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"Russell, A"
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MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites
Quality control of MRI is essential for excluding problematic acquisitions and avoiding bias in subsequent image processing and analysis. Visual inspection is subjective and impractical for large scale datasets. Although automated quality assessments have been demonstrated on single-site datasets, it is unclear that solutions can generalize to unseen data acquired at new sites. Here, we introduce the MRI Quality Control tool (MRIQC), a tool for extracting quality measures and fitting a binary (accept/exclude) classifier. Our tool can be run both locally and as a free online service via the OpenNeuro.org portal. The classifier is trained on a publicly available, multi-site dataset (17 sites, N = 1102). We perform model selection evaluating different normalization and feature exclusion approaches aimed at maximizing across-site generalization and estimate an accuracy of 76%±13% on new sites, using leave-one-site-out cross-validation. We confirm that result on a held-out dataset (2 sites, N = 265) also obtaining a 76% accuracy. Even though the performance of the trained classifier is statistically above chance, we show that it is susceptible to site effects and unable to account for artifacts specific to new sites. MRIQC performs with high accuracy in intra-site prediction, but performance on unseen sites leaves space for improvement which might require more labeled data and new approaches to the between-site variability. Overcoming these limitations is crucial for a more objective quality assessment of neuroimaging data, and to enable the analysis of extremely large and multi-site samples.
Journal Article
Normalizing the Use of Single-Item Measures
The application of single-item measures has the potential to help applied researchers address conceptual, methodological, and empirical challenges. Based on a large-scale evidence-based approach, we empirically examined the degree to which various constructs in the organizational sciences can be reliably and validly assessed with a single item. In study 1, across 91 selected constructs, 71.4% of the single-item measures demonstrated strong if not very strong definitional correspondence (as a measure of content validity). In study 2, based on a heterogeneous sample of working adults, we demonstrate that the majority of single-item measures examined demonstrated little to no comprehension or usability concerns. Study 3 provides evidence for the reliability of the proposed single-item measures based on test–retest reliabilities across the three temporal conditions (1 day, 2 weeks, 1 month). In study 4, we examined issues of construct and criterion validity using a multi-trait, multi-method approach. Collectively, 75 of the 91 focal measures demonstrated very good or extensive validity, evidencing moderate to high content validity, no usability concerns, moderate to high test–retest reliability, and extensive criterion validity. Finally, in study 5, we empirically examined the argument that only conceptually narrow constructs can be reliably and validly assessed with single-item measures. Results suggest that there is no relationship between subject matter expert evaluations of construct breadth and reliability and validity evidence collected across the first four studies. Beyond providing an off-the-shelf compendium of validated single-item measures, we abstract our validation steps providing a roadmap to replicate and build upon. Limitations and future directions are discussed.
Journal Article
The evolution of seasonal influenza viruses
Despite decades of surveillance and pharmaceutical and non-pharmaceutical interventions, seasonal influenza viruses continue to cause epidemics around the world each year. The key process underlying these recurrent epidemics is the evolution of the viruses to escape the immunity that is induced by prior infection or vaccination. Although we are beginning to understand the processes that underlie the evolutionary dynamics of seasonal influenza viruses, the timing and nature of emergence of new virus strains remain mostly unpredictable. In this Review, we discuss recent advances in understanding the molecular determinants of influenza virus immune escape, sources of evolutionary selection pressure, population dynamics of influenza viruses and prospects for better influenza virus control.
Journal Article
Orthogonalization of Regressors in fMRI Models
The occurrence of collinearity in fMRI-based GLMs (general linear models) may reduce power or produce unreliable parameter estimates. It is commonly believed that orthogonalizing collinear regressors in the model will solve this problem, and some software packages apply automatic orthogonalization. However, the effects of orthogonalization on the interpretation of the resulting parameter estimates is widely unappreciated or misunderstood. Here we discuss the nature and causes of collinearity in fMRI models, with a focus on the appropriate uses of orthogonalization. Special attention is given to how the two popular fMRI data analysis software packages, SPM and FSL, handle orthogonalization, and pitfalls that may be encountered in their usage. Strategies are discussed for reducing collinearity in fMRI designs and addressing their effects when they occur.
Journal Article
The new mind readers : what neuroimaging can and cannot reveal about our thoughts
The ability to read minds has long been a fascination of science fiction, but revolutionary new brain-imaging methods are bringing it closer to scientific reality. The New Mind Readers provides a compelling look at the origins, development, and future of these extraordinary tools, revealing how they are increasingly being used to decode our thoughts and experiences--and how this raises sometimes troubling questions about their application in domains such as marketing, politics, and the law. Russell Poldrack takes readers on a journey of scientific discovery, telling the stories of the visionaries behind these breakthroughs. Along the way, he gives an insider's perspective on what is perhaps the single most important technology in cognitive neuroscience today--functional magnetic resonance imaging, or fMRI, which is providing astonishing new insights into the contents and workings of the mind. He highlights both the amazing power and major limitations of these techniques and describes how applications outside the lab often exceed the bounds of responsible science. Poldrack also details the unique and sometimes disorienting experience of having his own brain scanned more than a hundred times as part of a landmark study of how human brain function changes over time. Written by one of the world's leading pioneers in the field, The New Mind Readers cuts through the hype and misperceptions surrounding these emerging new methods, offering needed perspective on what they can and cannot do--and demonstrating how they can provide new answers to age-old questions about the nature of consciousness and what it means to be human. -- Inside jacket flap.
BOOK
Functional boundaries in the human cerebellum revealed by a multi-domain task battery
There is compelling evidence that the human cerebellum is engaged in a wide array of motor and cognitive tasks. A fundamental question centers on whether the cerebellum is organized into distinct functional subregions. To address this question, we employed a rich task battery designed to tap into a broad range of cognitive processes. During four functional MRI sessions, participants performed a battery of 26 diverse tasks comprising 47 unique conditions. Using the data from this multi-domain task battery, we derived a comprehensive functional parcellation of the cerebellar cortex and evaluated it by predicting functional boundaries in a novel set of tasks. The new parcellation successfully identified distinct functional subregions, providing significant improvements over existing parcellations derived from task-free data. Lobular boundaries, commonly used to summarize functional data, did not coincide with functional subdivisions. The new parcellation provides a functional atlas to guide future neuroimaging studies.
Journal Article