marc Lina, Eliane Kobayashi, Christophe Grova, Gareth Robert Barnes
2013 PLoS ONE  
A Data Driven Parcellization (DDP) method was used to segment the cortical surface into non-overlapping parcels and diffusion-based spatial priors were used to model local spatial smoothness within parcels  ...  Source localization methods based on two types of realistic models have been investigated: (i) brain activity may be modeled using cortical parcels and (ii) brain activity is assumed to be locally smooth  ...  In order to implement these above-mentioned spatial models, we proposed two new source localization methods within the MEM framework (MEM-s and CMEM-s) and one within the HB framework (COH-s).  ... 
doi:10.1371/journal.pone.0055969 pmid:23418485 pmcid:PMC3572141 fatcat:64dzjvq4qvdtljnpgkdx6sw7b4
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