Using a novel source-localized phase regressor technique for evaluation of the vascular contribution to semantic category area localization in BOLD fMRI.

Numerous studies have shown that gradient-echo blood oxygen level dependent (BOLD) fMRI is biased toward large draining veins. However, the impact of this large vein bias on the localization and characterization of semantic category areas has not been examined. Here we address this issue by comparing standard magnitude measures of BOLD activity in the Fusiform Face Area (FFA) and Parahippocampal Place Area (PPA) to those obtained using a novel method that suppresses the contribution of large draining veins: source-localized phase regressor (sPR). Unlike previous suppression methods that utilize the phase component of the BOLD signal, sPR yields robust and unbiased suppression of large draining veins even in voxels with no task-related phase changes. This is confirmed in ideal simulated data as well as in FFA/PPA localization data from four subjects. It was found that approximately 38% of right PPA, 14% of left PPA, 16% of right FFA, and 6% of left FFA voxels predominantly reflect signal from large draining veins. Surprisingly, with the contributions from large veins suppressed, semantic category representation in PPA actually tends to be lateralized to the left rather than the right hemisphere. Furthermore, semantic category areas larger in volume and higher in fSNR were found to have more contributions from large veins. These results suggest that previous studies using gradient-echo BOLD fMRI were biased toward semantic category areas that receive relatively greater contributions from large veins

PrAGMATiC: a Probabilistic and Generative Model of Areas Tiling the Cortex

Much of the human cortex seems to be organized into topographic cortical maps. Yet few quantitative methods exist for characterizing these maps. To address this issue we developed a modeling framework that can reveal group-level cortical maps based on neuroimaging data. PrAGMATiC, a probabilistic and generative model of areas tiling the cortex, is a hierarchical Bayesian generative model of cortical maps. This model assumes that the cortical map in each individual subject is a sample from a single underlying probability distribution. Learning the parameters of this distribution reveals the properties of a cortical map that are common across a group of subjects while avoiding the potentially lossy step of co-registering each subject into a group anatomical space. In this report we give a mathematical description of PrAGMATiC, describe approximations that make it practical to use, show preliminary results from its application to a real dataset, and describe a number of possible future extensions

Pyrcca: Regularized Kernel Canonical Correlation Analysis in Python and Its Applications to Neuroimaging

Canonical correlation analysis (CCA) is a valuable method for interpreting cross-covariance across related datasets of different dimensionality. There are many potential applications of CCA to neuroimaging data analysis. For instance, CCA can be used for finding functional similarities across fMRI datasets collected from multiple subjects without resampling individual datasets to a template anatomy. In this paper, we introduce Pyrcca, an open-source Python module for executing CCA between two or more datasets. Pyrcca can be used to implement CCA with or without regularization, and with or without linear or a Gaussian kernelization of the datasets. We demonstrate an application of CCA implemented with Pyrcca to neuroimaging data analysis. We use CCA to find a data-driven set of functional response patterns that are similar across individual subjects in a natural movie experiment. We then demonstrate how this set of response patterns discovered by CCA can be used to accurately predict subject responses to novel natural movie stimuli

Pycortex: an interactive surface visualizer for fMRI.

Surface visualizations of fMRI provide a comprehensive view of cortical activity. However, surface visualizations are difficult to generate and most common visualization techniques rely on unnecessary interpolation which limits the fidelity of the resulting maps. Furthermore, it is difficult to understand the relationship between flattened cortical surfaces and the underlying 3D anatomy using tools available currently. To address these problems we have developed pycortex, a Python toolbox for interactive surface mapping and visualization. Pycortex exploits the power of modern graphics cards to sample volumetric data on a per-pixel basis, allowing dense and accurate mapping of the voxel grid across the surface. Anatomical and functional information can be projected onto the cortical surface. The surface can be inflated and flattened interactively, aiding interpretation of the correspondence between the anatomical surface and the flattened cortical sheet. The output of pycortex can be viewed using WebGL, a technology compatible with modern web browsers. This allows complex fMRI surface maps to be distributed broadly online without requiring installation of complex software

Reverse Spikeology Predicting Single Spikes

AbstractNeural models that simulate single spike trains can help us understand the basic principles of neural coding in vision. Keat et al. (2001) develop a hybrid model that combines spatiotemporal filtering with nonlinear spike generation. The model does a good job of predicting the responses of single retinal ganglion cells and thalamic relay neurons

Natural Scene Statistics Account for the Representation of Scene Categories in Human Visual Cortex

SummaryDuring natural vision, humans categorize the scenes they encounter: an office, the beach, and so on. These categories are informed by knowledge of the way that objects co-occur in natural scenes. How does the human brain aggregate information about objects to represent scene categories? To explore this issue, we used statistical learning methods to learn categories that objectively capture the co-occurrence statistics of objects in a large collection of natural scenes. Using the learned categories, we modeled fMRI brain signals evoked in human subjects when viewing images of scenes. We find that evoked activity across much of anterior visual cortex is explained by the learned categories. Furthermore, a decoder based on these scene categories accurately predicts the categories and objects comprising novel scenes from brain activity evoked by those scenes. These results suggest that the human brain represents scene categories that capture the co-occurrence statistics of objects in the world

RAPID PUBLICATION Responses in Area V4 Depend on the Spatial Relationship Between Stimulus and Attention

SUMMARY AND CONCLUSIONS I. We studied the spatial interaction between stimulus and attention in macaque area V4. Monkeys were required to fixate a small spot while continuously attending to a ring-shaped target within a large array of identical rings. Meanwhile, the response of the V4 cell under study was tested by flashing behaviorally irrelevant bar stimuli in the cell's classical receptive field (CRF). The location of the attended ring was varied across four positions surrounding the CRF, and the location of the bar stimulus was varied across five positions spanning the CRF. 2. Response strength depended on two aspects of the spatial relationship between the stimulus driving the cell (the bar) and the position of attention (the target ring). First, for 49% of the cells studied, responses were greater for bar stimuli near the attended ring; i.e., the receptive field profile shifted toward the attentional focus. Second, for 84% of the cells, the overall response level depended on the direction in which attention lay relative to the stimulus in the CRF (e.g., to the left, right, above, or below ) . 3. This study confirms a key prediction of spatial models of attention, which postulate enhanced processing of all stimuli near the attentional focus. It also introduces the novel finding that responses are influenced by the relative direction of attention. This result indicates that area V4 carries information about the spatial relationship between visual stimuli and attention