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Sarah Ryan

Publications and source records attributed to Sarah Ryan.

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Spatial Bayesian GLM on the cortical surface produces reliable task activations in individuals and groups

The general linear model (GLM) is a widely popular and convenient tool for estimating the functional brain response and identifying areas of significant activation during a task or stimulus. However, the classical GLM is based on a massive univariate approach that does not explicitly leverage the similarity of activation patterns among neighboring brain locations. As a result, it tends to produce noisy estimates and be underpowered to detect significant activations, particularly in individual subjects and small groups. A recent alternative, a cortical surface-based spatial Bayesian GLM, leverages spatial dependencies among neighboring cortical vertices to produce more accurate estimates and areas of functional activation. The spatial Bayesian GLM can be applied to individual and group-level analysis. In this study, we assess the reliability and power of individual and group-average measures of task activation produced via the surface-based spatial Bayesian GLM. We analyze motor task data from 45 subjects in the Human Connectome Project (HCP) and HCP Retest datasets. We also extend the model to multi-run analysis and employ subject-specific cortical surfaces rather than surfaces inflated to a sphere for more accurate distance-based modeling. Results show that the surface-based spatial Bayesian GLM produces highly reliable activations in individual subjects and is powerful enough to detect trait-like functional topologies. Additionally, spatial Bayesian modeling enhances reliability of group-level analysis even in moderately sized samples (n=45). The power of the spatial Bayesian GLM to detect activations above a scientifically meaningful effect size is nearly invariant to sample size, exhibiting high power even in small samples (n=10). The spatial Bayesian GLM is computationally efficient in individuals and groups and is convenient to implement with the open-source BayesfMRI R package.

stat.ME

Cluster Activation Mapping with Applications to Medical Imaging

An open question in deep clustering is how to understand what in the image is creating the cluster assignments. This visual understanding is essential to be able to trust the results of an inherently complex algorithm like deep learning, especially when the derived cluster assignments may be used to inform decision-making or create new disease sub-types. In this work, we developed novel methodology to generate CLuster Activation Mapping (CLAM) which combines an unsupervised deep clustering framework with a modification of Score-CAM, an approach for discriminative localization in the supervised setting. We evaluated our approach using a simulation study based on computed tomography scans of the lung, and applied it to 3D CT scans from a sarcoidosis population to identify new clusters of sarcoidosis based purely on CT scan presentation.

cs.CV