ninjaCap: A fully customizable and 3D printable headgear for fNIRS and EEG brain imaging.

Significance: Accurate sensor placement is vital for non-invasive brain imaging, particularly for functional near infrared spectroscopy (fNIRS) and diffuse optical tomography (DOT), which lack standardized layouts like EEG. Custom, manually prepared probe layouts on textile caps are often imprecise and labor-intensive. Aim: We introduce a method for creating personalized, 3D-printed headgear, enabling accurate translation of 3D brain coordinates to 2D printable panels for custom fNIRS and EEG sensor layouts, reducing costs and manual labor. Approach: Our approach uses atlas-based or subject-specific head models and a spring-relaxation algorithm for flattening 3D coordinates onto 2D panels, using 10-5 EEG coordinates for reference. This process ensures geometrical fidelity, crucial for accurate probe placement. Probe geometries and holder types are customizable and printed directly on the cap, making the approach agnostic to instrument manufacturers and probe types. Results: Our ninjaCap method offers 2.2±1.5 mm probe placement accuracy. Over the last five years, we have developed and validated this approach with over 50 cap models and 500 participants. A cloud-based ninjaCap generation pipeline along with detailed instructions is now available at openfnirs.org. Conclusions: The ninjaCap marks a significant advancement in creating individualized neuroimaging caps, reducing costs and labor while improving probe placement accuracy, thereby reducing variability in research.

fNIRS Dataset During Complex Scene Analysis.

When analyzing complex scenes, humans often focus their attention on an object at a particular spatial location. The ability to decode the attended spatial location would facilitate brain computer interfaces for complex scene analysis (CSA). Here, we investigated capability of functional near-infrared spectroscopy (fNIRS) to decode audio-visual spatial attention in the presence of competing stimuli from multiple locations. We targeted dorsal frontoparietal network including frontal eye field (FEF) and intra-parietal sulcus (IPS) as well as superior temporal gyrus/planum temporal (STG/PT). They all were shown in previous functional magnetic resonance imaging (fMRI) studies to be activated by auditory, visual, or audio-visual spatial tasks. To date, fNIRS has not been applied to decode auditory and visual-spatial attention during CSA, and thus, no such dataset exists yet. This report provides an open-access fNIRS dataset that can be used to develop, test, and compare machine learning algorithms for classifying attended locations based on the fNIRS signals on a single trial basis.

Short-separation regression incorporated diffuse optical tomography image reconstruction modeling for high-density functional near-infrared spectroscopy.

Significance: Short-separation (SS) regression and diffuse optical tomography (DOT) image reconstruction, two widely adopted methods in functional near-infrared spectroscopy (fNIRS), were demonstrated to individually facilitate the separation of brain activation and physiological signals, with further improvement using both sequentially. We hypothesized that doing both simultaneously would further improve the performance. Aim: Motivated by the success of these two approaches, we propose a method, SS-DOT, which applies SS and DOT simultaneously. Approach: The method, which employs spatial and temporal basis functions to represent the hemoglobin concentration changes, enables us to incorporate SS regressors into the time series DOT model. To benchmark the performance of the SS-DOT model against conventional sequential models, we use fNIRS resting state data augmented with synthetic brain response as well as data acquired during a ball squeezing task. The conventional sequential models comprise performing SS regression and DOT. Results: The results show that the SS-DOT model improves the image quality by increasing the contrast-to-background ratio by a threefold improvement. The benefits are marginal at small brain activation. Conclusions: The SS-DOT model improves the fNIRS image reconstruction quality.

Wearable, high-density fNIRS and diffuse optical tomography technologies: a perspective.

Recent progress in optoelectronics has made wearable and high-density functional near-infrared spectroscopy (fNIRS) and diffuse optical tomography (DOT) technologies possible for the first time. These technologies have the potential to open new fields of real-world neuroscience by enabling functional neuroimaging of the human cortex at a resolution comparable to fMRI in almost any environment and population. In this perspective article, we provide a brief overview of the history and the current status of wearable high-density fNIRS and DOT approaches, discuss the greatest ongoing challenges, and provide our thoughts on the future of this remarkable technology.

Introduction to the shared near infrared spectroscopy format.

Significance: Functional near-infrared spectroscopy (fNIRS) is a popular neuroimaging technique with proliferating hardware platforms, analysis approaches, and software tools. There has not been a standardized file format for storing fNIRS data, which has hindered the sharing of data as well as the adoption and development of software tools. Aim: We endeavored to design a file format to facilitate the analysis and sharing of fNIRS data that is flexible enough to meet the community's needs and sufficiently defined to be implemented consistently across various hardware and software platforms. Approach: The shared NIRS format (SNIRF) specification was developed in consultation with the academic and commercial fNIRS community and the Society for functional Near Infrared Spectroscopy. Results: The SNIRF specification defines a format for fNIRS data acquired using continuous wave, frequency domain, time domain, and diffuse correlation spectroscopy devices. Conclusions: We present the SNIRF along with validation software and example datasets. Support for reading and writing SNIRF data has been implemented by major hardware and software platforms, and the format has found widespread use in the fNIRS community.

Multivariate Kalman filter regression of confounding physiological signals for real-time classification of fNIRS data.

Significance: Functional near-infrared spectroscopy (fNIRS) is a noninvasive technique for measuring hemodynamic changes in the human cortex related to neural function. Due to its potential for miniaturization and relatively low cost, fNIRS has been proposed for applications, such as brain-computer interfaces (BCIs). The relatively large magnitude of the signals produced by the extracerebral physiology compared with the ones produced by evoked neural activity makes real-time fNIRS signal interpretation challenging. Regression techniques incorporating physiologically relevant auxiliary signals such as short separation channels are typically used to separate the cerebral hemodynamic response from the confounding components in the signal. However, the coupling of the extra-cerebral signals is often noninstantaneous, and it is necessary to find the proper delay to optimize nuisance removal. Aim: We propose an implementation of the Kalman filter with time-embedded canonical correlation analysis for the real-time regression of fNIRS signals with multivariate nuisance regressors that take multiple delays into consideration. Approach: We tested our proposed method on a previously acquired finger tapping dataset with the purpose of classifying the neural responses as left or right. Results: We demonstrate computationally efficient real-time processing of 24-channel fNIRS data (400 samples per second per channel) with a two order of selective magnitude decrease in cardiac signal power and up to sixfold increase in the contrast-to-noise ratio compared with the nonregressed signals. Conclusion: The method provides a way to obtain better distinction of brain from non-brain signals in real time for BCI application with fNIRS.

Towards Neuroscience of the Everyday World (NEW) using functional Near-Infrared Spectroscopy.

Functional Near-Infrared Spectroscopy (fNIRS) assesses human brain activity by noninvasively measuring changes of cerebral hemoglobin concentrations caused by modulation of neuronal activity. Recent progress in signal processing and advances in system design, such as miniaturization, wearability and system sensitivity, have strengthened fNIRS as a viable and cost-effective complement to functional Magnetic Resonance Imaging (fMRI), expanding the repertoire of experimental studies that can be performed by the neuroscience community. The availability of fNIRS and Electroencephalography (EEG) for routine, increasingly unconstrained, and mobile brain imaging is leading towards a new domain that we term "Neuroscience of the Everyday World" (NEW). In this light, we review recent advances in hardware, study design and signal processing, and discuss challenges and future directions towards achieving NEW.

Optical brain imaging and its application to neurofeedback.

Besides passive recording of brain electric or magnetic activity, also non-ionizing electromagnetic or optical radiation can be used for real-time brain imaging. Here, changes in the radiation's absorption or scattering allow for continuous in vivo assessment of regional neurometabolic and neurovascular activity. Besides magnetic resonance imaging (MRI), over the last years, also functional near-infrared spectroscopy (fNIRS) was successfully established in real-time metabolic brain imaging. In contrast to MRI, fNIRS is portable and can be applied at bedside or in everyday life environments, e.g., to restore communication and movement. Here we provide a comprehensive overview of the history and state-of-the-art of real-time optical brain imaging with a special emphasis on its clinical use towards neurofeedback and brain-computer interface (BCI) applications. Besides pointing to the most critical challenges in clinical use, also novel approaches that combine real-time optical neuroimaging with other recording modalities (e.g. electro- or magnetoencephalography) are described, and their use in the context of neuroergonomics, neuroenhancement or neuroadaptive systems discussed.

Using the General Linear Model to Improve Performance in fNIRS Single Trial Analysis and Classification: A Perspective.

Within a decade, single trial analysis of functional Near Infrared Spectroscopy (fNIRS) signals has gained significant momentum, and fNIRS joined the set of modalities frequently used for active and passive Brain Computer Interfaces (BCI). A great variety of methods for feature extraction and classification have been explored using state-of-the-art Machine Learning methods. In contrast, signal preprocessing and cleaning pipelines for fNIRS often follow simple recipes and so far rarely incorporate the available state-of-the-art in adjacent fields. In neuroscience, where fMRI and fNIRS are established neuroimaging tools, evoked hemodynamic brain activity is typically estimated across multiple trials using a General Linear Model (GLM). With the help of the GLM, subject, channel, and task specific evoked hemodynamic responses are estimated, and the evoked brain activity is more robustly separated from systemic physiological interference using independent measures of nuisance regressors, such as short-separation fNIRS measurements. When correctly applied in single trial analysis, e.g., in BCI, this approach can significantly enhance contrast to noise ratio of the brain signal, improve feature separability and ultimately lead to better classification accuracy. In this manuscript, we provide a brief introduction into the GLM and show how to incorporate it into a typical BCI preprocessing pipeline and cross-validation. Using a resting state fNIRS data set augmented with synthetic hemodynamic responses that provide ground truth brain activity, we compare the quality of commonly used fNIRS features for BCI that are extracted from (1) conventionally preprocessed signals, and (2) signals preprocessed with the GLM and physiological nuisance regressors. We show that the GLM-based approach can provide better single trial estimates of brain activity as well as a new feature type, i.e., the weight of the individual and channel-specific hemodynamic response function (HRF) regressor. The improved estimates yield features with higher separability, that significantly enhance accuracy in a binary classification task when compared to conventional preprocessing-on average +7.4% across subjects and feature types. We propose to adapt this well-established approach from neuroscience to the domain of single-trial analysis and preprocessing wherever the classification of evoked brain activity is of concern, for instance in BCI.

Improved physiological noise regression in fNIRS: A multimodal extension of the General Linear Model using temporally embedded Canonical Correlation Analysis.

For the robust estimation of evoked brain activity from functional Near-Infrared Spectroscopy (fNIRS) signals, it is crucial to reduce nuisance signals from systemic physiology and motion. The current best practice incorporates short-separation (SS) fNIRS measurements as regressors in a General Linear Model (GLM). However, several challenging signal characteristics such as non-instantaneous and non-constant coupling are not yet addressed by this approach and additional auxiliary signals are not optimally exploited. We have recently introduced a new methodological framework for the unsupervised multivariate analysis of fNIRS signals using Blind Source Separation (BSS) methods. Building onto the framework, in this manuscript we show how to incorporate the advantages of regularized temporally embedded Canonical Correlation Analysis (tCCA) into the supervised GLM. This approach allows flexible integration of any number of auxiliary modalities and signals. We provide guidance for the selection of optimal parameters and auxiliary signals for the proposed GLM extension. Its performance in the recovery of evoked HRFs is then evaluated using both simulated ground truth data and real experimental data and compared with the GLM with short-separation regression. Our results show that the GLM with tCCA significantly improves upon the current best practice, yielding significantly better results across all applied metrics: Correlation (HbO max. +45%), Root Mean Squared Error (HbO max. -55%), F-Score (HbO up to 3.25-fold) and p-value as well as power spectral density of the noise floor. The proposed method can be incorporated into the GLM in an easily applicable way that flexibly combines any available auxiliary signals into optimal nuisance regressors. This work has potential significance both for conventional neuroscientific fNIRS experiments as well as for emerging applications of fNIRS in everyday environments, medicine and BCI, where high Contrast to Noise Ratio is of importance for single trial analysis.

A new blind source separation framework for signal analysis and artifact rejection in functional Near-Infrared Spectroscopy.

In the analysis of functional Near-Infrared Spectroscopy (fNIRS) signals from real-world scenarios, artifact rejection is essential. However, currently there exists no gold-standard. Although a plenitude of methodological approaches implicitly assume the presence of latent processes in the signals, elaborate Blind-Source-Separation methods have rarely been applied. A reason are challenging characteristics such as Non-instantaneous and non-constant coupling, correlated noise and statistical dependencies between signal components. We present a novel suitable BSS framework that tackles these issues by incorporating A) Independent Component Analysis methods that exploit both higher order statistics and sample dependency, B) multimodality, i.e., fNIRS with accelerometer signals, and C) Canonical-Correlation Analysis with temporal embedding. This enables analysis of signal components and rejection of motion-induced physiological hemodynamic artifacts that would otherwise be hard to identify. We implement a method for Blind Source Separation and Accelerometer based Artifact Rejection and Detection (BLISSA2RD). It allows the analysis of a novel n-back based cognitive workload paradigm in freely moving subjects, that is also presented in this manuscript. We evaluate on the corresponding data set and simulated ground truth data, making use of metrics based on 1st and 2nd order statistics and SNR and compare with three established methods: PCA, Spline and Wavelet-based artifact removal. Across 17 subjects, the method is shown to reduce movement induced artifacts by up to two orders of magnitude, improves the SNR of continuous hemodynamic signals in single channels by up to 10dB, and significantly outperforms conventional methods in the extraction of simulated Hemodynamic Response Functions from strongly contaminated data. The framework and methods presented can serve as an introduction to a new type of multivariate methods for the analysis of fNIRS signals and as a blueprint for artifact rejection in complex environments beyond the applied paradigm.

Simultaneous acquisition of EEG and NIRS during cognitive tasks for an open access dataset.

We provide an open access multimodal brain-imaging dataset of simultaneous electroencephalography (EEG) and near-infrared spectroscopy (NIRS) recordings. Twenty-six healthy participants performed three cognitive tasks: 1) n-back (0-, 2- and 3-back), 2) discrimination/selection response task (DSR) and 3) word generation (WG) tasks. The data provided includes: 1) measured data, 2) demographic data, and 3) basic analysis results. For n-back (dataset A) and DSR tasks (dataset B), event-related potential (ERP) analysis was performed, and spatiotemporal characteristics and classification results for 'target' versus 'non-target' (dataset A) and symbol 'O' versus symbol 'X' (dataset B) are provided. Time-frequency analysis was performed to show the EEG spectral power to differentiate the task-relevant activations. Spatiotemporal characteristics of hemodynamic responses are also shown. For the WG task (dataset C), the EEG spectral power and spatiotemporal characteristics of hemodynamic responses are analyzed, and the potential merit of hybrid EEG-NIRS BCIs was validated with respect to classification accuracy. We expect that the dataset provided will facilitate performance evaluation and comparison of many neuroimaging analysis techniques.

M3BA: A Mobile, Modular, Multimodal Biosignal Acquisition Architecture for Miniaturized EEG-NIRS-Based Hybrid BCI and Monitoring.

OBJECTIVE: For the further development of the fields of telemedicine, neurotechnology, and brain-computer interfaces, advances in hybrid multimodal signal acquisition and processing technology are invaluable. Currently, there are no commonly available hybrid devices combining bioelectrical and biooptical neurophysiological measurements [here electroencephalography (EEG) and functional near-infrared spectroscopy (NIRS)]. Our objective was to design such an instrument in a miniaturized, customizable, and wireless form. METHODS: We present here the design and evaluation of a mobile, modular, multimodal biosignal acquisition architecture (M3BA) based on a high-performance analog front-end optimized for biopotential acquisition, a microcontroller, and our openNIRS technology. RESULTS: The designed M3BA modules are very small configurable high-precision and low-noise modules (EEG input referred noise @ 500 SPS 1.39 µVpp, NIRS noise equivalent power NEP750 nm = 5.92 pWpp, and NEP850 nm = 4.77 pWpp) with full input linearity, Bluetooth, 3-D accelerometer, and low power consumption. They support flexible user-specified biopotential reference setups and wireless body area/sensor network scenarios. CONCLUSION: Performance characterization and in-vivo experiments confirmed functionality and quality of the designed architecture. SIGNIFICANCE: Telemedicine and assistive neurotechnology scenarios will increasingly include wearable multimodal sensors in the future. The M3BA architecture can significantly facilitate future designs for research in these and other fields that rely on customized mobile hybrid biosignal modal biosignal acquisition architecture (M3BA), multimodal, near-infrared spectroscopy (NIRS), wireless body area network (WBAN), wireless body sensor network (WBSN).

Open Access Dataset for EEG+NIRS Single-Trial Classification.

We provide an open access dataset for hybrid brain-computer interfaces (BCIs) using electroencephalography (EEG) and near-infrared spectroscopy (NIRS). For this, we con-ducted two BCI experiments (left vs. right hand motor imagery; mental arithmetic vs. resting state). The dataset was validated using baseline signal analysis methods, with which classification performance was evaluated for each modality and a combination of both modalities. As already shown in previous literature, the capability of discriminating different mental states can be en-hanced by using a hybrid approach, when comparing to single modality analyses. This makes the provided data highly suitable for hybrid BCI investigations. Since our open access dataset also comprises motion artifacts and physiological data, we expect that it can be used in a wide range of future validation approaches in multimodal BCI research.

Toward a Wireless Open Source Instrument: Functional Near-infrared Spectroscopy in Mobile Neuroergonomics and BCI Applications.

Brain-Computer Interfaces (BCIs) and neuroergonomics research have high requirements regarding robustness and mobility. Additionally, fast applicability and customization are desired. Functional Near-Infrared Spectroscopy (fNIRS) is an increasingly established technology with a potential to satisfy these conditions. EEG acquisition technology, currently one of the main modalities used for mobile brain activity assessment, is widely spread and open for access and thus easily customizable. fNIRS technology on the other hand has either to be bought as a predefined commercial solution or developed from scratch using published literature. To help reducing time and effort of future custom designs for research purposes, we present our approach toward an open source multichannel stand-alone fNIRS instrument for mobile NIRS-based neuroimaging, neuroergonomics and BCI/BMI applications. The instrument is low-cost, miniaturized, wireless and modular and openly documented on www.opennirs.org. It provides features such as scalable channel number, configurable regulated light intensities, programmable gain and lock-in amplification. In this paper, the system concept, hardware, software and mechanical implementation of the lightweight stand-alone instrument are presented and the evaluation and verification results of the instrument's hardware and physiological fNIRS functionality are described. Its capability to measure brain activity is demonstrated by qualitative signal assessments and a quantitative mental arithmetic based BCI study with 12 subjects.