Publications

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

Delgado-Alvarado, M., Ferrer-Gallardo, V.J., Paz-Alonso, P.M., Caballero-Gaudes, C., & Rodríguez-Oroz, M.C. (2023). Interactions between functional networks in Parkinson's disease mild cognitive impairment. Scientific Reports, 13(1). Doi:10.1038/s41598-023-46991-3

Zvolanek, K.M., Moia, S., Dean, J.N., Stickland, R.C., Caballero-Gaudes, C., & Bright, M.G. (2023). Comparing end-tidal CO<inf>2</inf>, respiration volume per time (RVT), and average gray matter signal for mapping cerebrovascular reactivity amplitude and delay with breath-hold task BOLD fMRI. NeuroImage, 272. Doi:10.1016/j.neuroimage.2023.120038

Basaia, S., Agosta, F., Diez, I., Bueichekú, E., d'Oleire Uquillas, F., Delgado-Alvarado, M., Caballero-Gaudes, C., Rodriguez-Oroz, M.C., Stojkovic, T., Kostic, V.S., Filippi, M., & Sepulcre, J. (2022). Neurogenetic traits outline vulnerability to cortical disruption in Parkinson's disease. NeuroImage: Clinical, 33. Doi:10.1016/j.nicl.2022.102941

Bouziane, I., Das, M., Friston, K.J., Caballero-Gaudes, C., & Ray, D. (2022). Enhanced top-down sensorimotor processing in somatic anxiety. Translational Psychiatry, 12(1). Doi:10.1038/s41398-022-02061-2

Stickland, R.C., Zvolanek, K.M., Moia, S., Caballero-Gaudes, C., & Bright, M.G. (2022). Lag-Optimized Blood Oxygenation Level Dependent Cerebrovascular Reactivity Estimates Derived From Breathing Task Data Have a Stronger Relationship With Baseline Cerebral Blood Flow. Frontiers in Neuroscience, 16. Doi:10.3389/fnins.2022.910025

Zwiers, M.P., Moia, S., & Oostenveld, R. (2022). BIDScoin: A User-Friendly Application to Convert Source Data to Brain Imaging Data Structure. Frontiers in Neuroinformatics, 15. Doi:10.3389/fninf.2021.770608

Blanco, B., Molnar, M., Carreiras, M., Collins-Jones, L.H., Vidal, E., Cooper, R.J., & Caballero-Gaudes, C. (2021). Group-level cortical functional connectivity patterns using fNIRS: assessing the effect of bilingualism in young infants. Neurophotonics, 8(2). Doi:10.1117/1.NPh.8.2.025011

Gau, R., Noble, S., Heuer, K., Bottenhorn, K.L., Bilgin, I.P., Yang, Y.F., Huntenburg, J.M., Bayer, J.M.M., Bethlehem, R.A.I., Rhoads, S.A., Vogelbacher, C., Borghesani, V., Levitis, E., Wang, H.T., Van Den Bossche, S., Kobeleva, X., Legarreta, J.H., (2021). Brainhack: Developing a culture of open, inclusive, community-driven neuroscience. Neuron, 109(11), 1769-1775. Doi:10.1016/j.neuron.2021.04.001

Guediche, S., de Bruin, A., Caballero-Gaudes, C., Baart, M., & Samuel, A.G. (2021). Second-language word recognition in noise: Interdependent neuromodulatory effects of semantic context and crosslinguistic interactions driven by word form similarity. NeuroImage, 237. Doi:10.1016/j.neuroimage.2021.118168

Heunis, S., Breeuwer, M., Caballero-Gaudes, C., Hellrung, L., Huijbers, W., Jansen, J.F., Lamerichs, R., Zinger, S., & Aldenkamp, A.P. (2021). The effects of multi-echo fMRI combination and rapid T<inf>2</inf>*-mapping on offline and real-time BOLD sensitivity. NeuroImage, 238. Doi:10.1016/j.neuroimage.2021.118244

Heunis, S., Breeuwer, M., Caballero-Gaudes, C., Hellrung, L., Huijbers, W., Jansen, J.F.A., Lamerichs, R., Zinger, S., & Aldenkamp, A.P. (2021). rt-me-fMRI: a task and resting state dataset for real-time, multi-echo fMRI methods development and validation. F1000Research, 10, 1-21. Doi:10.12688/F1000RESEARCH.29988.1

Moia, S., Termenon, M., Uruñuela, E., Chen, G., Stickland, R.C., Bright, M.G., & Caballero-Gaudes, C. (2021). ICA-based denoising strategies in breath-hold induced cerebrovascular reactivity mapping with multi echo BOLD fMRI. NeuroImage, 233. Doi:10.1016/j.neuroimage.2021.117914

Stickland, R.C., Zvolanek, K.M., Moia, S., Ayyagari, A., Caballero-Gaudes, C., & Bright, M.G. (2021). A practical modification to a resting state fMRI protocol for improved characterization of cerebrovascular function. NeuroImage, 239. Doi:10.1016/j.neuroimage.2021.118306

Urunuela, E., Moia, S., & Caballero-Gaudes, C. (2021). A low rank and sparse paradigm free mapping algorithm for deconvolution of FMRI data. Proceedings - International Symposium on Biomedical Imaging, 2021-April, 1726-1729. Doi:10.1109/ISBI48211.2021.9433821

Bolton, T.A.W., Kebets, V., Glerean, E., Zöller, D., Li, J., Yeo, B.T.T., Caballero-Gaudes, C., & Van De Ville, D. (2020). Agito ergo sum: Correlates of spatio-temporal motion characteristics during fMRI. NeuroImage, 209. Doi:10.1016/j.neuroimage.2019.116433

Bolton, T.A.W., Urunuela, E., Tian, Y., Zalesky, A., Caballero-Gaudes, C., & Van De Ville, D. (2020). Sparse coupled logistic regression to estimate co-activation and modulatory influences of brain regions. Journal of Neural Engineering, 17(6). Doi:10.1088/1741-2552/aba55e

Correia, J.M., Caballero-Gaudes, C., Guediche, S., & Carreiras, M. (2020). Phonatory and articulatory representations of speech production in cortical and subcortical fMRI responses. Scientific Reports, 10(1). Doi:10.1038/s41598-020-61435-y

Heunis, S., Lamerichs, R., Zinger, S., Caballero-Gaudes, C., Jansen, J.F.A., Aldenkamp, B., & Breeuwer, M. (2020). Quality and denoising in real-time functional magnetic resonance imaging neurofeedback: A methods review. Human Brain Mapping, 41(12), 3439-3467. Doi:10.1002/hbm.25010

Lee, C.W., Blanco, B., Dempsey, L., Chalia, M., Hebden, J.C., Caballero-Gaudes, C., Austin, T., & Cooper, R.J. (2020). Sleep State Modulates Resting-State Functional Connectivity in Neonates. Frontiers in Neuroscience, 14. Doi:10.3389/fnins.2020.00347

Moia, S., Stickland, R.C., Ayyagari, A., Termenon, M., Caballero-Gaudes, C., & Bright, M.G. (2020). Voxelwise optimization of hemodynamic lags to improve regional CVR estimates in breath-hold fMRI. Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, 2020-July, 1489-1492. Doi:10.1109/EMBC44109.2020.9176225

Urunuela, E., Jones, S., Crawford, A., Shin, W., Oh, S., Lowe, M., & Caballero-Gaudes, C. (2020). Stability-Based Sparse Paradigm Free Mapping Algorithm for Deconvolution of Functional MRI Data. Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, 2020-July, 1092-1095. Doi:10.1109/EMBC44109.2020.9176137

Bastarrika-Iriarte, A., & Caballero-Gaudes, C. (2019). Closing eyes during auditory memory retrieval modulates alpha rhythm but does not alter tau rhythm. NeuroImage, 197, 60-68. Doi:10.1016/j.neuroimage.2019.04.053

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

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

Blanco, B., Molnar, M., & Caballero-Gaudes, C. (2018). Effect of prewhitening in resting-state functional near-infrared spectroscopy data. Neurophotonics, 5(4). Doi:10.1117/1.NPh.5.4.040401

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

Iglesias, J.E., Insausti, R., Lerma-Usabiaga, G., Bocchetta, M., Van Leemput, K., Greve, D.N., van der Kouwe, A., Fischl, B., Caballero-Gaudes, C., & Paz-Alonso, P.M. (2018). A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. NeuroImage, 183, 314-326. Doi:10.1016/j.neuroimage.2018.08.012

Paz-Alonso, P.M., Oliver, M., Lerma-Usabiaga, G., Caballero-Gaudes, C., Quiñones, I., Suárez-Coalla, P., Duñabeitia, J.A., Cuetos, F., & Carreiras, M. (2018). Neural correlates of phonological, orthographic and semantic reading processing in dyslexia. NeuroImage: Clinical, 20, 433-447. Doi:10.1016/j.nicl.2018.08.018

Rosenthal, C.R., Mallik, I., Caballero-Gaudes, C., Sereno, M.I., & Soto, D. (2018). Learning of goal-relevant and -irrelevant complex visual sequences in human V1. NeuroImage, 179, 215-224. Doi:10.1016/j.neuroimage.2018.06.023

Vuckovic, A., Gallardo, V.J.F., Jarjees, M., Fraser, M., & Purcell, M. (2018). Prediction of central neuropathic pain in spinal cord injury based on EEG classifier. Clinical Neurophysiology, 129(8), 1605-1617. Doi:10.1016/j.clinph.2018.04.750

Caballero-Gaudes, C., & Reynolds, R.C. (2017). Methods for cleaning the BOLD fMRI signal. NeuroImage, 154, 128-149. Doi:10.1016/j.neuroimage.2016.12.018

Keilholz, S., Caballero-Gaudes, C., Bandettini, P., Deco, G., & Calhoun, V. (2017). Time-Resolved Resting-State Functional Magnetic Resonance Imaging Analysis: Current Status, Challenges, and New Directions. Brain Connectivity, 7(8), 465-481. Doi:10.1089/brain.2017.0543

Tan, F.M., Caballero-Gaudes, C., Mullinger, K.J., Cho, S.Y., Zhang, Y., Dryden, I.L., Francis, S.T., & Gowland, P.A. (2017). Decoding fMRI events in sensorimotor motor network using sparse paradigm free mapping and activation likelihood estimates. Human Brain Mapping, 38(11), 5778-5794. Doi:10.1002/hbm.23767

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

Iglesias, J.E., Paz-Alonso, P., Lerma-Usabiaga, G., Insausti, R., Miller, K., & Caballero-Gaudes, C. (2016). Simultaneous Bayesian correction of slab boundary artifacts and bias field for high resolution ex vivo MRI. Proceedings - International Symposium on Biomedical Imaging, 2016-June, 1384-1387. Doi:10.1109/ISBI.2016.7493525

Allan, T.W., Francis, S.T., Caballero-Gaudes, C., Morris, P.G., Liddle, E.B., Liddle, P.F., Brookes, M.J., & Gowland, P.A. (2015). Functional connectivity in MRI is driven by spontaneous BOLD events. PLoS ONE, 10(4). Doi:10.1371/journal.pone.0124577

Caballero-Gaudes, C., Van de Ville, D., Grouiller, F., Thornton, R., Lemieux, L., Seeck, M., Lazeyras, F., & Vulliemoz, S. (2013). Mapping interictal epileptic discharges using mutual information between concurrent EEG and fMRI. NeuroImage, 68, 248-262. Doi:10.1016/j.neuroimage.2012.12.011

Karahanoǧlu, F.I., Caballero-Gaudes, C., Lazeyras, F., & Van De Ville, D. (2013). Total activation: FMRI deconvolution through spatio-temporal regularization. NeuroImage, 73, 121-134. Doi:10.1016/j.neuroimage.2013.01.067

Karahanoglu, F.I., Grouiller, F., Gaudes, C.C., Seeck, M., Vulliemoz, S., & Van De Ville, D. (2013). Spatial mapping of interictal epileptic discharges in fMRI with total activation. Proceedings - International Symposium on Biomedical Imaging, 1500-1503. Doi:10.1109/ISBI.2013.6556819

Gaudes, C.C., Karahanoǧlu, F.I., Lazeyras, F., & Van De Ville, D. (2012). Structured sparse deconvolution for paradigm free mapping of functional MRI data. Proceedings - International Symposium on Biomedical Imaging, 322-325. Doi:10.1109/ISBI.2012.6235549