CoSMoMVPA: Multi-Modal Multivariate Pattern Analysis of Neuroimaging Data in Matlab/GNU Octave

Recent years have seen an increase in the popularity of multivariate pattern (MVP) analysis of functional magnetic resonance (fMRI) data, and, to a much lesser extent, magneto- and electro-encephalography (M/EEG) data. We present CoSMoMVPA, a lightweight MVPA (MVP analysis) toolbox implemented in the intersection of the Matlab and GNU Octave languages, that treats both fMRI and M/EEG data as first-class citizens. CoSMoMVPA supports all state-of-the-art MVP analysis techniques, including searchlight analyses, classification, correlations, representational similarity analysis, and the time generalization method. These can be used to address both data-driven and hypothesis-driven questions about neural organization and representations, both within and across: space, time, frequency bands, neuroimaging modalities, individuals, and species. It uses a uniform data representation of fMRI data in the volume or on the surface, and of M/EEG data at the sensor and source level. Through various external toolboxes, it directly supports reading and writing a variety of fMRI and M/EEG neuroimaging formats, and, where applicable, can convert between them. As a result, it can be integrated readily in existing pipelines and used with existing preprocessed datasets. CoSMoMVPA overloads the traditional volumetric searchlight concept to support neighborhoods for M/EEG and surface-based fMRI data, which supports localization of multivariate effects of interest across space, time, and frequency dimensions. CoSMoMVPA also provides a generalized approach to multiple comparison correction across these dimensions using Threshold-Free Cluster Enhancement with state-of-the-art clustering and permutation techniques. CoSMoMVPA is highly modular and uses abstractions to provide a uniform interface for a variety of MVP measures. Typical analyses require a few lines of code, making it accessible to beginner users. At the same time, expert programmers can easily extend its functionality. CoSMoMVPA comes with extensive documentation, including a variety of runnable demonstration scripts and analysis exercises (with example data and solutions). It uses best software engineering practices including version control, distributed development, an automated test suite, and continuous integration testing. It can be used with the proprietary Matlab and the free GNU Octave software, and it complies with open source distribution platforms such as NeuroDebian. CoSMoMVPA is Free/Open Source Software under the permissive MIT license. Website: http://cosmomvpa.org Source code: https://github.com/CoSMoMVPA/CoSMoMVPA

Differential activation of frontoparietal attention networks by social and symbolic spatial cues

Perception of both gaze-direction and symbolic directional cues (e.g. arrows) orient an observer’s attention toward the indicated location. It is unclear, however, whether these similar behavioral effects are examples of the same attentional phenomenon and, therefore, subserved by the same neural substrate. It has been proposed that gaze, given its evolutionary significance, constitutes a ‘special’ category of spatial cue. As such, it is predicted that the neural systems supporting spatial reorienting will be different for gaze than for non-biological symbols. We tested this prediction using functional magnetic resonance imaging to measure the brain’s response during target localization in which laterally presented targets were preceded by uninformative gaze or arrow cues. Reaction times were faster during valid than invalid trials for both arrow and gaze cues. However, differential patterns of activity were evoked in the brain. Trials including invalid rather than valid arrow cues resulted in a stronger hemodynamic response in the ventral attention network. No such difference was seen during trials including valid and invalid gaze cues. This differential engagement of the ventral reorienting network is consistent with the notion that the facilitation of target detection by gaze cues and arrow cues is subserved by different neural substrates

Differential Activation of Frontoparietal Attention Networks by Social and Symbolic Spatial Cues

Perception of both gaze-direction and symbolic directional cues (e.g. arrows) orient an observer’s attention toward the indicated location. It is unclear, however, whether these similar behavioral effects are examples of the same attentional phenomenon and, therefore, subserved by the same neural substrate. It has been proposed that gaze, given its evolutionary significance, constitutes a ‘special’ category of spatial cue. As such, it is predicted that the neural systems supporting spatial reorienting will be different for gaze than for non-biological symbols. We tested this prediction using functional magnetic resonance imaging to measure the brain’s response during target localization in which laterally presented targets were preceded by uninformative gaze or arrow cues. Reaction times were faster during valid than invalid trials for both arrow and gaze cues. However, differential patterns of activity were evoked in the brain. Trials including invalid rather than valid arrow cues resulted in a stronger hemodynamic response in the ventral attention network. No such difference was seen during trials including valid and invalid gaze cues. This differential engagement of the ventral reorienting network is consistent with the notion that the facilitation of target detection by gaze cues and arrow cues is subserved by different neural substrates

The Neural Dynamics of Attentional Selection in Natural Scenes

The human visual system can only represent a small subset of the many objects present in cluttered scenes at any given time, such that objects compete for representation. Despite these processing limitations, the detection of object categories in cluttered natural scenes is remarkably rapid. How does the brain efficiently select goal-relevant objects from cluttered scenes? In the present study, we used multivariate decoding of magneto-encephalography (MEG) data to track the neural representation of within-scene objects as a function of top-down attentional set. Participants detected categorical targets (cars or people) in natural scenes. The presence of these categories within a scene was decoded from MEG sensor patterns by training linear classifiers on differentiating cars and people in isolation and testing these classifiers on scenes containing one of the two categories. The presence of a specific category in a scene could be reliably decoded from MEG response patterns as early as 160 ms, despite substantial scene clutter and variation in the visual appearance of each category. Strikingly, we find that these early categorical representations fully depend on the match between visual input and top-down attentional set: only objects that matched the current attentional set were processed to the category level within the first 200 ms after scene onset. A sensor-space searchlight analysis revealed that this early attention bias was localized to lateral occipitotemporal cortex, reflecting top-down modulation of visual processing. These results show that attention quickly resolves competition between objects in cluttered natural scenes, allowing for the rapid neural representation of goal-relevant objects. SIGNIFICANCE STATEMENT: Efficient attentional selection is crucial in many everyday situations. For example, when driving a car, we need to quickly detect obstacles, such as pedestrians crossing the street, while ignoring irrelevant objects. How can humans efficiently perform such tasks, given the multitude of objects contained in real-world scenes? Here we used multivariate decoding of magnetoencephalogaphy data to characterize the neural underpinnings of attentional selection in natural scenes with high temporal precision. We show that brain activity quickly tracks the presence of objects in scenes, but crucially only for those objects that were immediately relevant for the participant. These results provide evidence for fast and efficient attentional selection that mediates the rapid detection of goal-relevant objects in real-world environments

Task-invariant brain responses to the social value of faces

Abstract ■ In two fMRI experiments (n = 44) using tasks with different demands-approach-avoidance versus one-back recognition decisions-we measured the responses to the social value of faces. The face stimuli were produced by a parametric model of face evaluation that reduces multiple social evaluations to two orthogonal dimensions of valence and power [Oosterhof, N. N., & Todorov, A. The functional basis of face evaluation

Intravital correlated microscopy reveals differential macrophage and microglial dynamics during resolution of neuroinflammation

Many brain diseases involve activation of resident and peripheral immune cells to clear damaged and dying neurons. Which immune cells respond in what way to cues related to brain disease, however, remains poorly understood. To elucidate these in vivo immunological events in response to brain cell death we used genetically targeted cell ablation in zebrafish. Using intravital microscopy and large-scale electron microscopy, we defined the kinetics and nature of immune responses immediately following injury. Initially, clearance of dead cells occurs by mononuclear phagocytes, including resident microglia and macrophages of peripheral origin, whereas amoeboid microglia are exclusively involved at a later stage. Granulocytes, on the other hand, do not migrate towards the injury. Remarkably, following clearance, phagocyte numbers decrease, partly by phagocyte cell death and subsequent engulfment of phagocyte corpses by microglia. Here, we identify differential temporal involvement of microglia and peripheral macrophages in clearance of dead cells in the brain, revealing the chronological sequence of events in neuroinflammatory resolution. Remarkably, recruited phagocytes undergo cell death and are engulfed by microglia. Because adult zebrafish treated at the larval stage lack signs of pathology, it is likely that this mode of resolving immune responses in brain contributes to full tissue recovery. Therefore, these findings suggest that control of such immune cell behavior could benefit recovery from neuronal damage.</p

Colony-Stimulating Factor 1 Receptor (CSF1R) Regulates Microglia Density and Distribution, but Not Microglia Differentiation In Vivo

Microglia are brain-resident macrophages with trophic and phagocytic functions. Dominant loss-of-function mutations in a key microglia regulator, colony-stimulating factor 1 receptor (CSF1R), cause adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP), a progressive white matter disorder. Because it remains unclear precisely how CSF1R mutations affect microglia, we generated an allelic series of csf1r mutants in zebrafish to identify csf1r-dependent microglia changes. We found that csf1r mutations led to aberrant microglia density and distribution and regional loss of microglia. The remaining microglia still had a microglia-specific gene expression signature, indicating that they had differentiated normally. Strikingly, we also observed lower microglia numbers and widespread microglia depletion in postmortem brain tissue of ALSP patients. Both in zebrafish and in human disease, local microglia loss also presented in regions without obvious pathology. Together, this implies that CSF1R mainly regulates microglia density and that early loss of microglia may contribute to ALSP pathogenesis. Oosterhof et al. show that colony-stimulating factor 1 receptor (CSF1R) primarily regulates microglia density and not their normal differentiation. In addition, they find widespread depletion of microglia in CSF1R-haploinsufficient zebrafish and leukodystrophy patients, also in the absence of pathology, indicating that microglia depletion may contribute to loss of white matter

Passive tracer transport relevant to the TRACE A experiment

This paper explores some of the mechanisms governing the accumulation of passive tracers over the tropical southern Atlantic Ocean during the northern hemisphere fall season. There has been a pioneering observation regarding ozone maxima over the South Atlantic during austral spring. The understanding of the formation of this maxima has been the prime motivation for this study. Using a global model as a frame of reference, we have carried out three kinds of experiments during the period of the Transport and Atmospheric Chemistry Near the Equator-Atlantic (TRACE A) project of 1992. The first of these is a simple advection of total ozone (a passive tracer) in time using the Florida State University global spectral model. Integration over the period of roughly 1 week showed that the model quite closely replicates the behavior of the observed total ozone from the total ozone mapping spectrometer (TOMS). This includes many of the changes in the features of total ozone over the tropical and subtropical region of the southern Atlantic Ocean. These studies suggest a correlation of 0.8 between the observed ozone over this region and ozone modeled from “dynamics alone,” i.e., without recourse to any photochemistry. The second series of experiments invoke sustained sources of a tracer over the biomass burn region of Africa and Brazil. Furthermore, sustained sources were also introduced in the active frontal “descending air” region of the southern hemisphere and over the Asian monsoon's east-west circulation. These experiments strongly suggest that air motions help to accumulate tracer elements over the tropical southern Atlantic Ocean. A third series of experiments address what may be required to improve the deficiencies of the vertical stratification of ozone predicted by the model over the flight region of the tropical southern Atlantic during TRACE A. Here we use the global model to optimally derive plausible accumulation of burn elements over the fire count regions of Brazil and Africa to provide passive tracer advections to closely match what was observed from reconnaissance aircraft-based measurements of ozone over the tropical southern Atlantic Ocean.Engineering and Applied Science