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What is PHOEBE?

PHOEBE is a software that measures and displays, in real time, the optical coupling between fNIRS optodes and the scalp of a subject. The primary goal of PHOEBE is to help optimizing the placement of an fNIRS headgear in terms of both time efficiency and signal quality. Details on the methods used to quantify the scalp-optode coupling is described in this paper, whereas the following online manual aims at guiding the user in the installation and use of the software.

Why using PHOEBE?

Placing all optodes in good contact with the scalp can be a frustrating process, particularly for fNIRS investigators in their early experience. Usually, experimenters follow one of these two approaches:

  1. 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), and may not be acceptable in a clinical setting;

  2. Optodes previously mounted on a 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 with a low optical signal due to poor coupling between optodes and scalp. Although the instrument's software usually provides a graphical or numerical indication of which channels (i.e, optode pairings) have poor quality, the process of localizing and adjusting them may still be lengthy and complex for non-techical personnel.  

PHOEBE attempts to establish an optimum trade-off between these approaches by:

  1. Determining a quantitative measure of scalp coupling at the optode level rather that at the channel level, akin to electrical skin conductance used in EEG, and

  2. Visually indicating all optodes on a head model that have poor optical coupling with the scalp, so to guide the experimenter to a quick and intuitive adjustment.


PHOEBE must be installed on the computer (either desktop or laptop) controlling the fNIRS system, as it works in conjunction with the manufacturer’s software. At this time, PHOBE is compatible with NIRx products, but we are planning on expanding its use to other commercial fNIRS systems (as soon as time allows). In our experience, computers controlling fNIRS systems meet or exceed the requirements for using PHOEBE.

To install PHOBE, simply download and run the installation package,. If necessary, the installer will also downaload and install the appropriate version of the Matlab Runtime Compiler (MRC).

In addition, PHOBE will auto-update when new features or bug fixes become available.

First Time Use

When launched for the first time, PHOEBE will ask a series of questions to properly configure software and hardware settings.

Initially, PHOEBE asks which fNIRS device is in use (NIRx being the only option at this time) and will subsequently ask to select the location of the file "cfg.nrx" which cointains many settings information about the NIRx instrument. This file is usually isntalled the subfolder "Sys" of the NIRstar installation folder (e.g., C:/NIRx/NIRstar/.../Sys/).
If you happened to choose the NIRStar folder incorrectly or if you needed to re-install NIRStar to a different location, you would NOT need to re-install PHOEBE again. Simply go to menu Settings and choose the correct location of "cfg.nrx".

PHOEBE will also ask if Polhemus Patriot is used for digitization of the optodes' spatial coordinates, and if a previous digitization and source-detector pairings files (both in Homer format) are wanted to be used as default layout. The default layout can be changed at a later time.

PHOEBE will save all user's settings as soon as they are changed or upon closing the application. Hence, the latest settings (optodes layout, digitization parameters, GUI options) will remain in place for the next session of PHOEBE. Although this may be an inconvenience in multi-user labs, only few changes are required to switch from a preset optical layout to a different one. 

Optodes Placement 

The following is the procedure for using PHOEBE during the preparation of a subject for an fNIRS experiment:

  1. Obviously, the first step is to fit the subject with the fNIRS headgear.

NOTE: Originally, we developed PHOEBE as a tool meant to save time in placing headgear by providing an easily-understandable visual guidance. However, if no time constraints exist, you may choose to part hair before placing the optodes in order to converge faster to an optimal placement.

  1. Launch NIRStar and perform the instrument calibration to optimize light emission and detection levels on all optodes (see manifacturer's instruction). See figure below.

  2. Start a measurement on NIRStar by clicking START (not PREVIEW). This operation will collect fNIRS signals that PHOEBE will process in real time. You may discard this data later, as they are not specific to your experiment.

  3. Launch PHOEBE and click on the Monitor tab of the left frame. The main window will show one or two identical head models with the locations of all optodes of the default layout. You can change the default layout by: a) performing a new optodes digitization with Polhemus Patriot, b) loading a previously digitized layout by selecting the menu Probe->Load, or c) creating a new layout by using the point-and-click placement tool available in the menu Probe->Create.

  4. (Optional) If needed, change the Settings on the left panel. See Setting Parameters for more information.

  5. Click the START MONITOR button on the left panel. All optodes are now colored according to the following scheme:

GREEN (sufficient coupling): these optodes have sufficient coupling with the scalp and do not need any adjustement.

RED (insufficient coupling): these optodes need to be adjusted manually until they turn green or possibly yellow (see below). You may achieve a better scalp coupling by wiggling the optode in attempt to penetrate the hair layer, or by manually parting the hair underneath using a tool.

YELLOW (undetermined status): in certain cases, the coupling status of an optode cannot be determined when it is paired to one or more red optodes. In other words, some uncoupled optodes "overshadow" other optodes that they are linked to, causing them to be marked as yellow. Our paper describes this situation with more details and an example. To resolve the status of yellow optodes, the neighboring red optodes must be adjusted first. When these become coupled to the scalp, linked yellow optodes will turn green or red, depending on their actual coupling status.

  1. Manually adjust the placement of all optodes until they are coupled to the scalp. Depending on the subject’s hair characteristics (e.g., braids, thick and dark hair), it is possible that one or more optodes could not be coupled to the scalp satisfactorily even after prolonged adjustement.
Fun fact: During an experiment, a optode was marked as uncoupled even after meticulously parting hair, and it turned out that the corresponding 860 nm LED was burnt. Hard to diagnose that quickly by naked eye!

Setting Parameters

To be completed...

Optodes Digitization with Polhemus Patriot

Many fNIRS and EEG investigators use Polhemus Patriot to 3D-digitize the position of anatomical landmarks, optodes and/or electrode on the head. PHOEBE allows to interface to Patriot for a seamless acquisition of optodes coordinates in the 3D space. This feature is available also to users that do not intend to use PHOBE for determining the scalp coupling status of optodes.

Installation of Patriot

To interface with PHOEBE, Patriot must be connected to the computer using the RS-232 serial cable provided with the device. If you previously used Patriot via USB (e.g., with PMI-2 software), simply disconnect the USB cable and use the serial cable instead. It is not necessary to remove the Patriot software from the computer, if previously installed. If you computer does not have an RS-232 serial port, you can emulate it with an USB adapter (you can buy this or one of the many equivalents from Amazon). Before first use in PHOEBE, the serial port, baud rate and source hemisphere must be set and tested in the menu Settings (see figure). The button SAVE AND CLOSE will enable upon succesful connectivity with Patriot. These settings will be save permanently fo future use of PHOEBE, and will need to be checked only for troubleshooting.

Digitization of optodes

  1. On PHOEBE's left frame, click on the Digitizer tab.

  2. Using the drop-down lists, select the number of fiducials, sources and detectors to digitize.

  3. Set the distance range (minimum and maximum distance) that PHOEBE will use to automatically determine the source-detector pairings.

  4. Click the button DIGITIZATION to start the acquisition process. PHOEBE will sequentially call for the fiducials (NZ, AR, AL, and optionally CZ and IZ), then sources (S1, S2, S3,...) and finally detectors (D1, D2, D3,...), allowing 30 seconds to digitize the location of each by pressing the button on the Patriot's stylus.

Creating a new layout with the point-and-click tool

If Polhemus Patriot or a previously digitized layout files are not available, it is possible to create an fNIRS layout to be used with PHOEBE (and other fNIRS analysis tools like Homer) using a point-and-click tool.

To be completed... 


Although the software was developed by the Optical BioImaging Lab at the University of Houston, we acknowledge the grateful collaborative support of the Oghalai Lab at USC and the Bortfeld Lab at the University of California - Merced, whithout which PHOEBE couold not have been conceived.


If you use and find PHOBE helpful, please consider citing this paper:

L. Pollonini, H. Bortfeld, and J. Oghalai, "PHOEBE: a method for real time mapping of optodes-scalp coupling in functional near-infrared spectroscopy," Biomed. Opt. Express 7, 5104-5119 (2016) [link][pdf]