FreeSurfer

FreeSurfer is a suite of tools for the analysis of neuroimaging data that provides an array of algorithms to quantify the functional, connectional and structural properties of the human brain. It has evolved from a package primarily aimed at generating surface representations of the cerebral cortex into one that automatically creates models of most macroscopically visible structures in the human brain given any reasonable T1-weighted input image. It is freely available, runs on a wide variety of hardware and software platforms, and is open source.

[1]  Polina Golland,et al.  Automated segmentation of hippocampal subfields from ultra‐high resolution in vivo MRI , 2009, Hippocampus.

[2]  Anders M. Dale,et al.  Neuroanatomical aging: Universal but not uniform , 2005, Neurobiology of Aging.

[3]  A. Dale,et al.  Age does not increase rate of forgetting over weeks—Neuroanatomical volumes and visual memory across the adult life-span , 2005, Journal of the International Neuropsychological Society.

[4]  W. Eric L. Grimson,et al.  Active Contours Under Topology Control Genus Preserving Level Sets , 2005, CVBIA.

[5]  Lawrence L. Wald,et al.  Accurate prediction of V1 location from cortical folds in a surface coordinate system , 2008, NeuroImage.

[6]  Katrin Amunts,et al.  Cortical Folding Patterns and Predicting Cytoarchitecture , 2007, Cerebral cortex.

[7]  A. Dale,et al.  Age-related alterations in white matter microstructure measured by diffusion tensor imaging , 2005, Neurobiology of Aging.

[8]  Alan C. Evans,et al.  Automated 3-D Extraction of Inner and Outer Surfaces of Cerebral Cortex from MRI , 2000, NeuroImage.

[9]  Anders M. Dale,et al.  Genetic and environmental influences on the size of specific brain regions in midlife: The VETSA MRI study , 2010, NeuroImage.

[10]  Anders M. Dale,et al.  Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature , 2010, NeuroImage.

[11]  Xiao Han,et al.  Atlas Renormalization for Improved Brain MR Image Segmentation Across Scanner Platforms , 2007, IEEE Transactions on Medical Imaging.

[12]  Nikos Makris,et al.  Automatically parcellating the human cerebral cortex. , 2004, Cerebral cortex.

[13]  Mert R. Sabuncu,et al.  Task-Optimal Registration Cost Functions , 2009, MICCAI.

[14]  Bruce Fischl,et al.  Regional white matter volume differences in nondemented aging and Alzheimer's disease , 2009, NeuroImage.

[15]  Yuan Qi,et al.  Cortical Surface Shape Analysis Based on Spherical Wavelets , 2007, IEEE Transactions on Medical Imaging.

[16]  A. Dale,et al.  Age‐Related Changes in Prefrontal White Matter Measured by Diffusion Tensor Imaging , 2005, Annals of the New York Academy of Sciences.

[17]  A M Dale,et al.  Size does matter in the long run , 2004, Neurology.

[18]  A. Dale,et al.  Distinct genetic influences on cortical surface area and cortical thickness. , 2009, Cerebral cortex.

[19]  Anders M. Dale,et al.  An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest , 2006, NeuroImage.

[20]  Abraham Z. Snyder,et al.  Surface-Based Analyses of the Human Cerebral Cortex , 1999 .

[21]  A M Dale,et al.  Measuring the thickness of the human cerebral cortex from magnetic resonance images. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[22]  John W Belliveau,et al.  Monte Carlo simulation studies of EEG and MEG localization accuracy , 2002, Human brain mapping.

[23]  R. Andersen,et al.  Functional analysis of human MT and related visual cortical areas using magnetic resonance imaging , 1995, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[24]  S. Shergill,et al.  Cortical Thickness Reduction of Normal Appearing Cortex in Patients with Polymicrogyria , 2010, Journal of neuroimaging : official journal of the American Society of Neuroimaging.

[25]  David S Tuch,et al.  Diffusion tensor imaging in presymptomatic and early Huntington's disease: Selective white matter pathology and its relationship to clinical measures , 2006, Movement disorders : official journal of the Movement Disorder Society.

[26]  Richard M. Leahy,et al.  Automated graph-based analysis and correction of cortical volume topology , 2001, IEEE Transactions on Medical Imaging.

[27]  A. Dale,et al.  The Retinotopy of Visual Spatial Attention , 1998, Neuron.

[28]  Mert R. Sabuncu,et al.  Learning Task-Optimal Registration Cost Functions for Localizing Cytoarchitecture and Function in the Cerebral Cortex , 2010, IEEE Transactions on Medical Imaging.

[29]  A. M. Dale,et al.  A hybrid approach to the skull stripping problem in MRI , 2004, NeuroImage.

[30]  Bruce Fischl,et al.  Avoiding asymmetry-induced bias in longitudinal image processing , 2011, NeuroImage.

[31]  Mert R. Sabuncu,et al.  A Generative Model for Image Segmentation Based on Label Fusion , 2010, IEEE Transactions on Medical Imaging.

[32]  Bruce R. Rosen,et al.  Predicting the location of entorhinal cortex from MRI , 2009, NeuroImage.

[33]  A. Dale,et al.  Cerebral cortex thickness in 15-year-old adolescents with low birth weight measured by an automated MRI-based method. , 2005, Brain : a journal of neurology.

[34]  Alan C. Evans,et al.  Multiple surface identification and matching in magnetic resonance images , 1994, Other Conferences.

[35]  Bruce Fischl,et al.  Reduced microstructural integrity of the white matter underlying anterior cingulate cortex is associated with increased saccadic latency in schizophrenia , 2007, NeuroImage.

[36]  A. Dale,et al.  Effects of age on volumes of cortex, white matter and subcortical structures , 2005, Neurobiology of Aging.

[37]  B. T. Thomas Yeo,et al.  On the Construction of Invertible Filter Banks on the 2-Sphere , 2008, IEEE Transactions on Image Processing.

[38]  E. Halgren,et al.  Location of human face‐selective cortex with respect to retinotopic areas , 1999, Human brain mapping.

[39]  Anders M. Dale,et al.  Sequence-independent segmentation of magnetic resonance images , 2004, NeuroImage.

[40]  Xiao Han,et al.  A Topology Preserving Level Set Method for Geometric Deformable Models , 2003, IEEE Trans. Pattern Anal. Mach. Intell..

[41]  B Fischl,et al.  Regional cortical thinning in preclinical Huntington disease and its relationship to cognition , 2005, Neurology.

[42]  Bruce Fischl,et al.  Accurate and robust brain image alignment using boundary-based registration , 2009, NeuroImage.

[43]  B. Wandell.  Computational neuroimaging of human visual cortex. , 1999, Annual review of neuroscience.

[44]  MöllerTomas.  A fast triangle-triangle intersection test , 1997 .

[45]  A. Dale,et al.  Focal thinning of the cerebral cortex in multiple sclerosis. , 2003, Brain : a journal of neurology.

[46]  W. Eric L. Grimson,et al.  A Genetic Algorithm for the Topology Correction of Cortical Surfaces , 2005, IPMI.

[47]  Bruce Fischl,et al.  Combined Volumetric and Surface Registration , 2009, IEEE Transactions on Medical Imaging.

[48]  Anders M. Dale,et al.  Selective increase of cortical thickness in high-performing elderly—structural indices of optimal cognitive aging , 2006, NeuroImage.

[49]  D. Gadian,et al.  The Effect of Early Human Diet on Caudate Volumes and IQ , 2008, Pediatric Research.

[50]  Nicholas Ayache,et al.  Spherical Demons: Fast Diffeomorphic Landmark-Free Surface Registration , 2010, IEEE Transactions on Medical Imaging.

[51]  Anders M. Dale,et al.  Differing neuropsychological and neuroanatomical correlates of abnormal reading in early-stage semantic dementia and dementia of the Alzheimer type , 2005, Neuropsychologia.

[52]  Tomas Akenine-Möller,et al.  A Fast Triangle-Triangle Intersection Test , 1997, J. Graphics, GPU, & Game Tools.

[53]  A. Dale,et al.  Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System , 1999, NeuroImage.

[54]  M. Weiner,et al.  The dynamics of cortical and hippocampal atrophy in Alzheimer disease. , 2011, Archives of neurology.

[55]  P. Cavanagh,et al.  Retinotopy and color sensitivity in human visual cortical area V8 , 1998, Nature Neuroscience.

[56]  Bruce Fischl,et al.  IC-P2-077: Amyloid deposition related to cortical thinning , 2008, Alzheimer's & Dementia.

[57]  Bruce Fischl,et al.  Geometrically Accurate Topology-Correction of Cortical Surfaces Using Nonseparating Loops , 2007, IEEE Transactions on Medical Imaging.

[58]  Marianna D. Eddy,et al.  Regionally localized thinning of the cerebral cortex in schizophrenia , 2003, Schizophrenia Research.

[59]  N. Makris,et al.  A methodology for analyzing curvature in the developing brain from preterm to adult , 2008, Int. J. Imaging Syst. Technol..

[60]  Anders M. Dale,et al.  Regional cortical thickness matters in recall after months more than minutes , 2006, NeuroImage.

[61]  D. V. van Essen,et al.  Computerized Mappings of the Cerebral Cortex: A Multiresolution Flattening Method and a Surface-Based Coordinate System , 1996, Journal of Cognitive Neuroscience.

[62]  A. Dale,et al.  Regional and progressive thinning of the cortical ribbon in Huntington’s disease , 2002, Neurology.

[63]  Michael W. Weiner,et al.  Selective Disruption of the Cerebral Neocortex in Alzheimer's Disease , 2010, PloS one.

[64]  Alan C. Evans,et al.  A method for identifying geometrically simple surfaces from three-dimensional images , 1998 .

[65]  Donald Geman,et al.  Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images , 1984, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[66]  André J. W. van der Kouwe,et al.  Detection of cortical thickness correlates of cognitive performance: Reliability across MRI scan sessions, scanners, and field strengths , 2008, NeuroImage.

[67]  Bruce Fischl,et al.  Anatomical priors for global probabilistic diffusion tractography , 2009, 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro.

[68]  Brian A Wandell,et al.  Color Signals in Human Motion-Selective Cortex , 1999, Neuron.

[69]  J W Belliveau,et al.  Borders of multiple visual areas in humans revealed by functional magnetic resonance imaging. , 1995, Science.

[70]  W. Eric L. Grimson,et al.  Topological Correction of Subcortical Segmentation , 2003, MICCAI.

[71]  M. Weiner,et al.  Automated MRI measures predict progression to Alzheimer's disease , 2010, Neurobiology of Aging.

[72]  Bruce Fischl,et al.  Improved tractography alignment using combined volumetric and surface registration , 2010, NeuroImage.

[73]  A. Dale,et al.  The Representation of Illusory and Real Contours in Human Cortical Visual Areas Revealed by Functional Magnetic Resonance Imaging , 1999, The Journal of Neuroscience.

[74]  D. V. van Essen,et al.  Structural and Functional Analyses of Human Cerebral Cortex Using a Surface-Based Atlas , 1997, The Journal of Neuroscience.

[75]  E. Halgren,et al.  Dynamic Statistical Parametric Mapping Combining fMRI and MEG for High-Resolution Imaging of Cortical Activity , 2000, Neuron.

[76]  A. Dale,et al.  Thinning of the cerebral cortex in aging. , 2004, Cerebral cortex.

[77]  Anders M. Dale,et al.  Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex , 2001, IEEE Transactions on Medical Imaging.

[78]  G. Glover,et al.  Retinotopic organization in human visual cortex and the spatial precision of functional MRI. , 1997, Cerebral cortex.

[79]  D. Louis Collins,et al.  Animal: Validation and Applications of Nonlinear Registration-Based Segmentation , 1997, Int. J. Pattern Recognit. Artif. Intell..

[80]  Guillermo Sapiro,et al.  Creating connected representations of cortical gray matter for functional MRI visualization , 1997, IEEE Transactions on Medical Imaging.

[81]  S Marrett,et al.  Local and global attention are mapped retinotopically in human occipital cortex. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[82]  Jorge Sepulcre,et al.  Localization of focal epileptic discharges using functional connectivity magnetic resonance imaging. , 2011, Journal of neurosurgery.

[83]  Bruce Fischl,et al.  Thickness of ventromedial prefrontal cortex in humans is correlated with extinction memory. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[84]  Eric L. Schwartz,et al.  Computer-aided neuroanatomy of macaque visual cortex , 1993 .

[85]  A. Dale,et al.  High‐resolution intersubject averaging and a coordinate system for the cortical surface , 1999, Human brain mapping.

[86]  Eric L. Schwartz,et al.  A Numerical Solution to the Generalized Mapmaker's Problem: Flattening Nonconvex Polyhedral Surfaces , 1989, IEEE Trans. Pattern Anal. Mach. Intell..

[87]  J. Morris,et al.  The Cortical Signature of Alzheimer's Disease: Regionally Specific Cortical Thinning Relates to Symptom Severity in Very Mild to Mild AD Dementia and is Detectable in Asymptomatic Amyloid-Positive Individuals , 2008, Cerebral cortex.

[88]  Bruce Fischl,et al.  Orbitofrontal thickness, retention of fear extinction, and extraversion , 2005, Neuroreport.

[89]  Peng Yu,et al.  Altered white matter microstructure in the corpus callosum in Huntington's disease: Implications for cortical “disconnection” , 2010, NeuroImage.

[90]  Anders M. Dale,et al.  Cortical Surface-Based Analysis I. Segmentation and Surface Reconstruction , 1999, NeuroImage.

[91]  A. Dale,et al.  Whole Brain Segmentation Automated Labeling of Neuroanatomical Structures in the Human Brain , 2002, Neuron.

[92]  André J. W. van der Kouwe,et al.  Reliability of MRI-derived cortical and subcortical morphometric measures: Effects of pulse sequence, voxel geometry, and parallel imaging , 2009, NeuroImage.

[93]  D. Heeger,et al.  Linear Systems Analysis of Functional Magnetic Resonance Imaging in Human V1 , 1996, The Journal of Neuroscience.

[94]  Anders M. Dale,et al.  Reliability of MRI-derived measurements of human cerebral cortical thickness: The effects of field strength, scanner upgrade and manufacturer , 2006, NeuroImage.

[95]  Bruce Fischl,et al.  Highly accurate inverse consistent registration: A robust approach , 2010, NeuroImage.

[96]  Jerry L. Prince,et al.  An active contour model for mapping the cortex , 1995, IEEE Trans. Medical Imaging.

[97]  A. Dale,et al.  Functional Analysis of V3A and Related Areas in Human Visual Cortex , 1997, The Journal of Neuroscience.