1
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Soto FA, Narasiwodeyar S. Improving the validity of neuroimaging decoding tests of invariant and configural neural representation. PLoS Comput Biol 2023; 19:e1010819. [PMID: 36689555 PMCID: PMC9894561 DOI: 10.1371/journal.pcbi.1010819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 02/02/2023] [Accepted: 12/15/2022] [Indexed: 01/24/2023] Open
Abstract
Many research questions in sensory neuroscience involve determining whether the neural representation of a stimulus property is invariant or specific to a particular stimulus context (e.g., Is object representation invariant to translation? Is the representation of a face feature specific to the context of other face features?). Between these two extremes, representations may also be context-tolerant or context-sensitive. Most neuroimaging studies have used operational tests in which a target property is inferred from a significant test against the null hypothesis of the opposite property. For example, the popular cross-classification test concludes that representations are invariant or tolerant when the null hypothesis of specificity is rejected. A recently developed neurocomputational theory suggests two insights regarding such tests. First, tests against the null of context-specificity, and for the alternative of context-invariance, are prone to false positives due to the way in which the underlying neural representations are transformed into indirect measurements in neuroimaging studies. Second, jointly performing tests against the nulls of invariance and specificity allows one to reach more precise and valid conclusions about the underlying representations, particularly when the null of invariance is tested using the fine-grained information from classifier decision variables rather than only accuracies (i.e., using the decoding separability test). Here, we provide empirical and computational evidence supporting both of these theoretical insights. In our empirical study, we use encoding of orientation and spatial position in primary visual cortex as a case study, as previous research has established that these properties are encoded in a context-sensitive way. Using fMRI decoding, we show that the cross-classification test produces false-positive conclusions of invariance, but that more valid conclusions can be reached by jointly performing tests against the null of invariance. The results of two simulations further support both of these conclusions. We conclude that more valid inferences about invariance or specificity of neural representations can be reached by jointly testing against both hypotheses, and using neurocomputational theory to guide the interpretation of results.
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Affiliation(s)
- Fabian A. Soto
- Department of Psychology, Florida International University, Miami, Florida, United States of America
- * E-mail:
| | - Sanjay Narasiwodeyar
- Department of Psychology, Florida International University, Miami, Florida, United States of America
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2
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Natural scene sampling reveals reliable coarse-scale orientation tuning in human V1. Nat Commun 2022; 13:6469. [PMID: 36309512 PMCID: PMC9617970 DOI: 10.1038/s41467-022-34134-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 10/13/2022] [Indexed: 12/25/2022] Open
Abstract
Orientation selectivity in primate visual cortex is organized into cortical columns. Since cortical columns are at a finer spatial scale than the sampling resolution of standard BOLD fMRI measurements, analysis approaches have been proposed to peer past these spatial resolution limitations. It was recently found that these methods are predominantly sensitive to stimulus vignetting - a form of selectivity arising from an interaction of the oriented stimulus with the aperture edge. Beyond vignetting, it is not clear whether orientation-selective neural responses are detectable in BOLD measurements. Here, we leverage a dataset of visual cortical responses measured using high-field 7T fMRI. Fitting these responses using image-computable models, we compensate for vignetting and nonetheless find reliable tuning for orientation. Results further reveal a coarse-scale map of orientation preference that may constitute the neural basis for known perceptual anisotropies. These findings settle a long-standing debate in human neuroscience, and provide insights into functional organization principles of visual cortex.
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3
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Taylor J, Xu Y. Representation of Color, Form, and their Conjunction across the Human Ventral Visual Pathway. Neuroimage 2022; 251:118941. [PMID: 35122966 PMCID: PMC9014861 DOI: 10.1016/j.neuroimage.2022.118941] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/25/2022] [Indexed: 11/25/2022] Open
Abstract
Despite decades of research, our understanding of the relationship
between color and form processing in the primate ventral visual pathway remains
incomplete. Using fMRI multivoxel pattern analysis, we examined coding of color
and form, using a simple form feature (orientation) and a mid-level form feature
(curvature), in human ventral visual processing regions. We found that both
color and form could be decoded from activity in early visual areas V1 to V4, as
well as in the posterior color-selective region and shape-selective regions in
ventral and lateral occipitotemporal cortex defined based on their univariate
selectivity to color or shape, respectively (the central color region only
showed color but not form decoding). Meanwhile, decoding biases towards one
feature or the other existed in the color- and shape-selective regions,
consistent with their univariate feature selectivity reported in past studies.
Additional extensive analyses show that while all these regions contain
independent (linearly additive) coding for both features, several early visual
regions also encode the conjunction of color and the simple, but not the
complex, form feature in a nonlinear, interactive manner. Taken together, the
results show that color and form are encoded in a biased distributed and largely
independent manner across ventral visual regions in the human brain.
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Affiliation(s)
- JohnMark Taylor
- Visual Inference Laboratory, Zuckerman Institute, Columbia University.
| | - Yaoda Xu
- Department of Psychology, Yale University
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4
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Curtis CE, Sprague TC. Persistent Activity During Working Memory From Front to Back. Front Neural Circuits 2021; 15:696060. [PMID: 34366794 PMCID: PMC8334735 DOI: 10.3389/fncir.2021.696060] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/28/2021] [Indexed: 01/06/2023] Open
Abstract
Working memory (WM) extends the duration over which information is available for processing. Given its importance in supporting a wide-array of high level cognitive abilities, uncovering the neural mechanisms that underlie WM has been a primary goal of neuroscience research over the past century. Here, we critically review what we consider the two major "arcs" of inquiry, with a specific focus on findings that were theoretically transformative. For the first arc, we briefly review classic studies that led to the canonical WM theory that cast the prefrontal cortex (PFC) as a central player utilizing persistent activity of neurons as a mechanism for memory storage. We then consider recent challenges to the theory regarding the role of persistent neural activity. The second arc, which evolved over the last decade, stemmed from sophisticated computational neuroimaging approaches enabling researchers to decode the contents of WM from the patterns of neural activity in many parts of the brain including early visual cortex. We summarize key findings from these studies, their implications for WM theory, and finally the challenges these findings pose. Our goal in doing so is to identify barriers to developing a comprehensive theory of WM that will require a unification of these two "arcs" of research.
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Affiliation(s)
- Clayton E. Curtis
- Department of Psychology, New York University, New York, NY, United States
- Center for Neural Science, New York University, New York, NY, United States
| | - Thomas C. Sprague
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, Santa Barbara, CA, United States
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5
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Abstract
Selectivity for many basic properties of visual stimuli, such as orientation, is thought to be organized at the scale of cortical columns, making it difficult or impossible to measure directly with noninvasive human neuroscience measurement. However, computational analyses of neuroimaging data have shown that selectivity for orientation can be recovered by considering the pattern of response across a region of cortex. This suggests that computational analyses can reveal representation encoded at a finer spatial scale than is implied by the spatial resolution limits of measurement techniques. This potentially opens up the possibility to study a much wider range of neural phenomena that are otherwise inaccessible through noninvasive measurement. However, as we review in this article, a large body of evidence suggests an alternative hypothesis to this superresolution account: that orientation information is available at the spatial scale of cortical maps and thus easily measurable at the spatial resolution of standard techniques. In fact, a population model shows that this orientation information need not even come from single-unit selectivity for orientation tuning, but instead can result from population selectivity for spatial frequency. Thus, a categorical error of interpretation can result whereby orientation selectivity can be confused with spatial frequency selectivity. This is similarly problematic for the interpretation of results from numerous studies of more complex representations and cognitive functions that have built upon the computational techniques used to reveal stimulus orientation. We suggest in this review that these interpretational ambiguities can be avoided by treating computational analyses as models of the neural processes that give rise to measurement. Building upon the modeling tradition in vision science using considerations of whether population models meet a set of core criteria is important for creating the foundation for a cumulative and replicable approach to making valid inferences from human neuroscience measurements. Expected final online publication date for the Annual Review of Vision Science, Volume 7 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Justin L Gardner
- Department of Psychology, Stanford University, Stanford, California 94305, USA;
| | - Elisha P Merriam
- Laboratory of Brain and Cognition, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, USA;
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6
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Vizioli L, De Martino F, Petro LS, Kersten D, Ugurbil K, Yacoub E, Muckli L. Multivoxel Pattern of Blood Oxygen Level Dependent Activity can be sensitive to stimulus specific fine scale responses. Sci Rep 2020; 10:7565. [PMID: 32371891 PMCID: PMC7200825 DOI: 10.1038/s41598-020-64044-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/08/2020] [Indexed: 12/25/2022] Open
Abstract
At ultra-high field, fMRI voxels can span the sub-millimeter range, allowing the recording of blood oxygenation level dependent (BOLD) responses at the level of fundamental units of neural computation, such as cortical columns and layers. This sub-millimeter resolution, however, is only nominal in nature as a number of factors limit the spatial acuity of functional voxels. Multivoxel Pattern Analysis (MVPA) may provide a means to detect information at finer spatial scales that may otherwise not be visible at the single voxel level due to limitations in sensitivity and specificity. Here, we evaluate the spatial scale of stimuli specific BOLD responses in multivoxel patterns exploited by linear Support Vector Machine, Linear Discriminant Analysis and Naïve Bayesian classifiers across cortical depths in V1. To this end, we artificially misaligned the testing relative to the training portion of the data in increasing spatial steps, then investigated the breakdown of the classifiers’ performances. A one voxel shift led to a significant decrease in decoding accuracy (p < 0.05) across all cortical depths, indicating that stimulus specific responses in a multivoxel pattern of BOLD activity exploited by multivariate decoders can be as precise as the nominal resolution of single voxels (here 0.8 mm isotropic). Our results further indicate that large draining vessels, prominently residing in proximity of the pial surface, do not, in this case, hinder the ability of MVPA to exploit fine scale patterns of BOLD signals. We argue that tailored analytical approaches can help overcoming limitations in high-resolution fMRI and permit studying the mesoscale organization of the human brain with higher sensitivities.
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Affiliation(s)
- Luca Vizioli
- CMRR, University of Minnesota, Minneapolis, MN, United States.
| | - Federico De Martino
- CMRR, University of Minnesota, Minneapolis, MN, United States.,Maastricht University, Maastricht, Netherlands
| | | | - Daniel Kersten
- Department of Psychology, University of Minnesota, Minneapolis, MN, United States
| | - Kamil Ugurbil
- CMRR, University of Minnesota, Minneapolis, MN, United States
| | - Essa Yacoub
- CMRR, University of Minnesota, Minneapolis, MN, United States
| | - Lars Muckli
- University of Glasgow, Glasgow, United Kingdom
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7
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Representation of Auditory Motion Directions and Sound Source Locations in the Human Planum Temporale. J Neurosci 2019; 39:2208-2220. [PMID: 30651333 DOI: 10.1523/jneurosci.2289-18.2018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 11/21/2022] Open
Abstract
The ability to compute the location and direction of sounds is a crucial perceptual skill to efficiently interact with dynamic environments. How the human brain implements spatial hearing is, however, poorly understood. In our study, we used fMRI to characterize the brain activity of male and female humans listening to sounds moving left, right, up, and down as well as static sounds. Whole-brain univariate results contrasting moving and static sounds varying in their location revealed a robust functional preference for auditory motion in bilateral human planum temporale (hPT). Using independently localized hPT, we show that this region contains information about auditory motion directions and, to a lesser extent, sound source locations. Moreover, hPT showed an axis of motion organization reminiscent of the functional organization of the middle-temporal cortex (hMT+/V5) for vision. Importantly, whereas motion direction and location rely on partially shared pattern geometries in hPT, as demonstrated by successful cross-condition decoding, the responses elicited by static and moving sounds were, however, significantly distinct. Altogether, our results demonstrate that the hPT codes for auditory motion and location but that the underlying neural computation linked to motion processing is more reliable and partially distinct from the one supporting sound source location.SIGNIFICANCE STATEMENT Compared with what we know about visual motion, little is known about how the brain implements spatial hearing. Our study reveals that motion directions and sound source locations can be reliably decoded in the human planum temporale (hPT) and that they rely on partially shared pattern geometries. Our study, therefore, sheds important new light on how computing the location or direction of sounds is implemented in the human auditory cortex by showing that those two computations rely on partially shared neural codes. Furthermore, our results show that the neural representation of moving sounds in hPT follows a "preferred axis of motion" organization, reminiscent of the coding mechanisms typically observed in the occipital middle-temporal cortex (hMT+/V5) region for computing visual motion.
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8
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Roth ZN, Heeger DJ, Merriam EP. Stimulus vignetting and orientation selectivity in human visual cortex. eLife 2018; 7:e37241. [PMID: 30106372 PMCID: PMC6092116 DOI: 10.7554/elife.37241] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/01/2018] [Indexed: 01/03/2023] Open
Abstract
Neural selectivity to orientation is one of the simplest and most thoroughly-studied cortical sensory features. Here, we show that a large body of research that purported to measure orientation tuning may have in fact been inadvertently measuring sensitivity to second-order changes in luminance, a phenomenon we term 'vignetting'. Using a computational model of neural responses in primary visual cortex (V1), we demonstrate the impact of vignetting on simulated V1 responses. We then used the model to generate a set of predictions, which we confirmed with functional MRI experiments in human observers. Our results demonstrate that stimulus vignetting can wholly determine the orientation selectivity of responses in visual cortex measured at a macroscopic scale, and suggest a reinterpretation of a well-established literature on orientation processing in visual cortex.
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Affiliation(s)
- Zvi N Roth
- Laboratory of Brain and CognitionNational Institute of Mental Health, National Institutes of HealthBethesdaUnited States
| | - David J Heeger
- Department of PsychologyNew York UniversityNew YorkUnited States
- Center for Neural ScienceNew York UniversityNew YorkUnited States
| | - Elisha P Merriam
- Laboratory of Brain and CognitionNational Institute of Mental Health, National Institutes of HealthBethesdaUnited States
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9
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Thielen J, van Lier R, van Gerven M. No evidence for confounding orientation-dependent fixational eye movements under baseline conditions. Sci Rep 2018; 8:11644. [PMID: 30076355 PMCID: PMC6076314 DOI: 10.1038/s41598-018-30221-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 07/24/2018] [Indexed: 11/20/2022] Open
Abstract
Decoding has become a standard analysis technique for contemporary cognitive neuroscience. Already more than a decade ago, it was shown that orientation information could be decoded from functional magnetic resonance imaging voxel time series. However, the underlying neural mechanism driving the decodable information is still under debate. Here, we investigated whether eye movements and pupil dilation during attempted fixation and passive viewing of visually presented square-wave grating stimuli could explain orientation decoding. We hypothesized that there are confounding orientation-dependent fixational eye movements (e.g., microsaccades), which systematically alter brain activity, and hence can be the source of decodable information. We repeated one of the original orientation decoding studies, but recorded eye movements instead of brain activity. We found no evidence that stimulus orientation can be decoded from eye movements under baseline conditions, but cannot rule out the potential confounding effect of eye movements under different conditions. With this study, we emphasize the importance, and show the implications of such potential confounding eye movements for decoding studies and cognitive neuroscience in general.
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Affiliation(s)
- Jordy Thielen
- Radboud University, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.
| | - Rob van Lier
- Radboud University, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Marcel van Gerven
- Radboud University, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
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10
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Differential Sampling of Visual Space in Ventral and Dorsal Early Visual Cortex. J Neurosci 2018; 38:2294-2303. [PMID: 29382711 DOI: 10.1523/jneurosci.2717-17.2018] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/08/2018] [Accepted: 01/11/2018] [Indexed: 11/21/2022] Open
Abstract
A fundamental feature of cortical visual processing is the separation of visual processing for the upper and lower visual fields. In early visual cortex (EVC), the upper visual field is processed ventrally, with the lower visual field processed dorsally. This distinction persists into several category-selective regions of occipitotemporal cortex, with ventral and lateral scene-, face-, and object-selective regions biased for the upper and lower visual fields, respectively. Here, using an elliptical population receptive field (pRF) model, we systematically tested the sampling of visual space within ventral and dorsal divisions of human EVC in both male and female participants. We found that (1) pRFs tend to be elliptical and oriented toward the fovea with distinct angular distributions for ventral and dorsal divisions of EVC, potentially reflecting a radial bias; and (2) pRFs in ventral areas were larger (∼1.5×) and more elliptical (∼1.2×) than those in dorsal areas. These differences potentially reflect a tendency for receptive fields in ventral temporal cortex to overlap the fovea with less emphasis on precise localization and isotropic representation of space compared with dorsal areas. Collectively, these findings suggest that ventral and dorsal divisions of EVC sample visual space differently, likely contributing to and/or stemming from the functional differentiation of visual processing observed in higher-level regions of the ventral and dorsal cortical visual pathways.SIGNIFICANCE STATEMENT The processing of visual information from the upper and lower visual fields is separated in visual cortex. Although ventral and dorsal divisions of early visual cortex (EVC) are commonly assumed to sample visual space equivalently, we demonstrate systematic differences using an elliptical population receptive field (pRF) model. Specifically, we demonstrate that (1) ventral and dorsal divisions of EVC exhibit diverging distributions of pRF angle, which are biased toward the fovea; and (2) ventral pRFs exhibit higher aspect ratios and cover larger areas than dorsal pRFs. These results suggest that ventral and dorsal divisions of EVC sample visual space differently and that such differential sampling likely contributes to different functional roles attributed to the ventral and dorsal pathways, such as object recognition and visually guided attention, respectively.
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11
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Inverted Encoding Models of Human Population Response Conflate Noise and Neural Tuning Width. J Neurosci 2017; 38:398-408. [PMID: 29167406 DOI: 10.1523/jneurosci.2453-17.2017] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/08/2017] [Accepted: 11/10/2017] [Indexed: 01/02/2023] Open
Abstract
Channel-encoding models offer the ability to bridge different scales of neuronal measurement by interpreting population responses, typically measured with BOLD imaging in humans, as linear sums of groups of neurons (channels) tuned for visual stimulus properties. Inverting these models to form predicted channel responses from population measurements in humans seemingly offers the potential to infer neuronal tuning properties. Here, we test the ability to make inferences about neural tuning width from inverted encoding models. We examined contrast invariance of orientation selectivity in human V1 (both sexes) and found that inverting the encoding model resulted in channel response functions that became broader with lower contrast, thus apparently violating contrast invariance. Simulations showed that this broadening could be explained by contrast-invariant single-unit tuning with the measured decrease in response amplitude at lower contrast. The decrease in response lowers the signal-to-noise ratio of population responses that results in poorer population representation of orientation. Simulations further showed that increasing signal to noise makes channel response functions less sensitive to underlying neural tuning width, and in the limit of zero noise will reconstruct the channel function assumed by the model regardless of the bandwidth of single units. We conclude that our data are consistent with contrast-invariant orientation tuning in human V1. More generally, our results demonstrate that population selectivity measures obtained by encoding models can deviate substantially from the behavior of single units because they conflate neural tuning width and noise and are therefore better used to estimate the uncertainty of decoded stimulus properties.SIGNIFICANCE STATEMENT It is widely recognized that perceptual experience arises from large populations of neurons, rather than a few single units. Yet, much theory and experiment have examined links between single units and perception. Encoding models offer a way to bridge this gap by explicitly interpreting population activity as the aggregate response of many single neurons with known tuning properties. Here we use this approach to examine contrast-invariant orientation tuning of human V1. We show with experiment and modeling that due to lower signal to noise, contrast-invariant orientation tuning of single units manifests in population response functions that broaden at lower contrast, rather than remain contrast-invariant. These results highlight the need for explicit quantitative modeling when making a reverse inference from population response profiles to single-unit responses.
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12
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Local opposite orientation preferences in V1: fMRI sensitivity to fine-grained pattern information. Sci Rep 2017; 7:7128. [PMID: 28769042 PMCID: PMC5540976 DOI: 10.1038/s41598-017-07036-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 06/22/2017] [Indexed: 11/08/2022] Open
Abstract
The orientation of a visual grating can be decoded from human primary visual cortex (V1) using functional magnetic resonance imaging (fMRI) at conventional resolutions (2-3 mm voxel width, 3T scanner). It is unclear to what extent this information originates from different spatial scales of neuronal selectivity, ranging from orientation columns to global areal maps. According to the global-areal-map account, fMRI orientation decoding relies exclusively on fMRI voxels in V1 exhibiting a radial or vertical preference. Here we show, by contrast, that 2-mm isotropic voxels in a small patch of V1 within a quarterfield representation exhibit reliable opposite selectivities. Sets of voxels with opposite selectivities are locally intermingled and each set can support orientation decoding. This indicates that global areal maps cannot fully account for orientation information in fMRI and demonstrates that fMRI also reflects fine-grained patterns of neuronal selectivity.
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13
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Kumar S, Kaposvari P, Vogels R. Encoding of Predictable and Unpredictable Stimuli by Inferior Temporal Cortical Neurons. J Cogn Neurosci 2017; 29:1445-1454. [DOI: 10.1162/jocn_a_01135] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
Animals and humans learn statistical regularities that are embedded in sequences of stimuli. The neural mechanisms of such statistical learning are still poorly understood. Previous work in macaque inferior temporal (IT) cortex demonstrated suppressed spiking activity to visual images of a sequence in which the stimulus order was defined by transitional probabilities (labeled as “standard” sequence), compared with a sequence in which the stimulus order was random (“random” sequence). Here, we asked whether IT neurons encode the images of the standard sequence more accurately compared with images of the random sequence. Previous human fMRI studies in different sensory modalities also found a suppressed response to expected relative to unexpected stimuli but obtained various results regarding the effect of expectation on encoding, with one study reporting an improved classification accuracy of expected stimuli despite the reduced activation level. We employed a linear classifier to decode image identity from the spiking responses of the recorded IT neurons. We found a greater decoding accuracy for images of the standard compared with the random sequence during the early part of the stimulus presentation, but further analyses suggested that this reflected the sustained, stimulus-selective activity from the previous stimulus of the sequence, which is typical for IT neurons. However, the peak decoding accuracy was lower for the standard compared with the random sequence, in line with the reduced response to the former compared with the latter images. These data suggest that macaque IT neurons represent less accurately predictable compared with unpredictable images.
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14
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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: 1.4] [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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15
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Grootswagers T, Wardle SG, Carlson TA. Decoding Dynamic Brain Patterns from Evoked Responses: A Tutorial on Multivariate Pattern Analysis Applied to Time Series Neuroimaging Data. J Cogn Neurosci 2017; 29:677-697. [DOI: 10.1162/jocn_a_01068] [Citation(s) in RCA: 329] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Multivariate pattern analysis (MVPA) or brain decoding methods have become standard practice in analyzing fMRI data. Although decoding methods have been extensively applied in brain–computer interfaces, these methods have only recently been applied to time series neuroimaging data such as MEG and EEG to address experimental questions in cognitive neuroscience. In a tutorial style review, we describe a broad set of options to inform future time series decoding studies from a cognitive neuroscience perspective. Using example MEG data, we illustrate the effects that different options in the decoding analysis pipeline can have on experimental results where the aim is to “decode” different perceptual stimuli or cognitive states over time from dynamic brain activation patterns. We show that decisions made at both preprocessing (e.g., dimensionality reduction, subsampling, trial averaging) and decoding (e.g., classifier selection, cross-validation design) stages of the analysis can significantly affect the results. In addition to standard decoding, we describe extensions to MVPA for time-varying neuroimaging data including representational similarity analysis, temporal generalization, and the interpretation of classifier weight maps. Finally, we outline important caveats in the design and interpretation of time series decoding experiments.
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Affiliation(s)
- Tijl Grootswagers
- 1Macquarie University, Sydney, Australia
- 2ARC Centre of Excellence in Cognition and its Disorders
- 3University of Sydney
| | - Susan G. Wardle
- 1Macquarie University, Sydney, Australia
- 2ARC Centre of Excellence in Cognition and its Disorders
| | - Thomas A. Carlson
- 2ARC Centre of Excellence in Cognition and its Disorders
- 3University of Sydney
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16
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Baker DH. Decoding eye-of-origin outside of awareness. Neuroimage 2017; 147:89-96. [PMID: 27940075 DOI: 10.1016/j.neuroimage.2016.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 11/25/2016] [Accepted: 12/03/2016] [Indexed: 11/29/2022] Open
Abstract
In the primary visual cortex of many mammals, ocular dominance columns segregate information from the two eyes. Yet under controlled conditions, most human observers are unable to correctly report the eye to which a stimulus has been shown, indicating that this information is lost during subsequent processing. This study investigates whether eye-of-origin information is available in the pattern of electrophysiological activity evoked by visual stimuli, recorded using EEG and decoded using multivariate pattern analysis. Observers (N=24) viewed sine-wave grating and plaid stimuli of different orientations, shown to either the left or right eye (or both). Using a support vector machine, eye-of-origin could be decoded above chance at around 140 and 220ms post stimulus onset, yet observers were at chance for reporting this information. Other stimulus features, such as binocularity, orientation, spatial pattern, and the presence of interocular conflict (i.e. rivalry), could also be decoded using the same techniques, though all of these were perceptually discriminable above chance. A control analysis found no evidence to support the possibility that eye dominance was responsible for the eye-of-origin effects. These results support a structural explanation for multivariate decoding of electrophysiological signals - information organised in cortical columns can be decoded, even when observers are unaware of this information.
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Larsson J, Harrison C, Jackson J, Oh SM, Zeringyte V. Spatial scale and distribution of neurovascular signals underlying decoding of orientation and eye of origin from fMRI data. J Neurophysiol 2017; 117:818-835. [PMID: 27903637 DOI: 10.1152/jn.00590.2016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/29/2016] [Indexed: 12/29/2022] Open
Abstract
Multivariate pattern analysis of functional magnetic resonance imaging (fMRI) data is widely used, yet the spatial scales and origin of neurovascular signals underlying such analyses remain unclear. We compared decoding performance for stimulus orientation and eye of origin from fMRI measurements in human visual cortex with predictions based on the columnar organization of each feature and estimated the spatial scales of patterns driving decoding. Both orientation and eye of origin could be decoded significantly above chance in early visual areas (V1-V3). Contrary to predictions based on a columnar origin of response biases, decoding performance for eye of origin in V2 and V3 was not significantly lower than that in V1, nor did decoding performance for orientation and eye of origin differ significantly. Instead, response biases for both features showed large-scale organization, evident as a radial bias for orientation, and a nasotemporal bias for eye preference. To determine whether these patterns could drive classification, we quantified the effect on classification performance of binning voxels according to visual field position. Consistent with large-scale biases driving classification, binning by polar angle yielded significantly better decoding performance for orientation than random binning in V1-V3. Similarly, binning by hemifield significantly improved decoding performance for eye of origin. Patterns of orientation and eye preference bias in V2 and V3 showed a substantial degree of spatial correlation with the corresponding patterns in V1, suggesting that response biases in these areas originate in V1. Together, these findings indicate that multivariate classification results need not reflect the underlying columnar organization of neuronal response selectivities in early visual areas.NEW & NOTEWORTHY Large-scale response biases can account for decoding of orientation and eye of origin in human early visual areas V1-V3. For eye of origin this pattern is a nasotemporal bias; for orientation it is a radial bias. Differences in decoding performance across areas and stimulus features are not well predicted by differences in columnar-scale organization of each feature. Large-scale biases in extrastriate areas are spatially correlated with those in V1, suggesting biases originate in primary visual cortex.
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Affiliation(s)
- Jonas Larsson
- Department of Psychology, Royal Holloway, University of London, Egham, United Kingdom
| | - Charlotte Harrison
- Department of Psychology, Royal Holloway, University of London, Egham, United Kingdom
| | - Jade Jackson
- Department of Psychology, Royal Holloway, University of London, Egham, United Kingdom
| | - Seung-Mock Oh
- Department of Psychology, Royal Holloway, University of London, Egham, United Kingdom
| | - Vaida Zeringyte
- Department of Psychology, Royal Holloway, University of London, Egham, United Kingdom
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Philips RT, Chakravarthy VS. A Global Orientation Map in the Primary Visual Cortex (V1): Could a Self Organizing Model Reveal Its Hidden Bias? Front Neural Circuits 2017; 10:109. [PMID: 28111542 PMCID: PMC5216665 DOI: 10.3389/fncir.2016.00109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/14/2016] [Indexed: 11/13/2022] Open
Abstract
A remarkable accomplishment of self organizing models is their ability to simulate the development of feature maps in the cortex. Additionally, these models have been trained to tease out the differential causes of multiple feature maps, mapped on to the same output space. Recently, a Laterally Interconnected Synergetically Self Organizing Map (LISSOM) model has been used to simulate the mapping of eccentricity and meridional angle onto orthogonal axes in the primary visual cortex (V1). This model is further probed to simulate the development of the radial bias in V1, using a training set that consists of both radial (rectangular bars of random size and orientation) as well as non-radial stimuli. The radial bias describes the preference of the visual system toward orientations that match the angular position (meridional angle) of that orientation with respect to the point of fixation. Recent fMRI results have shown that there exists a coarse scale orientation map in V1, which resembles the meridional angle map, thereby providing a plausible neural basis for the radial bias. The LISSOM model, trained for the development of the retinotopic map, on probing for orientation preference, exhibits a coarse scale orientation map, consistent with these experimental results, quantified using the circular cross correlation (rc ). The rc between the orientation map developed on probing with a thin annular ring containing sinusoidal gratings with a spatial frequency of 0.5 cycles per degree (cpd) and the corresponding meridional map for the same annular ring, has a value of 0.8894. The results also suggest that the radial bias goes beyond the current understanding of a node to node correlation between the two maps.
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Affiliation(s)
- Ryan T Philips
- Computational Neuroscience Laboratory, Department of Biotechnology, Indian Institute of Technology Madras Chennai, India
| | - V Srinivasa Chakravarthy
- Computational Neuroscience Laboratory, Department of Biotechnology, Indian Institute of Technology Madras Chennai, India
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Edge-Related Activity Is Not Necessary to Explain Orientation Decoding in Human Visual Cortex. J Neurosci 2016; 37:1187-1196. [PMID: 28003346 DOI: 10.1523/jneurosci.2690-16.2016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/22/2016] [Accepted: 11/30/2016] [Indexed: 11/21/2022] Open
Abstract
Multivariate pattern analysis is a powerful technique; however, a significant theoretical limitation in neuroscience is the ambiguity in interpreting the source of decodable information used by classifiers. This is exemplified by the continued controversy over the source of orientation decoding from fMRI responses in human V1. Recently Carlson (2014) identified a potential source of decodable information by modeling voxel responses based on the Hubel and Wiesel (1972) ice-cube model of visual cortex. The model revealed that activity associated with the edges of gratings covaries with orientation and could potentially be used to discriminate orientation. Here we empirically evaluate whether "edge-related activity" underlies orientation decoding from patterns of BOLD response in human V1. First, we systematically mapped classifier performance as a function of stimulus location using population receptive field modeling to isolate each voxel's overlap with a large annular grating stimulus. Orientation was decodable across the stimulus; however, peak decoding performance occurred for voxels with receptive fields closer to the fovea and overlapping with the inner edge. Critically, we did not observe the expected second peak in decoding performance at the outer stimulus edge as predicted by the edge account. Second, we evaluated whether voxels that contribute most to classifier performance have receptive fields that cluster in cortical regions corresponding to the retinotopic location of the stimulus edge. Instead, we find the distribution of highly weighted voxels to be approximately random, with a modest bias toward more foveal voxels. Our results demonstrate that edge-related activity is likely not necessary for orientation decoding. SIGNIFICANCE STATEMENT A significant theoretical limitation of multivariate pattern analysis in neuroscience is the ambiguity in interpreting the source of decodable information used by classifiers. For example, orientation can be decoded from BOLD activation patterns in human V1, even though orientation columns are at a finer spatial scale than 3T fMRI. Consequently, the source of decodable information remains controversial. Here we test the proposal that information related to the stimulus edges underlies orientation decoding. We map voxel population receptive fields in V1 and evaluate orientation decoding performance as a function of stimulus location in retinotopic cortex. We find orientation is decodable from voxels whose receptive fields do not overlap with the stimulus edges, suggesting edge-related activity does not substantially drive orientation decoding.
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