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Digitization
Many fNIRS and EEG investigators use Polhemus Patriot to 3D-digitize the position of anatomical landmarks, optodes and/or electrodes on the head. PHOEBE interfaces to Patriot for a seamless acquisition of optodes coordinates in the MNI space. This feature can be used independently from the assessment of the scalp coupling status of optodes.
Polhemus Patriot must be connected using the RS-232 serial cable provided with the device. If you previously used Patriot via USB, simply disconnect the USB cable and use the serial cable instead. It is not necessary to remove the Patriot PMI-2 software from the computer, if previously installed. If your computer does not have an RS-232 serial port (i.e., most recent laptops no longer have one), you can emulate it with an USB adapter compatible with your operating system.
Before digitizing for the first time, the serial port (COM) number, baud rate and source hemisphere must be set and tested in the menu Digitizer->Settings. The button SAVE AND CLOSE will enable upon successful connectivity with Patriot. These settings will be saved permanently and should be changed only in case of troubleshooting.
In order for the optodes' coordinates to be digitized reliably, the digitizer's source and sensor (connected to PORT 1) must be accurately setup in the experimental room. The source should be stably located at no more than 5 feet from the subject's head, and its orientation in PHOEBE ("+X","-X","+Y","-Y","+Z","-Z") must be set consistently with the setup (see X, Y, Z markings on the source). The sensor must be mounted stably on the subject's headgear (e.g., underneath the cap, on eyeglass frames, etc.) so to follow any head movement during digitization. The optodes' digitization is performed using the stylus' button. Currently, the sensor must be connected to PORT 1 of the digitizer and the stylus must be connected to PORT 2.
##Digitization of optodes
On the Digitizer tab, select the number of fiducials, sources and detectors to digitize. Note that these may be different than the number of sources and detectors available in the fNIRS instrument. In this case, PHOEBE will only monitor the first S sources and D detectors of the instrument, where S and D are the selected number of sources and detectors respectively.
In the same panel, set the distance range (minimum and maximum Euclidean distance) that PHOEBE will use to automatically determine the source-detector pairings. The pairings can be re-computed with a different separation range by selecting the menu Tools -> Compute SD pairings from distance range
Click the button DIGITIZATION to start the digitization process. PHOEBE will audibly call for the name of fiducials ("NZ", "AR", "AL", and optionally "CZ" and "IZ"), followed by sources ("S1", "S2", "S3",...) and detectors ("D1", "D2", "D3",...). The coordinates of each optode are acquired and display immediately on the head model after pressing the button on the Patriots' stylus. There is a 30 seconds timeout period for each optode's digitization.