References

• [1] Avants, B., Epstein, C., Grossman, M., and Gee, J. 2008 February. Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain. Medical image analysis, 12 :1 , pp. 26–41 doi:10.1016/j.media.2007.06.004
• [2] Smith, S. M. 2002 November. Fast robust automated brain extraction. Human brain mapping, 17 :3 , pp. 143–155 doi:10.1002/hbm.10062
• [3] Cox, R. W. 1996 June. AFNI: Software for Analysis and Visualization of Functional Magnetic Resonance Neuroimages. Computers and biomedical research, 29 :3 , pp. 162–173 doi:10.1006/cbmr.1996.0014
• [4] (1,2) Zhang, Y., Brady, M., and Smith, S. Jan./2001. Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm. Ieee transactions on medical imaging, 20 :1 , pp. 45–57 doi:10.1109/42.906424
• [5] Smith, S. M., Jenkinson, M., Woolrich, M. W., Beckmann, C. F., Behrens, T. E.J., Johansen-Berg, H., Bannister, P. R., De Luca, M., Drobnjak, I., Flitney, D. E., Niazy, R. K., Saunders, J., Vickers, J., Zhang, Y., De Stefano, N., Brady, J. M., and Matthews, P. M. 2004 January. Advances in functional and structural MR image analysis and implementation as FSL. Neuroimage, 23 , pp. S208-S219 doi:10.1016/j.neuroimage.2004.07.051
• [6] Cox, R. W. and Jesmanowicz, A. 1999. Real-time 3D image registration for functional MRI. Magnetic resonance in medicine, 42 :6 , pp. 1014–1018 doi:10.1002/(SICI)1522-2594(199912)42:6<1014::AID-MRM4>3.0.CO;2-F
• [7] Friston, K. J., Williams, S., Howard, R., Frackowiak, R. S., and Turner, R. 1996 March. Movement-related effects in fMRI time-series. Magnetic resonance in medicine, 35 :3 , pp. 346–355 doi:10.1002/mrm.1910350312
• [8] Behzadi, Y., Restom, K., Liau, J., and Liu, T. T. 2007 August. A component based noise correction method (CompCor) for BOLD and perfusion based fMRI. Neuroimage, 37 :1 , pp. 90–101 doi:10.1016/j.neuroimage.2007.04.042
• [9] Zang, Y.-F., He, Y., Zhu, C.-Z., Cao, Q.-J., Sui, M.-Q., Liang, M., Tian, L.-X., Jiang, T.-Z., and Wang, Y.-F. 2007 March. Altered baseline brain activity in children with ADHD revealed by resting-state functional MRI. Brain & development, 29 :2 , pp. 83–91 doi:10.1016/j.braindev.2006.07.002
• [10] Zou, Q.-H., Zhu, C.-Z., Yang, Y., Zuo, X.-N., Long, X.-Y., Cao, Q.-J., Wang, Y.-F., and Zang, Y.-F. 2008 July. An improved approach to detection of amplitude of low-frequency fluctuation (ALFF) for resting-state fMRI: Fractional ALFF. Journal of neuroscience methods, 172 :1 , pp. 137–141 doi:10.1016/j.jneumeth.2008.04.012
• [11] Zang, Y., Jiang, T., Lu, Y., He, Y., and Tian, L. 2004 May. Regional homogeneity approach to fMRI data analysis. Neuroimage, 22 :1 , pp. 394–400 doi:10.1016/j.neuroimage.2003.12.030
• [12] Stark, D. E., Margulies, D. S., Shehzad, Z. E., Reiss, P., Kelly, A. M. C., Uddin, L. Q., Gee, D. G., Roy, A. K., Banich, M. T., Castellanos, F. X., and Milham, M. P. 2008 December. Regional Variation in Interhemispheric Coordination of Intrinsic Hemodynamic Fluctuations. The journal of neuroscience, 28 :51 , pp. 13754–13764 doi:10.1523/JNEUROSCI.4544-08.2008
• [13] Buckner, R. L., Sepulcre, J., Talukdar, T., Krienen, F. M., Liu, H., Hedden, T., Andrews-Hanna, J. R., Sperling, R. A., and Johnson, K. A. 2009 February. Cortical Hubs Revealed by Intrinsic Functional Connectivity: Mapping, Assessment of Stability, and Relation to Alzheimer’s Disease. The journal of neuroscience, 29 :6 , pp. 1860–1873 doi:10.1523/JNEUROSCI.5062-08.2009
• [14] Lohmann, G., Margulies, D. S., Horstmann, A., Pleger, B., Lepsien, J., Goldhahn, D., Schloegl, H., Stumvoll, M., Villringer, A., and Turner, R. 2010 April. Eigenvector Centrality Mapping for Analyzing Connectivity Patterns in fMRI Data of the Human Brain. Plos one, 5 :4 , pp. e10232 doi:10.1371/journal.pone.0010232
• [15] Tomasi, D. and Volkow, N. D. 2010 May. Functional connectivity density mapping. Proceedings of the national academy of sciences, 107 :21 , pp. 9885–9890 doi:10.1073/pnas.1001414107
• [16] Beckmann, C., Mackay, C., Filippini, N., and Smith, S. 2009 July. Group comparison of resting-state FMRI data using multi-subject ICA and dual regression. Neuroimage, 47 , pp. S148 doi:10.1016/S1053-8119(09)71511-3
• [17] Smith, S. M., Fox, P. T., Miller, K. L., Glahn, D. C., Fox, P. M., Mackay, C. E., Filippini, N., Watkins, K. E., Toro, R., Laird, A. R., and Beckmann, C. F. 2009 August. Correspondence of the brain’s functional architecture during activation and rest. Proceedings of the national academy of sciences, 106 :31 , pp. 13040–13045 doi:10.1073/pnas.0905267106
• [18](1,2) Dosenbach, N. U. F., Nardos, B., Cohen, A. L., Fair, D. A., Power, J. D., Church, J. A., Nelson, S. M., Wig, G. S., Vogel, A. C., Lessov-Schlaggar, C. N., Barnes, K. A., Dubis, J. W., Feczko, E., Coalson, R. S., Pruett, J. R., Barch, D. M., Petersen, S. E., and Schlaggar, B. L. 2010 September. Prediction of Individual Brain Maturity Using fMRI. Science, 329 :5997 , pp. 1358–1361 doi:10.1126/science.1194144
• [19] Tzourio-Mazoyer, N., Landeau, B., Papathanassiou, D., Crivello, F., Etard, O., Delcroix, N., Mazoyer, B., and Joliot, M. 2002 January. Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain. Neuroimage, 15 :1 , pp. 273–289 doi:10.1006/nimg.2001.0978
• [20] Eickhoff, S. B., Stephan, K. E., Mohlberg, H., Grefkes, C., Fink, G. R., Amunts, K., and Zilles, K. 2005 May. A new SPM toolbox for combining probabilistic cytoarchitectonic maps and functional imaging data. Neuroimage, 25 :4 , pp. 1325–1335 doi:10.1016/j.neuroimage.2004.12.034
• [21] Harvard-Oxford cortical and subcortical structural atlases, Fslwiki: atlases.
• [22] Lancaster, J. L., Woldorff, M. G., Parsons, L. M., Liotti, M., Freitas, C. S., Rainey, L., Kochunov, P. V., Nickerson, D., Mikiten, S. A., and Fox, P. T. 2000 July. Automated Talairach Atlas labels for functional brain mapping. Human brain mapping, 10 :3 , pp. 120–131 doi:10.1002/1097-0193(200007)10:3<120::AID-HBM30>3.0.CO;2-8
• [23] Craddock, R. C., James, G.Andrew, Holtzheimer, P. E., Hu, X. P., and Mayberg, H. S. 2012 August. A whole brain fMRI atlas generated via spatially constrained spectral clustering. Human brain mapping, 33 :8 , pp. 1914–1928 doi:10.1002/hbm.21333
• [24] fMRIPrep developers. 2016. fMRIPrep: A Robust Preprocessing Pipeline for fMRI Data — fMRIPrep stable version documentation.
• Kiar, G., Bridgeford, E. W., Roncal, W. R. G., Consortium for Reliability and Reproducibility (CoRR), Chandrashekhar, V., Mhembere, D., Ryman, S., Zuo, X.-N., Margulies, D. S., Craddock, R. C., Priebe, C. E., Jung, R., Calhoun, V. D., Caffo, B., Burns, R., Milham, M. P., and Vogelstein, J. T. 2018 April. A High-Throughput Pipeline Identifies Robust Connectomes But Troublesome Variability. doi:10.1101/188706
• NeuroData. NeuroData's MRI to Graphs.
• NeuroData. 2018 January. ndmg v0.1.0.
• [25] Hoffmann, M. S., Salum, G., Moore, T. M., Milham, M., and Satterthwaite, T. 2021 June. Reproducible Brain Charts initiative - Reliability and Validity of Bifactor Models of Dimensional Psychopathology in Youth. doi:10.17605/OSF.IO/UWY5N
• Ramirez, J. S. B., Graham, A. M., Thompson, J. R., Zhu, J. Y., Sturgeon, D., Bagley, J. L., Thomas, E., Papadakis, S., Bah, M., Perrone, A., Earl, E., Miranda-Dominguez, O., Feczko, E., Fombonne, E. J., Amaral, D. G., Nigg, J. T., Sullivan, E. L., and Fair, D. A. 2020 March. Maternal Interleukin-6 Is Associated With Macaque Offspring Amygdala Development and Behavior. Cerebral cortex, 30 :3 , pp. 1573–1585 doi:10.1093/cercor/bhz188
• Wang, X., Li, X.-H., Cho, J. W., Russ, B. E., Rajamani, N., Omelchenko, A., Ai, L., Korchmaros, A., Sawiak, S., Benn, R. A., Garcia-Saldivar, P., Wang, Z., Kalin, N. H., Schroeder, C. E., Craddock, R. C., Fox, A. S., Evans, A. C., Messinger, A., Milham, M. P., and Xu, T. 2021 July. U-net model for brain extraction: Trained on humans for transfer to non-human primates. Neuroimage, 235 , pp. 118001 doi:10.1016/j.neuroimage.2021.118001
• [26] Xu, T., Sturgeon, D., Ramirez, J. S. B., Froudist-Walsh, S., Margulies, D. S., Schroeder, C. E., Fair, D. A., and Milham, M. P. 2019 June. Interindividual variability of functional connectivity in awake and anesthetized rhesus macaque monkeys. Biological psychiatry: cognitive neuroscience and neuroimaging, 4 :6 , pp. 543–553 doi:10.1016/j.bpsc.2019.02.005
• [27] Sturgeon, D., Earl, E., Snider, K., Perrone, A., Ramirez, J., Mitchell, A. J., and Fair, D. Zenodo, 2020 June. DCAN-Labs/nhp-abcd-bids-pipeline Version 0.1.0. doi:10.5281/zenodo.3888969#.Xw31IpNKjyU