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The analysis of Functional Connectivity (FC) is a key technique of fMRI, having been used to distinguish brain states and conditions. While many approaches to calculating FC are available, there have been few assessments of their differences, making it difficult to choose approaches, and compare results. Here, we assess the impact of methodological choices on discriminability, using a fully controlled data set of continuous active states involving basic visual and motor tasks, providing robust localized FC changes. We tested a range of anatomical and functional parcellations, including the AAL atlas, parcellations derived from the Human Connectome Project and Independent Component Analysis (ICA) of many dimensionalities. We measure amplitude, covariance, correlation, and regularized partial correlation under different temporal filtering choices. We evaluate features derived from these methods for discriminating states using MVPA. We find that multidimensional parcellations derived from functional data performed similarly, outperforming an anatomical atlas, with correlation and partial correlation (p < .05, FDR). Partial correlation, with appropriate regularization, outperformed correlation. Amplitude and covariance generally discriminated less well, although gave good results with high‐dimensionality ICA. We found that discriminative FC properties are frequency specific; higher frequencies performed surprisingly well under certain configurations of atlas choices and dependency measures, with ICA‐based parcellations revealing greater discriminability at high frequencies compared to other parcellations. Methodological choices in FC analyses can have a profound impact on results and can be selected to optimize accuracy, interpretability, and sharing of results. This work contributes to a basis for consistent selection of approaches to estimating and analyzing FC. [ABSTRACT FROM AUTHOR]

Purpose Blood oxygen level dependent (BOLD) brain activity, measured using functional MRI (fMRI), is dependent on the echo time (TE) and the reversible spin-spin relaxation time constant ( [ABSTRACT FROM AUTHOR]

A decade of research and development in resting-state functional MRI (RSfMRI) has opened new translational and clinical research frontiers. This review aims to bridge between technical and clinical researchers who seek reliable neuroimaging biomarkers for studying drug interactions with the brain. About 85 pharma-RSfMRI studies using BOLD signal (75% of all) or arterial spin labeling (ASL) were surveyed to investigate the acute effects of psychoactive drugs. Experimental designs and objectives include drug fingerprinting dose-response evaluation, biomarker validation and calibration, and translational studies. Common biomarkers in these studies include functional connectivity, graph metrics, cerebral blood flow and the amplitude and spectrum of BOLD fluctuations. Overall, RSfMRI-derived biomarkers seem to be sensitive to spatiotemporal dynamics of drug interactions with the brain. However, drugs cause both central and peripheral effects, thus exacerbate difficulties related to biological confounds, structured noise from motion and physiological confounds, as well as modeling and inference testing. Currently, these issues are not well explored, and heterogeneities in experimental design, data acquisition and preprocessing make comparative or meta-analysis of existing reports impossible. A unifying collaborative framework for data-sharing and data-mining is thus necessary for investigating the commonalities and differences in biomarker sensitivity and specificity, and establishing guidelines. Multimodal datasets including sham-placebo or active control sessions and repeated measurements of various psychometric, physiological, metabolic and neuroimaging phenotypes are essential for pharmacokinetic/pharmacodynamic modeling and interpretation of the findings. We provide a list of basic minimum and advanced options that can be considered in design and analyses of future pharma-RSfMRI studies. Hum Brain Mapp 38:2276-2325, 2017. © 2017 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

FMRI has revealed the presence of correlated low-frequency cerebro-vascular oscillations within functional brain systems, which are thought to reflect an intrinsic feature of large-scale neural activity. The spatial correlations shown by these fluctuations has been their identifying feature, distinguishing them from fluctuations associated with other processes. Major analysis methods characterize these correlations, identifying networks and their interactions with various factors. However, other analysis approaches are required to fully characterize the regional signal dynamics contributing to these correlations between regions. In this study we show that analysis of the power spectral density (PSD) of regional signals can identify changes in oscillatory dynamics across conditions, and is able to characterize the nature and spatial extent of signal changes underlying changes in measures of connectivity. We analyzed spectral density changes in sessions consisting of both resting-state scans and scans recording 2 min blocks of continuous unilateral finger tapping and rest. We assessed the relationship of PSD and connectivity measures by additionally tracking correlations between selected motor regions. Spectral density gradually increased in gray and white matter during the experiment. Finger tapping produced widespread decreases in low-frequency spectral density. This change was symmetric across the cortex, and extended beyond both the lateralized task-related signal increases, and the established 'resting-state' motor network. Correlations between motor regions also reduced with task performance. In conclusion, analysis of PSD is a sensitive method for detecting and characterizing BOLD signal oscillations that can enhance the analysis of network connectivity. Hum Brain Mapp 2008. © 2008 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]