Methods for cleaning the BOLD fMRI signal

Available online 9 December 2016 http://www.sciencedirect.com/science/article/pii/S1053811916307418?via%3Dihubhttp://www.sciencedirect.com/science/article/pii/S1053811916307418?via%3DihubBlood oxygen-level-dependent functional magnetic resonance imaging (BOLD fMRI) has rapidly become a popular technique for the investigation of brain function in healthy individuals, patients as well as in animal studies. However, the BOLD signal arises from a complex mixture of neuronal, metabolic and vascular processes, being therefore an indirect measure of neuronal activity, which is further severely corrupted by multiple non-neuronal fluctuations of instrumental, physiological or subject-specific origin. This review aims to provide a comprehensive summary of existing methods for cleaning the BOLD fMRI signal. The description is given from a methodological point of view, focusing on the operation of the different techniques in addition to pointing out the advantages and limitations in their application. Since motion-related and physiological noise fluctuations are two of the main noise components of the signal, techniques targeting their removal are primarily addressed, including both data-driven approaches and using external recordings. Data-driven approaches, which are less specific in the assumed model and can simultaneously reduce multiple noise fluctuations, are mainly based on data decomposition techniques such as principal and independent component analysis. Importantly, the usefulness of strategies that benefit from the information available in the phase component of the signal, or in multiple signal echoes is also highlighted. The use of global signal regression for denoising is also addressed. Finally, practical recommendations regarding the optimization of the preprocessing pipeline for the purpose of denoising and future venues of research are indicated. Through the review, we summarize the importance of signal denoising as an essential step in the analysis pipeline of task-based and resting state fMRI studies.This work was supported by the Spanish Ministry of Economy and Competitiveness [Grant PSI 2013–42343 Neuroimagen Multimodal], the Severo Ochoa Programme for Centres/Units of Excellence in R & D [SEV-2015-490], and the research and writing of the paper were supported by the NIMH and NINDS Intramural Research Programs (ZICMH002888) of the NIH/HHS

FMRI Clustering and False Positive Rates

Recently, Eklund et al. (2016) analyzed clustering methods in standard FMRI packages: AFNI (which we maintain), FSL, and SPM [1]. They claimed: 1) false positive rates (FPRs) in traditional approaches are greatly inflated, questioning the validity of "countless published fMRI studies"; 2) nonparametric methods produce valid, but slightly conservative, FPRs; 3) a common flawed assumption is that the spatial autocorrelation function (ACF) of FMRI noise is Gaussian-shaped; and 4) a 15-year-old bug in AFNI's 3dClustSim significantly contributed to producing "particularly high" FPRs compared to other software. We repeated simulations from [1] (Beijing-Zang data [2], see [3]), and comment on each point briefly.Comment: 3 pages, 1 figure. A Letter accepted in PNA

XMM-Newton Archival Study of the ULX Population in Nearby Galaxies

We present the results of an archival XMM-Newton study of the bright X-ray point sources (L_X > 10^38 erg/s) in 32 nearby galaxies. From our list of approximately 100 point sources, we attempt to determine if there is a low-state counterpart to the Ultraluminous X-ray (ULX) population, searching for a soft-hard state dichotomy similar to that known for Galactic X-ray binaries and testing the specific predictions of the IMBH hypothesis. To this end, we searched for "low-state" objects, which we defined as objects within our sample which had a spectrum well fit by a simple absorbed power law, and "high-state" objects, which we defined as objects better fit by a combined blackbody and a power law. Assuming that ``low-state'' objects accrete at approximately 10% of the Eddington luminosity (Done & Gierlinski 2003) and that "high-state" objects accrete near the Eddington luminosity we further divided our sample of sources into low and high state ULX sources. We classify 16 sources as low-state ULXs and 26 objects as high-state ULXs. As in Galactic black hole systems, the spectral indices, Gamma, of the low-state objects, as well as the luminosities, tend to be lower than those of the high-state objects. The observed range of blackbody temperatures for the high state is 0.1-1 keV, with the most luminous systems tending toward the lowest temperatures. We therefore divide our high-state ULXs into candidate IMBHs (with blackbody temperatures of approximately 0.1 keV) and candidate stellar mass BHs (with blackbody temperatures of approximately 1.0 keV). A subset of the candidate stellar mass BHs have spectra that are well-fit by a Comptonization model, a property similar of Galactic BHs radiating in the "very-high" state near the Eddington limit.Comment: 54 pages, submitted to ApJ (March 2005), accepted (May 2006); changes to organization of pape

X-ray properties of an Unbiased Hard X-ray Detected Sample of AGN

The SWIFT gamma ray observatory's Burst Alert Telescope (BAT) has detected a sample of active galactic nuclei (AGN) based solely on their hard X-ray flux (14-195 keV). In this paper, we present for the first time {\it XMM-Newton} X-ray spectra for 22 BAT AGNs with no previously analyzed X-ray spectra. If our sources are a representative sample of the BAT AGN, as we claim, our results present for the first time global X-ray properties of an unbiased towards absorption (n$_H = 0.03$), AGN sample. We find 9/22 low absorption (n$_H < 10^{23}$ cm$^{-2}$), simple power law model sources, where 4 of these sources have a statistically significant soft component. Among these sources, we find the presence of a warm absorber statistically significant for only one Seyfert 1 source, contrasting with the ASCA results of \citet{rey97} and \citet{geo98}, who find signatures of warm absorption in half or more of their Seyfert 1 samples at similar redshifts. Additionally, the remaining sources (14/22) have more complex spectra, well-fit by an absorbed power law at $E > 2.0$ keV. Five of the complex sources are classified as Compton-thick candidates. Further, we find four more sources with properties consistent with the hidden/buried AGN reported by Ueda {\it et al.} (2007). Finally, we include a comparison of the {\it XMM-Newton} EPIC spectra with available SWIFT X-ray Telescope (XRT) observations. From these comparisons, we find 6/16 sources with varying column densities, 6/16 sources with varying power law indices, and 13/16 sources with varying fluxes, over periods of hours to months. Flux and power law index are correlated for objects where both parameters vary.Comment: 39 pages, 16 figures, accepted to Ap

The hard X-ray perspective on the soft X-ray excess

The X-ray spectra of many active galactic nuclei (AGN) exhibit a `soft excess' below 1keV, whose physical origin remains unclear. Diverse models have been suggested to account for it, including ionised reflection of X-rays from the inner part of the accretion disc, ionised winds/absorbers, and Comptonisation. The ionised reflection model suggests a natural link between the prominence of the soft excess and the Compton reflection hump strength above 10keV, but it has not been clear what hard X-ray signatures, if any, are expected from the other soft X-ray candidate models. Additionally, it has not been possible up until recently to obtain high-quality simultaneous measurements of both soft and hard X-ray emission necessary to distinguish these models, but upcoming joint XMM-NuSTAR programmes provide precisely this opportunity. In this paper, we present an extensive analysis of simulations of XMM+NuSTAR observations, using two candidate soft excess models as inputs, to determine whether such campaigns can disambiguate between them by using hard and soft X-ray observations in tandem. The simulated spectra are fit with the simplest "observer's model" of a black body and neutral reflection to characterise the strength of the soft and hard excesses. A plot of the strength of the hard excess against the soft excess strength provides a diagnostic plot which allows the soft excess production mechanism to be determined in individual sources and samples using current state-of-the-art and next generation hard X-ray enabled observatories. This approach can be straightforwardly extended to other candidate models for the soft excess.Comment: 12 pages, 11 figures, accepted for publication in ApJ. Added reference

Correlated X-ray and Optical Variability in Mkn 509

We present results of a 3 year monitoring campaign of the Seyfert 1 galaxy Markarian 509, using X-ray data from the Rossi X-ray Timing Explorer (RXTE) and optical data taken by the SMARTS consortium. Both light curves show significant variations, and are strongly correlated with the optical flux leading the X-ray flux by 15 days. The X-ray power spectrum shows a steep high-frequency slope of -2.0, breaking to a slope of -1.0 at at timescale of 34 days. The lag from optical to X-ray emission is most likely caused by variations in the accretion disk propagating inward.Comment: 13 pages, 3 figures. Accepted for publication in the Astrophysical Journa

Distribution of major anions and trace elements in the unsaturated zone at Franklin Lake Playa, California, USA

The composition of surficial salts formed near dry and drying saline lakes are partly the product of processes active in the unsaturated zone between the ground surface and the water table. These processes were investigated by determining the abundance of water-extractable solutes in sediment from the ground surface to the water table (~2.8 m) beneath Franklin Lake playa, California. Accumulation of solutes in the sediment is attributed to evaporation of aqueous solutions transported upward from the water table through the capillary fringe to an evaporation font that is currently 20-30 cm below the ground surface. Salts in the sediment from 0 to 20 cm depth are depleted in chloride and enriched in carbonate relative to deeper samples. Chloride depletion is most likely a product of selective dissolution by vertical recharge. The entire unsaturated zone contains greater amounts of carbonate than expected for evaporation of ground water and is best explained by preferential dissolution of more soluble salts in recharging precipitation but may also reflect the assimilation of CO2 as carbonate minerals precipitate. Variations in the concentrations of arsenic, molybdenum, tungsten, and uranium in the water-soluble fraction of the sediment are complex and suggest unique geochemical controls on the abundance of each element. The distribution of these trace element abundances indicates the arsenic is the element most likely to accumulate in near-surface salts

The Nuclear Spectral Energy Distribution of NGC 4395, The Least Luminous Type 1 Seyfert Galaxy

We present X-ray (ROSAT), infrared, and radio observations of NGC 4395, which harbors the optically least luminous type 1 Seyfert nucleus discovered thus far. In combination with published optical and ultraviolet spectra, we have used these data to assemble the broadband spectral energy distribution (SED) of the galaxy's nucleus. Interestingly, the SED of NGC 4395 differs markedly from the SEDs of both quasars and typical low-luminosity active galactic nuclei, which may be a manifestation of the different physical conditions (i.e., black hole masses, accretion rates, and/or accretion modes) that exist in these objects. The nuclear X-ray source in NGC 4395 is variable and has an observed luminosity of just ~ 10^38 ergs/s. Although this emission could plausibly be associated with either a weak active nucleus or a bright stellar-mass binary system, the optical and ultraviolet emission-line properties of the nucleus strongly suggest that the X-rays arise from a classical AGN.Comment: Accepted for publication in PASP (July 1999), 17 pages, including 4 Postscript figure

Intrinsic Absorption Lines in Seyfert 1 Galaxies. I. Ultraviolet Spectra from the Hubble Space Telescope

We present a study of the intrinsic absorption lines in the ultraviolet spectra of Seyfert 1 galaxies. We find that the fraction of Seyfert 1 galaxies that show absorption associated with their active nuclei is more than one-half (10/17), which is much higher than previous estimates (3 - 10%) . There is a one-to-one correspondence between Seyferts that show intrinsic UV absorption and X-ray ``warm absorbers''. The intrinsic UV absorption is generally characterized by high ionization: C IV and N V are seen in all 10 Seyferts with detected absorption (in addition to Ly-alpha), whereas Si IV is present in only four of these Seyferts, and Mg II absorption is only detected in NGC 4151. The absorption lines are blueshifted (or in a few cases at rest) with respect to the narrow emission lines, indicating that the absorbing gas is undergoing net radial outflow. At high resolution, the absorption often splits into distinct kinematic components that show a wide range in widths (20 - 400 km/s FWHM), indicating macroscopic motions (e.g., radial velocity subcomponents or turbulence) within a component. The strong absorption components have cores that are much deeper than the continuum flux levels, indicating that the regions responsible for these components lie completely outside of the broad emission-line regions. The covering factor of the absorbing gas in the line of sight, relative to the total underlying emission, is C > 0.86, on average. The global covering factor, which is the fraction of emission intercepted by the absorber averaged over all lines of sight, is C > 0.5.Comment: 56 pages, Latex, includes 4 figures (encapsulated postscript), Fig. 1 has 2 parts and Fig. 2 has 3 parts, to appear in the Astrophysical Journa