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Untangling the relatedness among correlations, part III: Inter-subject correlation analysis through Bayesian multilevel modeling for naturalistic scanning.

Chen G, Taylor PA, Qu X, Molfese PJ, Bandettini PA, Cox RW, Finn ES.

Neuroimage. 2019 Dec 27:116474. doi: 10.1016/j.neuroimage.2019.116474. [Epub ahead of print]


Fighting or embracing multiplicity in neuroimaging? neighborhood leverage versus global calibration.

Chen G, Taylor PA, Cox RW, Pessoa L.

Neuroimage. 2020 Feb 1;206:116320. doi: 10.1016/j.neuroimage.2019.116320. Epub 2019 Nov 5.


An integrative Bayesian approach to matrix-based analysis in neuroimaging.

Chen G, Bürkner PC, Taylor PA, Li Z, Yin L, Glen DR, Kinnison J, Cox RW, Pessoa L.

Hum Brain Mapp. 2019 Oct 1;40(14):4072-4090. doi: 10.1002/hbm.24686. Epub 2019 Jun 12.


Equitable Thresholding and Clustering: A Novel Method for Functional Magnetic Resonance Imaging Clustering in AFNI.

Cox RW.

Brain Connect. 2019 Sep;9(7):529-538. doi: 10.1089/brain.2019.0666.


Handling Multiplicity in Neuroimaging Through Bayesian Lenses with Multilevel Modeling.

Chen G, Xiao Y, Taylor PA, Rajendra JK, Riggins T, Geng F, Redcay E, Cox RW.

Neuroinformatics. 2019 Oct;17(4):515-545. doi: 10.1007/s12021-018-9409-6.


A tail of two sides: Artificially doubled false positive rates in neuroimaging due to the sidedness choice with t-tests.

Chen G, Cox RW, Glen DR, Rajendra JK, Reynolds RC, Taylor PA.

Hum Brain Mapp. 2019 Feb 15;40(3):1037-1043. doi: 10.1002/hbm.24399. Epub 2018 Sep 28.


Comparison of heritability estimates on resting state fMRI connectivity phenotypes using the ENIGMA analysis pipeline.

Adhikari BM, Jahanshad N, Shukla D, Glahn DC, Blangero J, Fox PT, Reynolds RC, Cox RW, Fieremans E, Veraart J, Novikov DS, Nichols TE, Hong LE, Thompson PM, Kochunov P.

Hum Brain Mapp. 2018 Dec;39(12):4893-4902. doi: 10.1002/hbm.24331. Epub 2018 Jul 27.


Heritability estimates on resting state fMRI data using ENIGMA analysis pipeline.

Adhikari BM, Jahanshad N, Shukla D, Glahn DC, Blangero J, Reynolds RC, Cox RW, Fieremans E, Veraart J, Novikov DS, Nichols TE, Hong LE, Thompson PM, Kochunov P.

Pac Symp Biocomput. 2018;23:307-318.


Intraclass correlation: Improved modeling approaches and applications for neuroimaging.

Chen G, Taylor PA, Haller SP, Kircanski K, Stoddard J, Pine DS, Leibenluft E, Brotman MA, Cox RW.

Hum Brain Mapp. 2018 Mar;39(3):1187-1206. doi: 10.1002/hbm.23909. Epub 2017 Dec 7.


Validity of a Smartphone Application for Measuring Ankle Plantar Flexion.

Cox RW, Martinez RE, Baker RT, Warren L.

J Sport Rehabil. 2018 May 1;27(3). doi: 10.1123/jsr.2017-0143. Epub 2018 Jun 22.


Temporal similarity perfusion mapping: A standardized and model-free method for detecting perfusion deficits in stroke.

Song S, Bokkers RPH, Luby M, Edwardson MA, Brown T, Shah S, Cox RW, Saad ZS, Reynolds RC, Glen DR, Cohen LG, Latour LL.

PLoS One. 2017 Oct 3;12(10):e0185552. doi: 10.1371/journal.pone.0185552. eCollection 2017.


fMRI clustering and false-positive rates.

Cox RW, Chen G, Glen DR, Reynolds RC, Taylor PA.

Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):E3370-E3371. doi: 10.1073/pnas.1614961114. Epub 2017 Apr 18. No abstract available.


FMRI Clustering in AFNI: False-Positive Rates Redux.

Cox RW, Chen G, Glen DR, Reynolds RC, Taylor PA.

Brain Connect. 2017 Apr;7(3):152-171. doi: 10.1089/brain.2016.0475.


Corrigendum to "Untangling the relatedness among correlations, Part I: Nonparametric approaches to inter-subject correlation analysis at the group level" [Neuroimage (in press)].

Chen G, Shin YW, Taylor PA, Glen DR, Reynolds RC, Israel RB, Cox RW.

Neuroimage. 2017 Jan 15;145(Pt A):130-132. doi: 10.1016/j.neuroimage.2016.10.021. Epub 2016 Oct 28. No abstract available.


Untangling the relatedness among correlations, Part II: Inter-subject correlation group analysis through linear mixed-effects modeling.

Chen G, Taylor PA, Shin YW, Reynolds RC, Cox RW.

Neuroimage. 2017 Feb 15;147:825-840. doi: 10.1016/j.neuroimage.2016.08.029. Epub 2016 Oct 15.


Is the statistic value all we should care about in neuroimaging?

Chen G, Taylor PA, Cox RW.

Neuroimage. 2017 Feb 15;147:952-959. doi: 10.1016/j.neuroimage.2016.09.066. Epub 2016 Oct 10. Review.


Untangling the relatedness among correlations, part I: Nonparametric approaches to inter-subject correlation analysis at the group level.

Chen G, Shin YW, Taylor PA, Glen DR, Reynolds RC, Israel RB, Cox RW.

Neuroimage. 2016 Nov 15;142:248-259. doi: 10.1016/j.neuroimage.2016.05.023. Epub 2016 May 17. Erratum in: Neuroimage. 2017 Jan 15;145(Pt A):130-132.


Detecting the subtle shape differences in hemodynamic responses at the group level.

Chen G, Saad ZS, Adleman NE, Leibenluft E, Cox RW.

Front Neurosci. 2015 Oct 26;9:375. doi: 10.3389/fnins.2015.00375. eCollection 2015.


Open Environment for Multimodal Interactive Connectivity Visualization and Analysis.

Taylor PA, Chen G, Cox RW, Saad ZS.

Brain Connect. 2016 Mar;6(2):109-21. doi: 10.1089/brain.2015.0363. Epub 2015 Nov 10.


Personal reflections on James S. Hyde.

Biswal B, Pawela C, Grist T, Meyerand ME, Nencka AS, DeYoe EA, Li SJ, Rowe DB, Kiviniemi V, Cox RW, Bodurka J, Ogawa S, Koretsky A, Hu X, Kim SG.

Brain Connect. 2014 Nov;4(9):631-5. doi: 10.1089/brain.2014.1503. No abstract available.


Task Dependence, Tissue Specificity, and Spatial Distribution of Widespread Activations in Large Single-Subject Functional MRI Datasets at 7T.

Gonzalez-Castillo J, Hoy CW, Handwerker DA, Roopchansingh V, Inati SJ, Saad ZS, Cox RW, Bandettini PA.

Cereb Cortex. 2015 Dec;25(12):4667-77. doi: 10.1093/cercor/bhu148. Epub 2014 Jul 1.


Applications of multivariate modeling to neuroimaging group analysis: a comprehensive alternative to univariate general linear model.

Chen G, Adleman NE, Saad ZS, Leibenluft E, Cox RW.

Neuroimage. 2014 Oct 1;99:571-88. doi: 10.1016/j.neuroimage.2014.06.027. Epub 2014 Jun 17.


Effective Preprocessing Procedures Virtually Eliminate Distance-Dependent Motion Artifacts in Resting State FMRI.

Jo HJ, Gotts SJ, Reynolds RC, Bandettini PA, Martin A, Cox RW, Saad ZS.

J Appl Math. 2013 May 21;2013. doi: 10.1155/2013/935154.


Two distinct forms of functional lateralization in the human brain.

Gotts SJ, Jo HJ, Wallace GL, Saad ZS, Cox RW, Martin A.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):E3435-44. doi: 10.1073/pnas.1302581110. Epub 2013 Aug 19.


The perils of global signal regression for group comparisons: a case study of Autism Spectrum Disorders.

Gotts SJ, Saad ZS, Jo HJ, Wallace GL, Cox RW, Martin A.

Front Hum Neurosci. 2013 Jul 12;7:356. doi: 10.3389/fnhum.2013.00356. eCollection 2013.


Correcting brain-wide correlation differences in resting-state FMRI.

Saad ZS, Reynolds RC, Jo HJ, Gotts SJ, Chen G, Martin A, Cox RW.

Brain Connect. 2013;3(4):339-52. doi: 10.1089/brain.2013.0156. Epub 2013 Jul 31.


Linear mixed-effects modeling approach to FMRI group analysis.

Chen G, Saad ZS, Britton JC, Pine DS, Cox RW.

Neuroimage. 2013 Jun;73:176-90. doi: 10.1016/j.neuroimage.2013.01.047. Epub 2013 Jan 30.


Quantifying agreement between anatomical and functional interhemispheric correspondences in the resting brain.

Jo HJ, Saad ZS, Gotts SJ, Martin A, Cox RW.

PLoS One. 2012;7(11):e48847. doi: 10.1371/journal.pone.0048847. Epub 2012 Nov 8. Erratum in: PLoS One. 2013;8(5). doi: 10.1371/annotation/cb15c6af-2153-49a9-8330-45e40e6c296d.


Fractionation of social brain circuits in autism spectrum disorders.

Gotts SJ, Simmons WK, Milbury LA, Wallace GL, Cox RW, Martin A.

Brain. 2012 Sep;135(Pt 9):2711-25. doi: 10.1093/brain/aws160. Epub 2012 Jul 11.


Trouble at rest: how correlation patterns and group differences become distorted after global signal regression.

Saad ZS, Gotts SJ, Murphy K, Chen G, Jo HJ, Martin A, Cox RW.

Brain Connect. 2012;2(1):25-32. doi: 10.1089/brain.2012.0080.


FMRI group analysis combining effect estimates and their variances.

Chen G, Saad ZS, Nath AR, Beauchamp MS, Cox RW.

Neuroimage. 2012 Mar;60(1):747-65. doi: 10.1016/j.neuroimage.2011.12.060. Epub 2011 Dec 30.


Vector autoregression, structural equation modeling, and their synthesis in neuroimaging data analysis.

Chen G, Glen DR, Saad ZS, Paul Hamilton J, Thomason ME, Gotlib IH, Cox RW.

Comput Biol Med. 2011 Dec;41(12):1142-55. doi: 10.1016/j.compbiomed.2011.09.004. Epub 2011 Oct 4.


AFNI: what a long strange trip it's been.

Cox RW.

Neuroimage. 2012 Aug 15;62(2):743-7. doi: 10.1016/j.neuroimage.2011.08.056. Epub 2011 Aug 27. Review.


Segmentation priors from local image properties: without using bias field correction, location-based templates, or registration.

Vovk A, Cox RW, Stare J, Suput D, Saad ZS.

Neuroimage. 2011 Mar 1;55(1):142-52. doi: 10.1016/j.neuroimage.2010.11.082. Epub 2010 Dec 10.


Mapping sources of correlation in resting state FMRI, with artifact detection and removal.

Jo HJ, Saad ZS, Simmons WK, Milbury LA, Cox RW.

Neuroimage. 2010 Aug 15;52(2):571-82. doi: 10.1016/j.neuroimage.2010.04.246. Epub 2010 Apr 24.


Defining functional SMA and pre-SMA subregions in human MFC using resting state fMRI: functional connectivity-based parcellation method.

Kim JH, Lee JM, Jo HJ, Kim SH, Lee JH, Kim ST, Seo SW, Cox RW, Na DL, Kim SI, Saad ZS.

Neuroimage. 2010 Feb 1;49(3):2375-86. doi: 10.1016/j.neuroimage.2009.10.016. Epub 2009 Oct 23.


Metabolically stable bradykinin B2 receptor agonists enhance transvascular drug delivery into malignant brain tumors by increasing drug half-life.

Sarin H, Kanevsky AS, Fung SH, Butman JA, Cox RW, Glen D, Reynolds R, Auh S.

J Transl Med. 2009 May 13;7:33. doi: 10.1186/1479-5876-7-33.


A new method for improving functional-to-structural MRI alignment using local Pearson correlation.

Saad ZS, Glen DR, Chen G, Beauchamp MS, Desai R, Cox RW.

Neuroimage. 2009 Feb 1;44(3):839-48. doi: 10.1016/j.neuroimage.2008.09.037. Epub 2008 Oct 11.


Two- and three-dimensional image rotation using the FFT.

Cox RW, Tong R.

IEEE Trans Image Process. 1999;8(9):1297-9. doi: 10.1109/83.784442.


Functional imaging analysis contest (FIAC) analysis according to AFNI and SUMA.

Saad ZS, Chen G, Reynolds RC, Christidis PP, Hammett KR, Bellgowan PS, Cox RW.

Hum Brain Mapp. 2006 May;27(5):417-24.


Experimental designs and processing strategies for fMRI studies involving overt verbal responses.

Birn RM, Cox RW, Bandettini PA.

Neuroimage. 2004 Nov;23(3):1046-58.


Single-shot magnetic field mapping embedded in echo-planar time-course imaging.

Roopchansingh V, Cox RW, Jesmanowicz A, Ward BD, Hyde JS.

Magn Reson Med. 2003 Oct;50(4):839-43.


Steady-state currents in sharp stochastic ratchets.

Kłosek MM, Cox RW.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 Oct;60(4 Pt A):3727-35.


Detection versus estimation in event-related fMRI: choosing the optimal stimulus timing.

Birn RM, Cox RW, Bandettini PA.

Neuroimage. 2002 Jan;15(1):252-64.


Analysis and use of FMRI response delays.

Saad ZS, Ropella KM, Cox RW, DeYoe EA.

Hum Brain Mapp. 2001 Jun;13(2):74-93.


Direct reconstruction of non-Cartesian k-space data using a nonuniform fast Fourier transform.

Sarty GE, Bennett R, Cox RW.

Magn Reson Med. 2001 May;45(5):908-15.


Specialized neural systems underlying representations of sequential movements.

Harrington DL, Rao SM, Haaland KY, Bobholz JA, Mayer AR, Binderx JR, Cox RW.

J Cogn Neurosci. 2000 Jan;12(1):56-77.


Real-time 3D image registration for functional MRI.

Cox RW, Jesmanowicz A.

Magn Reson Med. 1999 Dec;42(6):1014-8.

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