Optimizing Stimulation and Analysis Protocols for Neonatal fMRI

The development of brain function in young infants is poorly understood. The core challenge is that infants have a limited behavioral repertoire through which brain function can be expressed. Neuroimaging with fMRI has great potential as a way of characterizing typical development, and detecting abnormal development early. But, a number of methodological challenges must first be tackled to improve the robustness and sensitivity of neonatal fMRI. A critical one of these, addressed here, is that the hemodynamic response function (HRF) in pre-term and term neonates differs from that in adults, which has a number of implications for fMRI. We created a realistic model of noise in fMRI data, using resting-state fMRI data from infants and adults, and then conducted simulations to assess the effect of HRF of the power of different stimulation protocols and analysis assumptions (HRF modeling). We found that neonatal fMRI is most powerful if block-durations are kept at the lower range of those typically used in adults (full on/off cycle duration 25-30s). Furthermore, we show that it is important to use the age-appropriate HRF during analysis, as mismatches can lead to reduced power or even inverted signal. Where the appropriate HRF is not known (for example due to potential developmental delay), a flexible basis set performs well, and allows accurate post-hoc estimation of the HRF.     

Is Granger Causality a Viable Technique for Analyzing fMRI Data?

Multivariate neural data provide the basis for assessing interactions in brain networks. Among myriad connectivity measures, Granger causality (GC) has proven to be statistically intuitive, easy to implement, and generate meaningful results. Although its application to functional MRI (fMRI) data is increasing, several factors have been identified that appear to hinder its neural interpretability: (a) latency differences in hemodynamic response function (HRF) across different brain regions, (b) low-sampling rates, and (c) noise. Recognizing that in basic and clinical neuroscience, it is often the change of a dependent variable (e.g., GC) between experimental conditions and between normal and pathology that is of interest, we address the question of whether there exist systematic relationships between GC at the fMRI level and that at the neural level. Simulated neural signals were convolved with a canonical HRF, down-sampled, and noise-added to generate simulated fMRI data. As the coupling parameters in the model were varied, fMRI GC and neural GC were calculated, and their relationship examined. Three main results were found: (1) GC following HRF convolution is a monotonically increasing function of neural GC; (2) this monotonicity can be reliably detected as a positive correlation when realistic fMRI temporal resolution and noise level were used; and (3) although the detectability of monotonicity declined due to the presence of HRF latency differences, substantial recovery of detectability occurred after correcting for latency differences. These results suggest that Granger causality is a viable technique for analyzing fMRI data when the questions are appropriately formulated.     

Exploiting the potential of three dimensional spatial wavelet analysis to explore nesting of temporal oscillations and spatial variance in simultaneous EEG-fMRI data

Synchronization of the activity in neural networks is a fundamental mechanism of brain function, putatively serving the integration of computations on multiple spatial and temporal scales. Time scales are thought to be nested within distinct spatial scales, so that whereas fast oscillations may integrate local networks, slow oscillations might integrate computations across distributed brain areas. We here describe a newly developed approach that provides potential for the further substantiation of this hypothesis in future studies. We demonstrate the feasibility and important caveats of a novel wavelet-based means of relating time series of three-dimensional spatial variance (energy) of fMRI data to time series of temporal variance of EEG. The spatial variance of fMRI data was determined by employing the three-dimensional dual-tree complex wavelet transform. The temporal variance of EEG data was estimated by using traditional continuous complex wavelets. We tested our algorithm on artificial signals with known signal-to-noise ratios and on empirical resting state EEG-fMRI data obtained from four healthy human subjects. By employing the human posterior alpha rhythm as an exemplar, we demonstrated face validity of the approach. We believe that the proposed method can serve as a suitable tool for future research on the spatiotemporal properties of brain dynamics, hence moving beyond analyses based exclusively in one domain or the other.     

Identification of the self-interaction of rat TCTP/IgE-dependent histamine-releasing factor using yeast two-hybrid system

To further understand the biological function of translationally controlled tumor protein (TCTP), also known as IgE-dependent histamine-releasing factor (HRF), the yeast two-hybrid system was used to screen interacting molecules. We isolated cDNA clones coding for TCTP/HRF, suggesting that it may have a self-interacting property. Domain mapping of the interaction revealed that the C-terminal region of residue 126-172 is involved in self-interaction. The self-interacting property of TCTP/HRF was further supported by FPLC gel-filtration chromatography and coimmunoprecipitation analysis from transfected COS-7 cells. Our data suggests that TCTP/HRF may have a potential to self-interact through the C-terminal region, and the self-interaction property may be related to its biological function.     

Model Specification and the Reliability of fMRI Results: Implications for Longitudinal Neuroimaging Studies in Psychiatry

Functional Magnetic Resonance Imagine (fMRI) is an important assessment tool in longitudinal studies of mental illness and its treatment. Understanding the psychometric properties of fMRI-based metrics, and the factors that influence them, will be critical for properly interpreting the results of these efforts. The current study examined whether the choice among alternative model specifications affects estimates of test-retest reliability in key emotion processing regions across a 6-month interval. Subjects (N = 46) performed an emotional-faces paradigm during fMRI in which neutral faces dynamically morphed into one of four emotional faces. Median voxelwise intraclass correlation coefficients (mvICCs) were calculated to examine stability over time in regions showing task-related activity as well as in bilateral amygdala. Four modeling choices were evaluated: a default model that used the canonical hemodynamic response function (HRF), a flexible HRF model that included additional basis functions, a modified CompCor (mCompCor) model that added corrections for physiological noise in the global signal, and a final model that combined the flexible HRF and mCompCor models. Model residuals were examined to determine the degree to which each pipeline met modeling assumptions. Results indicated that the choice of modeling approaches impacts both the degree to which model assumptions are met and estimates of test-retest reliability. ICC estimates in the visual cortex increased from poor (mvICC = 0.31) in the default pipeline to fair (mvICC = 0.45) in the full alternative pipeline – an increase of 45%. In nearly all tests, the models with the fewest assumption violations generated the highest ICC estimates. Implications for longitudinal treatment studies that utilize fMRI are discussed.     

Accounting for movement increases sensitivity in detecting brain activity in Parkinson's disease

Parkinson's disease (PD) is manifested by motor impairment, which may impede the ability to accurately perform motor tasks during functional magnetic resonance imaging (fMRI). Both temporal and amplitude deviations of movement performance affect the blood oxygenation level-dependent (BOLD) response. We present a general approach for assessing PD patients' movement control employing simultaneously recorded fMRI time series and behavioral data of the patients' kinematics using MR-compatible gloves. Twelve male patients with advanced PD were examined with fMRI at 1.5T during epoch-based visually paced finger tapping. MR-compatible gloves were utilized online to quantify motor outcome in two conditions with or without dopaminergic medication. Modeling of individual-level brain activity included (i) a predictor consisting of a condition-specific, constant-amplitude boxcar function convolved with the canonical hemodynamic response function (HRF) as commonly used in fMRI statistics (standard model), or (ii) a custom-made predictor computed from glove time series convolved with the HRF (kinematic model). Factorial statistics yielded a parametric map for each modeling technique, showing the medication effect on the group level. Patients showed bilateral response to levodopa in putamen and globus pallidus during the motor experiment. Interestingly, kinematic modeling produced significantly higher activation in terms of both the extent and amplitude of activity. Our results appear to account for movement performance in fMRI motor experiments with PD and increase sensitivity in detecting brain response to levodopa. We strongly advocate quantitatively controlling for motor performance to reach more reliable and robust analyses in fMRI with PD patients.     

An empirical comparison of information-theoretic criteria in estimating the number of independent components of fMRI data

Background

Independent Component Analysis (ICA) has been widely applied to the analysis of fMRI data. Accurate estimation of the number of independent components of fMRI data is critical to reduce over/under fitting. Although various methods based on Information Theoretic Criteria (ITC) have been used to estimate the intrinsic dimension of fMRI data, the relative performance of different ITC in the context of the ICA model hasn''t been fully investigated, especially considering the properties of fMRI data. The present study explores and evaluates the performance of various ITC for the fMRI data with varied white noise levels, colored noise levels, temporal data sizes and spatial smoothness degrees.

Methodology

Both simulated data and real fMRI data with varied Gaussian white noise levels, first-order auto-regressive (AR(1)) noise levels, temporal data sizes and spatial smoothness degrees were carried out to deeply explore and evaluate the performance of different traditional ITC.

Principal Findings

Results indicate that the performance of ITCs depends on the noise level, temporal data size and spatial smoothness of fMRI data. 1) High white noise levels may lead to underestimation of all criteria and MDL/BIC has the severest underestimation at the higher Gaussian white noise level. 2) Colored noise may result in overestimation that can be intensified by the increase of AR(1) coefficient rather than the SD of AR(1) noise and MDL/BIC shows the least overestimation. 3) Larger temporal data size will be better for estimation for the model of white noise but tends to cause severer overestimation for the model of AR(1) noise. 4) Spatial smoothing will result in overestimation in both noise models.

Conclusions

1) None of ITC is perfect for all fMRI data due to its complicated noise structure. 2) If there is only white noise in data, AIC is preferred when the noise level is high and otherwise, Laplace approximation is a better choice. 3) When colored noise exists in data, MDL/BIC outperforms the other criteria.     

The NIRS Analysis Package: noise reduction and statistical inference

Near infrared spectroscopy (NIRS) is a non-invasive optical imaging technique that can be used to measure cortical hemodynamic responses to specific stimuli or tasks. While analyses of NIRS data are normally adapted from established fMRI techniques, there are nevertheless substantial differences between the two modalities. Here, we investigate the impact of NIRS-specific noise; e.g., systemic (physiological), motion-related artifacts, and serial autocorrelations, upon the validity of statistical inference within the framework of the general linear model. We present a comprehensive framework for noise reduction and statistical inference, which is custom-tailored to the noise characteristics of NIRS. These methods have been implemented in a public domain Matlab toolbox, the NIRS Analysis Package (NAP). Finally, we validate NAP using both simulated and actual data, showing marked improvement in the detection power and reliability of NIRS.     

On the Definition of Signal-To-Noise Ratio and Contrast-To-Noise Ratio for fMRI Data

Signal-to-noise ratio, the ratio between signal and noise, is a quantity that has been well established for MRI data but is still subject of ongoing debate and confusion when it comes to fMRI data. fMRI data are characterised by small activation fluctuations in a background of noise. Depending on how the signal of interest and the noise are identified, signal-to-noise ratio for fMRI data is reported by using many different definitions. Since each definition comes with a different scale, interpreting and comparing signal-to-noise ratio values for fMRI data can be a very challenging job. In this paper, we provide an overview of existing definitions. Further, the relationship with activation detection power is investigated. Reference tables and conversion formulae are provided to facilitate comparability between fMRI studies.     

Double‐wavelet transform for multisubject task‐induced functional magnetic resonance imaging data

The goal of this article is to model multisubject task‐induced functional magnetic resonance imaging (fMRI) response among predefined regions of interest (ROIs) of the human brain. Conventional approaches to fMRI analysis only take into account temporal correlations, but do not rigorously model the underlying spatial correlation due to the complexity of estimating and inverting the high dimensional spatio‐temporal covariance matrix. Other spatio‐temporal model approaches estimate the covariance matrix with the assumption of stationary time series, which is not always feasible. To address these limitations, we propose a double‐wavelet approach for modeling the spatio‐temporal brain process. Working with wavelet coefficients simplifies temporal and spatial covariance structure because under regularity conditions, wavelet coefficients are approximately uncorrelated. Different wavelet functions were used to capture different correlation structures in the spatio‐temporal model. The main advantages of the wavelet approach are that it is scalable and that it deals with nonstationarity in brain signals. Simulation studies showed that our method could reduce false‐positive and false‐negative rates by taking into account spatial and temporal correlations simultaneously. We also applied our method to fMRI data to study activation in prespecified ROIs in the prefontal cortex. Data analysis showed that the result using the double‐wavelet approach was more consistent than the conventional approach when sample size decreased.     

transition priors for protein hidden Markov models: an empirical study towards maximum discrimination.

Insertions and deletions in a profile hidden Markov model (HMM) are modeled by transition probabilities between insert, delete and match states. These are estimated by combining observed data and prior probabilities. The transition prior probabilities can be defined either ad hoc or by maximum likelihood (ML) estimation. We show that the choice of transition prior greatly affects the HMM's ability to discriminate between true and false hits. HMM discrimination was measured using the HMMER 2.2 package applied to 373 families from Pfam. We measured the discrimination between true members and noise sequences employing various ML transition priors and also systematically scanned the parameter space of ad hoc transition priors. Our results indicate that ML priors produce far from optimal discrimination, and we present an empirically derived prior that considerably decreases the number of misclassifications compared to ML. Most of the difference stems from the probabilities for exiting a delete state. The ML prior, which is unaware of noise sequences, estimates a delete-to-delete probability that is relatively high and does not penalize noise sequences enough for optimal discrimination.     

Studies of IgE-dependent histamine releasing factors: heterogeneity of IgE

Nasal lavage fluids from unstimulated individuals contain a histamine-releasing factor (HRF) similar to those which we have previously described from macrophages, platelets, and from blister fluids obtained during the late cutaneous reaction. The nasal HRF was partially purified by ion-exchange chromatography and gel filtration. Although some m.w. heterogeneity was observed, the majority of the HRF eluted at an apparent m.w. range of 15,000 to 30,000. This partially purified HRF induced histamine release from basophils of certain individuals. Histamine release occurred via a mechanism which is IgE-dependent in that: basophils desensitized by exposure to anti-IgE in the absence of calcium no longer respond to HRF, and desensitization with HRF reduces responsiveness to anti-IgE; and removal of IgE from the basophil surface by using lactic acid renders cells unresponsive to HRF. We have further defined this IgE dependence and have shown that the reason that only selected basophil donors respond to HRF is due to a previously unrecognized, functional heterogeneity of IgE. Thus, passive sensitization using sera from responders restored the responsiveness of acid-stripped basophils and conferred responsiveness to basophils of a nonresponder with naturally unoccupied IgE receptors. Sera from nonresponders failed to do this even though similar numbers of IgE molecules were put onto the basophil surface in each case. This property of responder sera was due to IgE because both heating sera at 56 degrees C for 2 hr and passage of sera over anti-IgE-Sepharose (which removes greater than 90% of the IgE) markedly reduced the ability of sera to induce responsiveness, and because an excess of either purified IgE myeloma or purified penicillin-specific IgE antibody from a nonresponder competitively inhibited the ability of IgE from responder sera to induce responsiveness to HRF. We conclude that nasal lavage fluids contain an HRF which induces basophil histamine release in a specific, IgE-dependent fashion but only from individuals with the appropriate type of IgE. Because we have shown that basophils are recruited into the nose during the late-phase reaction, we suggest that nasal HRF may induce these cells to release histamine and other mediators which could contribute to the symptomatology of the late-phase reaction.     

Quantitative Mapping of Protein Structure by Hydroxyl Radical Footprinting-Mediated Structural Mass Spectrometry: A Protection Factor?Analysis

Measurements from hydroxyl radical footprinting (HRF) provide rich information about the solvent accessibility of amino acid side chains of a protein. Traditional HRF data analyses focus on comparing the difference in the modification/footprinting rate of a specific site to infer structural changes across two protein states, e.g., between a free and ligand-bound state. However, the rate information itself is not fully used for the purpose of comparing different protein sites within a protein on an absolute scale. To provide such a cross-site comparison, we present a new, to our knowledge, data analysis algorithm to convert the measured footprinting rate constant to a protection factor (PF) by taking into account the known intrinsic reactivity of amino acid side chain. To examine the extent to which PFs can be used for structural interpretation, this PF analysis is applied to three model systems where radiolytic footprinting data are reported in the literature. By visualizing structures colored with the PF values for individual peptides, a rational view of the structural features of various protein sites regarding their solvent accessibility is revealed, where high-PF regions are buried and low-PF regions are more exposed to the solvent. Furthermore, a detailed analysis correlating solvent accessibility and local structural contacts for gelsolin shows a statistically significant agreement between PF values and various structure measures, demonstrating that the PFs derived from this PF analysis readily explain fundamental HRF rate measurements. We also tested this PF analysis on alternative, chemical-based HRF data, showing improved correlations of structural properties of a model protein barstar compared to examining HRF rate data alone. Together, this PF analysis not only permits a novel, to our knowledge, approach of mapping protein structures by using footprinting data, but also elevates the use of HRF measurements from a qualitative, cross-state comparison to a quantitative, cross-site assessment of protein structures in the context of individual conformational states of interest.     

A Review of fMRI Simulation Studies

Simulation studies that validate statistical techniques for fMRI data are challenging due to the complexity of the data. Therefore, it is not surprising that no common data generating process is available (i.e. several models can be found to model BOLD activation and noise). Based on a literature search, a database of simulation studies was compiled. The information in this database was analysed and critically evaluated focusing on the parameters in the simulation design, the adopted model to generate fMRI data, and on how the simulation studies are reported. Our literature analysis demonstrates that many fMRI simulation studies do not report a thorough experimental design and almost consistently ignore crucial knowledge on how fMRI data are acquired. Advice is provided on how the quality of fMRI simulation studies can be improved.     

Energy-Based Wavelet De-Noising of Hydrologic Time Series

De-noising is a substantial issue in hydrologic time series analysis, but it is a difficult task due to the defect of methods. In this paper an energy-based wavelet de-noising method was proposed. It is to remove noise by comparing energy distribution of series with the background energy distribution, which is established from Monte-Carlo test. Differing from wavelet threshold de-noising (WTD) method with the basis of wavelet coefficient thresholding, the proposed method is based on energy distribution of series. It can distinguish noise from deterministic components in series, and uncertainty of de-noising result can be quantitatively estimated using proper confidence interval, but WTD method cannot do this. Analysis of both synthetic and observed series verified the comparable power of the proposed method and WTD, but de-noising process by the former is more easily operable. The results also indicate the influences of three key factors (wavelet choice, decomposition level choice and noise content) on wavelet de-noising. Wavelet should be carefully chosen when using the proposed method. The suitable decomposition level for wavelet de-noising should correspond to series'' deterministic sub-signal which has the smallest temporal scale. If too much noise is included in a series, accurate de-noising result cannot be obtained by the proposed method or WTD, but the series would show pure random but not autocorrelation characters, so de-noising is no longer needed.     

Akaike causality in state space

We present a new approach of explaining instantaneous causality in multivariate fMRI time series by a state space model. A given single time series can be divided into two noise-driven processes, a common process shared among multivariate time series and a specific process refining the common process. By assuming that noises are independent, a causality map is drawn using Akaike noise contribution ratio theory. The method is illustrated by an application to fMRI data recorded under visual stimulation.     

Modelling Temporal Stability of EPI Time Series Using Magnitude Images Acquired with Multi-Channel Receiver Coils

In 2001, Krueger and Glover introduced a model describing the temporal SNR (tSNR) of an EPI time series as a function of image SNR (SNR₀). This model has been used to study physiological noise in fMRI, to optimize fMRI acquisition parameters, and to estimate maximum attainable tSNR for a given set of MR image acquisition and processing parameters. In its current form, this noise model requires the accurate estimation of image SNR. For multi-channel receiver coils, this is not straightforward because it requires export and reconstruction of large amounts of k-space raw data and detailed, custom-made image reconstruction methods. Here we present a simple extension to the model that allows characterization of the temporal noise properties of EPI time series acquired with multi-channel receiver coils, and reconstructed with standard root-sum-of-squares combination, without the need for raw data or custom-made image reconstruction. The proposed extended model includes an additional parameter κ which reflects the impact of noise correlations between receiver channels on the data and scales an apparent image SNR (SNR′₀) measured directly from root-sum-of-squares reconstructed magnitude images so that κ = SNR′₀/SNR₀ (under the condition of SNR₀>50 and number of channels ≤32). Using Monte Carlo simulations we show that the extended model parameters can be estimated with high accuracy. The estimation of the parameter κ was validated using an independent measure of the actual SNR₀ for non-accelerated phantom data acquired at 3T with a 32-channel receiver coil. We also demonstrate that compared to the original model the extended model results in an improved fit to human task-free non-accelerated fMRI data acquired at 7T with a 24-channel receiver coil. In particular, the extended model improves the prediction of low to medium tSNR values and so can play an important role in the optimization of high-resolution fMRI experiments at lower SNR levels.     

Reconstructing visual experiences from brain activity evoked by natural movies

Quantitative modeling of human brain activity can provide crucial insights about cortical representations [1, 2] and can form the basis for brain decoding devices [3-5]. Recent functional magnetic resonance imaging (fMRI) studies have modeled brain activity elicited by static visual patterns and have reconstructed these patterns from brain activity [6-8]. However, blood oxygen level-dependent (BOLD) signals measured via fMRI are very slow [9], so it has been difficult to model brain activity elicited by dynamic stimuli such as natural movies. Here we present a new motion-energy [10, 11] encoding model that largely overcomes this limitation. The model describes fast visual information and slow hemodynamics by separate components. We recorded BOLD signals in occipitotemporal visual cortex of human subjects who watched natural movies and fit the model separately to individual voxels. Visualization of the fit models reveals how early visual areas represent the information in movies. To demonstrate the power of our approach, we also constructed a Bayesian decoder [8] by combining estimated encoding models with a sampled natural movie prior. The decoder provides remarkable reconstructions of the viewed movies. These results demonstrate that dynamic brain activity measured under naturalistic conditions can be decoded using current fMRI technology.     

Human fetuses have nonlinear cardiac dynamics.

Approximate entropy (ApEn) is a statistic that quantifies regularity in time series data, and this parameter has several features that make it attractive for analyzing physiological systems. In this study, ApEn was used to detect nonlinearities in the heart rate (HR) patterns of 12 low-risk human fetuses between 38 and 40 wk of gestation. The fetal cardiac electrical signal was sampled at a rate of 1,024 Hz by using Ag-AgCl electrodes positioned across the mother's abdomen, and fetal R waves were extracted by using adaptive signal processing techniques. To test for nonlinearity, ApEn for the original HR time series was compared with ApEn for three dynamic models: temporally uncorrelated noise, linearly correlated noise, and linearly correlated noise with nonlinear distortion. Each model had the same mean and SD in HR as the original time series, and one model also preserved the Fourier power spectrum. We estimated that noise accounted for 17.2-44.5% of the total between-fetus variance in ApEn. Nevertheless, ApEn for the original time series data still differed significantly from ApEn for the three dynamic models for both group comparisons and individual fetuses. We concluded that the HR time series, in low-risk human fetuses, could not be modeled as temporally uncorrelated noise, linearly correlated noise, or static filtering of linearly correlated noise.     

Dynamic Causal Modeling and subspace identification methods

The main contribution of the paper is in formulating the problem of detection of brain regions structure within the framework of dynamic system theory. The motivation is to see if the mature domain of experimental identification of dynamic systems can provide a methodology alternative to Dynamic Causal Modeling (DCM) which is currently used as an exclusive tool to estimate the structure of interconnections among a given set of brain regions using the measured data from functional magnetic resonance imaging (fMRI). The key tool proposed for modeling the structure of brain interconnections in this paper is subspace identification methods which produce linear state-space model, thus neglecting the bilinear term from DCM. The procedure is illustrated using a simple two-region model with maximally simplified linearized hemodynamics. We assume that the underlying system can be modeled by a set of linear differential equations, and identify the parameters (in terms of state space matrices), without any a priori constraints. We then transform the hidden states so that the implicit state matrix has a form or structure that is consistent with the generation of (region-specific) hemodynamic signals by coupled neuronal states.