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PHOEBE (Placing Headgear Optodes Efficiently Before Experiment) is a MATLAB GUI application that measures and displays the optical coupling between fNIRS optodes and the scalp of a subject in real time.
The primary goal of PHOEBE is to help the experimenter optimize signal quality of fNIRS headgear in a time efficient manner prior to an fNIRS recording. For an assessment of data quality after recordings, please take a look at its sister project QT-NIRS. Both PHOEBE and QT-NIRS share the same quality assessment metrics (Scalp Coupling Index and Peak Spectral Power).
Details on the methods used to quantify the scalp-optode coupling is described in the paper linked at the bottom of this page.
Placing all optodes in good contact with the scalp can be a lengthy and often frustrating process, particularly for newer fNIRS investigators with less experience. Usually, experimenters will follow one of these two approaches:
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Optodes are placed on the scalp one-by-one after parting hair underneath each optode. When executed carefully, this method yields the best results. However, with recent fNIRS instrumentation encompassing tens of optodes, the preparation of a subject can take a considerable amount of time that may result in subjects to become tired and uncollaborative (particularly pediatric and elderly populations), which may not be acceptable in a clinical setting.
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Optodes pre-mounted on headgear are fitted all at once on the subject's scalp, without parting hair. This method is considerably quicker than individual optodes' placement, but often results in several channels containing low optical signal due to light blockage by hair creating poor coupling between optodes and scalp.
Although fNIRS instruments' software may provide a graphical and/or numerical indication of which optical channels (i.e, optode pairings) have poor signal quality, localizing and adjusting individual uncoupled optodes remains a lengthy and difficult process for non-technical personnel.
PHOEBE achieves an optimum trade-off between these approaches by:
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Determining a quantitative measure of scalp coupling of each individual optode, akin to electrical skin conductance used in EEG, and
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Displaying the scalp coupling status of all optodes on a head model, so to guide the experimenter to a quick and intuitive adjustment.
More traditionally, PHOEBE also allows to assess the quality of individual optical channels (source-detector pairings), as opposed to individual optodes.
PHOEBE uses LSL (Lab Streaming Layer) to capture and process data for quality assessment, hence any fNIRS instrument with LSL capability can be interfaced with PHOEBE. At this time, we have successfully tested PHOEBE with the following instruments/software:
- NIRx NIRScout/NIRStar
and we are currently developing extensions to:
- NIRx NIRSport/Aurora
- Artinis Brite/OxySoft
In addition, PHOEBE can be interfaced with Polhemus Patriot for a guided digitization of all optodes and fiducial points in the MNI space.
PHOEBE can be run directly from Matlab (2014b or newer). For an easier use, it is advised to install and launch PHOEBE from the same computer that interfaces with the fNIRS instrument, although LSL streaming allows to collect data from any computer on the same local network (LAN). The former setting simply avoids configuring networks in your working environment.
Unlike its previous version, PHOEBE no longer asks a series of questions to properly configure software and hardware settings. This significantly simplifies its first time use. All settings can be managed through menu items at anytime.
Also, PHOEBE no longer requires a source-detector pairings file to be loaded upfront. Optode locations can be provided either through a text file in Homer/AtlasViewer formats, or can be acquired on the spot through a Polhemus Patriot digitizer.
All PHOEBE settings (e.g., default probe path, GUI options, digitizer options) are saved in the file settings.json as soon as they are changed or upon closing the application, and will remain in place for the next session of PHOEBE.
PHOEBE requires pre-loading some information about the optical probe to monitor the quality of the incoming fNIRS data. Unlike previous versions of PHOEBE, this information consists only of the 3D location of all optodes (sources, detectors) and fiducial points, and it can be provided in different ways:
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Loading a TXT file containing all 3D locations formatted according to Homer/AtlasViewer (i.e., the typical digpts.txt)
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Loading a TXT file containing all 3D locations created with the user-friendly point-and-click tool NIRSite by NIRx (login required to download). The latest version of NIRSite saves locations in both Homer format and NIRX-specific format.
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Creating a new layout by digitizing optodes and fiducial points using Polhemus Patriot. After digitizing, PHOEBE will save the locations in AtlasViewer TXT format.
After fitting the participant with an fNIRS headgear with geometrical layout consistent with the probe loaded in PHOEBE, the quality of the incoming fNIRS can be measured and monitored in real time.
PHOEBE captures data streamed by any fNIRS instrument via LSL. It is critical that users stream either raw or optical density (OD) data, in addition to any other measures of interest (e.g., HbO/HbR, EEG, accelerometer/gyro, etc.). To setup LSL streaming, please refer to the operating manual of the instrument, and start streaming (either as a data preview or recording) to enable PHOEBE monitoring fNIRS signals.
PHOEBE can measure data quality at the optodes level or, more traditionally, at the optical channel level. Either modality can be selected on the left panel prior to starting monitoring.
Please note that PHOEBE monitors all optical channels defined and streamed by the fNIRS instrument, and not based on probe information pre-loaded in PHOEBE which only contain the location of all optodes necessary to display the assessment of data quality.
After setting the preferred parameters, launch PHOEBE and click the START MONITOR button on the Monitor panel.
All optodes are now colored according to the following scheme:
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GREEN (sufficient scalp coupling): these optodes do not need to be adjusted.
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RED (insufficient scalp coupling): these optodes need to be adjusted manually until their color turns green or possibly yellow (see below). An improved scalp coupling is usually achieved by wiggling the optode in attempt to penetrate the hair layer, or by manually parting the hair underneath.
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YELLOW (undetermined scalp status): in certain cases, the coupling status of an optode cannot be determined when paired to one or more red optodes in an optical channel(s) (see our paper for more details and an example). To resolve the status of yellow optodes, the neighboring red optodes must be adjusted first. As soon as red optodes become coupled to the scalp and their color turns green, the actual coupling status of all linked yellow optodes will be determined, hence turning green or red.
NOTE: Depending on the subject’s hair characteristics (e.g., braids, thick and dark hair), it is possible that not all optodes will be satisfactorily coupled to the scalp even after prolonged adjustment.
Fun fact: During one of our experiment, a optode was marked uncoupled even after parting hair meticulously, and it turned out that the corresponding 860 nm LED was burnt. Hard to diagnose that with naked eye!
All optical channels (i.e., links between sources and detectors) are colored in either GREEN (good quality) or RED (bad quality).
Please visit this page for more on how to digitize optodes positions using Polhemus Patriot.
To report bugs and suggest additional features, please use the Issues page.
PHOEBE has been coded by Luca Pollonini, Ph.D., Jonathan Perry, M.S., Samuel Montero-Hernandez, PhD. and Raian Ferdous, B.S. with the Optical BioImaging Lab at the University of Houston.
If you find PHOEBE helpful for your work, please consider citing this paper:
PHOEBE is distributed under the Creative Commons BY-NC-SA 4.0 License