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Journal ArticleDOI

An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest.

TL;DR: An automated labeling system for subdividing the human cerebral cortex into standard gyral-based neuroanatomical regions is both anatomically valid and reliable and may be useful for both morphometric and functional studies of the cerebral cortex.
About: This article is published in NeuroImage.The article was published on 2006-07-01. It has received 9940 citations till now.
Citations
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Journal ArticleDOI
TL;DR: The minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space are described.

3,992 citations


Cites background from "An automated labeling system for su..."

  • ..., 1999b), and automated segmentation of sulci and gyri (Desikan et al., 2006) are among the steps done during this recon-all stage....

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  • ...Spherical inflation of the white matter surface (Fischl et al., 1999a), registration to the fsaverage surface template based on cortical folding patterns (Fischl et al., 1999b), and automated segmentation of sulci and gyri (Desikan et al., 2006) are among the steps done during this recon-all stage....

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Journal ArticleDOI
11 Aug 2016-Nature
TL;DR: Using multi-modal magnetic resonance images from the Human Connectome Project and an objective semi-automated neuroanatomical approach, 180 areas per hemisphere are delineated bounded by sharp changes in cortical architecture, function, connectivity, and/or topography in a precisely aligned group average of 210 healthy young adults.
Abstract: Understanding the amazingly complex human cerebral cortex requires a map (or parcellation) of its major subdivisions, known as cortical areas. Making an accurate areal map has been a century-old objective in neuroscience. Using multi-modal magnetic resonance images from the Human Connectome Project (HCP) and an objective semi-automated neuroanatomical approach, we delineated 180 areas per hemisphere bounded by sharp changes in cortical architecture, function, connectivity, and/or topography in a precisely aligned group average of 210 healthy young adults. We characterized 97 new areas and 83 areas previously reported using post-mortem microscopy or other specialized study-specific approaches. To enable automated delineation and identification of these areas in new HCP subjects and in future studies, we trained a machine-learning classifier to recognize the multi-modal 'fingerprint' of each cortical area. This classifier detected the presence of 96.6% of the cortical areas in new subjects, replicated the group parcellation, and could correctly locate areas in individuals with atypical parcellations. The freely available parcellation and classifier will enable substantially improved neuroanatomical precision for studies of the structural and functional organization of human cerebral cortex and its variation across individuals and in development, aging, and disease.

3,414 citations


Cites methods from "An automated labeling system for su..."

  • ...We used a coordinate system based on the FreeSurfer ‘fsaverage’ template (Desikan et al., 2006) after registration to a standard mesh sphere that accurately aligns geographically corresponding features in the left and right hemispheres (Van Essen et al....

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  • ...We used a coordinate system based on the FreeSurfer ‘fsaverage’ template (Desikan et al., 2006) after registration to a standard mesh sphere that accurately aligns geographically corresponding features in the left and right hemispheres (Van Essen et al., 2012)....

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Journal ArticleDOI
TL;DR: Although resting state functional connectivity is variable and is frequently present between regions without direct structural linkage, its strength, persistence, and spatial statistics are nevertheless constrained by the large-scale anatomical structure of the human cerebral cortex.
Abstract: In the cerebral cortex, the activity levels of neuronal populations are continuously fluctuating. When neuronal activity, as measured using functional MRI (fMRI), is temporally coherent across 2 populations, those populations are said to be functionally connected. Functional connectivity has previously been shown to correlate with structural (anatomical) connectivity patterns at an aggregate level. In the present study we investigate, with the aid of computational modeling, whether systems-level properties of functional networks—including their spatial statistics and their persistence across time—can be accounted for by properties of the underlying anatomical network. We measured resting state functional connectivity (using fMRI) and structural connectivity (using diffusion spectrum imaging tractography) in the same individuals at high resolution. Structural connectivity then provided the couplings for a model of macroscopic cortical dynamics. In both model and data, we observed (i) that strong functional connections commonly exist between regions with no direct structural connection, rendering the inference of structural connectivity from functional connectivity impractical; (ii) that indirect connections and interregional distance accounted for some of the variance in functional connectivity that was unexplained by direct structural connectivity; and (iii) that resting-state functional connectivity exhibits variability within and across both scanning sessions and model runs. These empirical and modeling results demonstrate that although resting state functional connectivity is variable and is frequently present between regions without direct structural linkage, its strength, persistence, and spatial statistics are nevertheless constrained by the large-scale anatomical structure of the human cerebral cortex.

2,771 citations

Journal ArticleDOI
TL;DR: Visual inspection and fMRI results show that BBR is more accurate than correlation ratio or normalized mutual information and is considerably more robust to even strong intensity inhomogeneities.

2,679 citations


Cites background or methods from "An automated labeling system for su..."

  • ...), and these areas are automatically labeled in FreeSurfer (Desikan et al., 2006)....

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  • ...The metric and intensity distortions tend to occur in known anatomical locations (e.g., orbital frontal, medial temporal gyrus, etc.), and these areas are automatically labeled in FreeSurfer (Desikan et al., 2006)....

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Journal ArticleDOI
TL;DR: A precisely defined method for automatically labeling the cortical surface in standard terminology using standard internationally accepted nomenclature and criteria is presented.

2,190 citations


Cites background from "An automated labeling system for su..."

  • ..., 1998) may be more appropriate for the anatomy of the brain than classical volume based coordinate systems (Talairach and Tournoux, 1988): they provide better inter-subject averaging and allow the development of tools for automatically parcellating the cortex in a reproducible and accurate way (Desikan et al., 2006; Fischl et al., 2004)....

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  • ..., 1990) and in many atlases used in the neuroimaging community (Desikan et al., 2006; Lancaster et al., 1997; Talairach and Tournoux, 1988), gyri are defined as the cortex joining the bottom of two neighboring sulci, sulci being only consider as virtual landmarks between them....

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  • ...Due to the sheetlike topology of the cortex, surface based coordinate systems (Fischl et al., 1999a,b; Thompson et al., 2000; Van Essen et al., 1998) may be more appropriate for the anatomy of the brain than classical volume based coordinate systems (Talairach and Tournoux, 1988): they provide better inter-subject averaging and allow the development of tools for automatically parcellating the cortex in a reproducible and accurate way (Desikan et al., 2006; Fischl et al., 2004)....

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  • ..., 1991; Talairach and Szikla, 1967; Talairach and Tournoux, 1988) and most of the available atlases (Desikan et al., 2006; Lancaster et al., 2000; Shattuck et al., 2008) use a gyral based parcellation of the brain....

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  • ..., 1997) and the surface-based parcellation proposed by Desikan (Desikan et al., 2006) defined 48 and 34 gyral regions per hemisphere respectively....

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References
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Book
01 Jan 1993
TL;DR: This article presents bootstrap methods for estimation, using simple arguments, with Minitab macros for implementing these methods, as well as some examples of how these methods could be used for estimation purposes.
Abstract: This article presents bootstrap methods for estimation, using simple arguments. Minitab macros for implementing these methods are given.

37,183 citations

Journal ArticleDOI
TL;DR: An anatomical parcellation of the spatially normalized single-subject high-resolution T1 volume provided by the Montreal Neurological Institute was performed and it is believed that this tool is an improvement for the macroscopical labeling of activated area compared to labeling assessed using the Talairach atlas brain.

13,678 citations


"An automated labeling system for su..." refers methods in this paper

  • ...Using a volumetric labeling technique, Tzourio-Mazoyer et al. (2002) manually delineated regions of interest for a single subject existing in common stereotaxic space in order to provide a more robust anatomic basis for functional activation studies, not for determining the absolute anatomic…...

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  • ...Using a volumetric labeling technique, Tzourio-Mazoyer et al. (2002) manually delineated regions of interest for a single subject existing in common stereotaxic space in order to provide a more robust anatomic basis for functional activation studies, not for determining the absolute anatomic localization of brain structures that is required formorphometricstudies.Otherexamplesofparcellationtechniques involve the spatial transformation to a ......

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Journal ArticleDOI
TL;DR: A set of automated procedures for obtaining accurate reconstructions of the cortical surface are described, which have been applied to data from more than 100 subjects, requiring little or no manual intervention.

9,599 citations


"An automated labeling system for su..." refers methods in this paper

  • ...…using curvature based information (i.e., sulcal representations) available on images of the cortex that are Finflated_ (Dale and Sereno, 1993; Dale et al., 1999; Fischl et al., 1999a,b, 2001; Fischl and Dale, 2000); anatomic curvature is visually represented well on inflated images as they…...

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  • ...First, we have developed the definitions of the regions of interest using curvature based information (i.e., sulcal representations) available on images of the cortex that are Finflated_ (Dale and Sereno, 1993; Dale et al., 1999; Fischl et al., 1999a, b, 2001; Fischl and Dale, 2000); anatomic curvature is visually represented well on inflated images as they provide a view of the brain in which the entire cortical surface is exposed, ......

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  • ...…a skull-stripping algorithm (Ségonne et al., 2004) and the images were segmented to identify the dorsal, ventral and lateral extent of the gray/white matter boundary to provide a surface representation of the cortical white matter (Dale and Sereno, 1993; Dale et al., 1999; Fischl et al., 1999a)....

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  • ...…for motion, averaged, normalized for intensity and resampled to isotropic dimensions of 1 1 1 mm using previously published algorithms that are distributed in the FreeSurfer software package (http://www.martinos.org/ freesurfer) (Dale and Sereno, 1993; Dale et al., 1999; Fischl et al., 1999a)....

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  • ...Each scan was first corrected for motion, averaged, normalized for intensity and resampled to isotropic dimensions of 1 ! 1 ! 1 mm using previously published algorithms that are distributed in the FreeSurfer software package (http://www.martinos.org/ freesurfer) (Dale and Sereno, 1993; Dale et al., 1999; Fischl et al., 1999a )....

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Book
07 Dec 1989
TL;DR: In this article, the authors propose three basic concepts: devising the items, selecting the items and selecting the responses, from items to scales, reliability and validity of the responses.
Abstract: 1. Introduction 2. Basic concepts 3. Devising the items 4. Scaling responses 5. Selecting the items 6. Biases in responding 7. From items to scales 8. Reliability 9. Generalizability theory 10. Validity 11. Measuring change 12. Item response theory 13. Methods of administration 14. Ethical considerations 15. Reporting test results Appendices

9,316 citations

Journal ArticleDOI

8,086 citations


"An automated labeling system for su..." refers background or methods in this paper

  • ...Adults 60 and over were also clinically screened for dementia and classified based on the Clinical Dementia Rating (Morris, 1993)....

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  • ...For example, MRI is now a secondary endpoint in clinical trials of patients with multiple sclerosis (MS), as MS lesions can now be quantified quickly and reliably (see Bakshi et al., 2005)....

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