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Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex
, 2001
"... Highly accurate surface models of the cerebral cortex are becoming increasingly important as tools in the investigation of the functional organization of the human brain. The construction of such models is difficult using current neuroimaging technology due to the high degree of cortical folding. E ..."
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Cited by 167 (25 self)
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Highly accurate surface models of the cerebral cortex are becoming increasingly important as tools in the investigation of the functional organization of the human brain. The construction of such models is difficult using current neuroimaging technology due to the high degree of cortical folding. Even single voxel misclassifications can result in erroneous connections being created between adjacent banks of a sulcus, resulting in a topologically inaccurate model. These topological defects cause the cortical model to no longer be homeomorphic to a sheet, preventing the accurate inflation, flattening, or spherical morphing of the reconstructed cortex. Surface deformation techniques can guarantee the topological correctness of a model, but are timeconsuming and may result in geometrically inaccurate models. In order to address this need we have developed a technique for taking a model of the cortex, detecting and fixing the topological defects while leaving that majority of the model intact, resulting in a surface that is both geometrically accurate and topologically correct.
A topology preserving level set method for geometric deformable models
 IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
, 2003
"... Active contour and surface models, also known as deformable models, are powerful image segmentation techniques. Geometric deformable models implemented using level set methods have advantages over parametric models due to their intrinsic behavior, parameterization independence, and ease of implement ..."
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Cited by 117 (7 self)
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Active contour and surface models, also known as deformable models, are powerful image segmentation techniques. Geometric deformable models implemented using level set methods have advantages over parametric models due to their intrinsic behavior, parameterization independence, and ease of implementation. However, a long claimed advantage of geometric deformable models—the ability to automatically handle topology changes—turns out to be a liability in applications where the object to be segmented has a known topology that must be preserved. In this paper, we present a new class of geometric deformable models designed using a novel topologypreserving level set method, which achieves topology preservation by applying the simple point concept from digital topology. These new models maintain the other advantages of standard geometric deformable models including subpixel accuracy and production of nonintersecting curves or surfaces. Moreover, since the topologypreserving constraint is enforced efficiently through local computations, the resulting algorithm incurs only nominal computational overhead over standard geometric deformable models. Several experiments on simulated and real data are provided to demonstrate the performance of this new deformable model algorithm.
Image segmentation using deformable models
 Handbook of Medical Imaging. Vol.2 Medical Image Processing and Analysis
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Topology correction in brain cortex segmentation using a multiscale, graphbased algorithm
 IEEE Trans. Med. Imaging
, 2002
"... Abstract — Reconstructing an accurate and topologically correct representation of the cortical surface of the brain is an important objective in various neuroscience applications. Most cortical surface reconstruction methods either ignore topology or correct it using manual editing or methods that l ..."
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Cited by 66 (7 self)
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Abstract — Reconstructing an accurate and topologically correct representation of the cortical surface of the brain is an important objective in various neuroscience applications. Most cortical surface reconstruction methods either ignore topology or correct it using manual editing or methods that lead to inaccurate reconstructions. Shattuck and Leahy recently reported a fullyautomatic method that yields a topologically correct representation with little distortion of the underlying segmentation. We provide an alternate approach that has several advantages over their approach, including the use of arbitrary digital connectivities, a flexible morphologybased multiscale approach, and the option of foregroundonly or backgroundonly correction. A detailed analysis of the method's performance on 15 magnetic resonance brain images is provided.
Computational anatomy: Shape, growth, and atrophy comparison via diffeomorphisms
 NeuroImage
, 2004
"... Computational anatomy (CA) is the mathematical study of anatomy I a I = I a BG, an orbit under groups of diffeomorphisms (i.e., smooth invertible mappings) g a G of anatomical exemplars Iaa I. The observable images are the output of medical imaging devices. There are three components that CA examine ..."
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Cited by 62 (2 self)
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Computational anatomy (CA) is the mathematical study of anatomy I a I = I a BG, an orbit under groups of diffeomorphisms (i.e., smooth invertible mappings) g a G of anatomical exemplars Iaa I. The observable images are the output of medical imaging devices. There are three components that CA examines: (i) constructions of the anatomical submanifolds, (ii) comparison of the anatomical manifolds via estimation of the underlying diffeomorphisms g a G defining the shape or geometry of the anatomical manifolds, and (iii) generation of probability laws of anatomical variation P(d) on the images I for inference and disease testing within anatomical models. This paper reviews recent advances in these three areas applied to shape, growth, and atrophy.
Fast and robust parameter estimation for statistical partial volume models in brain MRI
 NEUROIMAGE
, 2004
"... Due to the finite spatial resolution of imaging devices, a single voxel in a medical image may be composed of mixture of tissue types, an effect known as partial volume effect (PVE). Partial volume estimation, that is, the estimation of the amount of each tissue type within each voxel, has received ..."
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Cited by 54 (11 self)
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Due to the finite spatial resolution of imaging devices, a single voxel in a medical image may be composed of mixture of tissue types, an effect known as partial volume effect (PVE). Partial volume estimation, that is, the estimation of the amount of each tissue type within each voxel, has received considerable interest in recent years. Much of this work has been focused on the mixel model, a statistical model of PVE. We propose a novel trimmed minimum covariance determinant (TMCD) method for the estimation of the parameters of the mixel PVE model. In this method, each voxel is first labeled according to the most dominant tissue type. Voxels that are prone to PVE are removed from this labeled set, following which robust location estimators with high breakdown points are used to estimate the mean and the covariance of each tissue class. Comparisons between different methods for parameter estimation based on classified images as well as expectation–maximizationlike (EMlike) procedure for simultaneous parameter and
An Eulerian PDE approach for computing tissue thickness
 IEEE Transactions on Medical Imaging
, 2003
"... Abstract—We outline an Eulerian framework for computing the thickness of tissues between two simply connected boundaries that does not require landmark points or parameterizations of either boundary. Thickness is defined as the length of correspondence trajectories, which run from one tissue boundar ..."
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Cited by 39 (5 self)
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Abstract—We outline an Eulerian framework for computing the thickness of tissues between two simply connected boundaries that does not require landmark points or parameterizations of either boundary. Thickness is defined as the length of correspondence trajectories, which run from one tissue boundary to the other, and which follow a smooth vector field constructed in the region between the boundaries. A pair of partial differential equations (PDEs) that are guided by this vector field are then solved over this region, and the sum of their solutions yields the thickness of the tissue region. Unlike other approaches, this approach does not require explicit construction of any correspondence trajectories. An efficient, stable, and computationally fast solution to these PDEs is found by careful selection of finite differences according to an upwinding condition. The behavior and performance of our method is demonstrated on two simulations and two magnetic resonance imaging data sets in two and three dimensions. These experiments reveal very good performance and show strong potential for application in tissue thickness visualization and quantification. Index Terms—Correspondence trajectory, numerical methods, partial differential equations (PDEs), thickness. I.
CRUISE: Cortical reconstruction using implicit surface evolution
 NeuroImage
, 2004
"... Segmentation and representation of the human cerebral cortex from magnetic resonance (MR) images play an important role in neuroscience and medicine. A successful segmentation method must be robust to various imaging artifacts and produce anatomically meaningful and consistent cortical representatio ..."
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Cited by 33 (3 self)
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Segmentation and representation of the human cerebral cortex from magnetic resonance (MR) images play an important role in neuroscience and medicine. A successful segmentation method must be robust to various imaging artifacts and produce anatomically meaningful and consistent cortical representations. A method for the automatic reconstruction of the inner, central, and outer surfaces of the cerebral cortex from T1weighted MR brain images is presented. The method combines a fuzzy tissue classification method, an efficient topology correction algorithm, and a topologypreserving 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. Validation results on real MR data are presented to demonstrate the performance of the method.
Deformable Registration of Cortical Structures Via Hybrid Volumetric and Surface Warping
, 2004
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Atlas Renormalization for Improved Brain MR Image Segmentation Across Scanner Platforms
"... Abstract—Atlasbased approaches have demonstrated the ability to automatically identify detailed brain structures from 3D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse se ..."
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Cited by 30 (2 self)
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Abstract—Atlasbased approaches have demonstrated the ability to automatically identify detailed brain structures from 3D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlasbased whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10 % or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. Index Terms—Brain atlas, brain imaging, computational neuroanatomy, magnetic resonance imaging (MRI) segmentation. I.