scholarly journals Anatomically informed bayesian spatial priors for fmri analysis

2019 ◽  
Author(s):  
David Abramian ◽  
Per Sidén ◽  
Hans Knutsson ◽  
Mattias Villani ◽  
Anders Eklund
Keyword(s):  
Posterior Probability ◽  
Spatial Models ◽  
Anatomical Structure ◽  
Fmri Data ◽  
Local Smoothing ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
Anatomical Image ◽  
Fmri Analysis ◽  
Bayesian Spatial Models

ABSTRACTExisting Bayesian spatial priors for functional magnetic resonance imaging (fMRI) data correspond to stationary isotropic smoothing filters that may oversmooth at anatomical boundaries. We propose two anatomically informed Bayesian spatial models for fMRI data with local smoothing in each voxel based on a tensor field estimated from a T1-weighted anatomical image. We show that our anatomically informed Bayesian spatial models results in posterior probability maps that follow the anatomical structure.

scholarly journals Informative Biomarkers for Autism Spectrum Disorder Diagnosis in Functional Magnetic Resonance Imaging Data on the Default Mode Network

2021 ◽  
Vol 11 (13) ◽  
pp. 6216
Author(s):  
Aikaterini S. Karampasi ◽  
Antonis D. Savva ◽  
Vasileios Ch. Korfiatis ◽  
Ioannis Kakkos ◽  
George K. Matsopoulos
Keyword(s):  
Magnetic Resonance Imaging ◽  
Autism Spectrum Disorder ◽  
Magnetic Resonance ◽  
Functional Magnetic Resonance Imaging ◽  
Default Mode Network ◽  
Autism Spectrum ◽  
Fmri Data ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
Dynamic Connectivity

Effective detection of autism spectrum disorder (ASD) is a complicated procedure, due to the hundreds of parameters suggested to be implicated in its etiology. As such, machine learning methods have been consistently applied to facilitate diagnosis, although the scarcity of potent autism-related biomarkers is a bottleneck. More importantly, the variability of the imported attributes among different sites (e.g., acquisition parameters) and different individuals (e.g., demographics, movement, etc.) pose additional challenges, eluding adequate generalization and universal modeling. The present study focuses on a data-driven approach for the identification of efficacious biomarkers for the classification between typically developed (TD) and ASD individuals utilizing functional magnetic resonance imaging (fMRI) data on the default mode network (DMN) and non-physiological parameters. From the fMRI data, static and dynamic connectivity were calculated and fed to a feature selection and classification framework along with the demographic, acquisition and motion information to obtain the most prominent features in regard to autism discrimination. The acquired results provided high classification accuracy of 76.63%, while revealing static and dynamic connectivity as the most prominent indicators. Subsequent analysis illustrated the bilateral parahippocampal gyrus, right precuneus, midline frontal, and paracingulate as the most significant brain regions, in addition to an overall connectivity increment.

Statistical Analysis of Functional Magnetic Resonance Imaging Data

2017 ◽  
pp. 103-114
Author(s):  
Nicole A. Lazar
Keyword(s):  
Magnetic Resonance Imaging ◽  
Data Analysis ◽  
Statistical Analysis ◽  
Magnetic Resonance ◽  
Functional Magnetic Resonance Imaging ◽  
Temporal Correlation ◽  
Fmri Data ◽  
Imaging Data ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging

The analysis of functional magnetic resonance imaging (fMRI) data poses many statistical challenges. The data are massive, noisy, and have a complicated spatial and temporal correlation structure. This chapter introduces the basics of fMRI data collection and surveys common approaches for data analysis.

Language Functional Magnetic Resonance Imaging in Preoperative Assessment of Language Areas: Correlation with Direct Cortical Stimulation

Neurosurgery ◽  
2003 ◽  
Vol 52 (6) ◽  
pp. 1335-1347 ◽  
Author(s):  
Franck-Emmanuel Roux ◽  
Kader Boulanouar ◽  
Jean-Albert Lotterie ◽  
Mehdi Mejdoubi ◽  
James P. LeSage ◽  
...  
Keyword(s):  
Magnetic Resonance Imaging ◽  
Magnetic Resonance ◽  
Functional Magnetic Resonance Imaging ◽  
Left Hemisphere ◽  
Brain Mapping ◽  
Fmri Data ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
Verb Generation ◽  
Language Areas

Abstract OBJECTIVE The aim of this study was to analyze the usefulness of preoperative language functional magnetic resonance imaging (fMRI), by correlating fMRI data with intraoperative cortical stimulation results for patients with brain tumors. METHODS Naming and verb generation tasks were used, separately or in combination, for 14 right-handed patients with tumors in the left hemisphere. fMRI data obtained were analyzed with SPM software, with two standard analysis thresholds (P < 0.005 and then P < 0.05). The fMRI data were then registered in a frameless stereotactic neuronavigational device and correlated with direct brain mapping results. We used a statistical model with the fMRI information as a predictor, spatially correlating each intraoperatively mapped cortical site with fMRI data integrated in the neuronavigational system (site-by-site correlation). Eight patients were also studied with language fMRI postoperatively, with the same acquisition protocol. RESULTS We observed high variability in signal extents and locations among patients with both tasks. The activated areas were located mainly in the left hemisphere in the middle and inferior frontal gyri (F2 and F3), the superior and middle temporal gyri (T1 and T2), and the supramarginal and angular gyri. A total of 426 cortical sites were tested for each task among the 14 patients. In frontal and temporoparietal areas, poor sensitivity of the fMRI technique was observed for the naming and verb generation tasks (22 and 36%, respectively) with P < 0.005 as the analysis threshold. Although not perfect, the specificity of the fMRI technique was good in all conditions (97% for the naming task and 98% for the verb generation task). Better correlation (sensitivity, 59%; specificity, 97%) was achieved by combining the two fMRI tasks. Variation of the analysis threshold to P < 0.05 increased the sensitivity to 66% while decreasing the specificity to 91%. Postoperative fMRI data (for the cortical brain areas studied intraoperatively) were in accordance with brain mapping results for six of eight patients. Complete agreement between pre- and postoperative fMRI studies and direct brain mapping results was observed for only three of eight patients. CONCLUSION With the paradigms and analysis thresholds used in this study, language fMRI data obtained with naming or verb generation tasks, before and after surgery, were imperfectly correlated with intraoperative brain mapping results. A better correlation could be obtained by combining the fMRI tasks. The overall results of this study demonstrated that language fMRI could not be used to make critical surgical decisions in the absence of direct brain mapping. Other acquisition protocols are required for evaluation of the potential role of language fMRI in the accurate detection of essential cortical language areas.

Methods of Predicting the Brain Activity Based on Noun

2013 ◽  
Vol 347-350 ◽  
pp. 2516-2520
Author(s):  
Jian Hua Jiang ◽  
Xu Yu ◽  
Zhi Xing Huang
Keyword(s):  
Brain Activity ◽  
Past Research ◽  
Neural Representation ◽  
Fmri Data ◽  
Semantic Features ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
The Past ◽  
Machine Learning Methods ◽  
The Brain

Over the last decade, functional magnetic resonance imaging (fMRI) has become a primary tool to predict the brain activity.During the past research, researchers transfer the focus from the picture to the word.The results of these researches are relatively successful. In this paper, several typical methods which are machine learning methods are introduced. And most of the methods are by using fMRI data associated with words features. The semantic features (properties or factors) support words neural representation, and have a certain commonality in the people.The purpose of the application of these methods is used for prediction or classification.

scholarly journals The context-dependent nature of the neural implementation of intentions

2018 ◽  
Author(s):  
Sebo Uithol ◽  
Kai Görgen ◽  
Doris Pischedda ◽  
Ivan Toni ◽  
John-Dylan Haynes
Keyword(s):  
Essential Feature ◽  
Intentional Action ◽  
Context Dependency ◽  
Voluntary Action ◽  
Fmri Data ◽  
Experimental Setup ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
Neural Representations ◽  
Neural Processes

AbstractMany studies have identified networks in parietal and prefrontal cortex that are involved in intentional action. Yet, knowledge about what these networks exactly encoded is still scarce. In this study we look into the content of those processes. We ask whether the neural representations of intentions are context- and reason-invariant, or whether these processes depend on the context we are in, and the reasons we have for choosing an action. We use a combination of functional magnetic resonance imaging and multivariate decoding to directly assess the context- and reason-dependency of the processes underlying intentional action. We were able to decode action decisions in the same context and for the same reasons from the fMRI data, in line with previous decoding studies. Furthermore, we could decode action decisions across different reasons for choosing an action. Importantly, though, decoding decisions across different contexts was at chance level. These results suggest that for voluntary action, there is considerable context-dependency in intention representations. This suggests that established invariance in neural processes may not reflect an essential feature of a certain process, but that this stable character could be dependent on invariance in the experimental setup, in line with predictions from situated cognition theory.

scholarly journals A Hilbert-based method for processing respiratory timeseries

2020 ◽  
Author(s):  
Samuel J. Harrison ◽  
Samuel Bianchi ◽  
Jakob Heinzle ◽  
Klaas Enno Stephan ◽  
Sandra Iglesias ◽  
...  
Keyword(s):  
Magnetic Resonance Imaging ◽  
Magnetic Resonance ◽  
Time Resolution ◽  
Technical Note ◽  
Fmri Data ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
Physiological Noise ◽  
Noise Correction ◽  
The Hilbert Transform

In this technical note, we introduce a new method for estimating changes in respiratory volume per unit time (RVT) from respiratory bellows recordings. By using techniques from the electrophysiological literature, in particular the Hilbert transform, we show how we can better characterise breathing rhythms, with the goal of improving physiological noise correction in functional magnetic resonance imaging (fMRI). Specifically, our approach leads to a representation with higher time resolution and better captures atypical breathing events than current peak-based RVT estimators. Finally, we demonstrate that this leads to an increase in the amount of respiration-related variance removed from fMRI data when used as part of a typical preprocessing pipeline. Our implementation will be publicly available as part of the PhysIO package, which is distributed as part of the open-source TAPAS toolbox (https://translationalneuromodeling.org/tapas).

scholarly journals Understanding multivariate brain activity: evaluating the effect of voxelwise noise correlations on population codes in functional magnetic resonance imaging

2019 ◽  
Author(s):  
Ru-Yuan Zhang ◽  
Xue-Xin Wei ◽  
Kendrick Kay
Keyword(s):  
Magnetic Resonance Imaging ◽  
Magnetic Resonance ◽  
Functional Magnetic Resonance Imaging ◽  
Brain Activity ◽  
Neuronal Population ◽  
Fmri Data ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
Correlated Activity ◽  
Population Codes

ABSTRACTPrevious studies have shown that neurons exhibit trial-by-trial correlated activity and that such noise correlations (NCs) greatly impact the accuracy of population codes. Meanwhile, multivariate pattern analysis (MVPA) has become a mainstream approach in functional magnetic resonance imaging (fMRI), but it remains unclear how NCs between voxels influence MVPA performance. Here, we tackle this issue by combining voxel-encoding modeling and MVPA. We focus on a well-established form of NC, tuning-compatible noise correlation (TCNC), whose sign and magnitude are systematically related to the tuning similarity between two units. We first replicate the classical finding that TCNCs impair population codes in a standard neuronal population. We then extend our analysis to fMRI data, and show that voxelwise TCNCs do not impair and can even improve MVPA performance when TCNCs are strong or the number of voxels is large. We also confirm these results using standard information-theoretic analyses in computational neuroscience. Further computational analyses demonstrate that the discrepancy between the effect of TCNCs in neuronal and voxel populations can be explained by tuning heterogeneity and pool sizes. Our results provide a theoretical foundation to understand the effect of correlated activity on population codes in macroscopic fMRI data. Our results also suggest that future fMRI research could benefit from a closer examination of the correlational structure of multivariate responses, which is not directly revealed by conventional MVPA approaches.

scholarly journals Estimates of locus coeruleus function with functional magnetic resonance imaging are influenced by localization approaches and the use of multi-echo data

2019 ◽  
Author(s):  
Hamid B. Turker ◽  
Elizabeth Riley ◽  
Wen-Ming Luh ◽  
Stan J. Colcombe ◽  
Khena M. Swallow
Keyword(s):  
Magnetic Resonance Imaging ◽  
Time Series ◽  
Magnetic Resonance ◽  
Functional Magnetic Resonance Imaging ◽  
Locus Coeruleus ◽  
Signal To Noise Ratio ◽  
Fmri Data ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
Signal To Noise

AbstractThe locus coeruleus (LC) plays a central role in regulating human cognition, arousal, and autonomic states. Efforts to characterize the LC’s function in humans using functional magnetic resonance imaging have been hampered by its small size and location near a large source of noise, the fourth ventricle. We tested whether the ability to characterize LC function is improved by employing neuromelanin-T1 weighted images (nmT1) for LC localization and multi-echo functional magnetic resonance imaging (ME-fMRI) for estimating intrinsic functional connectivity (iFC). Analyses indicated that, relative to a probabilistic atlas, utilizing nmT1 images to individually localize the LC increases the specificity of seed time series and clusters in the iFC maps. When combined with independent components analysis (ME-ICA), ME-fMRI data provided significant gains in the temporal signal to noise ratio relative to denoised single-echo (1E) data. The effects of acquiring nmT1 images and ME-fMRI data did not appear to only reflect increases in power: iFC maps for each approach only moderately overlapped. This is consistent with findings that ME-fMRI offers substantial advantages over 1E data acquisition and denoising. It also suggests that individually identifying LC with nmT1 scans is likely to reduce the influence of other nearby brainstem regions on estimates of LC function.HighlightsManual tracing of locus coeruleus increased specificity of seed time seriesManual tracing of locus coeruleus increased specificity of intrinsic connectivityMulti-echo fMRI increased temporal signal-to-noise ratio compared to single-echo fMRIConnectivity maps across methodologies overlapped only moderatelyMeasurement of LC function benefits from multi-echo fMRI and tracing ROIs

scholarly journals Bayesian MEG time courses with fMRI priors

2021 ◽  
Author(s):  
Yingying Wang ◽  
Scott K. Holland
Keyword(s):  
Spatial Resolution ◽  
Brain Activity ◽  
Fmri Data ◽  
Source Reconstruction ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
Good Spatial Resolution ◽  
Excellent Spatial Resolution ◽  
Inverse Solutions ◽  
Time Courses

Magnetoencephalography (MEG) records brain activity with excellent temporal and good spatial resolution, while functional magnetic resonance imaging (fMRI) offers good temporal and excellent spatial resolution. The aim of this study is to implement a Bayesian framework to use fMRI data as spatial priors for MEG inverse solutions. We used simulated MEG data with both evoked and induced activity and experimental MEG data from sixteen participants to examine the effectiveness of using fMRI spatial priors in MEG source reconstruction. Our results provide empirical evidence that the use of fMRI spatial priors improves the accuracy of MEG source reconstruction.

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