An integrated framework for joint HRF and drift estimation and HbO/HbR signal improvement in fNIRS data

Artifact Management for Cerebral Near-Infrared Spectroscopy Signals: A Systematic Scoping Review

Artifacts induced during patient monitoring are a main limitation for near-infrared spectroscopy (NIRS) as a non-invasive method of cerebral hemodynamic monitoring. There currently does not exist a robust "gold-standard" method for artifact management for these signals. The objective of this review is to comprehensively examine the literature on existing artifact management methods for cerebral NIRS signals recorded in animals and humans. A search of five databases was conducted based on the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. The search yielded 806 unique results. There were 19 articles from these results that were included in this review based on the inclusion/exclusion criteria. There were an additional 36 articles identified in the references of select articles that were also included. The methods outlined in these articles were grouped under two major categories: (1) motion and other disconnection artifact removal methods; (2) data quality improvement and physiological/other noise artifact filtering methods. These were sub-categorized by method type. It proved difficult to quantitatively compare the methods due to the heterogeneity of the effectiveness metrics and definitions of artifacts. The limitations evident in the existing literature justify the need for more comprehensive comparisons of artifact management. This review provides insights into the available methods for artifact management in cerebral NIRS and justification for a homogenous method to quantify the effectiveness of artifact management methods. This builds upon the work of two existing reviews that have been conducted on this topic; however, the scope is extended to all artifact types and all NIRS recording types. Future work by our lab in cerebral NIRS artifact management will lie in a layered artifact management method that will employ different techniques covered in this review (including dynamic thresholding, autoregressive-based methods, and wavelet-based methods) amongst others to remove varying artifact types.

Deconvolution of the Functional Ultrasound Response in the Mouse Visual Pathway Using Block-Term Decomposition

Functional ultrasound (fUS) indirectly measures brain activity by detecting changes in cerebral blood volume following neural activation. Conventional approaches model such functional neuroimaging data as the convolution between an impulse response, known as the hemodynamic response function (HRF), and a binarized representation of the input signal based on the stimulus onsets, the so-called experimental paradigm (EP). However, the EP may not characterize the whole complexity of the activity-inducing signals that evoke the hemodynamic changes. Furthermore, the HRF is known to vary across brain areas and stimuli. To achieve an adaptable framework that can capture such dynamics of the brain function, we model the multivariate fUS time-series as convolutive mixtures and apply block-term decomposition on a set of lagged fUS autocorrelation matrices, revealing both the region-specific HRFs and the source signals that induce the hemodynamic responses. We test our approach on two mouse-based fUS experiments. In the first experiment, we present a single type of visual stimulus to the mouse, and deconvolve the fUS signal measured within the mouse brain's lateral geniculate nucleus, superior colliculus and visual cortex. We show that the proposed method is able to recover back the time instants at which the stimulus was displayed, and we validate the estimated region-specific HRFs based on prior studies. In the second experiment, we alter the location of the visual stimulus displayed to the mouse, and aim at differentiating the various stimulus locations over time by identifying them as separate sources.

Adaptive Brain Activity Detection in Structured Interference and Partially Homogeneous Locally Correlated Disturbance

OBJECTIVE

In this paper, we aim to address the problem of subspace detection in the presence of locally-correlated complex Gaussian noise and interference. For applications like brain activity detection using functional magnetic resonance imaging (fMRI) data where the noise is possibly locally correlated, using the sample covariance estimator is not a suitable choice due to significant dependency of its accuracy on the number of observations.

METHODS

In this study, we take advantage of an assumed banded structure in the covariance matrix to model the local dependence in the noise and propose a new covariance estimation approach. In particular, we use the idea of fac-torizing the joint likelihood function into a few conditional likelihood terms and maximizing each term independently of the others. This process leads to an explicit estimator for banded covariance matrices which requires fewer observations to achieve the same accuracy as the sample covari-ance. This estimate is then fed into an adaptive matched filter, two-step Rao and two-step Wald tests for detection.

RESULTS

Simulation results reveal the superiority of the proposed methods over well known classical detectors. Finally, the proposed methods are applied to functional magnetic resonance imaging (fMRI) data to localize neural activities in the brain.

CONCLUSION

The proposed method can offer better activation maps in terms of accuracy and spatial smoothness.

SIGNIFICANCE

The proposed methods can be seen as alternatives for standard detection approaches which are not perfectly aligned with the properties of fMRI data.

Joint direct estimation of hemodynamic response function and activation level in brain functional high density diffuse optical tomography

High density diffuse optical tomography has become increasingly important to detect underlying neuronal activities. Conventional methods first estimate the time courses of the changes in the absorption coefficients for all the voxels, and then estimate the hemodynamic response function (HRF). Activation-level maps are extracted at last based on this HRF. However, the error propagation among the successive processes degrades and even misleads the final results. Besides, the computation burden is heavy. To address the above problems, a direct method is proposed in this paper to simultaneously estimate the HRF and the activation-level maps from the boundary fluxes. It is assumed that all the voxels in the same activated brain region share the same HRF but differ in the activation levels, and no prior information is imposed on the specific shape of the HRF. The dynamic simulation and phantom experiments demonstrate that the proposed method outperforms the conventional one in terms of the estimation accuracy and computation speed.

Initial-Dip Existence and Estimation in Relation to DPF and Data Drift

Early de-oxygenation (initial dip) is an indicator of the primal cortical activity source in functional neuro-imaging. In this study, initial dip's existence and its estimation in relation to the differential pathlength factor (DPF) and data drift were investigated in detail. An efficient algorithm for estimation of drift in fNIRS data is proposed. The results favor the shifting of the fNIRS signal to a transformed coordinate system to infer correct information. Additionally, in this study, the effect of the DPF on initial dip was comprehensively analyzed. Four different cases of initial dip existence were treated, and the resultant characteristics of the hemodynamic response function (HRF) for DPF variation corresponding to particular near-infrared (NIR) wavelengths were summarized. A unique neuro-activation model and its iterative optimization solution that can estimate drift in fNIRS data and determine the best possible fit of HRF with free parameters were developed and herein proposed. The results were verified on simulated data sets. The algorithm is applied to free available datasets in addition to six healthy subjects those were experimented using fNIRS and observations and analysis regarding shape of HRF were summarized as well. A comparison with standard GLM is also discussed and effects of activity strength parameters have also been analyzed.

Sequential Dictionary Learning From Correlated Data: Application to fMRI Data Analysis

Sequential dictionary learning via the K-SVD algorithm has been revealed as a successful alternative to conventional data driven methods, such as independent component analysis for functional magnetic resonance imaging (fMRI) data analysis. fMRI data sets are however structured data matrices with notions of spatio-temporal correlation and temporal smoothness. This prior information has not been included in the K-SVD algorithm when applied to fMRI data analysis. In this paper, we propose three variants of the K-SVD algorithm dedicated to fMRI data analysis by accounting for this prior information. The proposed algorithms differ from the K-SVD in their sparse coding and dictionary update stages. The first two algorithms account for the known correlation structure in the fMRI data by using the squared Q, R-norm instead of the Frobenius norm for matrix approximation. The third and last algorithms account for both the known correlation structure in the fMRI data and the temporal smoothness. The temporal smoothness is incorporated in the dictionary update stage via regularization of the dictionary atoms obtained with penalization. The performance of the proposed dictionary learning algorithms is illustrated through simulations and applications on real fMRI data.

Bundled-Optode Method in Functional Near-Infrared Spectroscopy

In this paper, a theory for detection of the absolute concentrations of oxy-hemoglobin (HbO) and deoxy-hemoglobin (HbR) from hemodynamic responses using a bundled-optode configuration in functional near-infrared spectroscopy (fNIRS) is proposed. The proposed method is then applied to the identification of two fingers (i.e., little and thumb) during their flexion and extension. This experiment involves a continuous-wave-type dual-wavelength (760 and 830 nm) fNIRS and five healthy male subjects. The active brain locations of two finger movements are identified based on the analysis of the t- and p-values of the averaged HbOs, which are quite distinctive. Our experimental results, furthermore, revealed that the hemodynamic responses of two-finger movements are different: The mean, peak, and time-to-peak of little finger movements are higher than those of thumb movements. It is noteworthy that the developed method can be extended to 3-dimensional fNIRS imaging.

Connectivity in Language Areas of the Brain in Cochlear Implant Users as Revealed by fNIRS

Many studies, using a variety of imaging techniques, have shown that deafness induces functional plasticity in the brain of adults with late-onset deafness, and in children changes the way the auditory brain develops. Cross modal plasticity refers to evidence that stimuli of one modality (e.g. vision) activate neural regions devoted to a different modality (e.g. hearing) that are not normally activated by those stimuli. Other studies have shown that multimodal brain networks (such as those involved in language comprehension, and the default mode network) are altered by deafness, as evidenced by changes in patterns of activation or connectivity within the networks. In this paper, we summarise what is already known about brain plasticity due to deafness and propose that functional near-infra-red spectroscopy (fNIRS) is an imaging method that has potential to provide prognostic and diagnostic information for cochlear implant users. Currently, patient history factors account for only 10 % of the variation in post-implantation speech understanding, and very few post-implantation behavioural measures of hearing ability correlate with speech understanding. As a non-invasive, inexpensive and user-friendly imaging method, fNIRS provides an opportunity to study both pre- and post-implantation brain function. Here, we explain the principle of fNIRS measurements and illustrate its use in studying brain network connectivity and function with example data.

Recovering HRFs from overlapping ROIs in fMRI data using thresholding correlations for sparse dictionary learning

Recovering region-specific hemodynamic response function (HRF) in noisy fMRI data is essential to characterize the temporal dynamics of functionally coherent brain regions during activation. Data-driven techniques not based on sparsity fails to recover sub-region HRFs from overlapping regions of interest (ROIs) in task-related activations. This paper exploits spatial sparsity for recovering distinct HRFs from un-delineated overlapping ROIs in fMRI data. Spatial sparsity is realized using thresholding correlation for dictionary learning. The effectiveness of the proposed procedure is illustrated on both simulated and an experimental fMRI data obtained during a visual-task.