23 papers · ranked by Valyu relevance
Hyemin Han
BayesFactorFMRI is a tool developed with R and Python to allow neuroimaging researchers to conduct Bayesian second-level analysis and Bayesian meta-analysis of fMRI image data with multiprocessing. This tool expedites computationally intensive Bayesian fMRI analysis through multiprocessing. Its GUI allows researchers…
Hyemin Han
Previous research has shown the potential value of Bayesian methods in fMRI (functional magnetic resonance imaging) analysis. For instance, the results from Bayes factor-applied second-level fMRI analysis showed a higher hit rate compared with frequentist second-level fMRI analysis, suggesting greater sensitivity.…
Hyemin Han, Leonardo Gollo
Previous research has shown the potential value of Bayesian methods in fMRI (functional magnetic resonance imaging) analysis. For instance, the results from Bayes factor-applied second-level fMRI analysis showed a higher hit rate compared with frequentist second-level fMRI analysis, suggesting greater sensitivity.…
Xuan Guo, Bing Liu, Le Chen, Guantao Chen + 2 more
This paper aims to review state-of-the-art Bayesian-inference-based methods applied to functional magnetic resonance imaging (fMRI) data. Particularly, we focus on one specific long-standing challenge in the computational modeling of fMRI datasets: how to effectively explore typical functional interactions from fMRI…
Hyemin Han, Joonsuk Park
Recent debates about the conventional traditional threshold used in the fields of neuroscience and psychology, namely P < 0.05, have spurred researchers to consider alternative ways to analyze fMRI data. A group of methodologists and statisticians have considered Bayesian inference as a candidate methodology. However…
Ruslan Masharipov, Irina Knyazeva, Yaroslav Nikolaev, Alexander Korotkov + 3 more
Classical null hypothesis significance testing is limited to the rejection of the point-null hypothesis; it does not allow the interpretation of non-significant results. This leads to a bias against the null hypothesis. Herein, we discuss statistical approaches to ‘null effect’ assessment focusing on the Bayesian…
Amanda F. Mejia, Yu Ryan Yue, David Bolin, Finn Lindren + 1 more
'Martin A. Lindquist'] Cortical surface fMRI (cs-fMRI) has recently grown in popularity versus traditional volumetric fMRI, as it allows for more meaningful spatial smoothing and is more compatible with the common assumptions of isotropy and stationarity in Bayesian spatial models. However, as no Bayesian spatial model…
Hyemin Han
We developed and tested Bayesian multiple comparison correction method for Bayesian voxelwise second-level fMRI analysis with R. The performance of the developed method was tested with simulation and real image datasets. First, we compared false alarm and hit rates, which were used as proxies for selectivity and…
Daniel Spencer, David Bolin, Amanda F. Mejia
Task functional magnetic resonance imaging (fMRI) is a type of neuroimaging data used to identify areas of the brain that activate during specific tasks or stimuli. These data are conventionally modeled using a massive univariate approach across all data locations, which ignores spatial dependence at the cost of model…
Johnatan Cardona Jiménez, Carlos Alberto de Bragança Pereira, Victor Fossaluza
'Victor Fossaluza'] Functional magnetic resonance imaging or functional MRI (fMRI) is a non-invasive way to assess brain activity by detecting changes associated with blood flow. In this work, we propose a full Bayesian procedure to analyze fMRI data for individual and group stages. For the individual stage we use a…
Gang Chen, Yaqiong Xiao, Paul A. Taylor, Tracy Riggins + 3 more
In neuroimaging, the multiplicity issue may sneak into data analysis through several channels, affecting expected false positive rates (FPRs; type I errors) in diverse ways. One widely recognized aspect of multiplicity, multiple testing, occurs when the investigator fits a separate model for each voxel in the brain.…
Andrew S. Whiteman, Andreas J. Bartsch, Jian Kang, Timothy D. Johnson
'Timothy D. Johnson'] Abstract: Neuroradiologists and neurosurgeons increasingly opt to use functional magnetic resonance imaging (fMRI) to map functionally relevant brain regions for noninvasive presurgical planning and intraoperative neuronavigation. This application requires a high degree of spatial accuracy, but…
Daniel I. R. Spencer, Yu, Yue Yue, David Bolin + 2 more
'Amanda F. Mejia'] 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…
Daniel Spencer, Yu Ryan Yue, David Bolin, Sarah Ryan + 1 more
'Amanda F. Mejia'] 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…
Bertil Wegmann, Anders Eklund, Mattias Villani
We propose a regression model for non-central χ (NC-χ) distributed functional magnetic resonance imaging (fMRI) and diffusion weighted imaging (DWI) data, with the heteroscedastic Rician regression model as a prominent special case. The model allows both parameters in the NC-χ distribution to be linked to explanatory…
Michelle F. Miranda, Jeffrey S. Morris
In this paper, we introduce a new Bayesian approach for analyzing task fMRI data that simultaneously detects activation signatures and background connectivity. Our modeling involves a new hybrid tensor spatial-temporal basis strategy that enables scalable computing yet captures nearby and distant intervoxel correlation…
Gang Chen, Paul A. Taylor, Robert W. Cox, Luiz Pessoa
Neuroimaging faces the daunting challenge of multiple testing – an instance of multiplicity – that is associated with two other issues to some extent: low inference efficiency and poor reproducibility. Typically, the same statistical model is applied to each spatial unit independently in the approach of massively…
Jens Sjölund, Anders Eklund, Evren Özarslan, Magnus Herberthson + 2 more
'Maria Bånkestad' 'Hans Knutsson'] Diffusion MRI (dMRI) is a valuable tool in the assessment of tissue microstructure. By fitting a model to the dMRI signal it is possible to derive various quantitative features. Several of the most popular dMRI signal models are expansions in an appropriately chosen basis, where the…
Authors not listed
Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline and widespread neurovascular disturbances. Traditional fMRI provides valuable spatial maps of blood-oxygen-level-dependent (BOLD) changes but often lacks the capacity to quantify the interplay of cerebral blood flow…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? This type of solution degeneracy often exists in physics-based simulations and wet-lab experiments, but constraining these degeneracies is often unsupported or difficult to implement in many optimization packages, requiring additional time and…
Yifan Wu, Aron Walsh, Alex Ganose
What is the minimum number of experiments, or calculations, required to find an optimal solution? Relevant chemical problems range from identifying a compound with target functionality within a given phase space to controlling materials synthesis and device fabrication conditions. A common feature in this application…
Lucian Chan, Geoffrey Hutchison, Garrett Morris
Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generating geometrically diverse conformers rather than finding the most probable or energetically lowest minima. Here…
Lucian Chan, Geoffrey Hutchison, Garrett Morris
Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generating geometrically diverse conformers rather than finding the most probable or energetically lowest minima. Here…