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Vitória MA, Fernandes FG, van den Boom M, Ramsey N, Raemaekers M. Decoding Single and Paired Phonemes Using 7T Functional MRI. Brain Topogr 2024; 37:731-747. [PMID: 38261272 PMCID: PMC11393141 DOI: 10.1007/s10548-024-01034-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
Several studies have shown that mouth movements related to the pronunciation of individual phonemes are represented in the sensorimotor cortex. This would theoretically allow for brain computer interfaces that are capable of decoding continuous speech by training classifiers based on the activity in the sensorimotor cortex related to the production of individual phonemes. To address this, we investigated the decodability of trials with individual and paired phonemes (pronounced consecutively with one second interval) using activity in the sensorimotor cortex. Fifteen participants pronounced 3 different phonemes and 3 combinations of two of the same phonemes in a 7T functional MRI experiment. We confirmed that support vector machine (SVM) classification of single and paired phonemes was possible. Importantly, by combining classifiers trained on single phonemes, we were able to classify paired phonemes with an accuracy of 53% (33% chance level), demonstrating that activity of isolated phonemes is present and distinguishable in combined phonemes. A SVM searchlight analysis showed that the phoneme representations are widely distributed in the ventral sensorimotor cortex. These findings provide insights about the neural representations of single and paired phonemes. Furthermore, it supports the notion that speech BCI may be feasible based on machine learning algorithms trained on individual phonemes using intracranial electrode grids.
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Affiliation(s)
- Maria Araújo Vitória
- Brain Center Rudolf Magnus, Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Francisco Guerreiro Fernandes
- Brain Center Rudolf Magnus, Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Max van den Boom
- Brain Center Rudolf Magnus, Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Nick Ramsey
- Brain Center Rudolf Magnus, Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mathijs Raemaekers
- Brain Center Rudolf Magnus, Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands.
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2
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Faes LK, Lage-Castellanos A, Valente G, Yu Z, Cloos MA, Vizioli L, Moeller S, Yacoub E, De Martino F. Evaluating the effect of denoising submillimeter auditory fMRI data with NORDIC. IMAGING NEUROSCIENCE (CAMBRIDGE, MASS.) 2024; 2:1-18. [PMID: 39810817 PMCID: PMC11726685 DOI: 10.1162/imag_a_00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 07/22/2024] [Accepted: 07/22/2024] [Indexed: 01/16/2025]
Abstract
Functional magnetic resonance imaging (fMRI) has emerged as an essential tool for exploring human brain function. Submillimeter fMRI, in particular, has emerged as a tool to study mesoscopic computations. The inherently low signal-to-noise ratio (SNR) at submillimeter resolutions warrants the use of denoising approaches tailored at reducing thermal noise-the dominant contributing noise component in high-resolution fMRI. NOise Reduction with DIstribution Corrected Principal Component Analysis (NORDIC PCA) is one of such approaches, and has been benchmarked against other approaches in several applications. Here, we investigate the effects that two versions of NORDIC denoising have on auditory submillimeter data. While investigating auditory functional responses poses unique challenges, we anticipated NORDIC to have a positive impact on the data on the basis of previous applications. Our results show that NORDIC denoising improves the detection sensitivity and the reliability of estimates in submillimeter auditory fMRI data. These effects can be explained by the reduction of the noise-induced signal variability. However, we did observe a reduction in the average response amplitude (percent signal change) within regions of interest, which may suggest that a portion of the signal of interest, which could not be distinguished from general i.i.d. noise, was also removed. We conclude that, while evaluating the effects of the signal reduction induced by NORDIC may be necessary for each application, using NORDIC in high-resolution auditory fMRI studies may be advantageous because of the large reduction in variability of the estimated responses.
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Affiliation(s)
- Lonike K. Faes
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Agustin Lage-Castellanos
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Department of Neuroinformatics, Cuban Neuroscience Center, Havana City, Cuba
| | - Giancarlo Valente
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Zidan Yu
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University School of Medicine, New York, NY, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, United States
- MRI Research Center, University of Hawaii, Honolulu, HI, United States
| | - Martijn A. Cloos
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University School of Medicine, New York, NY, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, United States
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St. Lucia, Australia
| | - Luca Vizioli
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, United States
| | - Steen Moeller
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, United States
| | - Essa Yacoub
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, United States
| | - Federico De Martino
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, United States
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3
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Liu X, Jiao G, Zhou F, Kendrick KM, Yao D, Gong Q, Xiang S, Jia T, Zhang XY, Zhang J, Feng J, Becker B. A neural signature for the subjective experience of threat anticipation under uncertainty. Nat Commun 2024; 15:1544. [PMID: 38378947 PMCID: PMC10879105 DOI: 10.1038/s41467-024-45433-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Uncertainty about potential future threats and the associated anxious anticipation represents a key feature of anxiety. However, the neural systems that underlie the subjective experience of threat anticipation under uncertainty remain unclear. Combining an uncertainty-variation threat anticipation paradigm that allows precise modulation of the level of momentary anxious arousal during functional magnetic resonance imaging (fMRI) with multivariate predictive modeling, we train a brain model that accurately predicts subjective anxious arousal intensity during anticipation and test it across 9 samples (total n = 572, both gender). Using publicly available datasets, we demonstrate that the whole-brain signature specifically predicts anxious anticipation and is not sensitive in predicting pain, general anticipation or unspecific emotional and autonomic arousal. The signature is also functionally and spatially distinguishable from representations of subjective fear or negative affect. We develop a sensitive, generalizable, and specific neuroimaging marker for the subjective experience of uncertain threat anticipation that can facilitate model development.
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Affiliation(s)
- Xiqin Liu
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- MOE Key Laboratory for Neuroinformation, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- The Center of Psychosomatic Medicine, Sichuan Provincial Center for Mental Health, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Guojuan Jiao
- MOE Key Laboratory for Neuroinformation, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Feng Zhou
- Faculty of Psychology, Southwest University, Chongqing, China
- MOE Key Laboratory of Cognition and Personality, Chongqing, China
| | - Keith M Kendrick
- MOE Key Laboratory for Neuroinformation, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Dezhong Yao
- MOE Key Laboratory for Neuroinformation, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Qiyong Gong
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Department of Radiology, West China Xiamen Hospital of Sichuan University, Xiamen, Fujian, China
| | - Shitong Xiang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, (Fudan University), Ministry of Education, Shanghai, China
| | - Tianye Jia
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, (Fudan University), Ministry of Education, Shanghai, China
- The Centre for Population Neuroscience and Stratified Medicine (PONS), ISTBI, Fudan University, Shanghai, China
- SGDP Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Xiao-Yong Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, (Fudan University), Ministry of Education, Shanghai, China
| | - Jie Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, (Fudan University), Ministry of Education, Shanghai, China
| | - Jianfeng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, (Fudan University), Ministry of Education, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
| | - Benjamin Becker
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, China.
- Department of Psychology, The University of Hong Kong, Hong Kong, China.
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4
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Faes LK, Lage-Castellanos A, Valente G, Yu Z, Cloos MA, Vizioli L, Moeller S, Yacoub E, De Martino F. Evaluating the effect of denoising submillimeter auditory fMRI data with NORDIC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577070. [PMID: 38328173 PMCID: PMC10849717 DOI: 10.1101/2024.01.24.577070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Functional magnetic resonance imaging (fMRI) has emerged as an essential tool for exploring human brain function. Submillimeter fMRI, in particular, has emerged as a tool to study mesoscopic computations. The inherently low signal-to-noise ratio (SNR) at submillimeter resolutions warrants the use of denoising approaches tailored at reducing thermal noise - the dominant contributing noise component in high resolution fMRI. NORDIC PCA is one of such approaches, and has been benchmarked against other approaches in several applications. Here, we investigate the effects that two versions of NORDIC denoising have on auditory submillimeter data. As investigating auditory functional responses poses unique challenges, we anticipated that the benefit of this technique would be especially pronounced. Our results show that NORDIC denoising improves the detection sensitivity and the reliability of estimates in submillimeter auditory fMRI data. These effects can be explained by the reduction of the noise-induced signal variability. However, we also observed a reduction in the average response amplitude (percent signal), which may suggest that a small amount of signal was also removed. We conclude that, while evaluating the effects of the signal reduction induced by NORDIC may be necessary for each application, using NORDIC in high resolution auditory fMRI studies may be advantageous because of the large reduction in variability of the estimated responses.
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Affiliation(s)
- Lonike K. Faes
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, 6200 MD, Maastricht, The Netherlands
| | - Agustin Lage-Castellanos
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, 6200 MD, Maastricht, The Netherlands
- Department of Neuroinformatics, Cuban Neuroscience Center, Havana City 11600, Cuba
| | - Giancarlo Valente
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, 6200 MD, Maastricht, The Netherlands
| | - Zidan Yu
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University School of Medicine, New York, NY, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA
- MRI Research Center, University of Hawaii, United States
| | - Martijn A. Cloos
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University School of Medicine, New York, NY, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia 4066, Australia
| | - Luca Vizioli
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Steen Moeller
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Essa Yacoub
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Federico De Martino
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, 6200 MD, Maastricht, The Netherlands
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, United States
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5
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Sandhaeger F, Siegel M. Testing the generalization of neural representations. Neuroimage 2023; 278:120258. [PMID: 37429371 PMCID: PMC10443234 DOI: 10.1016/j.neuroimage.2023.120258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/27/2023] [Accepted: 06/28/2023] [Indexed: 07/12/2023] Open
Abstract
Multivariate analysis methods are widely used in neuroscience to investigate the presence and structure of neural representations. Representational similarities across time or contexts are often investigated using pattern generalization, e.g. by training and testing multivariate decoders in different contexts, or by comparable pattern-based encoding methods. It is however unclear what conclusions can be validly drawn on the underlying neural representations when significant pattern generalization is found in mass signals such as LFP, EEG, MEG, or fMRI. Using simulations, we show how signal mixing and dependencies between measurements can drive significant pattern generalization even though the true underlying representations are orthogonal. We suggest that, using an accurate estimate of the expected pattern generalization given identical representations, it is nonetheless possible to test meaningful hypotheses about the generalization of neural representations. We offer such an estimate of the expected magnitude of pattern generalization and demonstrate how this measure can be used to assess the similarity and differences of neural representations across time and contexts.
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Affiliation(s)
- Florian Sandhaeger
- Department of Neural Dynamics and Magnetoencephalography, Hertie Institute for Clinical Brain Research, University of Tübingen, Germany; Centre for Integrative Neuroscience, University of Tübingen, Germany; MEG Center, University of Tübingen, Germany; IMPRS for Cognitive and Systems Neuroscience, University of Tübingen, Germany.
| | - Markus Siegel
- Department of Neural Dynamics and Magnetoencephalography, Hertie Institute for Clinical Brain Research, University of Tübingen, Germany; Centre for Integrative Neuroscience, University of Tübingen, Germany; MEG Center, University of Tübingen, Germany.
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6
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Ruiz MJ, Dojat M, Hupé JM. Multivariate pattern analysis of fMRI data for imaginary and real colours in grapheme-colour synaesthesia. Eur J Neurosci 2020; 52:3434-3456. [PMID: 32384170 DOI: 10.1111/ejn.14774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/22/2020] [Accepted: 05/03/2020] [Indexed: 11/29/2022]
Abstract
Grapheme-colour synaesthesia is a subjective phenomenon related to perception and imagination, in which some people involuntarily but systematically associate specific, idiosyncratic colours to achromatic letters or digits. Its investigation is relevant to unravel the neural correlates of colour perception in isolation from low-level neural processing of spectral components, as well as the neural correlates of imagination by being able to reliably trigger imaginary colour experiences. However, functional MRI studies using univariate analyses failed to provide univocal evidence of the activation of the "colour network" by synaesthesia. Applying multivariate (multivoxel) pattern analysis (MVPA) on 20 synaesthetes and 20 control participants, we tested whether the neural processing of real colours (concentric rings) and synaesthetic colours (black graphemes) shared patterns of activations. Region of interest analyses in retinotopically and anatomically defined visual areas revealed neither evidence of shared circuits for real and synaesthetic colour processing, nor processing difference between synaesthetes and controls. We also found no correlation with individual experiences, characterised by measuring the strength of synaesthetic associations. The whole brain searchlight analysis led to similar results. We conclude that revealing the neural coding of the synaesthetic experience of colours is a hard task which requires the improvement of our current methodology: for example involving more individuals and achieving higher MR signal to noise ratio and spatial resolution. So far, we have not found any evidence of the involvement of the cortical colour network in the subjective experience of synaesthetic colours.
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Affiliation(s)
- Mathieu J Ruiz
- Centre de Recherche Cerveau et Cognition, Université de Toulouse Paul Sabatier & CNRS, Toulouse, France.,Grenoble Institut des Neurosciences, Université Grenoble Alpes, INSERM & CHU Grenoble Alpes, Grenoble, France
| | - Michel Dojat
- Grenoble Institut des Neurosciences, Université Grenoble Alpes, INSERM & CHU Grenoble Alpes, Grenoble, France
| | - Jean-Michel Hupé
- Centre de Recherche Cerveau et Cognition, Université de Toulouse Paul Sabatier & CNRS, Toulouse, France
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7
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Kriegeskorte N, Diedrichsen J. Inferring brain-computational mechanisms with models of activity measurements. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0278. [PMID: 27574316 PMCID: PMC5003864 DOI: 10.1098/rstb.2016.0278] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2016] [Indexed: 12/18/2022] Open
Abstract
High-resolution functional imaging is providing increasingly rich measurements of brain activity in animals and humans. A major challenge is to leverage such data to gain insight into the brain's computational mechanisms. The first step is to define candidate brain-computational models (BCMs) that can perform the behavioural task in question. We would then like to infer which of the candidate BCMs best accounts for measured brain-activity data. Here we describe a method that complements each BCM by a measurement model (MM), which simulates the way the brain-activity measurements reflect neuronal activity (e.g. local averaging in functional magnetic resonance imaging (fMRI) voxels or sparse sampling in array recordings). The resulting generative model (BCM-MM) produces simulated measurements. To avoid having to fit the MM to predict each individual measurement channel of the brain-activity data, we compare the measured and predicted data at the level of summary statistics. We describe a novel particular implementation of this approach, called probabilistic representational similarity analysis (pRSA) with MMs, which uses representational dissimilarity matrices (RDMs) as the summary statistics. We validate this method by simulations of fMRI measurements (locally averaging voxels) based on a deep convolutional neural network for visual object recognition. Results indicate that the way the measurements sample the activity patterns strongly affects the apparent representational dissimilarities. However, modelling of the measurement process can account for these effects, and different BCMs remain distinguishable even under substantial noise. The pRSA method enables us to perform Bayesian inference on the set of BCMs and to recognize the data-generating model in each case. This article is part of the themed issue ‘Interpreting BOLD: a dialogue between cognitive and cellular neuroscience’.
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Affiliation(s)
| | - Jörn Diedrichsen
- Brain and Mind Institute, Department of Computer Science and Department of Statistical and Actuarial Sciences, Western University, London, Ontario, Canada
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8
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Gravel N, Harvey BM, Renken RJ, Dumoulin SO, Cornelissen FW. Phase-synchronization-based parcellation of resting state fMRI signals reveals topographically organized clusters in early visual cortex. Neuroimage 2017; 170:424-433. [PMID: 28867341 DOI: 10.1016/j.neuroimage.2017.08.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 08/02/2017] [Accepted: 08/28/2017] [Indexed: 01/29/2023] Open
Abstract
Resting-state fMRI is widely used to study brain function and connectivity. However, interpreting patterns of resting state (RS) fMRI activity remains challenging as they may arise from different neuronal mechanisms than those triggered by exogenous events. Currently, this limits the use of RS-fMRI for understanding cortical function in health and disease. Here, we examine the phase synchronization (PS) properties of blood-oxygen level dependent (BOLD) signals obtained during visual field mapping (VFM) and RS with 7T fMRI. This data-driven approach exploits spatiotemporal covariations in the phase of BOLD recordings to establish the presence of clusters of synchronized activity. We find that, in both VFM and RS data, selecting the most synchronized neighboring recording sites identifies spatially localized PS clusters that follow the topographic organization of the visual cortex. However, in activity obtained during VFM, PS is spatially more extensive than in RS activity, likely reflecting stimulus-driven interactions between local responses. Nevertheless, the similarity of the PS clusters obtained for RS and stimulus-driven fMRI suggest that they share a common neuroanatomical origin. Our finding justifies and facilitates direct comparison of RS and stimulus-evoked activity.
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Affiliation(s)
- Nicolás Gravel
- Laboratory of Experimental Ophthalmology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Ben M Harvey
- Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, The Netherlands; Faculty of Psychology and Education Sciences, University of Coimbra, Coimbra, Portugal
| | - Remco J Renken
- NeuroImaging Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Serge O Dumoulin
- Faculty of Psychology and Education Sciences, University of Coimbra, Coimbra, Portugal
| | - Frans W Cornelissen
- Laboratory of Experimental Ophthalmology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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9
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Optimization of functional MRI for detection, decoding and high-resolution imaging of the response patterns of cortical columns. Neuroimage 2017; 164:67-99. [PMID: 28461061 DOI: 10.1016/j.neuroimage.2017.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/26/2017] [Accepted: 04/05/2017] [Indexed: 11/20/2022] Open
Abstract
The capacity of functional MRI (fMRI) to resolve cortical columns depends on several factors. These include the spatial scale of the columnar pattern, the point-spread of the fMRI response, the voxel size, and the signal-to-noise ratio (SNR) considering thermal and physiological noise. However, it remains unknown how these factors combine, and what is the voxel size that optimizes fMRI of cortical columns. Here we combine current knowledge into a quantitative model of fMRI of realistic patterns of cortical columns with different spatial scales and degrees of irregularity. We compare different approaches for identifying patterns of cortical columns, including univariate and multivariate based detection, multi-voxel pattern analysis (MVPA) based decoding, and high-resolution imaging and reconstruction of the pattern of cortical columns. We present the dependence of the performance of each approach on the parameters of the imaged pattern as well as those of the data acquisition. In addition, we predict voxel sizes that optimize fMRI of cortical columns under various scenarios. We found that all measures associated with multivariate detection and decoding could be approximately calculated from a measure we termed "multivariate contrast-to-noise ratio" (mv-CNR), which is a function of the contrast-to-noise ratio (CNR) and number of voxels. Furthermore, mv-CNR implied that the optimal voxel width for detection and decoding is independent of changes in response amplitude, SNR and imaged volume that are not caused by changes in voxel size. For regular patterns, optimal voxel widths for detection, decoding and imaging/reconstructing the pattern of cortical columns were approximately half the main cycle length of the organization. Optimal voxel widths for irregular patterns were less dependent on the main cycle length, and differed between univariate detection, multivariate detection and decoding, and reconstruction. We compared the effects of different factors of Gradient Echo fMRI at 3 Tesla (T), Gradient Echo fMRI at 7T, and Spin-Echo fMRI at 7T on the detection, decoding, and reconstruction measures considered and found that in all cases the width of the fMRI point-spread had the most significant effect. In contrast, different response amplitudes and noise characteristics played a relatively minor role. We recommend specific voxel widths for optimal univariate detection, for multivariate detection and decoding, and for high-resolution imaging of cortical columns under these three data-acquisition scenarios. Our study supports the planning, optimization, and interpretation of high-resolution fMRI of cortical columns and the decoding of information conveyed by these columns.
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10
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Moerel M, De Martino F, Kemper VG, Schmitter S, Vu AT, Uğurbil K, Formisano E, Yacoub E. Sensitivity and specificity considerations for fMRI encoding, decoding, and mapping of auditory cortex at ultra-high field. Neuroimage 2017; 164:18-31. [PMID: 28373123 DOI: 10.1016/j.neuroimage.2017.03.063] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 12/18/2016] [Accepted: 03/29/2017] [Indexed: 01/05/2023] Open
Abstract
Following rapid technological advances, ultra-high field functional MRI (fMRI) enables exploring correlates of neuronal population activity at an increasing spatial resolution. However, as the fMRI blood-oxygenation-level-dependent (BOLD) contrast is a vascular signal, the spatial specificity of fMRI data is ultimately determined by the characteristics of the underlying vasculature. At 7T, fMRI measurement parameters determine the relative contribution of the macro- and microvasculature to the acquired signal. Here we investigate how these parameters affect relevant high-end fMRI analyses such as encoding, decoding, and submillimeter mapping of voxel preferences in the human auditory cortex. Specifically, we compare a T2* weighted fMRI dataset, obtained with 2D gradient echo (GE) EPI, to a predominantly T2 weighted dataset obtained with 3D GRASE. We first investigated the decoding accuracy based on two encoding models that represented different hypotheses about auditory cortical processing. This encoding/decoding analysis profited from the large spatial coverage and sensitivity of the T2* weighted acquisitions, as evidenced by a significantly higher prediction accuracy in the GE-EPI dataset compared to the 3D GRASE dataset for both encoding models. The main disadvantage of the T2* weighted GE-EPI dataset for encoding/decoding analyses was that the prediction accuracy exhibited cortical depth dependent vascular biases. However, we propose that the comparison of prediction accuracy across the different encoding models may be used as a post processing technique to salvage the spatial interpretability of the GE-EPI cortical depth-dependent prediction accuracy. Second, we explored the mapping of voxel preferences. Large-scale maps of frequency preference (i.e., tonotopy) were similar across datasets, yet the GE-EPI dataset was preferable due to its larger spatial coverage and sensitivity. However, submillimeter tonotopy maps revealed biases in assigned frequency preference and selectivity for the GE-EPI dataset, but not for the 3D GRASE dataset. Thus, a T2 weighted acquisition is recommended if high specificity in tonotopic maps is required. In conclusion, different fMRI acquisitions were better suited for different analyses. It is therefore critical that any sequence parameter optimization considers the eventual intended fMRI analyses and the nature of the neuroscience questions being asked.
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Affiliation(s)
- Michelle Moerel
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA; Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands; Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center (MBIC), Maastricht, The Netherlands.
| | - Federico De Martino
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA; Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center (MBIC), Maastricht, The Netherlands.
| | - Valentin G Kemper
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center (MBIC), Maastricht, The Netherlands.
| | - Sebastian Schmitter
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA; Department of Biomedical Magnetic Resonance, Physikalisch-Technische Bundesanstalt, Berlin, Germany.
| | - An T Vu
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA; Advanced MRI Technologies, Sebastopol, CA, USA.
| | - Kâmil Uğurbil
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA.
| | - Elia Formisano
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands; Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center (MBIC), Maastricht, The Netherlands.
| | - Essa Yacoub
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA.
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11
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Cichy RM, Teng S. Resolving the neural dynamics of visual and auditory scene processing in the human brain: a methodological approach. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0108. [PMID: 28044019 PMCID: PMC5206276 DOI: 10.1098/rstb.2016.0108] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2016] [Indexed: 01/06/2023] Open
Abstract
In natural environments, visual and auditory stimulation elicit responses across a large set of brain regions in a fraction of a second, yielding representations of the multimodal scene and its properties. The rapid and complex neural dynamics underlying visual and auditory information processing pose major challenges to human cognitive neuroscience. Brain signals measured non-invasively are inherently noisy, the format of neural representations is unknown, and transformations between representations are complex and often nonlinear. Further, no single non-invasive brain measurement technique provides a spatio-temporally integrated view. In this opinion piece, we argue that progress can be made by a concerted effort based on three pillars of recent methodological development: (i) sensitive analysis techniques such as decoding and cross-classification, (ii) complex computational modelling using models such as deep neural networks, and (iii) integration across imaging methods (magnetoencephalography/electroencephalography, functional magnetic resonance imaging) and models, e.g. using representational similarity analysis. We showcase two recent efforts that have been undertaken in this spirit and provide novel results about visual and auditory scene analysis. Finally, we discuss the limits of this perspective and sketch a concrete roadmap for future research. This article is part of the themed issue ‘Auditory and visual scene analysis’.
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Affiliation(s)
| | - Santani Teng
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
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12
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Chang C, Raven EP, Duyn JH. Brain-heart interactions: challenges and opportunities with functional magnetic resonance imaging at ultra-high field. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0188. [PMID: 27044994 PMCID: PMC4822447 DOI: 10.1098/rsta.2015.0188] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/05/2016] [Indexed: 05/24/2023]
Abstract
Magnetic resonance imaging (MRI) at ultra-high field (UHF) strengths (7 T and above) offers unique opportunities for studying the human brain with increased spatial resolution, contrast and sensitivity. However, its reliability can be compromised by factors such as head motion, image distortion and non-neural fluctuations of the functional MRI signal. The objective of this review is to provide a critical discussion of the advantages and trade-offs associated with UHF imaging, focusing on the application to studying brain-heart interactions. We describe how UHF MRI may provide contrast and resolution benefits for measuring neural activity of regions involved in the control and mediation of autonomic processes, and in delineating such regions based on anatomical MRI contrast. Limitations arising from confounding signals are discussed, including challenges with distinguishing non-neural physiological effects from the neural signals of interest that reflect cardiorespiratory function. We also consider how recently developed data analysis techniques may be applied to high-field imaging data to uncover novel information about brain-heart interactions.
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Affiliation(s)
- Catie Chang
- Advanced Magnetic Resonance Imaging Section, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erika P Raven
- Advanced Magnetic Resonance Imaging Section, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA Center for Functional and Molecular Imaging, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Jeff H Duyn
- Advanced Magnetic Resonance Imaging Section, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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13
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Gardumi A, Ivanov D, Hausfeld L, Valente G, Formisano E, Uludağ K. The effect of spatial resolution on decoding accuracy in fMRI multivariate pattern analysis. Neuroimage 2016; 132:32-42. [PMID: 26899782 DOI: 10.1016/j.neuroimage.2016.02.033] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/21/2016] [Accepted: 02/10/2016] [Indexed: 11/15/2022] Open
Affiliation(s)
- Anna Gardumi
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center, Maastricht University, Maastricht, The Netherlands.
| | - Dimo Ivanov
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center, Maastricht University, Maastricht, The Netherlands
| | - Lars Hausfeld
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center, Maastricht University, Maastricht, The Netherlands
| | - Giancarlo Valente
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center, Maastricht University, Maastricht, The Netherlands
| | - Elia Formisano
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center, Maastricht University, Maastricht, The Netherlands
| | - Kâmil Uludağ
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center, Maastricht University, Maastricht, The Netherlands
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14
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Yang Z, Zhen Z, Huang L, Kong XZ, Wang X, Song Y, Liu J. Neural Univariate Activity and Multivariate Pattern in the Posterior Superior Temporal Sulcus Differentially Encode Facial Expression and Identity. Sci Rep 2016; 6:23427. [PMID: 26997104 PMCID: PMC4800450 DOI: 10.1038/srep23427] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 03/04/2016] [Indexed: 11/23/2022] Open
Abstract
Faces contain a variety of information such as one’s identity and expression. One prevailing model suggests a functional division of labor in processing faces that different aspects of facial information are processed in anatomically separated and functionally encapsulated brain regions. Here, we demonstrate that facial identity and expression can be processed in the same region, yet with different neural coding strategies. To this end, we employed functional magnetic resonance imaging to examine two types of coding schemes, namely univariate activity and multivariate pattern, in the posterior superior temporal cortex (pSTS) - a face-selective region that is traditionally viewed as being specialized for processing facial expression. With the individual difference approach, we found that participants with higher overall face selectivity in the right pSTS were better at differentiating facial expressions measured outside of the scanner. In contrast, individuals whose spatial pattern for faces in the right pSTS was less similar to that for objects were more accurate in identifying previously presented faces. The double dissociation of behavioral relevance between overall neural activity and spatial neural pattern suggests that the functional-division-of-labor model on face processing is over-simplified, and that coding strategies shall be incorporated in a revised model.
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Affiliation(s)
- Zetian Yang
- State Key Laboratory of Cognitive Neuroscience and Learning &IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China.,The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Zonglei Zhen
- State Key Laboratory of Cognitive Neuroscience and Learning &IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Lijie Huang
- State Key Laboratory of Cognitive Neuroscience and Learning &IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Xiang-Zhen Kong
- State Key Laboratory of Cognitive Neuroscience and Learning &IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Xu Wang
- State Key Laboratory of Cognitive Neuroscience and Learning &IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Yiying Song
- State Key Laboratory of Cognitive Neuroscience and Learning &IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Jia Liu
- Beijing Key Laboratory of Applied Experimental Psychology, School of Psychology, Beijing Normal University, Beijing, 100875, China
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15
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Stallen M, Sanfey AG. The neuroscience of social conformity: implications for fundamental and applied research. Front Neurosci 2015; 9:337. [PMID: 26441509 PMCID: PMC4585332 DOI: 10.3389/fnins.2015.00337] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/07/2015] [Indexed: 11/24/2022] Open
Abstract
The development of closer ties between researchers and practitioners in the domain of behavior and behavioral change offers useful opportunities for better informing public policy campaigns via a deeper understanding of the psychological processes that operate in real-world decision-making. Here, we focus on the domain of social conformity, and suggest that the recent emergence of laboratory work using neuroscientific techniques to probe the brain basis of social influence can prove a useful source of data to better inform models of conformity. In particular, we argue that this work can have an important role to play in better understanding the specific mechanisms at work in social conformity, in both validating and extending current psychological theories of this process, and in assessing how behavioral change can take place as a result of exposure to the judgments of others. We conclude by outlining some promising future directions in this domain, and indicating how this research could potentially be usefully applied to policy issues.
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Affiliation(s)
- Mirre Stallen
- Department of Psychology, Stanford University Stanford, CA, USA
| | - Alan G Sanfey
- Behavioural Science Institute, Radboud University Nijmegen Nijmegen, Netherlands ; Donders Institute for Brain, Cognition and Behaviour Nijmegen, Netherlands
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16
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“Domain gauges”: A reference system for multivariate profiling of brain fMRI activation patterns induced by psychoactive drugs in rats. Neuroimage 2015. [DOI: 10.1016/j.neuroimage.2015.02.032 [doi]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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17
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Bruns A, Mueggler T, Künnecke B, Risterucci C, Prinssen EP, Wettstein JG, von Kienlin M. “Domain gauges”: A reference system for multivariate profiling of brain fMRI activation patterns induced by psychoactive drugs in rats. Neuroimage 2015. [DOI: 10.1016/j.neuroimage.2015.02.032 [doi].] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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18
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Bruns A, Mueggler T, Künnecke B, Risterucci C, Prinssen EP, Wettstein JG, von Kienlin M. "Domain gauges": A reference system for multivariate profiling of brain fMRI activation patterns induced by psychoactive drugs in rats. Neuroimage 2015; 112:70-85. [PMID: 25724758 DOI: 10.1016/j.neuroimage.2015.02.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 02/06/2015] [Accepted: 02/16/2015] [Indexed: 01/01/2023] Open
Abstract
Pharmacological magnetic resonance imaging (phMRI) of the brain has become a widely used tool in both preclinical and clinical drug research. One of its challenges is to condense the observed complex drug-induced brain-activation patterns into semantically meaningful metrics that can then serve as a basis for informed decision making. To aid interpretation of spatially distributed activation patterns, we propose here a set of multivariate metrics termed "domain gauges", which have been calibrated based on different classes of marketed or validated reference drugs. Each class represents a particular "domain" of interest, i.e., a specific therapeutic indication or mode of action. The drug class is empirically characterized by the unique activation pattern it evokes in the brain-the "domain profile". A domain gauge provides, for any tested intervention, a "classifier" as a measure of response strength with respect to the domain in question, and a "differentiator" as a measure of deviation from the domain profile, both along with error ranges. Capitalizing on our in-house database with an unprecedented wealth of standardized perfusion-based phMRI data obtained from rats subjected to various validated treatments, we exemplarily focused on 3 domains based on therapeutic indications: an antipsychotic, an antidepressant and an anxiolytic domain. The domain profiles identified as part of the gauge definition process, as well as the outputs of the gauges when applied to both reference and validation data, were evaluated for their reconcilability with prior biological knowledge and for their performance in drug characterization. The domain profiles provided quantitative activation patterns with high biological plausibility. The antipsychotic profile, for instance, comprised key areas (e.g., cingulate cortex, nucleus accumbens, ventral tegmental area, substantia nigra) which are believed to be strongly involved in mediating an antipsychotic effect, and which are in line with network-level dysfunctions observed in schizophrenia. The domain gauges plausibly positioned the vast majority of the pharmacological and even non-pharmacological treatments. The results also suggest the segregation of sub-domains based on, e.g., the mode of action. Upon judicious selection of domains and careful calibration of the gauges, our approach represents a valuable analytical tool for biological interpretation and decision making in drug discovery.
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Affiliation(s)
- Andreas Bruns
- Roche Pharmaceutical Research & Early Development, Neuroscience Discovery, Roche Innovation Center Basel, Switzerland.
| | - Thomas Mueggler
- Roche Pharmaceutical Research & Early Development, Neuroscience Discovery, Roche Innovation Center Basel, Switzerland
| | - Basil Künnecke
- Roche Pharmaceutical Research & Early Development, Neuroscience Discovery, Roche Innovation Center Basel, Switzerland
| | - Céline Risterucci
- Roche Pharmaceutical Research & Early Development, Neuroscience Discovery, Roche Innovation Center Basel, Switzerland
| | - Eric P Prinssen
- Roche Pharmaceutical Research & Early Development, Neuroscience Discovery, Roche Innovation Center Basel, Switzerland
| | - Joseph G Wettstein
- Roche Pharmaceutical Research & Early Development, Neuroscience Discovery, Roche Innovation Center Basel, Switzerland
| | - Markus von Kienlin
- Roche Pharmaceutical Research & Early Development, Neuroscience Discovery, Roche Innovation Center Basel, Switzerland
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19
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Abstract
Magnetic resonance imaging can now provide human brain images of structure, function, and connectivity with isotropic voxels smaller than one millimeter, and thus much smaller than the cortical thickness. This resolution, achievable in a scan time of less than 1 h, enables visualization of myeloarchitectural layer structure, intracortical variations in functional activity--recorded in changes in blood oxygenation level dependent signal or cerebral blood volume CBV--and intracortical axonal orientational structure via diffusion-weighted magnetic resonance imaging. While recent improvements in radiofrequency receiver coils now enable excellent image data to be obtained at 3T, scanning at the ultra-high field of 7 T offers further gains in signal-to-noise ratio and speed of image acquisition, with a structural image resolution of about 300 μm. These improvements throw into sharp question the strategies that have become conventional for the analysis of functional imaging data, especially the practice of spatial smoothing of raw functional data before further analysis. Creation of a native cortical map for each human subject that provides a reliable individual parcellation into cortical areas related to Brodmann Areas enables a strikingly different approach to functional image analysis. This proposed approach involves surface registration of the cortices of groups of subjects using maps of the longitudinal relaxation time T1 as an index of myelination, and methods for inferring statistical significance that do not entail spatial smoothing. The outcome should be a far more precise comparison of like-with-like cortical areas across subjects, with the potential to greatly increase experimental power, to discriminate activity in neighboring cortical areas, and to enable correlation of function and connectivity with specific cytoarchitecture. Such analyses should enable a far more convincing modeling of brain mechanisms than current graph-based methods that require gross over-simplification of brain activity patterns in order to be computationally tractable.
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Affiliation(s)
- Robert Turner
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences , Leipzig, Germany
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20
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Nili H, Wingfield C, Walther A, Su L, Marslen-Wilson W, Kriegeskorte N. A toolbox for representational similarity analysis. PLoS Comput Biol 2014; 10:e1003553. [PMID: 24743308 PMCID: PMC3990488 DOI: 10.1371/journal.pcbi.1003553] [Citation(s) in RCA: 517] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 01/24/2014] [Indexed: 11/18/2022] Open
Abstract
Neuronal population codes are increasingly being investigated with multivariate pattern-information analyses. A key challenge is to use measured brain-activity patterns to test computational models of brain information processing. One approach to this problem is representational similarity analysis (RSA), which characterizes a representation in a brain or computational model by the distance matrix of the response patterns elicited by a set of stimuli. The representational distance matrix encapsulates what distinctions between stimuli are emphasized and what distinctions are de-emphasized in the representation. A model is tested by comparing the representational distance matrix it predicts to that of a measured brain region. RSA also enables us to compare representations between stages of processing within a given brain or model, between brain and behavioral data, and between individuals and species. Here, we introduce a Matlab toolbox for RSA. The toolbox supports an analysis approach that is simultaneously data- and hypothesis-driven. It is designed to help integrate a wide range of computational models into the analysis of multichannel brain-activity measurements as provided by modern functional imaging and neuronal recording techniques. Tools for visualization and inference enable the user to relate sets of models to sets of brain regions and to statistically test and compare the models using nonparametric inference methods. The toolbox supports searchlight-based RSA, to continuously map a measured brain volume in search of a neuronal population code with a specific geometry. Finally, we introduce the linear-discriminant t value as a measure of representational discriminability that bridges the gap between linear decoding analyses and RSA. In order to demonstrate the capabilities of the toolbox, we apply it to both simulated and real fMRI data. The key functions are equally applicable to other modalities of brain-activity measurement. The toolbox is freely available to the community under an open-source license agreement (http://www.mrc-cbu.cam.ac.uk/methods-and-resources/toolboxes/license/).
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Affiliation(s)
- Hamed Nili
- MRC Cognition and Brain Sciences Unit, Cambridge, United Kingdom
- * E-mail: (HN); (NK)
| | - Cai Wingfield
- Department of Computer Science, University of Bath, Bath, United Kingdom
| | | | - Li Su
- MRC Cognition and Brain Sciences Unit, Cambridge, United Kingdom
- Department of Experimental Psychology, University of Cambridge, Cambridge, United Kingdom
| | - William Marslen-Wilson
- Department of Experimental Psychology, University of Cambridge, Cambridge, United Kingdom
| | - Nikolaus Kriegeskorte
- MRC Cognition and Brain Sciences Unit, Cambridge, United Kingdom
- * E-mail: (HN); (NK)
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21
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Shen G, Zhang J, Wang M, Lei D, Yang G, Zhang S, Du X. Decoding the individual finger movements from single-trial functional magnetic resonance imaging recordings of human brain activity. Eur J Neurosci 2014; 39:2071-82. [PMID: 24661456 DOI: 10.1111/ejn.12547] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/29/2014] [Accepted: 02/04/2014] [Indexed: 12/11/2022]
Abstract
Multivariate pattern classification analysis (MVPA) has been applied to functional magnetic resonance imaging (fMRI) data to decode brain states from spatially distributed activation patterns. Decoding upper limb movements from non-invasively recorded human brain activation is crucial for implementing a brain-machine interface that directly harnesses an individual's thoughts to control external devices or computers. The aim of this study was to decode the individual finger movements from fMRI single-trial data. Thirteen healthy human subjects participated in a visually cued delayed finger movement task, and only one slight button press was performed in each trial. Using MVPA, the decoding accuracy (DA) was computed separately for the different motor-related regions of interest. For the construction of feature vectors, the feature vectors from two successive volumes in the image series for a trial were concatenated. With these spatial-temporal feature vectors, we obtained a 63.1% average DA (84.7% for the best subject) for the contralateral primary somatosensory cortex and a 46.0% average DA (71.0% for the best subject) for the contralateral primary motor cortex; both of these values were significantly above the chance level (20%). In addition, we implemented searchlight MVPA to search for informative regions in an unbiased manner across the whole brain. Furthermore, by applying searchlight MVPA to each volume of a trial, we visually demonstrated the information for decoding, both spatially and temporally. The results suggest that the non-invasive fMRI technique may provide informative features for decoding individual finger movements and the potential of developing an fMRI-based brain-machine interface for finger movement.
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Affiliation(s)
- Guohua Shen
- Shanghai Key Laboratory of Magnetic Resonance, Department of Physics, East China Normal University, 3663 North Zhong-Shan Road, 200062, Shanghai, China
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22
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Perdue KL, Diamond SG. Effects of spatial pattern scale of brain activity on the sensitivity of DOT, fMRI, EEG and MEG. PLoS One 2013; 8:e83299. [PMID: 24376684 PMCID: PMC3871678 DOI: 10.1371/journal.pone.0083299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 11/06/2013] [Indexed: 11/18/2022] Open
Abstract
The objective of this work is to quantify how patterns of cortical activity at different spatial scales are measured by noninvasive functional neuroimaging sensors. We simulated cortical activation patterns at nine different spatial scales in a realistic head model and propagated this activity to magnetoencephalography (MEG), electroencephalography (EEG), diffuse optical tomography (DOT), and functional magnetic resonance imaging (fMRI) sensors in arrangements that are typically used in functional neuroimaging studies. We estimated contrast transfer functions (CTF), correlation distances in sensor space, and the minimum resolvable spatial scale of cortical activity for each modality. We found that CTF decreases as the spatial extent of cortical activity decreases, and that correlations between nearby sensors depend on the spatial extent of cortical activity. For cortical activity on the intermediate spatial scale of 6.7 cm(2), the correlation distances (r>0.5) were 1.0 cm for fMRI, 2.0 cm for DOT, 12.8 for EEG, 9.5 cm for MEG magnetometers and 9.7 cm for MEG gradiometers. The resolvable spatial pattern scale was found to be 1.43 cm(2) for MEG magnetometers, 0.88 cm(2) for MEG gradiometers, 376 cm(2) for EEG, 0.75 cm(2) for DOT, and 0.072 cm(2) for fMRI. These findings show that sensitivity to cortical activity varies substantially as a function of spatial scale within and between the different imaging modalities. This information should be taken into account when interpreting neuroimaging data and when choosing the number of nodes for network analyses in sensor space.
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Affiliation(s)
- Katherine L. Perdue
- Thayer School of Engineering at Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail:
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23
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Abstract
In this paper, I will review why psychotherapy is relevant to the question of how consciousness relates to brain plasticity. A great deal of the research and theorizing on consciousness and the brain, including my own on hallucinations for example (Collerton and Perry, 2011) has focused upon specific changes in conscious content which can be related to temporal changes in restricted brain systems. I will argue that psychotherapy, in contrast, allows only a focus on holistic aspects of consciousness; an emphasis which may usefully complement what can be learnt from more specific methodologies.
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Affiliation(s)
- Daniel Collerton
- Clinical Psychology, Northumberland, Tyne and Wear NHS Foundation Trust Gateshead, UK ; Newcastle upon Tyne Newcastle University, UK
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24
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McNamee D, Rangel A, O'Doherty JP. Category-dependent and category-independent goal-value codes in human ventromedial prefrontal cortex. Nat Neurosci 2013; 16:479-85. [PMID: 23416449 DOI: 10.1038/nn.3337] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 01/24/2013] [Indexed: 11/09/2022]
Abstract
To choose between manifestly distinct options, it is suggested that the brain assigns values to goals using a common currency. Although previous studies have reported activity in ventromedial prefrontal cortex (vmPFC) correlating with the value of different goal stimuli, it remains unclear whether such goal-value representations are independent of the associated stimulus categorization, as required by a common currency. Using multivoxel pattern analyses on functional magnetic resonance imaging (fMRI) data, we found a region of medial prefrontal cortex to contain a distributed goal-value code that is independent of stimulus category. More ventrally in the vmPFC, we found spatially distinct areas of the medial orbitofrontal cortex to contain unique category-dependent distributed value codes for food and consumer items. These results implicate the medial prefrontal cortex in the implementation of a common currency and suggest a ventral versus dorsal topographical organization of value signals in the vmPFC.
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Affiliation(s)
- Daniel McNamee
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin,
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