Javier González-Castillo

Taylor, P.A., Aggarwal, H., Bandettini, P.A., Barilari, M., Bright, M.G., Caballero-Gaudes, C., Calhoun, V.D., Chakravarty, M., Devenyi, G.A., Evans, J.W., Garza-Villarreal, E.A., Gau, R., Glen, D.R., Goebel, R., Gonzalez-Castillo, J., Gulban, O.F., Halchenko, Y., Handwerker, D.A., Hanayik, T., Lauren, P.D., Leopold, D.A., Lerch, J.P., Mathys, C., McCarthy, P., McLeod, A., Mejia, A.F., Moia, S., Nichols, T.E., Pernet, C., Pessoa, L., Pfleiderer, B., Rajendra, J.K., Rasgado-Toledo, J., Reyes, L.D., Reynolds, R.C., Roopchansingh, V., Rorden, C., Russ, B.E., Sundermann, B., Thirion, B., Torrisi, S., & Chen, G. (In press). Go figure: transparency in neuroscience images preserves context and clarifies interpretation. Nature Methods. Doi:10.1038/s41592-026-03206-7

Faskowitz, J., Bandettini, P.A., & Gonzalez-Castillo, J. (2026). Mapping high-amplitude fMRI edge time series events across space and time. Imaging Neuroscience, 4. Doi:10.1162/IMAG.a.1126

Gonzalez-Castillo, J., Spurney, M.A., Lam, K.C., Gephart, I.S., Pereira, F., Handwerker, D.A., Kam, J.W.Y., & Bandettini, P.A. (2026). In-scanner thoughts contribute to resting-state functional connectivity. Nature Communications, 17(1). Doi:10.1038/s41467-026-74953-6

Kumar, S.S., Arzi, A., Bareham, C.A., Gonzalez-Castillo, J., Fernandez, I., Tagliazucchi, E., Mediano, P.A.M., Bandettini, P.A., & Bekinschtein, T.A. (2026). Brain network dynamics in the wake-sleep transition reorganize according to task engagement. Imaging Neuroscience, 4. Doi:10.1162/IMAG.a.1336

Kronemer, S.I., Gobo, V.E., Walsh, C.R., Teves, J.B., Burk, D.C., Shahsavarani, S., Gonzalez-Castillo, J., & Bandettini, P.A. (2025). Cross-species real-time detection of trends in pupil size fluctuation. Behavior Research Methods, 57(1). Doi:10.3758/s13428-024-02545-7

Kronemer, S.I., Bandettini, P.A., & Gonzalez-Castillo, J. (2025). Sleuthing subjectivity: a review of covert measures of consciousness. Nature Reviews Neuroscience, 26(8), 476-496. Doi:10.1038/s41583-025-00934-1

Kronemer, S.I., Holness, M., Morgan, A.T., Teves, J.B., Gonzalez-Castillo, J., Handwerker, D.A., & Bandettini, P.A. (2024). Visual imagery vividness correlates with afterimage conscious perception. Neuroscience of Consciousness, 2024(1). Doi:10.1093/nc/niae032

Uruñuela, E., Gonzalez-Castillo, J., Zheng, C., Bandettini, P., & Caballero-Gaudes, C. (2024). Whole-brain multivariate hemodynamic deconvolution for functional MRI with stability selection. Medical Image Analysis, 91. Doi:10.1016/j.media.2023.103010

Gaggi, N.L., Collins, K.A., Gonzalez-Castillo, J., Hurtado, A.M., Castellanos, F.X., Osorio, R., Cassano, P., & Iosifescu, D.V. (2024). Transcranial photobiomodulation increases intrinsic brain activity within irradiated areas in early Alzheimer's disease: Potential link with cerebral metabolism. Brain Stimulation, 17(2), 208-210. Doi:10.1016/j.brs.2024.02.012

Gonzalez-Castillo, J., Fernandez, I.S., Lam, K.C., Handwerker, D.A., Pereira, F., & Bandettini, P.A. (2023). Manifold learning for fMRI time-varying functional connectivity. Frontiers in Human Neuroscience, 17. Doi:10.3389/fnhum.2023.1134012

Shahsavarani, S., Thibodeaux, D.N., Xu, W., Kim, S.H., Lodgher, F., Nwokeabia, C., Cambareri, M., Yagielski, A.J., Zhao, H.T., Handwerker, D.A., Gonzalez-Castillo, J., Bandettini, P.A., & Hillman, E.M.C. (2023). Cortex-wide neural dynamics predict behavioral states and provide a neural basis for resting-state dynamic functional connectivity. Cell Reports, 42(6). Doi:10.1016/j.celrep.2023.112527

Taylor, P.A., Reynolds, R.C., Calhoun, V., Gonzalez-Castillo, J., Handwerker, D.A., Bandettini, P.A., Mejia, A.F., & Chen, G. (2023). Highlight results, don't hide them: Enhance interpretation, reduce biases and improve reproducibility. Neuroimage, 274. Doi:10.1016/j.neuroimage.2023.120138

Teves, J.B., Gonzalez-Castillo, J., Holness, M., Spurney, M., Bandettini, P.A., & Handwerker, D.A. (2023). The art and science of using quality control to understand and improve fMRI data. Frontiers in Neuroscience, 17. Doi:10.3389/fnins.2023.1100544

Gonzalez-Castillo, J. (2022). Traveling and standing waves in the brain. Nature Neuroscience, 25(8), 980-981. Doi:10.1038/s41593-022-01119-0

Gonzalez-Castillo, J., Fernandez, I.S., Handwerker, D.A., & Bandettini, P.A. (2022). Ultra-slow fMRI fluctuations in the fourth ventricle as a marker of drowsiness. Neuroimage, 259. Doi:10.1016/j.neuroimage.2022.119424

Bandettini, P.A., Gonzalez-Castillo, J., Handwerker, D., Taylor, P., Chen, G., & Thomas, A. (2022). The challenge of BWAs: Unknown unknowns in feature space and variance. Med, 3(8), 526-531. Doi:10.1016/j.medj.2022.07.002

Gonzalez-Castillo, J., Kam, J.W.Y., Hoy, C.W., & Bandettini, P.A. (2021). How to interpret resting-state fMRI: Ask your participants. Journal of Neuroscience, 41(6), 1130-1141. Doi:10.1523/JNEUROSCI.1786-20.2020

Handwerker, D.A., Ianni, G., Gutierrez, B., Roopchansingh, V., Gonzalez-Castillo, J., Chen, G., Bandettini, P.A., Ungerleider, L.G., & Pitcher, D. (2020). Theta-burst TMS to the posterior superior temporal sulcus decreases resting-state fMRI connectivity across the face processing network. Network Neuroscience, 4(3), 746-760. Doi:10.1162/netn_a_00145

Rolinski, R., You, X., Gonzalez-Castillo, J., Norato, G., Reynolds, R.C., Inati, S.K., & Theodore, W.H. (2020). Language lateralization from task-based and resting state functional MRI in patients with epilepsy. Human Brain Mapping, 41(11), 3133-3146. Doi:10.1002/hbm.25003

Gonzalez-Castillo, J., Ramot, M., & Momenan, R. (2020). Editorial: Towards Expanded Utility of Real Time fMRI Neurofeedback in Clinical Applications. Frontiers in Human Neuroscience, 14. Doi:10.3389/fnhum.2020.606868

Caballero-Gaudes, C., Moia, S., Panwar, P., Bandettini, P.A., & Gonzalez-Castillo, J. (2019). A deconvolution algorithm for multi-echo functional MRI: Multi-echo Sparse Paradigm Free Mapping. Neuroimage, 202. Doi:10.1016/j.neuroimage.2019.116081

Chai, Y., Handwerker, D.A., Marrett, S., Gonzalez-Castillo, J., Merriam, E.P., Hall, A., Molfese, P.J., & Bandettini, P.A. (2019). Visual temporal frequency preference shows a distinct cortical architecture using fMRI. Neuroimage, 197, 13-23. Doi:10.1016/j.neuroimage.2019.04.048

Gonzalez-Castillo, J., Caballero-Gaudes, C., Topolski, N., Handwerker, D.A., Pereira, F., & Bandettini, P.A. (2019). Imaging the spontaneous flow of thought: Distinct periods of cognition contribute to dynamic functional connectivity during rest. Neuroimage, 202. Doi:10.1016/j.neuroimage.2019.116129

Ramot, M., & Gonzalez-Castillo, J. (2019). A framework for offline evaluation and optimization of real-time algorithms for use in neurofeedback, demonstrated on an instantaneous proxy for correlations. Neuroimage, 188, 322-334. Doi:10.1016/j.neuroimage.2018.12.006

Xie, H., Zheng, C.Y., Handwerker, D.A., Bandettini, P.A., Calhoun, V.D., Mitra, S., & Gonzalez-Castillo, J. (2019). Efficacy of different dynamic functional connectivity methods to capture cognitively relevant information. Neuroimage, 188, 502-514. Doi:10.1016/j.neuroimage.2018.12.037

Jangraw, D.C., Gonzalez-Castillo, J., Handwerker, D.A., Ghane, M., Rosenberg, M.D., Panwar, P., & Bandettini, P.A. (2018). A functional connectivity-based neuromarker of sustained attention generalizes to predict recall in a reading task. Neuroimage, 166, 99-109. Doi:10.1016/j.neuroimage.2017.10.019

Saggar, M., Sporns, O., Gonzalez-Castillo, J., Bandettini, P.A., Carlsson, G., Glover, G., & Reiss, A.L. (2018). Towards a new approach to reveal dynamical organization of the brain using topological data analysis. Nature Communications, 9(1). Doi:10.1038/s41467-018-03664-4

Xie, H., Gonzalez-Castillo, J., Handwerker, D.A., Bandettini, P.A., Calhoun, V.D., Chen, G., Damaraju, E., Liu, X., & Mitra, S. (2018). Time-varying whole-brain functional network connectivity coupled to task engagement. Network Neuroscience, 3(1), 49-66. Doi:10.1162/netn_a_00051

Caballero-Gaudes, C., Moia, S., Bandettini, P.A., & Gonzalez-Castillo, J. (2018). Quantitative deconvolution of fmri data with multi-echo sparse paradigm free mapping. Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics, 11072 LNCS, 311-319. Doi:10.1007/978-3-030-00931-1_36

Gaudes, C.C., Bandettini, P.A., & Gonzalez-Castillo, J. (2018). A temporal deconvolution algorithm for multiecho functional MRI. Proceedings International Symposium on Biomedical Imaging, 2018-April, 608-611. Doi:10.1109/ISBI.2018.8363649

Gonzalez-Castillo, J., & Bandettini, P.A. (2018). Task-based dynamic functional connectivity: Recent findings and open questions. Neuroimage, 180, 526-533. Doi:10.1016/j.neuroimage.2017.08.006

Torrisi, S., Gorka, A.X., Gonzalez-Castillo, J., O'Connell, K., Balderston, N., Grillon, C., & Ernst, M. (2018). Extended amygdala connectivity changes during sustained shock anticipation. Translational Psychiatry, 8(1). Doi:10.1038/s41398-017-0074-6

Xie, H., Calhoun, V.D., Gonzalez-Castillo, J., Damaraju, E., Miller, R., Bandettini, P.A., & Mitra, S. (2018). Whole-brain connectivity dynamics reflect both task-specific and individual-specific modulation: A multitask study. Neuroimage, 180, 495-504. Doi:10.1016/j.neuroimage.2017.05.050

Degryse, J., Seurinck, R., Durnez, J., Gonzalez-Castillo, J., Bandettini, P.A., & Moerkerke, B. (2017). Introducing alternative-based thresholding for defining functional regions of interest in fMRI. Frontiers in Neuroscience, 11(APR). Doi:10.3389/fnins.2017.00222

Gonzalez-Castillo, J., Chen, G., Nichols, T.E., & Bandettini, P.A. (2017). Variance decomposition for single-subject task-based fMRI activity estimates across many sessions. Neuroimage, 154, 206-218. Doi:10.1016/j.neuroimage.2016.10.024

Huber, L., Handwerker, D.A., Jangraw, D.C., Chen, G., Hall, A., Stüber, C., Gonzalez-Castillo, J., Ivanov, D., Marrett, S., Guidi, M., Goense, J., Poser, B.A., & Bandettini, P.A. (2017). High-Resolution CBV-fMRI Allows Mapping of Laminar Activity and Connectivity of Cortical Input and Output in Human M1. Neuron, 96(6), 1253-1263.e7. Doi:10.1016/j.neuron.2017.11.005

Ramot, M., Kimmich, S., Gonzalez-Castillo, J., Roopchansingh, V., Popal, H., White, E., Gotts, S.J., & Martin, A. (2017). Direct modulation of aberrant brain network connectivity through real-time NeuroFeedback. Elife, 6. Doi:10.7554/eLife.28974

Gonzalez-Castillo, J., Panwar, P., Buchanan, L.C., Caballero-Gaudes, C., Handwerker, D.A., Jangraw, D.C., Zachariou, V., Inati, S., Roopchansingh, V., Derbyshire, J.A., & Bandettini, P.A. (2016). Evaluation of multi-echo ICA denoising for task based fMRI studies: Block designs, rapid event-related designs, and cardiac-gated fMRI. Neuroimage, 141, 452-468. Doi:10.1016/j.neuroimage.2016.07.049

Gonzalez-Castillo, J., Hoy, C.W., Handwerker, D.A., Robinson, M.E., Buchanan, L.C., Saad, Z.S., & Bandettini, P.A. (2015). Tracking ongoing cognition in individuals using brief, whole-brain functional connectivity patterns. Proceedings of the National Academy of Sciences of the United States of America, 112(28), 8762-8767. Doi:10.1073/pnas.1501242112

Gonzalez-Castillo, J., Hoy, C.W., Handwerker, D.A., Roopchansingh, V., Inati, S.J., Saad, Z.S., Cox, R.W., & Bandettini, P.A. (2015). Task dependence, tissue specificity, and spatial distribution of widespread activations in large single-subject functional MRI datasets at 7T. Cerebral Cortex, 25(12), 4667-4677. Doi:10.1093/cercor/bhu148

Gonzalez-Castillo, J., & Bandettini, P.A. (2015). What Cascade Spreading Models Can Teach Us about the Brain. Neuron, 86(6), 1327-1329. Doi:10.1016/j.neuron.2015.06.006

Gonzalez-Castillo, J., Handwerker, D.A., Robinson, M.E., Hoy, C.W., Buchanan, L.C., Saad, Z.S., & Bandettini, P.A. (2014). The spatial structure of resting state connectivity stability on the scale of minutes. Frontiers in Neuroscience(8 JUN). Doi:10.3389/fnins.2014.00138

Yang, Z., Huang, Z., Gonzalez-Castillo, J., Dai, R., Northoff, G., & Bandettini, P. (2014). Using fMRI to decode true thoughts independent of intention to conceal. Neuroimage, 99, 80-92. Doi:10.1016/j.neuroimage.2014.05.034

Talavage, T.M., Gonzalez-Castillo, J., & Scott, S.K. (2014). Auditory neuroimaging with fMRI and PET. Hearing Research, 307, 4-15. Doi:10.1016/j.heares.2013.09.009

Gonzalez-Castillo, J., Duthie, K.N., Saad, Z.S., Chu, C., Bandettini, P.A., & Luh, W.M. (2013). Effects of image contrast on functional MRI image registration. Neuroimage, 67, 163-174. Doi:10.1016/j.neuroimage.2012.10.076

Hutchison, R.M., Womelsdorf, T., Allen, E.A., Bandettini, P.A., Calhoun, V.D., Corbetta, M., Della Penna, S., Duyn, J.H., Glover, G.H., Gonzalez-Castillo, J., Handwerker, D.A., Keilholz, S., Kiviniemi, V., Leopold, D.A., de Pasquale, F., Sporns, O., Walter, M., & Chang, C. (2013). Dynamic functional connectivity: Promise, issues, and interpretations. Neuroimage, 80, 360-378. Doi:10.1016/j.neuroimage.2013.05.079

Smalt, C.J., Gonzalez-Castillo, J., Talavage, T.M., Pisoni, D.B., & Svirsky, M.A. (2013). Neural correlates of adaptation in freely-moving normal hearing subjects under cochlear implant acoustic simulations. Neuroimage, 82, 500-509. Doi:10.1016/j.neuroimage.2013.06.001

Bandettini, P.A., Kundu, P., Gonzalez-Castillo, J., Misaki, M., & Guillod, P. (2013). Characterizing and utilizing fMRI fluctuations, patterns, and dynamics. Progress in Biomedical Optics and Imaging Proceedings of SPIE, 8672. Doi:10.1117/12.2012737

Gonzalez-Castillo, J., Olulade, O.A., & Talavage, T.M. (2012). Using functional MRI to study auditory comprehension. Imaging in Medicine, 4(1), 137-143. Doi:10.2217/iim.11.74

Gonzalez-Castillo, J., Saad, Z.S., Handwerker, D.A., Inati, S.J., Brenowitz, N., & Bandettini, P.A. (2012). Whole-brain, time-locked activation with simple tasks revealed using massive averaging and model-free analysis. Proceedings of the National Academy of Sciences of the United States of America, 109(14), 5487-5492. Doi:10.1073/pnas.1121049109

Handwerker, D.A., Roopchansingh, V., Gonzalez-Castillo, J., & Bandettini, P.A. (2012). Periodic changes in fMRI connectivity. Neuroimage, 63(3), 1712-1719. Doi:10.1016/j.neuroimage.2012.06.078

Handwerker, D.A., Gonzalez-Castillo, J., D'Esposito, M., & Bandettini, P.A. (2012). The continuing challenge of understanding and modeling hemodynamic variation in fMRI. Neuroimage, 62(2), 1017-1023. Doi:10.1016/j.neuroimage.2012.02.015

Gonzalez-Castillo, J., Roopchansingh, V., Bandettini, P.A., & Bodurka, J. (2011). Physiological noise effects on the flip angle selection in BOLD fMRI. Neuroimage, 54(4), 2764-2778. Doi:10.1016/j.neuroimage.2010.11.020

Gonzalez-Castillo, J., & Talavage, T.M. (2011). Reproducibility of fMRI activations associated with auditory sentence comprehension. Neuroimage, 54(3), 2138-2155. Doi:10.1016/j.neuroimage.2010.09.082

Olulade, O., Hu, S., Gonzalez-Castillo, J., Tamer, G.G., Luh, W.M., Ulmer, J.L., & Talavage, T.M. (2011). Assessment of temporal state-dependent interactions between auditory fMRI responses to desired and undesired acoustic sources. Hearing Research, 277(1-2), 67-77. Doi:10.1016/j.heares.2011.03.008

Soltysik, D.A., Thomasson, D., Rajan, S., Gonzalez-Castillo, J., DiCamillo, P., & Biassou, N. (2011). Head-repositioning does not reduce the reproducibility of fMRI activation in a block-design motor task. Neuroimage, 56(3), 1329-1337. Doi:10.1016/j.neuroimage.2011.03.023

Hu, S., Olulade, O., Castillo, J.G., Santos, J., Kim, S., Tamer, G.G., Luh, W.M., & Talavage, T.M. (2010). Modeling hemodynamic responses in auditory cortex at 1.5 T using variable duration imaging acoustic noise. Neuroimage, 49(4), 3027-3038. Doi:10.1016/j.neuroimage.2009.11.051

Kemmerer, D., & Gonzalez-Castillo, J. (2010). The Two-Level Theory of verb meaning: An approach to integrating the semantics of action with the mirror neuron system. Brain and Language, 112(1), 54-76. Doi:10.1016/j.bandl.2008.09.010

Kemmerer, D., Castillo, J.G., Talavage, T., Patterson, S., & Wiley, C. (2008). Neuroanatomical distribution of five semantic components of verbs: Evidence from fMRI. Brain and Language, 107(1), 16-43. Doi:10.1016/j.bandl.2007.09.003