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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  
across a less restricted range of cortical thickness values.  ...  In the surface-based evaluation, using synthesized thick cortex, the average difference between simulated and extracted surfaces was 4.6 T 1.4 mm for conventional ASP and 0.5 T 0.4 mm for CLASP.  ...  Acknowledgments This work was supported by the Post-doctoral Fellowship Program of Korea Science and Engineering Foundation (KOSEF).  ... 
doi:10.1016/j.neuroimage.2005.03.036 pmid:15896981 fatcat:vtohlijhoja3plmlwwdku4eqii

Small focal cortical dysplasia lesions are located at the bottom of a deep sulcus

Pierre Besson, Frederick Andermann, Francois Dubeau, Andrea Bernasconi
2008 Brain  
Visual assessment of morphological characteristics of FCD and sulci harbouring them is difficult due to the complexity of brain convolutions.  ...  Sulci were identified and labelled automatically using an algorithm based on a congregation of neural networks. Segmented FCD lesions and sulci were then simultaneously visualized in 3D.  ...  A detailed histological examination of surgically resected tissue of patients with pharmacoresistant epilepsy has shown that major gyri may be composed of microscopic gyri with corresponding sulci (Kaufmann  ... 
doi:10.1093/brain/awn224 pmid:18812443 fatcat:xtse7b3hgre5jch7w6oab2hrti

A Library of Cortical Morphology Analysis Tools to Study Development, Aging and Genetics of Cerebral Cortex

Peter Kochunov, William Rogers, Jean-Francois Mangin, Jack Lancaster
2011 Neuroinformatics  
We provide a description of each tool and examples for several case studies to demonstrate their use.  ...  We describe a library of tools developed to quantify global and regional differences in cortical anatomy in high resolution structural MR images.  ...  Acknowledgments This research was supported by the National Institute of Biomedical Imaging and Bioengineering (K01 EB006395) grant to P.K.  ... 
doi:10.1007/s12021-011-9127-9 pmid:21698393 pmcid:PMC3471145 fatcat:awmuxx2g7bhr3humkrephmarnq

Using sulcal and gyral measures of brain structure to investigate benefits of an active lifestyle

Ashley J. Lamont, Moyra E. Mortby, Kaarin J. Anstey, Perminder S. Sachdev, Nicolas Cherbuin
2014 NeuroImage  
However, cortical sulci may provide additional information to these more standard measures.  ...  Method: Associations between physical activity, brain structure, and cognition were investigated in a large, community-based sample of cognitively healthy individuals (N=317) using both sulcal and volumetric  ...  Independent measures of mean depth and width were assessed in both the left and right hemispheres for these five sulci (Figure 2) .  ... 
doi:10.1016/j.neuroimage.2014.01.008 pmid:24434675 fatcat:uqgsoh5hovfxbpeyx64gsnwr24

Robust Cortical Thickness Morphometry of Neonatal Brain and Systematic Evaluation Using Multi-Site MRI Datasets

Mengting Liu, Claude Lepage, Sharon Y. Kim, Seun Jeon, Sun Hyung Kim, Julia Pia Simon, Nina Tanaka, Shiyu Yuan, Tasfiya Islam, Bailin Peng, Knarik Arutyunyan, Wesley Surento (+8 others)
2021 Frontiers in Neuroscience  
Qualitative assessment for reconstructed cortical surfaces shows that 86.9% are rated as accurate across the three site datasets.  ...  The range of the cortical thickness measured was biologically congruent (1.3 mm at 28 weeks of PMA to 1.8 mm at term equivalent).  ...  FUNDING This study was supported by the National Institutes of Health grants (P41EB015922; U54EB020406; U19AG024904; U01NS086090; and 003585-00001).  ... 
doi:10.3389/fnins.2021.650082 pmid:33815050 pmcid:PMC8010150 fatcat:375ffvilgrdq7hgdvxc3emna2e

Cortical thinning in obsessive compulsive disorder

Yong-Wook Shin, So Young Yoo, Jun Ki Lee, Tae Hyon Ha, Kyung Jin Lee, Jong Min Lee, In Young Kim, Sun I. Kim, Jun Soo Kwon
2007 Human Brain Mapping  
With recent advances in neuroimaging technology, it is now possible to study cortical thickness based on cortical surfaces, which offers a direct quantitative index of cortical mass.  ...  Using the constrained Laplacian-based automated segmentation with proximities (CLASP) algorithm, we measured cortical thickness of 55 patients with OCD (33 men and 22 women) and 52 ageand sex-matched healthy  ...  Except part of the posterior central gyri and parietal sulci, most regions had a negative cortical thickness difference (OCD-normal group).  ... 
doi:10.1002/hbm.20338 pmid:17525985 fatcat:5r2qoxsvgbexvbkhnbng7smqbu

Optimized Cortical Subdivision for Classification of Alzheimer's Disease With Cortical Thickness [chapter]

Mirco Richter, Dorit Merhof
2013 Bildverarbeitung für die Medizin 2013  
In several studies, brain atrophy measured by cortical thickness has shown to be a meaningful biomarker for Alzheimer's disease.  ...  In every aspect, superior classification performance was observed as compared to the original parcellation scheme which can be explained by the increased locality of cortical thickness measures and the  ...  By measuring geodesic distances T between those surface points, a pruning function is defined that can be thresholded to separate gyri and sulci at different height levels.  ... 
doi:10.1007/978-3-642-36480-8_8 dblp:conf/bildmed/RichterM13 fatcat:hnctn6d7ejgcla5wezhohfedmq

A comparison between voxel-based cortical thickness and voxel-based morphometry in normal aging

Chloe Hutton, Bogdan Draganski, John Ashburner, Nikolaus Weiskopf
2009 NeuroImage  
The morphology of cortical grey matter is commonly assessed using T1-weighted MRI together with automated computerised methods such as voxel-based morphometry (VBM) and cortical thickness measures.  ...  Our findings suggest that while VBCT selectively investigates cortical thickness, VBM provides a mixed measure of grey matter including cortical surface area or cortical folding, as well as cortical thickness  ...  ., 2006) was used for this purpose. The second modification used a skeletonized representation of the binarised CSF segment to improve the delineation of deep sulci in the brain.  ... 
doi:10.1016/j.neuroimage.2009.06.043 pmid:19559801 pmcid:PMC2741580 fatcat:5rmqz6ol7zhx7nbpsvbnrmhcia

Mindboggling morphometry of human brains [article]

Arno Klein, Satrajit S. Ghosh, Forrest S. Bao, Joachim Giard, Yrjo Hame, Eliezer Stavsky, Noah Lee, Brian Rossa, Martin Reuter, Elias Chaibub Neto, Anisha Keshavan
2016 bioRxiv   pre-print
Mindboggle computes a variety of (primarily surface-based) shapes: area, volume, thickness, curvature, depth, Laplace-Beltrami spectra, Zernike moments, etc.  ...  Very few software algorithms provide more than measures of volume and cortical thickness, and more subtle shape measures may provide more sensitive and specific biomarkers.  ...  For 16 cortical regions in the 40 subjects, we measured scan-rescan reliability of 745 cortical thickness measures, and we compared thickness measures with published estimates based on 746 manual delineations  ... 
doi:10.1101/091322 fatcat:kfgcikresvcntlem6eyrjh2lmu

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  
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.  ...  This paper describes a comprehensive approach for cortical reconstruction, flattening, and sulcal segmentation.  ...  Noor Kabani for providing the hand-labeled atlas data and Kirsten Behnke for assistance with the atlas data. This work was supported in part by NIH/NINDS Grant R01NS37747.  ... 
doi:10.1016/j.neuroimage.2004.07.042 pmid:15501080 pmcid:PMC4587756 fatcat:5poegzjszvhnpfq7zha2haka24

Altered grey matter volume, perfusion and white matter integrity in very low birthweight adults

Maddie J. Pascoe, Tracy R. Melzer, L. John Horwood, Lianne J. Woodward, Brian A. Darlow
2019 NeuroImage: Clinical  
MRI analyses included: a) structural MRI to assess grey matter (GM) volume and cortical thickness; b) arterial spin labelling (ASL) to quantify GM perfusion; and c) diffusion tensor imaging (DTI) to measure  ...  Of the 338 who survived to discharge, 229 were assessed at age 27-29 years. Of these, 150 had a 3 T MRI scan alongside 50 healthy term-born controls.  ...  Acknowledgements We thank all of the young participants for their willingness to take part in this study. We are grateful to Julia Martin, the Project Manager, and Dr.  ... 
doi:10.1016/j.nicl.2019.101780 pmid:30925384 pmcid:PMC6438988 fatcat:2ok2x2oe3nbztksu56dfgyhafu

System for Integrated Neuroimaging Analysis and Processing of Structure

Bennett A. Landman, John A. Bogovic, Aaron Carass, Min Chen, Snehashis Roy, Navid Shiee, Zhen Yang, Bhaskar Kishore, Dzung Pham, Pierre-Louis Bazin, Susan M. Resnick, Jerry L. Prince
2012 Neuroinformatics  
Mapping brain structure in relation to neurological development, function, plasticity, and disease is widely considered to be one of the most essential challenges for opening new lines of neuro-scientific  ...  Robust and consistent estimates of the cortical surface extraction, cortical labeling, diffusion-inferred contrasts, diffusion tractography, and subcortical parcellation are demonstrated in a scan-rescan  ...  Acknowledgments The authors are appreciative of the careful feedback from the anonymous reviewers and editor (Dr. David Kennedy).  ... 
doi:10.1007/s12021-012-9159-9 pmid:22932976 pmcid:PMC3511612 fatcat:krgqmregs5hqnm3isklageiqi4

Voxel-based cortical thickness measurements in MRI

Chloe Hutton, Enrico De Vita, John Ashburner, Ralf Deichmann, Robert Turner
2008 NeuroImage  
Here we present a method for automatically generating voxel-based cortical thickness (VBCT) maps. This technique results in maps where each voxel in the grey matter is assigned a thickness value.  ...  Sub-voxel measurements of thickness are possible using sub-sampling and interpolation of the image information.  ...  Automated methods for measuring cortical thickness in MRI may be categorized as either surface-based, voxel-based or a mixture of the two.  ... 
doi:10.1016/j.neuroimage.2008.01.027 pmid:18325790 pmcid:PMC2330066 fatcat:x4kryszslzbjjceeqho57xuzwa

Measurement of cortical thickness from MRI by minimum line integrals on soft-classified tissue

Iman Aganj, Guillermo Sapiro, Neelroop Parikshak, Sarah K. Madsen, Paul M. Thompson
2009 Human Brain Mapping  
In this work, we present a framework for measuring the cortical thickness, based on minimizing line integrals over the probability map of the gray matter in the MRI volume.  ...  Then, the thickness is basically defined for each voxel as the minimum line integral of the probability map on line segments centered at the point of interest.  ...  Acknowledgments This work was supported in part by the National Institutes of Health (NIH), the National Science Foundation (NSF), the National Center for Research Resources (P41 RR14075), the National  ... 
doi:10.1002/hbm.20740 pmid:19219850 pmcid:PMC2903209 fatcat:yybvw3c2ovgmjjw3kynpestdsq

Mindboggling morphometry of human brains

Arno Klein, Satrajit S. Ghosh, Forrest S. Bao, Joachim Giard, Yrjö Häme, Eliezer Stavsky, Noah Lee, Brian Rossa, Martin Reuter, Elias Chaibub Neto, Anisha Keshavan, Dina Schneidman
2017 PLoS Computational Biology  
Mindboggle computes a variety of (primarily surface-based) shapes: area, volume, thickness, curvature, depth, Laplace-Beltrami spectra, Zernike moments, etc.  ...  Very few software algorithms provide more than measures of volume and cortical thickness, while more subtle shape measures may provide more sensitive and specific biomarkers.  ...  Software and online resources that have benefitted the project include:,, and PyCharm for software development; Open Science Framework, Harvard Dataverse, and for  ... 
doi:10.1371/journal.pcbi.1005350 pmid:28231282 pmcid:PMC5322885 fatcat:lsqa2kigtzfivlkqzrnmkri37u
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