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Automatic feature-based surface mapping for brain cortices

Fabien Vivodtzev, David F. Wiley, Lars Linsen, James Jones, Nina Amenta, Bernd Hamann, Kenneth I. Joy, Robert F. Erbacher, Jonathan C. Roberts, Matti T. Gröhn, Katy Börner
2006 Visualization and Data Analysis 2006  
One main objective of our effort is to develop technology for automatically transferring surface annotations from an atlas brain to a subject brain.  ...  The result is a mapping between topological components of the input surfaces allowing for transfer of annotations.  ...  We thank the members of the Visualization and Computer Graphics Research Group at the Institute for Data Analysis and Visualization (IDAV) at the University of California, Davis.  ... 
doi:10.1117/12.644541 dblp:conf/vda/VivodtzevWLJAHJ06 fatcat:nsag23zbg5h4dfxl4fsu7grtza

A Landmark-Based Brain Conformal Parametrization with Automatic Landmark Tracking Technique [chapter]

Lok Ming Lui, Yalin Wang, Tony F. Chan, Paul M. Thompson
2006 Lecture Notes in Computer Science  
In this paper, we present algorithms to automatically detect and match landmark curves on cortical surfaces to get an optimized brain conformal parametrization.  ...  Next, we applied these automatically labeled landmark curves to generate an optimized conformal parametrization of the cortical surface, in the sense that homologous features across subjects are caused  ...  Introduction Parametrization of the cortical surfaces is an important process in the brain mapping research for data comparison.  ... 
doi:10.1007/11866763_38 fatcat:ge2nhc6vfbgltooknmuomz33oi

Brain anatomical feature detection by solving partial differential equations on general manifolds

Paul Thompson, Tony Chan, Yalin Wang, Lok Lui
2007 Discrete and continuous dynamical systems. Series B  
One important problem in human brain mapping research is to locate the important anatomical features.  ...  These landmark curves are important information for neuroscientists to study brain disease and to match different cortical surfaces.  ...  One important problem in human brain mapping research is to locate the important anatomical features.  ... 
doi:10.3934/dcdsb.2007.7.605 fatcat:klir2aeevncf5njvns6paj3gq4

Evaluating the accuracy of cortical registration using landmark-based and automatic methods

D Pantazis, A Joshi, J Jintao, D Shattuck, LE Bernstein, H Damasio, RM Leahy
2009 NeuroImage  
Surface-based registration methods differ mainly in the features or similarity metrics that are used when aligning cortical surfaces.  ...  The second approach allows automatic registration by optimizing the alignment of shape metrics, such as sulcal depth and cortical convexity, computed over the entire cortical surface.  ...  Introduction: Surface-based registration methods differ mainly in the features or similarity metrics that are used when aligning cortical surfaces.  ... 
doi:10.1016/s1053-8119(09)71159-0 fatcat:gyhkd76opfeudnichg4efzbovu

Brain image registration using cortically constrained harmonic mappings

Anand Joshi, David Shattuck, Paul Thompson, Richard Leahy
2007 Information processing in medical imaging : proceedings of the ... conference  
We then extrapolate this mapping from the cortical surface to the entire brain volume using a harmonic mapping procedure.  ...  The resulting maps retain the one-to-one correspondence between cortical surfaces while also aligning volumetric features via the intensity-driven registration.  ...  Acknowledgment The authors would like to thank the Center for Morphometric Analysis at Massachusetts General Hospital for providing the MRI brain data sets and their manual segmentations.  ... 
pmid:17633713 pmcid:PMC4511383 fatcat:hs3q6jtcc5edbkjw52jhwu7h7m

Brain Morphometry Analysis with Surface Foliation Theory [article]

Chengfeng Wen, Na Lei, Ming Ma, Xin Qi, Wen Zhang, Yalin Wang, David Xianfeng Gu
2018 arXiv   pre-print
Given brain cortical surfaces with automatically extracted landmark curves, we first construct finite foliations on surfaces.  ...  Brain morphometry study plays a fundamental role in neuroimaging research. In this work, we propose a novel method for brain surface morphometry analysis based on surface foliation theory.  ...  For comparison purpose, we also computed cortical surface area and cortical surface mean curvatures, two cortical surface features frequently adopted in prior structural MRI analyses [18] .  ... 
arXiv:1809.02870v1 fatcat:p3ddmywe6bexxn37edw64aedwq

Comparison of landmark-based and automatic methods for cortical surface registration

Dimitrios Pantazis, Anand Joshi, Jintao Jiang, David W. Shattuck, Lynne E. Bernstein, Hanna Damasio, Richard M. Leahy
2010 NeuroImage  
A surface-based approach to this problem treats the cortex as a convoluted surface and coregisters across subjects so that cortical landmarks or features are aligned.  ...  Alternatively, registration can be based on the alignment of curvature metrics computed over the entire cortical surface.  ...  Surface-based registration methods differ mainly in the features or similarity metrics that are used when aligning cortical surfaces.  ... 
doi:10.1016/j.neuroimage.2009.09.027 pmid:19796696 pmcid:PMC2818237 fatcat:u4cc7ixitrfrvfl2o7u5ndstky

A Deep Attentive Convolutional Neural Network for Automatic Cortical Plate Segmentation in Fetal MRI [article]

Haoran Dou, Davood Karimi, Caitlin K. Rollins, Cynthia M. Ortinau, Lana Vasung, Clemente Velasco-Annis, Abdelhakim Ouaalam, Xin Yang, Dong Ni, Ali Gholipour
2021 arXiv   pre-print
Automatic segmentation of the cortical plate, on the other hand, is challenged by the relatively low resolution of the reconstructed fetal brain MRI scans compared to the thin structure of the cortical  ...  Manual segmentation of the cortical plate, or manual refinement of automatic segmentations is tedious and time-consuming.  ...  /fetal brain atlas/ feature maps in a stage-wise manner.  ... 
arXiv:2004.12847v3 fatcat:r26i6yn4tnhhrn66ld2kfnrp6m

Automatic cortical thickness analysis on rodent brain

Joohwi Lee, Cindy Ehlers, Fulton Crews, Marc Niethammer, Francois Budin, Beatriz Paniagua, Kathy Sulik, Josephine Johns, Martin Styner, Ipek Oguz, David R. Haynor, Benoit M. Dawant
2011 Medical Imaging 2011: Image Processing  
This paper describes an algorithm for automatically measuring the cortical thickness of mouse and rat brains.  ...  There are many tools and methods already developed to automatically measure and analyze cortical thickness for the human brain.  ...  Acknowledgments We are grateful to Clement Vachet for his insights and technical support.  ... 
doi:10.1117/12.878305 pmid:21909228 pmcid:PMC3168533 dblp:conf/miip/LeeECNBPSJSO11 fatcat:ehkmbf3bofffvoynxt5yhkxwx4

Optimized Conformal Parameterization of Cortical Surfaces Using Shape Based Matching of Landmark Curves [chapter]

Lok Ming Lui, Sheshadri Thiruvenkadam, Yalin Wang, Tony Chan, Paul Thompson
2008 Lecture Notes in Computer Science  
The utility of our model is demonstrated in experiments on cortical surfaces with landmarks delineated, which show that our computed maps give a shape-based alignment of the sulcal curves without significantly  ...  In this work, we find meaningful parameterizations of cortical surfaces utilizing prior anatomical information in the form of anatomical landmarks (sulci curves) on the surfaces.  ...  Introduction Parametrization of the cortical surface is a key problem in brain mapping research.  ... 
doi:10.1007/978-3-540-85988-8_59 fatcat:q5md63dxnnevret4z6klziubv4

A Geometry-Driven Optical Flow Warping for Spatial Normalization of Cortical Surfaces

D. Tosun, J.L. Prince
2008 IEEE Transactions on Medical Imaging  
The work presented in this paper is motivated by the need for an automated cortical surface normalization technique that will automatically identify homologous cortical landmarks and map them to the same  ...  data mapped to the surfaces.  ...  Noor Kabani for constructing the atlas of anatomical features, Dr. Maryam E. Rettmann for manually labeling the sulcal regions, and Dr. Susan M.  ... 
doi:10.1109/tmi.2008.925080 pmid:19033090 pmcid:PMC2597639 fatcat:6uyatqb3dffvdma4wrizp2abpa

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)  
Automatic and accurate parcellation of cortical surfaces into anatomically and functionally meaningful regions is of fundamental importance in brain mapping.  ...  Particularly, to capitalize on random forests, we propose a novel definition of Haar-like features on cortical surfaces based on spherical 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

Atlas-Free Surface Reconstruction of the Cortical Grey-White Interface in Infants

François Leroy, Jean-François Mangin, François Rousseau, Hervé Glasel, L. Hertz-Pannier, Jessica Dubois, Ghislaine Dehaene-Lambertz, Antoni Rodriguez-Fornells
2011 PLoS ONE  
We used a broad characterization of tissue using features based not only on local contrast but also on geometric properties.  ...  Furthermore, inaccuracies in localization were reduced by the convergence of two evolving surfaces located on each side of the inner cortical surface.  ...  Introduction Accurate reconstruction of the cortical border from MRI is an important issue in visualization, cortical mapping and quantitative brain analysis.  ... 
doi:10.1371/journal.pone.0027128 pmid:22110604 pmcid:PMC3217936 fatcat:i52g3h5m5jdd3gadaxfn6andgu

Cortical correspondence via sulcal curve-constrained spherical registration with application to Macaque studies

Ilwoo Lyu, Sun Hyung Kim, Joon-Kyung Seong, Sang Wook Yoo, Alan C. Evans, Yundi Shi, Mar Sanchez, Marc Niethammer, Martin A. Styner, David R. Haynor, Sebastien Ourselin
2013 Medical Imaging 2013: Image Processing  
Starting from structural MR images, we first apply existing preprocessing steps: brain tissue segmentation using the Automatic Brain Classification tool (ABC), as well as cortical surface reconstruction  ...  and spherical parametrization of the cortical surface via Constrained Laplacian-based Automated Segmentation with Proximities (CLASP).  ...  Since volume-based registration is limited to image intensities as features, better correspondence is established via registration on cortical surfaces that preserve geometry properties of the cortex.  ... 
doi:10.1117/12.2006459 pmid:24357916 pmcid:PMC3865241 dblp:conf/miip/LyuKSYESSNS13 fatcat:rgeaytwshjc57kdl6jn2hvozue

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 parcellation is obtained using an anatomically constrained surface-based coordinate system from which we define a complete partition of the surface.  ...  The aim of our method is to exhibit a new way to describe the cortical surface organization, in both anatomical and functional terms.  ...  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
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