Amir Shmuel, PhD

Amir Shmuel, PhD
Contact Information
Email address: 
amir.shmuel [at]
BIC Core Faculty

Dr. Amir Shmuel is the director of the Brain Imaging Signals Lab and a core faculty member of the McConnell Brain Imaging Centre of the Montreal Neurological Institute. He is an Associate Professor of McGill University’s Departments of Neurology, Neurosurgery, Physiology, and Biomedical Engineering. Dr. Shmuel served as the chair of the organizing committee and chair of the sixth conference of the International Society for Brain Connectivity in 2018. He is the PI of an $18.7M grant funded by the Canada Foundation for Innovation to install the first large bore 7 Tesla MRI scanner in Quebec. His research program focuses on understanding the mechanisms of resting-state functional connectivity, understanding functional brain imaging signals and evaluating the degree to which they reflect the underlying neuronal activity, cortical lamina resolved neurophysiology and neuroimaging, and computational modeling of these themes.

His lab employs an integrative approach, using a combination of imaging and electrical recording techniques. These include functional Magnetic Resonance Imaging (fMRI), optical imaging using intrinsic signals and voltage-sensitive dyes, multi-channel neurophysiological recordings, and optogenetics. Together, these techniques encompass multiple levels of spatial and temporal resolution. The measurements are recorded while presenting different types of sensory stimuli or during spontaneous activity. In each of the themes Dr. Shmuel’s lab investigates, it emphasizes the development of models in parallel to obtaining experimental data, with the aim of fitting the models to the experimental data. Dr. Shmuel’s research is currently funded by the Canadian Institut of Health Research, the Natural Sciences and Engineering Research Council of Canada, and the US Department of Defense.

Selected publications: 

*Chaimow D, Shmuel A (Neuroimage, under revision) A more accurate account of the effect of k-space sampling and signal decay on the effective spatial resolution in functional MRI. Available as pre-print in: BioRxiv 097154, doi:

*Pilgram R, Shmuel A (NeuroImage, under revision) 3D Rodent Image Fusion Workbench: multimodal atlas-based region- and lamina-specific linkage between histo-chemistry and MRI.

*Bortel A, *Yao Z-S, Shmuel A (Frontiers in Brain Imaging Methods, under revision) Dexmedetomitine – commonly used in functional imaging studies – increases susceptibility to seizures in rats but not in wild type mice. Available as pre-print in: BioRxiv 890525; doi:

*Bortel A, *Yao Z-S, Shmuel A (2019) A rat model of somatosensory-evoked reflex seizures induced by peripheral stimulation. Epilepsy Research, 157:106209. doi:

*Lahmiri S, Shmuel A (2019) Performance of machine learning methods applied to structural MRI and ADAS cognitive scores in diagnosing Alzheimer's disease. Biomedical Signal Processing and Control, 52:414-419,

*Pizarro R, Assemlal HE, De Nigris D, Elliot C, Antel S, Arnold D, Shmuel A (2019) Using deep learning algorithms to automatically identify the brain MRI contrast: implications for managing large databases. NeuroInformatics, 17(1):115-130.

*Lahmiri S, Shmuel A (2019) Detection of Parkinson’s Disease Based on Voice Pattern Ranking and Optimized Support Vector Machine. Biomedical Signal Processing and Control, 49 (2019) 427–433.

*Lahmiri S, Shmuel A (2019) Accurate Classification of Seizure and Seizure-Free Intervals of Intra-Cranial EEG Signals from Epileptic Patients. IEEE Transactions on Instrumentation & Measurement. 68:791-796.

Milham MP et al. (2018) An open resource for non-human primate imaging. Neuron. Oct 10;100(1):61-74.e2. doi: 10.1016/j.neuron.2018.08.039. Epub 2018 Sep 27.

Mendola JD, *Lam J, Rosenstein M, Lewis LB, Shmuel A (2018) Partial correlation analysis reveals abnormal retinotopically organized functional connectivity of visual areas in amblyopia. NeuroImage Clinical, 18:192-201.

*Chaimow D, Yacoub E, Uğurbil K, Shmuel A (2018) Spatial specificity of the functional MRI blood oxygenation response relative to neuronal activity. NeuroImage, 164:32-47.

*Chaimow D, Uğurbil K, Shmuel A (2018) Optimization of functional MRI for detection, decoding and high-resolution imaging of the response patterns of cortical columns. NeuroImage, 164:67-99.

*Kropf P, Shmuel A (2016) 1-D current-source density (CSD) estimation in inverse theory: a unified framework for higher-order spectral regularization of quadrature and expansion type CSD methods. Neural Computation, 28:1305-1355.

*Dawson DA, Lewis LB, *Carbonell F, Mendola JD, Shmuel A (2016) Partial-correlation based retinotopically organized resting-state functional connectivity within and between areas of the visual cortex reflects more than cortical distance. Brain Connectivity, 6(1):57-75. doi: 10.1089/brain.2014.0331.

*Sotero RC, Bortel A, *Na’aman S, *Mocanu MV, *Kropf P, *Villeneuve M, Shmuel A (2015) Laminar distribution of phase-amplitude coupling of spontaneous current sources and sinks. Front. Neurosci. 9:454. doi: 10.3389/fnins.2015.00454.

Buxton RB, Griffeth VE, Simon AB, Moradi F, Shmuel A (2014) Variability of the coupling of blood flow and oxygen metabolism responses in the brain: a problem for interpreting BOLD studies but potentially a new window on the underlying neural activity. Front Neurosci., 8:139. Corrigendum DOI: 10.3389/fnins.2014.00241.

*Carbonell F, Bellec P, Shmuel A (2014) Quantification of the impact of a confounding variable on functional connectivity confirms anti-correlated networks in the resting-state. Neuroimage, 86:343-53.

*Dawson DA, Cha K, Lewis LB, Mendola JD, Shmuel A (2013) Evaluation and calibration of functional network modeling methods based on known anatomical connections. Neuroimage, 67: 331–343.

*Sotero RC, Shmuel A (2012) Energy-based stochastic control of neural mass models suggests time-varying effective connectivity in the resting-state. Journal of Computational Neuroscience, 32 (3): 563-576 (doi: 10.1007/s10827-011-0370-8).

*Carbonell F, Bellec P, Shmuel A (2012) Global and system-specific resting-state BOLD fluctuations are uncorrelated: principal component analysis reveals anti-correlated networks. Brain Connectivity, 1 (6): 496-510. *Chaimow D, Yacoub E, Ugurbil K, Shmuel A (2011) Modeling and analysis of mechanisms underlying fMRI-based decoding of information conveyed in cortical columns. Neuroimage, 56 (2): 627-642.

*Sotero RC, *Bortel A, Martínez-Cancino R, *Neupane S, *O’Connor P, *Carbonell F, Shmuel A (2010) Anatomically-constrained effective connectivity among layers in a cortical column modeled and estimated from local field potentials. Journal of Integrative Neuroscience, 9: 355–379. Shmuel A, *Chaimow D, Raddatz G, Ugurbil K, Yacoub E (2010) Mechanisms underlying decoding at 7 T: Ocular dominance columns, broad structures, and macroscopic blood vessels in V1 convey information on the stimulated eye. Neuroimage, 49:1957–1964.

Shmuel A, Leopold DA (2008) Neuronal correlates of spontaneous fluctuations in fMRI signals in monkey visual cortex: implications for functional connectivity at rest. Human Brain Mapping, 29:751-761.

Keliris G*, Shmuel A* (* co-first authors), Ku SP, Pfeuffer J, Oeltermann A, Steudel T, Ku SP, Logothetis NK (2007), Robust controlled functional MRI in alert monkeys at high magnetic field: effects of jaw and body movements. NeuroImage, 36(3):550-570.

Yacoub E*, Shmuel A* (* co-first authors), Logothetis NK, Ugurbil K (2007), Robust detection of ocular dominance columns in humans using Hahn spin-echo BOLD functional MRI at high field. NeuroImage, 37(4):1161–1177.

Shmuel A, Yacoub E, Chaimow D, Logothetis NK, Ugurbil K (2007), Spatio-temporal point-spread function of fMRI signal in human gray matter at 7 Tesla. NeuroImage, 35(2):539-552.

Shmuel A, Augath M, Oeltermann A, Logothetis NK (2006) Negative functional MRI response correlates with decreases in neuronal activity in monkey visual area V1. Nature Neuroscience, 9(4):569-577.

Shmuel A, Korman M, Melnik A, Harel M, Ullman S, Malach R, Grinvald A (2005) Retinotopic axis specificity and selective clustering of feedback projections from V2 to V1 in the owl monkey. The Journal of Neuroscience, 25(8):2117-31.

Swindale NV, Grinvald A, Shmuel A (2003) The spatial pattern of response magnitude and selectivity for orientation and direction in cat visual cortex. Cerebral Cortex, 13(3):225-238.

Shmuel A, Yacoub E, Pfeuffer J, Van De Moortele PF, Adriany G, Hu X, Ugurbil K (2002) Sustained negative BOLD, blood flow and oxygen consumption response and its coupling to the positive response in the human brain. Neuron, 36(6):1195-1210.

Shmuel A, Grinvald A (2000) Coexistence of linear zones and pinwheels within orientation maps in cat visual cortex. Proceedings of the National Academy of Sciences USA 97(10):5568- 5573.

Shmuel A, Grinvald A (1996) Functional organization for direction of motion and its relationship to orientation maps in cat area 18. The Journal of Neuroscience, 16(21):6945-6964, and cover illustration.

Research areas: 
Neuroimaging and Neuroinformatics

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