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ABLE: Automated Brain Lines Extraction Based on Laplacian Surface Collapse [article]

Alberto Fernández-Pena, Daniel Martín de Blas, Francisco J. Navas-Sánchez, Luis Marcos-Vidal, Pedro M. Gordaliza, Javier Santonja, Joost Janssen, Susanna Carmona, Manuel Desco, Yasser Alemán-Gómez
2022 bioRxiv   pre-print
We present Automated Brain Lines Extraction (ABLE), a method based on Laplacian surface collapse to segment sulcal fundi and gyral crown lines reliably.  ...  This problem can be avoided by focusing on sulcal fundi and gyral crowns which represent the topological opposites of cortical folding.  ...  To solve this problem, some methods extract the endpoints directly during the sulcal eroding step 26 or using adaptive thresholding of the Geodesic Path Density Maps (GPDM) 22 .  ... 
doi:10.1101/2022.01.18.476370 fatcat:zd7mojixdzd55jn6leptm5dz5a

A Geometric Method for Automatic Extraction of Sulcal Fundi

Chiu-Yen Kao, Michael Hofer, Guillermo Sapiro, Josh Stern, Kelly Rehm, David A. Rottenberg
2007 IEEE Transactions on Medical Imaging  
We present a sequence of geometric algorithms which automatically extract the sulcal fundi from magnetic resonance images and represent them as smooth polylines lying on the cortical surface.  ...  First we compute a geometric depth measure for each point on the cortical surface, and based on this information we extract sulcal regions by checking the connectivity above a depth threshold.  ...  a flat map of the cortical surface [15] .  ... 
doi:10.1109/tmi.2006.886810 pmid:17427740 fatcat:qex7s2vpyfgtrcwieqoeqzvzwi

Joint Sulcal Detection on Cortical Surfaces With Graphical Models and Boosted Priors

Yonggang Shi, Zhuowen Tu, A.L. Reiss, R.A. Dutton, A.D. Lee, A.M. Galaburda, I. Dinov, P.M. Thompson, A.W. Toga
2009 IEEE Transactions on Medical Imaging  
In this paper, we propose an automated approach for the joint detection of major sulci on cortical surfaces.  ...  Using the AdaBoost algorithm, we learn both individual and pairwise shape priors of sulcal curves from training data, which are then used to define potential functions in the graphical model based on the  ...  of anatomical quantities defined on cortical surfaces such as gray matter densities.  ... 
doi:10.1109/tmi.2008.2004402 pmid:19244008 pmcid:PMC2754577 fatcat:qxc66v74pvblpewexuo2u2fx6q

Consistent sulcal parcellation of longitudinal cortical surfaces

Gang Li, Dinggang Shen
2011 NeuroImage  
However, applying the existing methods (which were typically developed for cortical sulcal parcellation of a single cortical surface) independently to longitudinal cortical surfaces might generate longitudinally-inconsistent  ...  The proposed method has been successfully applied to sulcal parcellation of both real and simulated longitudinal inner cortical surfaces of human brain MR images.  ...  In addition, automatic sulcal parcellation of cortical surfaces is of great importance in structural and functional mapping of human brains.  ... 
doi:10.1016/j.neuroimage.2011.03.064 pmid:21473919 pmcid:PMC3101304 fatcat:btnrmb7ryfbu3eus3cdm2ugp6u

Hamilton–Jacobi Skeleton on Cortical Surfaces

Yonggang Shi, P.M. Thompson, I. Dinov, A.W. Toga
2008 IEEE Transactions on Medical Imaging  
Compared with previous work that uses skeletons of 3D volumes to represent sulcal patterns, the skeletons on cortical surfaces can be easily decomposed into branches and provide a simpler way to construct  ...  In our approach, a cortical surface is first partitioned into sulcal and gyral regions via the solution of a variational problem using graph cuts, which can guarantee global optimality.  ...  Using the skeleton of the sulcal regions on a cortical surface, our system generates a sample space for each major sulcal line.  ... 
doi:10.1109/tmi.2007.913279 pmid:18450539 pmcid:PMC2754588 fatcat:6ibv3kci6jd7nnv6fkyk4n2tmm

A cortical shape-adaptive approach to local gyrification index

Ilwoo Lyu, Sun Hyung Kim, Jessica B. Girault, John H. Gilmore, Martin A. Styner
2018 Medical Image Analysis  
The amount of cortical folding, or gyrification, is typically measured within local cortical regions covered by an equidistant geodesic or nearest neighborhood-ring kernel.  ...  In general, our method yields sharper and more detailed statistical maps that associate cortical folding with sex and gestational age.  ...  Pizer for his consultation on differential geometry issues, Joohwi Lee for his help with the hull correspondence, and Shaili C. Jha for her support of the cortical surface reconstruction.  ... 
doi:10.1016/ pmid:29990689 pmcid:PMC6167255 fatcat:br77lsfdtbb3llstnktvzvinhq

Characterization of U-shape streamline fibers: Methods and applications

Tuo Zhang, Hanbo Chen, Lei Guo, Kaiming Li, Longchuan Li, Shu Zhang, Dinggang Shen, Xiaoping Hu, Tianming Liu
2014 Medical Image Analysis  
sulci based on DTI, HARDI, and DSI datasets of human, chimpanzee and macaque brains.  ...  Diffusion tensor imaging (DTI), high angular resolution diffusion imaging (HARDI), and Diffusion Spectrum Imaging (DSI) have been widely used in the neuroimaging field to examine the macro-scale fiber  ...  Supplementary Material Refer to Web version on PubMed Central for supplementary material. (a) Illustration of extracting gyral crest line on cortical surface.  ... 
doi:10.1016/ pmid:24835185 pmcid:PMC4122429 fatcat:xkllcu5fqzc3flmepgmi3a6lte

Cortical Shape Analysis in the Laplace-Beltrami Feature Space [chapter]

Yonggang Shi, Ivo Dinov, Arthur W. Toga
2009 Lecture Notes in Computer Science  
Using the eigenfunction of the Laplace-Beltrami operator, we propose in this paper a novel feature space to characterize the cortical geometry.  ...  For the automated analysis of cortical morphometry, it is critical to develop robust descriptions of the position of anatomical structures on the convoluted cortex.  ...  The automatically detected sulcal curves on these surfaces are plotted in Fig. 5 .  ... 
doi:10.1007/978-3-642-04271-3_26 fatcat:drn3my7pyjf6hensu2pnivc6hi

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  
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.  ...  In this article, we document the software and demonstrate its use in studies of shape variation in healthy and diseased humans.  ...  The travel depth algorithm constructs a combination of Euclidean paths outside the cortical surface and estimated geodesic paths along the cortical surface.  ... 
doi:10.1371/journal.pcbi.1005350 pmid:28231282 pmcid:PMC5322885 fatcat:lsqa2kigtzfivlkqzrnmkri37u

Anatomo-functional correspondence in the superior temporal sulcus

C. Bodin, S. Takerkart, P. Belin, O. Coulon
2017 Brain Structure and Function  
To do so, anatomical and functional scans of 116 subjects were processed such as to generate individual surface maps on which both depth and functional voice activity can be analyzed.  ...  Individual depth profiles of manually drawn STS and functional profiles from a voice localizer (voice [ non-voice) maps were extracted and compared to assess anatomo-functional correspondences.  ...  Surface-based functional maps Individual 3D functional maps were projected on the corresponding 2D cortical mesh representation (Fig. 1b) using the method presented in Operto et al. (2008) , resulting  ... 
doi:10.1007/s00429-017-1483-2 pmid:28756487 fatcat:vjjot22nezfobfxs5w4bq4rmpa

Cortical hot spots and labyrinths: why cortical neuromodulation for episodic migraine with aura should be personalized

Markus A. Dahlem, Bernd Schmidt, Ingo Bojak, Sebastian Boie, Frederike Kneer, Nouchine Hadjikhani, Jürgen Kurths
2015 Frontiers in Computational Neuroscience  
In particular, we firstly focus exclusively on curvature-induced dynamical properties by studying a generic reaction-diffusion model of SD on the folded cortical surface.  ...  This surface is described with increasing level of details, including finally personalized simulations using patient's magnetic resonance imaging (MRI) scanner readings.  ...  Gaussian Curvature K for a Discretised Cortical Surface To determine the Gaussian curvature, we use a cortical surface originally extracted with CIVET (Kim et al., 2005) .  ... 
doi:10.3389/fncom.2015.00029 pmid:25798103 pmcid:PMC4350394 fatcat:7zqhm5mupnby3bzxkiysl5fuu4

Multimodal MRI profiling of focal cortical dysplasia type II

Seok-Jun Hong, Boris C. Bernhardt, Benoit Caldairou, Jeffery A. Hall, Marie C. Guiot, Dewi Schrader, Neda Bernasconi, Andrea Bernasconi
2017 Neurology  
Geodesic distance mapping quantified the same features in the lesion perimeter.  ...  A multisurface approach operating on manual consensus labels systematically sampled intracortical and subcortical lesional features.  ...  to the Euclidian distance that measures the straight line distance, the geodesic distance, defined as the length of the shortest path between 2 vertices along the cortical surface, respects topology.  ... 
doi:10.1212/wnl.0000000000003632 pmid:28130467 pmcid:PMC5344077 fatcat:2gvlvhplcfesxcq5t456hlrjsy

Statistical Computing on Non-Linear Spaces for Computational Anatomy [chapter]

X. Pennec, P. Fillard
2015 Handbook of Biomedical Imaging  
Moreover, the geometric nature of the anatomical features usually extracted raises the need for statistics on objects like curves, surfaces and deformations that do not belong to standard Euclidean spaces  ...  This computational framework is illustrated with the analysis of the shape of the scoliotic spine and the modeling of the brain variability from sulcal lines where the results suggest new anatomical findings  ...  lines [44, 41, 29] , surfaces like the cortical surface or sulcal ribbons [68, 1, 72] , images seen as 3D functions, which lead to voxel-based morphometry (VBM) [6] , diffusion imaging or rigid, multiaffine  ... 
doi:10.1007/978-0-387-09749-7_8 fatcat:c5o4rmqf6jahtag34zsilzhavy

Entropy-based particle correspondence for shape populations

Ipek Oguz, Josh Cates, Manasi Datar, Beatriz Paniagua, Thomas Fletcher, Clement Vachet, Martin Styner, Ross Whitaker
2015 International Journal of Computer Assisted Radiology and Surgery  
The alignment is based on two curvature-related measures; a multi-spectral optical flow algorithm is used to warp the subject cortical surface into the atlas.  ...  Wang et al. [20] propose using geodesic interpolation of a sparse set of corresponding points. Oguz et al.  ...  For example, to align cortical surfaces, we extract the sulcal curves and align these in a pairwise manner to initialize the entropy-based correspondence in [11] .  ... 
doi:10.1007/s11548-015-1319-6 pmid:26646417 pmcid:PMC4899300 fatcat:zcjbu3z2tnex5kqwqzdbrjx77e

Adaptive reproducing kernel particle method for extraction of the cortical surface

Meihe Xu, P.M. Thompson, A.W. Toga
2006 IEEE Transactions on Medical Imaging  
We also compare the proposed method to the finite element method, and to a commonly used cortical surface extraction approach, the CRUISE method.  ...  We propose a novel adaptive approach based on the Reproducing Kernel Particle Method (RKPM) to extract the cortical surfaces of the brain from three-dimensional (3-D) magnetic resonance images (MRIs).  ...  Information on the National Centers for Biomedical Computing can be obtained from  ... 
doi:10.1109/tmi.2006.873614 pmid:16768240 fatcat:nqe3ti6wvfgfzlmo55zhtqbhl4
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