References#
The Voxelwise Encoding Model (VEM) framework is a powerful approach for functional magnetic resonance imaging (fMRI) data analysis. Over the years, VEM has led to many high profile publications [Huth et al., 2012, Nishimoto et al., 2011, Dupré la Tour et al., 2022, Nunez-Elizalde et al., 2019, de Heer et al., 2017, Deniz et al., 2019, Huth et al., 2016, Kay et al., 2008, LeBel et al., 2021, Lescroart and Gallant, 2019, Naselaris et al., 2009, Popham et al., 2021, Stansbury et al., 2013, Çukur et al., 2013, Çukur et al., 2013].
Datasets#
Shortclips dataset [Huth et al., 2022]
Vim-2 dataset [Nishimoto et al., 2014]
Packages#
voxelwise_tutorials[Dupré la Tour et al., 2024]himalaya[Dupré la Tour et al., 2022]pycortex[Gao et al., 2015]pymoten[Nunez-Elizalde et al., 2021]
Bibliography#
W. A. de Heer, A. G. Huth, T. L. Griffiths, J. L. Gallant, and F. E. Theunissen. The hierarchical cortical organization of human speech processing. Journal of Neuroscience, 37(27):6539–6557, 2017.
F. Deniz, A. O. Nunez-Elizalde, A. G. Huth, and J. L. Gallant. The representation of semantic information across human cerebral cortex during listening versus reading is invariant to stimulus modality. Journal of Neuroscience, 39(39):7722–7736, 2019.
T. Dupré la Tour, M. Eickenberg, A.O. Nunez-Elizalde, and J. L. Gallant. Feature-space selection with banded ridge regression. NeuroImage, 267:119728, 2022. doi:10.1016/j.neuroimage.2022.119728.
T. Dupré la Tour, M. Visconti di Oleggio Castello, and J. L. Gallant. The voxelwise encoding model framework: a tutorial introduction to fitting encoding models to fMRI data. PsyArXiv, 2024. doi:10.31234/osf.io/t975e.
J. S. Gao, A. G. Huth, M. D. Lescroart, and J. L. Gallant. Pycortex: an interactive surface visualizer for fMRI. Frontiers in Neuroinformatics, 2015. doi:10.3389/fninf.2015.00023.
A. G. Huth, W. A. De Heer, T. L. Griffiths, F. E. Theunissen, and J. L. Gallant. Natural speech reveals the semantic maps that tile human cerebral cortex. Nature, 532(7600):453–458, 2016.
A. G. Huth, S. Nishimoto, A. T. Vu, T. Dupré la Tour, and J. L. Gallant. Gallant lab natural short clips 3t fMRI data. 2022. doi:10.12751/g-node.vy1zjd.
A. G. Huth, S. Nishimoto, A. T. Vu, and J. L. Gallant. A continuous semantic space describes the representation of thousands of object and action categories across the human brain. Neuron, 76(6):1210–1224, 2012.
K. N. Kay, T. Naselaris, R. J. Prenger, and J. L. Gallant. Identifying natural images from human brain activity. Nature, 452(7185):352–355, 2008.
A. LeBel, S. Jain, and A. G. Huth. Voxelwise encoding models show that cerebellar language representations are highly conceptual. Journal of Neuroscience, 41(50):10341–10355, 2021.
M. D. Lescroart and J. L. Gallant. Human scene-selective areas represent 3d configurations of surfaces. Neuron, 101(1):178–192, 2019.
T. Naselaris, R. J. Prenger, K. N. Kay, M. Oliver, and J. L. Gallant. Bayesian reconstruction of natural images from human brain activity. Neuron, 63(6):902–915, 2009.
S. Nishimoto, A. T. Vu, T. Naselaris, Y. Benjamini, B. Yu, and J. L. Gallant. Reconstructing visual experiences from brain activity evoked by natural movies. Current Biology, 21(19):1641–1646, 2011.
S. Nishimoto, A. T. Vu, T. Naselaris, Y. Benjamini, B. Yu, and J. L. Gallant. Gallant lab natural movie 4t fMRI data. 2014. doi:10.6080/K00Z715X.
A. O. Nunez-Elizalde, A. G. Huth, and J. L. Gallant. Voxelwise encoding models with non-spherical multivariate normal priors. Neuroimage, 197:482–492, 2019.
A.O. Nunez-Elizalde, F. Deniz, T. Dupré la Tour, M. Visconti di Oleggio Castello, and J.L. Gallant. Pymoten: scientific python package for computing motion energy features from video. 2021. doi:10.5281/zenodo.6349625.
S. F. Popham, A. G. Huth, N. Y. Bilenko, F. Deniz, J. S. Gao, A. O. Nunez-Elizalde, and J. L. Gallant. Visual and linguistic semantic representations are aligned at the border of human visual cortex. Nature Neuroscience, 24(11):1628–1636, 2021.
D. E. Stansbury, T. Naselaris, and J. L. Gallant. Natural scene statistics account for the representation of scene categories in human visual cortex. Neuron, 79(5):1025–1034, 2013.
T. Çukur, A. G. Huth, S. Nishimoto, and J. L. Gallant. Functional subdomains within human ffa. Journal of Neuroscience, 33(42):16748–16766, 2013.
T. Çukur, S. Nishimoto, A. G. Huth, and J. L. Gallant. Attention during natural vision warps semantic representation across the human brain. Nature neuroscience, 16(6):763–770, 2013.