Category: fNIRS Glossary Project

Definition: A range of algebraic operations that introduce a small perturbation on a tensor in order to alter its determinant. Consequently, regularization changes the condition number of a matrix. The range of applications of regularization is vast e.g. perhaps for enabling or stabilizing matrix inversion, for altering the prominence of some dimensions of the tensor over others, for increasing derivability e.g. smoothing, etc. By and large, the most popular regularization approach is Tikhonov’s which attacks the main diagonal isotropically and only has 1 parameter, but certainly many other regularization approaches exist with different purposes. A popular use in fNIRS is to improve the stability and accuracy of the reconstruction algorithm by introducing additional constraints. It is often used in solving the ill-posed inverse problem in image reconstruction when the data being used for reconstruction is noisy and can help to reduce the effects of these sources of error on the final reconstructed image. Another form of regularization that has been used in fNIRS analysis is sparsity regularization, which adds a penalty term proportional to the L1 norm of the changes in hemoglobin concentration. This penalty term encourages the solution to be sparse, meaning that it has many zero or near-zero coefficients, which can help identify the brain regions that are most active.

Category: Math

Related terms: Moore-Penrose Pseudoinverse

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https://doi.org/10.1063/5.0015512

https://doi.org/10.1117%2F1.JBO.26.5.056001

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Definition: A block average is the response obtained from segmenting the fNIRS measurement with respect to the task or stimulus onset and offset and averaging these segments across trials of a given condition. The time window for block averaging usually starts with a baseline period and is long enough to capture the hemodynamic response to the stimulus presented. Block averaging can be done on the single-subject level or/and on the group level.

Category: Analysis

Related terms: block design, event-related averaging

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https://doi.org/10.1117/1.NPh.8.2.025008

https://doi.org/10.1016/j.dcn.2010.07.004

https://doi.org/10.1111/nyas.13948

https://doi.org/10.1117/1.2166632

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Definition: The Brain Imaging Data Structure (BIDS) is a standardized format for organizing and describing neuroimaging data such as fMRI, EEG, fNIRS as well as behavioral data, among others, making it accessible to and shareable with a wide range of researchers from diverse backgrounds. It is based on a formalized file and folder structure and JSON (Javascript Object Notation)-based metadata files with controlled vocabulary. The top-level directory contains subdirectories for each subject, and each subject directory contains subdirectories for each session and modality. It includes the core specification as well as extensions for specific brain imaging modalities and other types of data. (https://bids.neuroimaging.io/)

Category: Analysis

Related terms: SNIRF, Open Science, Open Data, Data Structure, Standardization

Abbreviation or symbol: BIDS

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References: https://doi.org/10.1038/sdata.2016.44

https://doi.org/10.1117/1.NPh.10.2.023515

https://doi.org/10.1162/imag_a_00103

https://doi.org/10.31219/osf.io/7nmcp

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Definition: A baseline shift is an artifact in the signal that specifically refers to a rapid change in the amplitude of the signal, typically taking a few seconds or less, which results in a discontinuity in the signal. For example, when an optode moves relative to the scalp and fails to return to its original position, this will create a baseline shift in the signal.

Category: Analysis

Related terms: artifact, spikes, motion artifacts, noise, baseline drift

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Synonym: shift artifacts, step-like artifacts

References: https://doi.org/10.1109/EMBC46164.2021.9631014

https://doi.org/10.3389/fnins.2012.00147

https://doi.org/10.3390/brainsci11050606

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Definition: A baseline drift refers to a gradual change or deviation in a signal’s behavior or output over time. Changes in the contact between the sensors and the scalp, temperature variations, instrument instability, and other variables can all contribute to this change.

Category: Analysis

Related terms: Motion artifact, baseline shift

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Synonym: Signal drift

References: https://doi.org/10.3389/fnhum.2015.00617

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Related terms (alternative definition): Trend, detrending

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Definition: A band-pass filter is a combination of a low-pass and a high-pass filter and has the effect of attenuating frequencies above and below the passband frequencies. In the context of fNIRS, band-pass filtering is used as a signal processing step to reduce undesired fNIRS signal frequency components that are irrelevant to the brain functions of interest, i.e. task or stimulus evoked hemodynamic responses or resting-state hemodynamics.

Category: Analysis

Related terms: high-pass filtering, low-pass filtering, wavelet, temporal filtering

Abbreviation or symbol: bpf

Synonym: filtering

References:

https://doi.org/10.3389/fnhum.2019.00331

https://doi.org/10.1542/peds.2015-2326

http://dx.doi.org/10.1136/adc.76.2.151

https://doi.org/10.3389/fnhum.2013.00864

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Definition: In the context of fNIRS, an artifact is a disturbance of the fNIRS signal that makes the identification of physiologically relevant information in the fNIRS signal difficult or impossible. Generally it is a component of the fNIRS signal that is not induced by neuronal activity and may thus contaminate the measured hemodynamic response. Common sources of artifact in fNIRS data include relative movement between the optodes and the scalp (i.e. motion artifacts), optical signal changes caused by non-brain function related physiological variations (e.g., effects of blood flow changes in the scalp or respiration), environmental variations (e.g., due to stray or ambient light), as well as undesired instrument fluctuations (i.e., related to the measurement equipment).

Category: Analysis

Related terms: Physiological Noise, Filtering, Noise, Motion Correction, Accelerometer, Gyroscope, Inertial measurement Unit (IMU), Low-Pass Filter, High-Pass Filter, Band Pass Filter, baseline shift, baseline drift

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https://doi.org/10.3389/fnins.2012.00147

https://doi.org/10.1016/j.neuroimage.2013.04.082

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Definition: Avalanche photodiodes utilize the avalanche multiplication process to achieve higher electric output. The avalanche photodiode resembles a PIN photodiode except for the insertion of an additional p-type multiplying region. Most of the incident photons are absorbed in the intrinsic (‘I’) region and electron-hole pairs are first generated in this region as in the PIN photodiode. The holes drift toward the p-type region (‘P’) and the electrons toward the n-type (‘N’). The electrons, before reaching the n-type region, pass through a p-type multiplying region. If the electrons have undergone sufficient acceleration on reaching the multiplying region, new electron-hole pairs are generated by the collision- ionization process. The newly generated electron-hole pairs themselves generate more electron-hole pairs. The drawbacks to avalanche photodiodes are the high bias voltage needed, and the temperature compensation necessary for stable operation.

Category: Hardware

Related terms: Photomultiplier tube, Detector, Sensor, Silicon Photomultiplier

Abbreviation or symbol: APD

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References: E. Hui Pan. Fiber Optics Weekly Update. Information Gatekeepers Inc.

Alternative definition: An avalanche photodiode (APD) is a type of semiconductor photodetector used to detect low levels of light in applications such as fNIRS. It is based on the principle of avalanche multiplication, which occurs when an electron in the photodiode collides with an atom and generates a cascade of secondary electrons, resulting in a much larger current than would be caused by a single photon.

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Definition: An optode is the distal end of an fNIRS system which interfaces with the surface of the tissue being measured. Optodes can contain a single source (source optode), a single detector (detector optode), or a source accompanied by a short-separation detector.

Category: Hardware

Related terms: source; detector; emitter; emission, receiver, transmitter

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References: https://doi.org/10.1016/j.neuroimage.2005.08.008

https://biomedical.njit.edu/sites/biomedical/files/fNIRS%20Optode%20Helmet%20Construct.pdf

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Definition: Relative arrangement of linked sources and detectors on a region of interest.

Category: Hardware

Related terms: Probe design; Optode placement, topographic layout, Montage

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Synonym: Probe array; fNIRS array; Channel configuration; fNIRS-sensor configuration; Source–detector array, fNIRS Montage

References: https://doi.org/10.1117/1.NPh.5.3.035010

https://doi.org/10.1117/1.NPh.8.1.012101

Alternative definition: A schematic arrangement of sources and detectors to create a pattern of measurement channels.

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References (alternative definition): https://doi.org/10.1117/1.NPh.8.1.012101