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Automated 3-D extraction and evaluation of the inner and outer cortical surfaces using a Laplacian map and partial volume effect classification

June Sic Kim, Vivek Singh, Jun Ki Lee, Jason Lerch, Yasser Ad-Dab'bagh, David MacDonald, Jong Min Lee, Sun I. Kim, Alan C. Evans
2005 NeuroImage  
In the volume-based evaluation, the volume enclosed by the CLASP WM and GM surfaces matched the classified GM volume 13% more accurately than using conventional ASP.  ...  This paper presents a novel method for improving the conventional ASP algorithm by making use of partial volume information through probabilistic classification in order to allow for topology preservation  ...  The process is guided (in a manner that is outlined in the next section) by the use of partial volume CSF in order to insure correct sulcal morphology.  ... 
doi:10.1016/j.neuroimage.2005.03.036 pmid:15896981 fatcat:vtohlijhoja3plmlwwdku4eqii

Loss of cerebral white matter structural integrity tracks the gray matter metabolic decline in normal aging☆

P. Kochunov, A.E. Ramage, J.L. Lancaster, D.A. Robin, S. Narayana, T. Coyle, D.R. Royall, P. Fox
2009 NeuroImage  
measurements were converted to standard uptake values and corrected for partial volume artifact.  ...  span and HWM volumes.  ...  Surface-based analysis of cortical 18 FDG GM uptake-Cortical 18 FDG PET uptake measurements were calculated using a surface-based analysis before and after correction for partial volume averaging artifact  ... 
doi:10.1016/j.neuroimage.2008.11.010 pmid:19095067 pmcid:PMC2734283 fatcat:yo64lrezkna5tndoeg2nyvg6f4

FDDNP binding using MR derived cortical surface maps

H.D. Protas, S.-C. Huang, V. Kepe, K. Hayashi, A. Klunder, M.N. Braskie, L. Ercoli, S. Bookheimer, P.M. Thompson, G.W. Small, J.R. Barrio
2010 NeuroImage  
movement and partial volume (PV), and optimized for kernel size.  ...  Discriminant analysis was used to order the FDDNP DVR cortical surfaces based on subjects' disease state. Linear regression was used to assess the rate of change of DVR vs.  ...  Koon-Pong Wong, and Weber Shao for their help with movement correction of PET images.  ... 
doi:10.1016/j.neuroimage.2009.08.035 pmid:19703569 pmcid:PMC2764817 fatcat:gqaziarmtjberkwl6zpo3yv5oi

Automatic Delineation of Sulci and Improved Partial Volume Classification for Accurate 3D Voxel-Based Cortical Thickness Estimation from MR [chapter]

Oscar Acosta, Pierrick Bourgeat, Jurgen Fripp, Erik Bonner, Sébastien Ourselin, Olivier Salvado
2008 Lecture Notes in Computer Science  
When using magnetic resonance images (MRI), accuracy may be hampered by artifacts such as partial volume (PV) as the cortex spans only a few voxels.  ...  The aim of this work is to propose a voxel-based cortical thickness estimation method from MR by integrating a mechanism for correcting sulci delineation after an improved partial volume classification  ...  Then, the resulting skeletonized surface combined with the partial volume maps are used to correct the hard segmentations for computing the thickness.  ... 
doi:10.1007/978-3-540-85988-8_31 fatcat:mrptrrbwsrcvtpx4y5z3dbhptm

A framework to analyze cerebral mean diffusivity using surface guided diffusion mapping in diffusion tensor imaging

Oh-Hun Kwon, Hyunjin Park, Sang-Won Seo, Duk L. Na, Jong-Min Lee
2015 Frontiers in Neuroscience  
Diffusion tensor imaging of the brain: review of and outer cortical surfaces using a laplacian map and partial volume clinical applications.  ...  (B) The cortical surface superimposed in the MD volume. The MD volume was aligned the T1-weighted volume to correct for contamination by CSF.  ... 
doi:10.3389/fnins.2015.00236 pmid:26236180 pmcid:PMC4500906 fatcat:pncr75klbncz3jl4vythjrvj7m

Cortical surface segmentation and mapping

Duygu Tosun, Maryam E. Rettmann, Xiao Han, Xiaodong Tao, Chenyang Xu, Susan M. Resnick, Dzung L. Pham, Jerry L. Prince
2004 NeuroImage  
This paper describes a comprehensive approach for cortical reconstruction, flattening, and sulcal segmentation.  ...  Results demonstrating the application of this approach to a study of cortical thickness changes in aging are presented. D 2004 Elsevier Inc. All rights reserved.  ...  We note that all processing is done on the original cortical surface-the partially flattened surface is used for visualization only.  ... 
doi:10.1016/j.neuroimage.2004.07.042 pmid:15501080 pmcid:PMC4587756 fatcat:5poegzjszvhnpfq7zha2haka24

CRUISE: Cortical reconstruction using implicit surface evolution

Xiao Han, Dzung L. Pham, Duygu Tosun, Maryam E. Rettmann, Chenyang Xu, Jerry L. Prince
2004 NeuroImage  
The method combines a fuzzy tissue classification method, an efficient topology correction algorithm, and a topology-preserving geometric deformable surface model (TGDM).  ...  The algorithm is fast and numerically stable, and yields accurate brain surface reconstructions that are guaranteed to be topologically correct and free from selfintersections.  ...  Xiaodong Tao for providing software that was used in the validation studies. This work was supported in part by NIH/NINDS Grant R01NS37747.  ... 
doi:10.1016/j.neuroimage.2004.06.043 pmid:15528100 fatcat:hv3wfe2i4jcljbcgj2435oawpy

Regionally Specific Cortical Thinning and Gray Matter Abnormalities in the Healthy Relatives of Schizophrenia Patients

V. M. Goghari, K. Rehm, C. S. Carter, A. W. MacDonald
2006 Cerebral Cortex  
To investigate the nature of cortical abnormalities in the healthy relatives of patients, this study used magnetic resonance imaging to evaluate gray matter volume, surface area, and thickness of 13 regions  ...  Cortical thickness and surface area are additional indicators of cortical cytoarchitectural integrity.  ...  To improve the accuracy of tissue classification and cortical surface extraction, whole-brain volumes were intensity corrected using nonparametric nonuniform intensity normalization (N3, Sled and others  ... 
doi:10.1093/cercor/bhj158 pmid:16547347 fatcat:t24lwc34ujfopfsbm6ykno377e

Diffusion properties of cortical and pericortical tissue: regional variations, reliability and methodological issues

Xiaojian Kang, Timothy J. Herron, U. Turken, David L. Woods
2012 Magnetic Resonance Imaging  
The measurement of FA, MD and cPDD near the cortical surface clarifies the organization of fiber projections to and from the cortex.  ...  5 mm from the pial surface into white matter.  ...  The views expressed herein do not necessarily reflect the views of the US Department of Veterans Affairs or the United States Government.  ... 
doi:10.1016/j.mri.2012.04.004 pmid:22698767 fatcat:dlyube46ffemnbtqysz7qydaqa

BrainSuite: An Automated Cortical Surface Identification Tool [chapter]

David W. Shattuck, Richard M. Leahy
2000 Lecture Notes in Computer Science  
In this paper we describe the theory of each stage of the cortical surface identification process. We then present validation results using real and phantom data.  ...  We describe a new magnetic resonance (MR) image analysis tool that produces cortical surface representations with spherical topology from MR images of the human brain.  ...  MR imaging offers neuroanatomical detail, but extraction of cortical surfaces from MR imagery faces several problems, including measurement noise, partial volume effects, and image nonuniformity due to  ... 
doi:10.1007/978-3-540-40899-4_6 fatcat:qy22ko42dfcpffp54rwljuceym

BrainSuite: An automated cortical surface identification tool

David W Shattuck, Richard M Leahy
2002 Medical Image Analysis  
In this paper we describe the theory of each stage of the cortical surface identification process. We then present validation results using real and phantom data.  ...  We describe a new magnetic resonance (MR) image analysis tool that produces cortical surface representations with spherical topology from MR images of the human brain.  ...  MR imaging offers neuroanatomical detail, but extraction of cortical surfaces from MR imagery faces several problems, including measurement noise, partial volume effects, and image nonuniformity due to  ... 
doi:10.1016/s1361-8415(02)00054-3 pmid:12045000 fatcat:twtgqwnxhfahhlqwuexjfvlliu

Regional growth and atlasing of the developing human brain

Antonios Makropoulos, Paul Aljabar, Robert Wright, Britta Hüning, Nazakat Merchant, Tomoki Arichi, Nora Tusor, Joseph V. Hajnal, A. David Edwards, Serena J. Counsell, Daniel Rueckert
2016 NeuroImage  
Whole brain volume, the absolute volume of all structures studied, cortical curvature and cortical surface area increased with increasing age at scan.  ...  Preterm infants at term had smaller whole brain volumes, reduced regional white matter and cortical and subcortical grey matter volumes, and reduced cortical surface area compared with term born controls  ...  without correction for the CGM-WM partial volume and sulci correction.  ... 
doi:10.1016/j.neuroimage.2015.10.047 pmid:26499811 pmcid:PMC4692521 fatcat:ihpvnbpfkrfhngp4ld4bimjz4q

Relationships between IQ and Regional Cortical Gray Matter Thickness in Healthy Adults

K. L. Narr, R. P. Woods, P. M. Thompson, P. Szeszko, D. Robinson, T. Dimtcheva, M. Gurbani, A. W. Toga, R. M. Bilder
2006 Cerebral Cortex  
Cortical thickness may more closely reflect cytoarchitectural characteristics than gray matter density or volume estimates.  ...  Positive relationships were found between FSIQ and intracranial gray and white matter but not cerebrospinal fluid volumes.  ...  of gray matter, white matter, and cerebrospinal fluid (CSF) using a partial volume correction method (Shattuck et al. 2001) .  ... 
doi:10.1093/cercor/bhl125 pmid:17118969 fatcat:v3o6muqizbdohasn7izapmuplq

An Automated Pipeline for the Analysis of PET Data on the Cortical Surface

Arnaud Marcoux, Ninon Burgos, Anne Bertrand, Marc Teichmann, Alexandre Routier, Junhao Wen, Jorge Samper-González, Simona Bottani, Stanley Durrleman, Marie-Odile Habert, Olivier Colliot, for the Alzheimer's Disease Neuroimaging Initiative
2018 Frontiers in Neuroinformatics  
Our pipeline combines tools from FreeSurfer and PETPVC, and consists of (i) co-registration of PET and T1-w MRI (T1) images, (ii) intensity normalization, (iii) partial volume correction, (iv) robust projection  ...  We present a fully automatic pipeline for the analysis of PET data on the cortical surface.  ...  The PET image, after partial volume correction performed using the parcellation, is robustly projected onto the cortical surface.  ... 
doi:10.3389/fninf.2018.00094 pmid:30618699 pmcid:PMC6296445 fatcat:5u4tcsec5jgsfmsu2n5a5slyc4

Joint Analysis of Cortical Area and Thickness as a Replacement for the Analysis of the Volume of the Cerebral Cortex

Anderson M Winkler, Douglas N Greve, Knut J Bjuland, Thomas E Nichols, Mert R Sabuncu, Asta K Håberg, Jon Skranes, Lars M Rimol
2017 Cerebral Cortex  
Cortical surface area is an increasingly used brain morphology metric that is ontogenetically and phylogenetically distinct from cortical thickness and offers a separate index of neurodevelopment and disease  ...  We use the methods to analyze area, thickness and volume in young adults born preterm with very low birth weight, and show that NPC analysis is a more sensitive option for studying joint effects on area  ...  Volume can be estimated through the use of voxelwise partial volume effects using a volume-based representation of the brain, such as in VBM, or from a surface representation, in which it can be measured  ... 
doi:10.1093/cercor/bhx308 pmid:29190325 pmcid:PMC5972607 fatcat:tcb4gnzpefdademztlq3oai5wa
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