/** automatically generated by AFNI program quotize **/ static char *afni_papers[] = { "\n" , " ****************************************************\n" , " ***** This is a list of papers about AFNI, SUMA, *****\n" , " ****** and various algorithms implemented therein ******\n" , "----------------------------------------------------------------------------\n" , "RW Cox.\n" , " AFNI: Software for analysis and visualization of functional\n" , " magnetic resonance neuroimages. Computers and Biomedical Research,\n" , " 29: 162-173, 1996.\n" , "\n" , " * The very first AFNI paper, and the one I prefer you cite if you want\n" , " to refer to the AFNI package as a whole.\n" , " * https://sscc.nimh.nih.gov/sscc/rwcox/papers/CBM_1996.pdf\n" , "----------------------------------------------------------------------------\n" , "RW Cox, A Jesmanowicz, JS Hyde.\n" , " Real-time functional magnetic resonance imaging.\n" , " Magnetic Resonance in Medicine, 33: 230-236, 1995.\n" , "\n" , " * The first paper on realtime FMRI; describes the algorithm used in\n" , " in the realtime plugin for time series regression analysis.\n" , " * https://sscc.nimh.nih.gov/sscc/rwcox/papers/Realtime_FMRI.pdf\n" , "----------------------------------------------------------------------------\n" , "RW Cox, JS Hyde.\n" , " Software tools for analysis and visualization of FMRI Data.\n" , " NMR in Biomedicine, 10: 171-178, 1997.\n" , "\n" , " * A second paper about AFNI and design issues for FMRI software tools.\n" , "----------------------------------------------------------------------------\n" , "RW Cox, A Jesmanowicz.\n" , " Real-time 3D image registration for functional MRI.\n" , " Magnetic Resonance in Medicine, 42: 1014-1018, 1999.\n" , "\n" , " * Describes the algorithm used for image registration in 3dvolreg\n" , " and in the realtime plugin.\n" , " * The first paper to demonstrate realtime MRI volume image\n" , " registration running on a standard workstation (not a supercomputer).\n" , " * https://sscc.nimh.nih.gov/sscc/rwcox/papers/RealtimeRegistration.pdf\n" , "----------------------------------------------------------------------------\n" , "ZS Saad, KM Ropella, RW Cox, EA DeYoe.\n" , " Analysis and use of FMRI response delays.\n" , " Human Brain Mapping, 13: 74-93, 2001.\n" , "\n" , " * Describes the algorithm used in 3ddelay (cf. '3ddelay -help').\n" , " * https://sscc.nimh.nih.gov/sscc/rwcox/papers/Delays2001.pdf\n" , "----------------------------------------------------------------------------\n" , "ZS Saad, RC Reynolds, BD Argall, S Japee, RW Cox.\n" , " SUMA: An interface for surface-based intra- and inter-subject analysis\n" , " within AFNI. 2004 IEEE International Symposium on Biomedical Imaging:\n" , " from Nano to Macro. IEEE, Arlington VA, pp. 1510-1513.\n" , "\n" , " * A brief description of SUMA.\n" , " * https://dx.doi.org/10.1109/ISBI.2004.1398837\n" , " * https://sscc.nimh.nih.gov/sscc/rwcox/papers/SUMA2004paper.pdf\n" , "----------------------------------------------------------------------------\n" , "ZS Saad, G Chen, RC Reynolds, PP Christidis, KR Hammett, PSF Bellgowan,\n" , " RW Cox.\n" , " FIAC Analysis According to AFNI and SUMA.\n" , " Human Brain Mapping, 27: 417-424, 2006.\n" , "\n" , " * Describes how we used AFNI to analyze the FIAC contest data.\n" , " * https://dx.doi.org/10.1002/hbm.20247\n" , " * https://sscc.nimh.nih.gov/sscc/rwcox/papers/FIAC_AFNI_2006.pdf\n" , "----------------------------------------------------------------------------\n" , "BD Argall, ZS Saad, MS Beauchamp.\n" , " Simplified intersubject averaging on the cortical surface using SUMA.\n" , " Human Brain Mapping 27: 14-27, 2006.\n" , "\n" , " * Describes the 'standard mesh' surface approach used in SUMA.\n" , " * https://dx.doi.org/10.1002/hbm.20158\n" , " * https://sscc.nimh.nih.gov/sscc/rwcox/papers/SUMA2006paper.pdf\n" , "----------------------------------------------------------------------------\n" , "ZS Saad, DR Glen, G Chen, MS Beauchamp, R Desai, RW Cox.\n" , " A new method for improving functional-to-structural MRI alignment\n" , " using local Pearson correlation. NeuroImage 44: 839-848, 2009.\n" , "\n" , " * Describes the algorithm used in 3dAllineate (and thence in\n" , " align_epi_anat.py) for EPI-to-structural volume image registration.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2649831/\n" , " * https://dx.doi.org/10.1016/j.neuroimage.2008.09.037\n" , " * https://sscc.nimh.nih.gov/sscc/rwcox/papers/LocalPearson2009.pdf\n" , "----------------------------------------------------------------------------\n" , "H Sarin, AS Kanevsky, SH Fung, JA Butman, RW Cox, D Glen, R Reynolds, S Auh.\n" , " Metabolically stable bradykinin B2 receptor agonists enhance transvascular\n" , " drug delivery into malignant brain tumors by increasing drug half-life.\n" , " Journal of Translational Medicine, 7: #33, 2009.\n" , "\n" , " * Describes the method used in AFNI for modeling dynamic contrast enhanced\n" , " (DCE) MRI for analysis of brain tumors.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689161/\n" , " * https://dx.doi.org/10.1186/1479-5876-7-33\n" , "----------------------------------------------------------------------------\n" , "HJ Jo, ZS Saad, WK Simmons, LA Milbury, RW Cox.\n" , " Mapping sources of correlation in resting state FMRI, with artifact detection\n" , " and removal. NeuroImage, 52: 571-582, 2010.\n" , "\n" , " * Describes the ANATICOR method for de-noising FMRI datasets.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897154/\n" , " * https://dx.doi.org/10.1016/j.neuroimage.2010.04.246\n" , "----------------------------------------------------------------------------\n" , "A Vovk, RW Cox, J Stare, D Suput, ZS Saad.\n" , " Segmentation Priors From Local Image Properties: Without Using Bias Field\n" , " Correction, Location-based Templates, or Registration.\n" , " Neuroimage, 55: 142-152, 2011.\n" , "\n" , " * Describes the earliest basis for 3dSeg.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3031751/\n" , " * https://dx.doi.org/10.1016/j.neuroimage.2010.11.082\n" , "----------------------------------------------------------------------------\n" , "G Chen, ZS Saad, DR Glen, JP Hamilton, ME Thomason, IH Gotlib, RW Cox.\n" , " Vector Autoregression, Structural Equation Modeling, and Their Synthesis in\n" , " Neuroimaging Data Analysis.\n" , " Computers in Biology and Medicine, 41: 1142-1155, 2011.\n" , "\n" , " * Describes the method implemented in 1dSVAR (Structured Vector AutoRegression).\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3223325/\n" , " * https://dx.doi.org/10.1016/j.compbiomed.2011.09.004\n" , "----------------------------------------------------------------------------\n" , "RW Cox.\n" , " AFNI: what a long strange trip it's been. NeuroImage, 62: 747-765, 2012.\n" , "\n" , " * A Brief History of AFNI, from its inception to speculation about the future.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246532/\n" , " * https://dx.doi.org/10.1016/j.neuroimage.2011.08.056\n" , "----------------------------------------------------------------------------\n" , "ZS Saad, RC Reynolds.\n" , " SUMA. Neuroimage. 62: 768-773, 2012.\n" , "\n" , " * The biography of SUMA.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3260385/\n" , " * https://dx.doi.org/10.1016/j.neuroimage.2011.09.016\n" , "----------------------------------------------------------------------------\n" , "G Chen, ZS Saad, AR Nath, MS Beauchamp, RW Cox.\n" , " FMRI Group Analysis Combining Effect Estimates and Their Variances.\n" , " Neuroimage, 60: 747-765, 2012.\n" , "\n" , " * The math behind 3dMEMA (Mixed Effects Meta-Analysis) -- AKA super-3dttest.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3404516/\n" , " * https://dx.doi.org/10.1016/j.neuroimage.2011.12.060\n" , "----------------------------------------------------------------------------\n" , "ZS Saad, SJ Gotts, K Murphy, G Chen, HJ Jo, A Martin, RW Cox.\n" , " Trouble at Rest: How Correlation Patterns and Group Differences Become\n" , " Distorted After Global Signal Regression.\n" , " Brain Connectivity, 2: 25-32, 2012.\n" , "\n" , " * Our first paper on why Global Signal Regression in resting state FMRI is\n" , " a bad idea when doing any form of group analysis.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3484684/\n" , " * https://dx.doi.org/10.1089/brain.2012.0080\n" , "----------------------------------------------------------------------------\n" , "SJ Gotts, WK Simmons, LA Milbury, GL Wallace, RW Cox, A Martin.\n" , " Fractionation of Social Brain Circuits in Autism Spectrum Disorders.\n" , " Brain, 135: 2711-2725, 2012.\n" , "\n" , " * In our humble opinion, this shows how to use resting state FMRI correctly when\n" , " making inter-group comparisons (hint: no global signal regression is used).\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3437021/\n" , " * https://dx.doi.org/10.1093/brain/aws160\n" , "----------------------------------------------------------------------------\n" , "HJ Jo, ZS Saad, SJ Gotts, A Martin, RW Cox.\n" , " Quantifying Agreement between Anatomical and Functional Interhemispheric\n" , " Correspondences in the Resting Brain.\n" , " PLoS ONE, 7: art.no. e48847, 2012.\n" , "\n" , " * A numerical method for measuring symmetry in brain functional imaging data.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3493608/\n" , " * https://dx.doi.org/10.1371/journal.pone.0048847\n" , "----------------------------------------------------------------------------\n" , "ZS Saad, SJ Gotts, K Murphy, G Chen, HJ Jo, A Martin, RW Cox.\n" , " Trouble at Rest: How Correlation Patterns and Group Differences Become\n" , " Distorted After Global Signal Regression. Brain Connectivity, 2012: 25-32.\n" , "\n" , " * Another paper in the battle against Global Signal Regression.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3484684/\n" , " * https://dx.doi.org/10.1089/brain.2012.0080\n" , "----------------------------------------------------------------------------\n" , "G Chen, ZS Saad, JC Britton, DS Pine, RW Cox\n" , " Linear mixed-effects modeling approach to FMRI group analysis.\n" , " NeuroImage, 73: 176-190, 2013.\n" , "\n" , " * The math behind 3dLME.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3404516/\n" , " * https://dx.doi.org/10.1016/j.neuroimage.2011.12.060\n" , "----------------------------------------------------------------------------\n" , "SJ Gotts, ZS Saad, HJ Jo, GL Wallace, RW Cox, A Martin.\n" , " The perils of global signal regression for group comparisons: A case study\n" , " of Autism Spectrum Disorders.\n" , " Frontiers in Human Neuroscience: art.no. 356, 2013.\n" , "\n" , " * The long twilight struggle against Global Signal Regression continues.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3709423/\n" , " * https://dx.doi.org/10.3389/fnhum.2013.00356\n" , "----------------------------------------------------------------------------\n" , "HJ Jo, SJ Gotts, RC Reynolds, PA Bandettini, A Martin, RW Cox, ZS Saad.\n" , " Effective preprocessing procedures virtually eliminate distance-dependent\n" , " motion artifacts in resting state FMRI.\n" , " Journal of Applied Mathematics: art.no. 935154, 2013.\n" , "\n" , " * A reply to the Power 2012 paper on pre-processing resting state FMRI data,\n" , " showing how they got it wrong.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886863/\n" , " * https://dx.doi.org/10.1155/2013/935154\n" , "----------------------------------------------------------------------------\n" , "SJ Gotts, HJ Jo, GL Wallace, ZS Saad, RW Cox, A Martin.\n" , " Two distinct forms of functional lateralization in the human brain.\n" , " PNAS, 110: E3435-E3444, 2013.\n" , "\n" , " * More about methodology and results for symmetry in brain function.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767540/\n" , " * https://dx.doi.org/10.1073/pnas.1302581110\n" , "----------------------------------------------------------------------------\n" , "ZS Saad, RC Reynolds, HJ Jo, SJ Gotts, G Chen, A Martin, RW Cox.\n" , " Correcting Brain-Wide Correlation Differences in Resting-State FMRI.\n" , " Brain Connectivity, 2013: 339-352.\n" , "\n" , " * Just when you thought it was safe to go back into the waters of resting\n" , " state FMRI, another paper explaining why global signal regression is a\n" , " bad idea and a tentative step towards a different solution.\n" , " * https://www.ncbi.nlm.nih.gov/pubmed/23705677\n" , " * https://dx.doi.org/10.1089/brain.2013.0156\n" , "----------------------------------------------------------------------------\n" , "P Kundu, ND Brenowitz, V Voon, Y Worbe, PE Vertes, SJ Inati, ZS Saad,\n" , " PA Bandettini, ET Bullmore.\n" , " Integrated strategy for improving functional connectivity mapping using\n" , " multiecho fMRI. PNAS 110: 16187-16192, 2013.\n" , "\n" , " * A data acquisition and processing strategy for improving resting state FMRI.\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791700/\n" , " * https://dx.doi.org/10.1073/pnas.1301725110\n" , "----------------------------------------------------------------------------\n" , "PA Taylor, ZS Saad.\n" , " FATCAT: (An Efficient) Functional And Tractographic Connectivity Analysis\n" , " Toolbox. Brain Connectivity 3:523-535, 2013.\n" , "\n" , " * Introducing diffusion-based tractography tools in AFNI, with particular\n" , " emphases on complementing FMRI analysis and in performing interactive\n" , " visualization with SUMA.\n" , " * https://www.ncbi.nlm.nih.gov/pubmed/23980912\n" , " * https://dx.doi.org/10.1089/brain.2013.0154\n" , "----------------------------------------------------------------------------\n" , "G Chen, NE Adleman, ZS Saad, E Leibenluft, RW Cox.\n" , " Applications of multivariate modeling to neuroimaging group analysis:\n" , " A comprehensive alternative to univariate general linear model.\n" , " NeuroImage 99:571-588, 2014.\n" , "\n" , " * The fun stuff behind 3dMVM == more complex linear modeling for groups.\n" , " * https://dx.doi.org/10.1016/j.neuroimage.2014.06.027\n" , " * https://sscc.nimh.nih.gov/pub/dist/doc/papers/3dMVM_2014.pdf\n" , "----------------------------------------------------------------------------\n" , "Taylor PA, Chen G, Cox RW, Saad ZS.\n" , " Open Environment for Multimodal Interactive Connectivity\n" , " Visualization and Analysis. Brain Connectivity 6(2):109-21, 2016.\n" , "\n" , " * Visualization and MVM stats tools using tracking (or even functional\n" , " connectivity).\n" , " * https://dx.doi.org/10.1089/brain.2015.0363\n" , " * https://sscc.nimh.nih.gov/pub/dist/papers/ASF_2015_draft_BCinpress.pdf\n" , "----------------------------------------------------------------------------\n" , "G Chen, Y-W Shin, PA Taylor, DR GLen, RC Reynolds, RB Israel, RW Cox.\n" , " Untangling the relatedness among correlations, part I: Nonparametric\n" , " approaches to inter-subject correlation analysis at the group level.\n" , " NeuroImage 142:248-259, 2016.\n" , "\n" , " Proper statistical analysis (FPR control) when correlating FMRI time\n" , " series data amongst multiple subjects, using nonparametric methods.\n" , " * https://doi.org/10.1016/j.neuroimage.2016.05.023\n" , "----------------------------------------------------------------------------\n" , "G Chen, PA Taylor, Y-W Shin, RC Reynolds, RW Cox.\n" , " Untangling the relatedness among correlations, Part II: Inter-subject\n" , " correlation group analysis through linear mixed-effects modeling.\n" , " NeuroImage 147:825-840 2017.\n" , "\n" , " * Just when you thought it was safe to go back into the brain data:\n" , " this time, using parametric methods.\n" , " * https://doi.org/10.1016/j.neuroimage.2016.08.029\n" , "----------------------------------------------------------------------------\n" , "G Chen, PA Taylor, X Qu, PJ Molfese, PA Bandettini, RW Cox, ES Finn.\n" , " Untangling the relatedness among correlations, part III: Inter-subject\n" , " correlation analysis through Bayesian multilevel modeling for naturalistic\n" , " scanning.\n" , " NeuroImage, 2019.\n" , "\n" , " * https://doi.org/10.1016/j.neuroimage.2019.116474\n" , " * https://www.ncbi.nlm.nih.gov/pubmed/31884057\n" , " * https://www.biorxiv.org/content/10.1101/655738v1.full\n" , "----------------------------------------------------------------------------\n" , "RW Cox, G Chen, DR Glen, RC Reynolds, PA Taylor.\n" , " fMRI clustering and false-positive rates.\n" , " PNAS 114:E3370-E3371, 2017.\n" , "\n" , " * Response to Eklund's (et al.) paper about clustering in PNAS 2016.\n" , " * https://arxiv.org/abs/1702.04846\n" , " * https://doi.org/10.1073/pnas.1614961114\n" , "----------------------------------------------------------------------------\n" , "RW Cox, G Chen, DR Glen, RC Reynolds, PA Taylor.\n" , " FMRI Clustering in AFNI: False Positive Rates Redux.\n" , " Brain Connectivity 7:152-171, 2017.\n" , "\n" , " * A discussion of the cluster-size thresholding updates made to\n" , " AFNI in early 2017.\n" , " * https://arxiv.org/abs/1702.04845\n" , " * https://doi.org/10.1089/brain.2016.0475\n" , "----------------------------------------------------------------------------\n" , "S Song, RPH Bokkers, MA Edwardson, T Brown, S Shah, RW Cox, ZS Saad,\n" , " RC Reynolds, DR Glen, LG Cohen LG, LL Latour.\n" , " Temporal similarity perfusion mapping: A standardized and model-free method\n" , " for detecting perfusion deficits in stroke.\n" , " PLoS ONE 12, Article number e0185552, 2017.\n" , "\n" , " * Applying AFNI's InstaCorr module to stroke perfusion mapping.\n" , " * https://doi.org/10.1371/journal.pone.0185552\n" , " * https://www.ncbi.nlm.nih.gov/pubmed/28973000\n" , "----------------------------------------------------------------------------\n" , "G Chen, PA Taylor, SP Haller, K Kircanski, J Stoddard, DS Pine, E Leibenluft,\n" , " Brotman MA, RW Cox.\n" , " Intraclass correlation: Improved modeling approaches and applications for\n" , " neuroimaging.\n" , " Human Brain Mapping, 39:1187-1206 2018.\n" , "\n" , " * Discussion of ICC methods, and distinctions among them.\n" , " * https://doi.org/10.1002/hbm.23909\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807222/\n" , "----------------------------------------------------------------------------\n" , "PA Taylor, G Chen, DR Glen, JK Rajendra, RC Reynolds, RW Cox.\n" , " FMRI processing with AFNI: Some comments and corrections on 'Exploring the\n" , " Impact of Analysis Software on Task fMRI Results'.\n" , "\n" , " * https://www.biorxiv.org/content/10.1101/308643v1.abstract\n" , " * https://doi.org/10.1101/308643\n" , "----------------------------------------------------------------------------\n" , "RW Cox.\n" , " Equitable Thresholding and Clustering: A Novel Method for Functional\n" , " Magnetic Resonance Imaging Clustering in AFNI.\n" , " Brain Connectivity 9:529-538, 2019.\n" , "\n" , " * https://doi.org/10.1089/brain.2019.0666\n" , "----------------------------------------------------------------------------\n" , "G Chen, RW Cox, DR Glen, JK Rajendra, RC Reynolds, PA Taylor.\n" , " A tail of two sides: Artificially doubled false positive rates in\n" , " neuroimaging due to the sidedness choice with t-tests.\n" , " Human Brain Mapping 40:1037-1043, 2019.\n" , "\n" , " * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6328330/\n" , " * https://dx.doi.org/10.1002/hbm.24399\n" , "----------------------------------------------------------------------------\n" , "G Chen, Y Xiao, PA Taylor, JK Rajendra, T Riggins, F Geng, E Redcay, RW Cox.\n" , " Handling Multiplicity in Neuroimaging Through Bayesian Lenses with\n" , " Multilevel Modeling.\n" , " Neuroinformatics 17:515-545, 2019.\n" , "\n" , " * https://link.springer.com/article/10.1007/s12021-018-9409-6\n" , " * https://www.biorxiv.org/content/10.1101/238998v1.abstract\n" , "----------------------------------------------------------------------------\n" , "DR Glen, PA Taylor, BR Buchsbaum, RW Cox, and RC Reynolds.\n" , " Beware (Surprisingly Common) Left-Right Flips in Your MRI Data:\n" , " An Efficient and Robust Method to Check MRI Dataset Consistency Using AFNI.\n" , " Frontiers in Neuroinformatics, 25 May 2020.\n" , "\n" , " * https://doi.org/10.3389/fninf.2020.00018\n" , " * https://www.medrxiv.org/content/10.1101/19009787v4\n" , "----------------------------------------------------------------------------\n" , "V Roopchansingh, JJ French Jr, DM Nielson, RC Reynolds, DR Glen, P D’Souza,\n" , " PA Taylor, RW Cox, AE Thurm.\n" , " EPI Distortion Correction is Easy and Useful, and You Should Use It:\n" , " A case study with toddler data.\n" , "\n" , " * https://www.biorxiv.org/content/10.1101/2020.09.28.306787v1\n" , "----------------------------------------------------------------------------\n" , "G Chen, TA Nash, KM Cole, PD Kohn, S-M Wei, MD Gregory, DP Eisenberg,\n" , " RW Cox, KF Berman, JS Kippenham.\n" , " Beyond linearity in neuroimaging: Capturing nonlinear relationships with\n" , " application to longitudinal studies.\n" , "\n" , " * https://doi.org/10.1016/j.neuroimage.2021.117891\n" , " * https://pubmed.ncbi.nlm.nih.gov/33667672/\n" , "----------------------------------------------------------------------------\n" , NULL } ; #define NUM_afni_papers 375