Gray Matter Analysis of MRI Images: Introduction to Current Research Practice

[1]  N. Makris,et al.  Decreased volume of left and total anterior insular lobule in schizophrenia , 2006, Schizophrenia Research.

[2]  Stine K. Krogsrud,et al.  Neurodevelopmental origins of lifespan changes in brain and cognition , 2016, Proceedings of the National Academy of Sciences.

[3]  Brian A. Nosek,et al.  The preregistration revolution , 2018, Proceedings of the National Academy of Sciences.

[4]  Stephen M. Smith,et al.  A global optimisation method for robust affine registration of brain images , 2001, Medical Image Anal..

[5]  R. Lanfear,et al.  Evidence of Experimental Bias in the Life Sciences: Why We Need Blind Data Recording , 2015, PLoS biology.

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

[7]  Meritxell Bach Cuadra,et al.  A Surface-Based Approach to Quantify Local Cortical Gyrification , 2008, IEEE Transactions on Medical Imaging.

[8]  Rainer Goebel,et al.  Analysis of functional image analysis contest (FIAC) data with brainvoyager QX: From single‐subject to cortically aligned group general linear model analysis and self‐organizing group independent component analysis , 2006, Human brain mapping.

[9]  Karl J. Friston,et al.  Why Voxel-Based Morphometry Should Be Used , 2001, NeuroImage.

[10]  Scott D. Brown,et al.  A purely confirmatory replication study of structural brain-behavior correlations , 2015, Cortex.

[11]  Alan C. Evans,et al.  Applications of random field theory to functional connectivity , 1998, Human brain mapping.

[12]  Armin Raznahan,et al.  The Dynamic Associations Between Cortical Thickness and General Intelligence are Genetically Mediated. , 2019, Cerebral cortex.

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

[14]  Arno Klein,et al.  Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements , 2014, NeuroImage.

[15]  N. Makris,et al.  Hypothalamic Abnormalities in Schizophrenia: Sex Effects and Genetic Vulnerability , 2007, Biological Psychiatry.

[16]  John P. A. Ioannidis,et al.  p-Curve and p-Hacking in Observational Research , 2016, PloS one.

[17]  Ayse Pinar Saygin,et al.  Smoothing and cluster thresholding for cortical surface-based group analysis of fMRI data , 2006, NeuroImage.

[18]  Nikolaus Weiskopf,et al.  Quantitative multi-parameter mapping of R1, PD*, MT, and R2* at 3T: a multi-center validation , 2013, Front. Neurosci..

[19]  Robbie C. M. van Aert,et al.  Degrees of Freedom in Planning, Running, Analyzing, and Reporting Psychological Studies: A Checklist to Avoid p-Hacking , 2016, Front. Psychol..

[20]  Alan C. Evans,et al.  Intellectual ability and cortical development in children and adolescents , 2006, Nature.

[21]  Stephen M. Smith,et al.  Age-related changes in grey and white matter structure throughout adulthood , 2010, NeuroImage.

[22]  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.

[23]  S. Belleville,et al.  Relationships between years of education, regional grey matter volumes, and working memory-related brain activity in healthy older adults , 2017, Brain Imaging and Behavior.

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

[25]  Abel Brodeur,et al.  Star Wars: The Empirics Strike Back , 2012, SSRN Electronic Journal.

[26]  Jia-Hong Gao,et al.  Sample sizes and population differences in brain template construction , 2020, NeuroImage.

[27]  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.

[28]  Brian B. Avants,et al.  Registration based cortical thickness measurement , 2009, NeuroImage.

[29]  Robert Turner,et al.  Voxel-based cortical thickness measurements in MRI , 2008, NeuroImage.

[30]  E. Bora,et al.  Gray matter abnormalities in Major Depressive Disorder: a meta-analysis of voxel based morphometry studies. , 2012, Journal of affective disorders.

[31]  Reza Shoorangiz,et al.  Test-retest reliability and sample size estimates after MRI scanner relocation , 2020, NeuroImage.

[32]  Michael Brady,et al.  Improved Optimization for the Robust and Accurate Linear Registration and Motion Correction of Brain Images , 2002, NeuroImage.

[33]  Richard A. Bettis,et al.  The search for asterisks: Compromised statistical tests and flawed theories , 2012 .

[34]  J. Mumford.  A power calculation guide for fMRI studies. , 2012, Social cognitive and affective neuroscience.

[35]  P. Pan,et al.  Voxel‐wise meta‐analysis of gray matter abnormalities in idiopathic Parkinson’s disease , 2012, European journal of neurology.

[36]  Russell A. Poldrack,et al.  OpenfMRI: Open sharing of task fMRI data , 2017, NeuroImage.

[37]  Kei Majima,et al.  BrainLiner: A Neuroinformatics Platform for Sharing Time-Aligned Brain-Behavior Data , 2016, Front. Neuroinform..

[38]  Lutz Jäncke,et al.  Reliability and statistical power analysis of cortical and subcortical FreeSurfer metrics in a large sample of healthy elderly , 2015, NeuroImage.

[39]  Brian A. Nosek,et al.  An Open, Large-Scale, Collaborative Effort to Estimate the Reproducibility of Psychological Science , 2012, Perspectives on psychological science : a journal of the Association for Psychological Science.

[40]  L. Westlye,et al.  Differential Longitudinal Changes in Cortical Thickness, Surface Area and Volume across the Adult Life Span: Regions of Accelerating and Decelerating Change , 2014, The Journal of Neuroscience.

[41]  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.

[42]  Stephen M. Smith,et al.  Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm , 2001, IEEE Transactions on Medical Imaging.

[43]  Christopher J. Wertz,et al.  Structural correlates of Openness and Intellect: Implications for the contribution of personality to creativity , 2018, Human brain mapping.

[44]  Alan C. Evans,et al.  Changes in thickness and surface area of the human cortex and their relationship with intelligence. , 2015, Cerebral cortex.

[45]  Lorne Campbell,et al.  Preregistration Is Hard, And Worthwhile , 2019, Trends in Cognitive Sciences.

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

[47]  Karl J. Friston,et al.  Unified segmentation , 2005, NeuroImage.

[48]  R Saxe,et al.  People thinking about thinking people The role of the temporo-parietal junction in “theory of mind” , 2003, NeuroImage.

[49]  Thomas E. Nichols,et al.  Validating cluster size inference: random field and permutation methods , 2003, NeuroImage.

[50]  G. Busatto,et al.  Neurostructural predictors of Alzheimer's disease: A meta-analysis of VBM studies , 2011, Neurobiology of Aging.

[51]  Salvatore Nigro,et al.  Surface-based morphometry reveals the neuroanatomical basis of the five-factor model of personality , 2017, Social cognitive and affective neuroscience.

[52]  Jianfeng Feng,et al.  Automated anatomical labelling atlas 3 , 2020, NeuroImage.

[53]  Karl J. Friston,et al.  Diffeomorphic registration using geodesic shooting and Gauss–Newton optimisation , 2011, NeuroImage.

[54]  E. Wagenmakers,et al.  Detecting and avoiding likely false‐positive findings – a practical guide , 2017, Biological reviews of the Cambridge Philosophical Society.

[55]  Yi Chen,et al.  Statistical inference and multiple testing correction in classification-based multi-voxel pattern analysis (MVPA): Random permutations and cluster size control , 2011, NeuroImage.

[56]  M C Keuken,et al.  A test-retest reliability analysis of diffusion measures of white matter tracts relevant for cognitive control. , 2017, Psychophysiology.

[57]  Karl J. Friston,et al.  Voxel-based morphometry of the human brain: Methods and applications , 2005 .

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

[59]  P. Basser,et al.  MR diffusion tensor spectroscopy and imaging. , 1994, Biophysical journal.

[60]  N. Kanwisher,et al.  The fusiform face area: a cortical region specialized for the perception of faces , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[61]  Christian Gaser,et al.  Cortical thickness and central surface estimation , 2013, NeuroImage.

[62]  Arno Klein,et al.  Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration , 2009, NeuroImage.

[63]  S. Rauch,et al.  Structural brain magnetic resonance imaging of limbic and thalamic volumes in pediatric bipolar disorder. , 2005, The American journal of psychiatry.

[64]  Arthur W Toga,et al.  Relationships between IQ and regional cortical gray matter thickness in healthy adults. , 2007, Cerebral cortex.

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

[66]  Cathy J. Price,et al.  The impact of sample size on the reproducibility of voxel-based lesion-deficit mappings , 2018, Neuropsychologia.

[67]  Thomas E. Nichols,et al.  Nonstationary cluster-size inference with random field and permutation methods , 2004, NeuroImage.

[68]  John E. Richards,et al.  A database of age-appropriate average MRI templates , 2016, NeuroImage.

[69]  S. Beugelsdijk,et al.  What’s in a p? Reassessing best practices for conducting and reporting hypothesis-testing research , 2017, Journal of International Business Studies.

[70]  Learning from replication , 2018, Nature Human Behaviour.

[71]  Promoting reproducibility with registered reports , 2017, Nature Human Behaviour.

[72]  Matthew F. Glasser,et al.  The Brain Analysis Library of Spatial maps and Atlases (BALSA) database , 2017, NeuroImage.

[73]  Bruce Fischl,et al.  FreeSurfer , 2012, NeuroImage.

[74]  Stuart J. Ritchie,et al.  Structural brain imaging correlates of general intelligence in UK Biobank , 2019, Intelligence.

[75]  Bruce Fischl,et al.  Within-subject template estimation for unbiased longitudinal image analysis , 2012, NeuroImage.

[76]  D. V. van Essen,et al.  Mapping Human Cortical Areas In Vivo Based on Myelin Content as Revealed by T1- and T2-Weighted MRI , 2011, The Journal of Neuroscience.

[77]  Geraint Rees,et al.  Quantitative MRI provides markers of intra-, inter-regional, and age-related differences in young adult cortical microstructure , 2017, NeuroImage.

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

[79]  Angela R. Laird,et al.  Comparison of the disparity between Talairach and MNI coordinates in functional neuroimaging data: Validation of the Lancaster transform , 2010, NeuroImage.

[80]  John Ashburner,et al.  A fast diffeomorphic image registration algorithm , 2007, NeuroImage.

[81]  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.

[82]  H. Hotelling.  Relations Between Two Sets of Variates , 1936 .

[83]  Daniel S. Margulies,et al.  NeuroVault.org: A repository for sharing unthresholded statistical maps, parcellations, and atlases of the human brain , 2016, NeuroImage.

[84]  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.

[85]  Wendy Johnson,et al.  Cognitive ability changes and dynamics of cortical thickness development in healthy children and adolescents , 2014, NeuroImage.

[86]  Wei Li,et al.  Fast magnetic resonance diffusion‐weighted imaging of acute human stroke , 1992, Neurology.

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

[88]  Russell A. Poldrack,et al.  Large-scale automated synthesis of human functional neuroimaging data , 2011, Nature Methods.

[89]  R. Kanai.  Open questions in conducting confirmatory replication studies: Commentary on Boekel et al., 2015 , 2016, Cortex.

[90]  A. Dale,et al.  High consistency of regional cortical thinning in aging across multiple samples. , 2009, Cerebral cortex.

[91]  N. Kerr.  HARKing: Hypothesizing After the Results are Known , 1998, Personality and social psychology review : an official journal of the Society for Personality and Social Psychology, Inc.

[92]  Matthias L. Schroeter,et al.  When less is more: Structural correlates of core executive functions in young adults – A VBM and cortical thickness study , 2019, NeuroImage.

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

[94]  H. Knutsson,et al.  Detection of neural activity in functional MRI using canonical correlation analysis , 2001, Magnetic resonance in medicine.

[95]  K Kazemi,et al.  Quantitative Comparison of SPM, FSL, and Brainsuite for Brain MR Image Segmentation , 2014, Journal of biomedical physics & engineering.

[96]  Jesper Andersson,et al.  A multi-modal parcellation of human cerebral cortex , 2016, Nature.

[97]  Steven C. R. Williams,et al.  Mapping IQ and gray matter density in healthy young people , 2004, NeuroImage.

[98]  Christian Gaser,et al.  Topological correction of brain surface meshes using spherical harmonics , 2010, MICCAI.

[99]  Birte U. Forstmann,et al.  Challenges in replicating brain-behavior correlations: Rejoinder to Kanai (2015) and Muhlert and Ridgway (2015) , 2016, Cortex.

[100]  Alan C. Evans,et al.  Brain size and cortical structure in the adult human brain. , 2008, Cerebral cortex.

[101]  Robert D. McIntosh,et al.  Exploratory reports: A new article type for Cortex , 2017, Cortex.

[102]  Arno Klein,et al.  A reproducible evaluation of ANTs similarity metric performance in brain image registration , 2011, NeuroImage.

[103]  N. Muhlert,et al.  Failed replications, contributing factors and careful interpretations: Commentary on Boekel et al., 2015 , 2016, Cortex.

[104]  Rupert Lanzenberger,et al.  Cortical Thickness Estimations of FreeSurfer and the CAT12 Toolbox in Patients with Alzheimer's Disease and Healthy Controls , 2018, Journal of neuroimaging : official journal of the American Society of Neuroimaging.

[105]  Marisa O. Hollinshead,et al.  The organization of the human cerebral cortex estimated by intrinsic functional connectivity. , 2011, Journal of neurophysiology.

[106]  Michael C. Frank,et al.  Estimating the reproducibility of psychological science , 2015, Science.

[107]  Timothy D. Wilson,et al.  Comment on “Estimating the reproducibility of psychological science” , 2016, Science.

[108]  L. Gray,et al.  Cardiovascular disease risk factors in chronic kidney disease: A systematic review and meta-analysis , 2018, PloS one.

[109]  Courtland S. Hyatt,et al.  No evidence for morphometric associations of the amygdala and hippocampus with the five-factor model personality traits in relatively healthy young adults , 2018, PloS one.

[110]  Jennifer L. Whitwell,et al.  Accurate automatic estimation of total intracranial volume: A nuisance variable with less nuisance , 2015, NeuroImage.

[111]  S. Kiebel,et al.  An Introduction to Random Field Theory , 2003 .

[112]  Hallvard Røe Evensmoen,et al.  Marked effects of intracranial volume correction methods on sex differences in neuroanatomical structures: a HUNT MRI study , 2015, Front. Neurosci..

[113]  Harlan M. Krumholz,et al.  Trial Publication after Registration in ClinicalTrials.Gov: A Cross-Sectional Analysis , 2009, PLoS medicine.

[114]  Satrajit S. Ghosh,et al.  Instrumentation bias in the use and evaluation of scientific software: recommendations for reproducible practices in the computational sciences , 2013, Front. Neurosci..

[115]  Herman Aguinis,et al.  HARKing's Threat to Organizational Research: Evidence From Primary and Meta‐Analytic Sources , 2016 .

[116]  G. Prendergast,et al.  Encouraging pre-registration of research studies , 2019, International journal of audiology.

[117]  Ariel Deardorff,et al.  Open Science Framework (OSF) , 2017, Journal of the Medical Library Association : JMLA.