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NIRx NIRSport User Manual

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NIRStar™
14.1
User Manual
For use with NIRx NIRSport™, NIRScout™ and NIRScoutX™ Imagers.
NIRx Medical Technologies LLC
15 Cherry Lane
Glen Head, NY 11545, USA
www.nirx.net
NIRStar14-1_Manual_R15_2015-06-23.doc

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  • Page 1 NIRStar™ 14.1 User Manual For use with NIRx NIRSport™, NIRScout™ and NIRScoutX™ Imagers. NIRx Medical Technologies LLC 15 Cherry Lane Glen Head, NY 11545, USA www.nirx.net NIRStar14-1_Manual_R15_2015-06-23.doc...
  • Page 2 NIRx NIRS imaging systems are NOT intended for use as a clinical diagnostic or treatment guidance tool. Neither the system hardware (NIRSport, NIRScout, NIRScoutX) nor system control software (NIRStar) has FDA Approval. Use of these resources is for investigational use only...
  • Page 3 All rights reserved, including the right to translate the document. The content of the manual is the intellectual property of NIRx Medical Technologies, LLC. No part of the manual may be reproduced or distributed in any form without the express written permission of NIRx Medical Technologies, LLC.
  • Page 4 NIRStar 14.1 - User Manual Blank Page...

  • Page 5: Table Of Contents

    NIRStar 14.1 - User Manual Table of Contents Release Notes ............................11 General Remarks........................11 New Features ..........................11 Improvements/Enhancements ....................11 Bug Fixes ............................ 12 Introduction ............................13 NIRS Fundamentals ........................13 Intended Readership ........................14 Related Documents ........................14 Problem Reporting Instructions ....................
  • Page 6 NIRStar 14.1 - User Manual Data Streaming .......................... 36 Advanced Setup ......................... 39 Additional Functionality ......................39 Additional Menu Bar Items ......................... 40 Digital I/O ........................... 40 Diagnostics ..........................43 File Options ..........................44 About ............................46 Operating Panel ........................... 47 Review ............................
  • Page 7 NIRStar 14.1 - User Manual 10.3 Triggers and Timestamps ......................62 11 Subject Demographics ........................64 12 Integrated Stimulus Presentation......................65 12.1 NIRStim Features ........................65 12.2 NIRStim event synchronization ....................66 13 Data File Formats ..........................67 13.1 File Naming and Organization ....................67 13.2 Detector Readings: *.wl1, *.wl2 ....................
  • Page 8 15.1 Online/Offline Mode ........................76 15.2 Reviewer Function ........................78 16 Device-Specific Information ........................ 80 16.1 NIRSport ............................. 80 16.1.1 Hardware Configuration ....................80 16.1.2 Setup Screen ........................81 16.1.3 Dynamic Range Consideration: Detector Gain and Source Amplitude ......82 16.1.4...
  • Page 9 NIRStar 14.1 - User Manual 17.2.4 Block Average Display ....................... 95 18 Topographic Rendering ........................99 18.1 Installation ..........................99 18.2 Use of Topographic Rendering Displays ..................99 18.2.1 Real-Time Display ......................102 18.2.2 Quick Guide ........................103 18.2.3 FAQ ..........................104 19 Hyperscanning ...........................
  • Page 10 NIRStar 14.1 - User Manual Blank Page...

  • Page 11: Release Notes

    The release of NIRStar 14.1 includes important new functional features and bug fixes. We recommend that all users of NIRx systems update to this newest version. New functionalities of this version of NIRStar are highlighted throughout the text by the following tag:...

  • Page 12: Bug Fixes

    The user is now warned if a TopoLayout that exceeds the Block Average boundaries is created.  If a measurement starts with an empty data root directory, C:\NIRx\Data will now be used.  Entries from File Options (section 6.3) are now saved along with the Hardware Configuration.

  • Page 13: Introduction

    To achieve spatial mapping (or imaging) of brain activity, arrays of multiple source-detector pairs are placed over the area of interest. The NIRS imaging equipment developed by NIRx employs a unique measurement strategy in which EACH source channel forms a measurement channel with EACH detector channel.

  • Page 14: Intended Readership

    7.1. Intended Readership Familiarity with this document is strongly recommended for operators of the NIRx NIRS imaging devices including the NIRScout™ product family and the NIRSport™, to avoid instrument misuse that potentially can lead to hardware malfunction or data corruption.

  • Page 15: Installation

    (3D displays) may require computational performance exceeding these minimum specification. Download and Updates To obtain the software and to check for updates, please contact support@nirx.net. NIRStar 14.1 can be downloaded in an optimized version for two different screen resolutions: ...

  • Page 16: Additional Software Requirements

    NIRStar 14.1 - User Manual Additional Software Requirements Some NIRStar features, such as the ‘NIRStim’ experimental control software and the ‘Topographic Rendering’ capabilities, used to require the installation of a separate software packages on NIRStar14-0. Starting on NIRStar14-1, the software installer (LowRes/HighRes) already comprehends all the additional packages and toolboxes that may be needed to run any feature available on the acquisition software.

  • Page 17: Overview

    NIRx line of NIRSport and NIRScout functional imaging systems can explore. Whether your aim is to perform mobile studies with the NIRSport or high density hyperscanning measurements with the NIRScoutX, NIRStar gives you a wealth of system control and real-time display capabilities that are designed to maximize the investigational opportunities accessible with NIRS.
  • Page 18 NIRStar 14.1 - User Manual  Automated helpful suggestions to facilitate system use.  Real-time system status reporting display.  User directed comment box for information logging.  Up to 4-wavelength laser operation (optional equipment required) Functional Features of NIRStar: The NIRStar software screen, shown in Figure 4, is subdivided into four principal functional components.
  • Page 19 NIRStar 14.1 - User Manual i. Menu Bar: The Menu Bar at the top of the software screen allows access to several configuration and status functions of the imager along with tools for system diagnostics and specification of data path. A principal control feature is the Configure Hardware menu described in Section 5.

  • Page 20: Hardware Configuration

    ‘on’ position, launching NIRStar will cause the software to automatically identify the imager type (i.e., NIRSport, NIRScout, NIRScoutX). Because some system types are scalable, it is important that the hardware specifications listed in this section matches the hardware configuration present in the connected device.
  • Page 21 ‘Phantom’ (40% LED power level); for all physiologic experiments, please use the setting ‘Human Subject’ (full LED power). This feature is only available for NIRScout and NIRscout Extended devices. NIRSport devices employ an automated LED intensity adjustment feature (see section 16.1.3).

  • Page 22: Predefined Montages

    Moreover, a picture of the chosen layout is displayed for the user, where the positions of each source and detector on the 10-10 standard NIRx cap is shown to the user (Figure 6). Figure 6. Montage Motor_8x8 has been chosen under Predefined Montages tab and cap layout is displayed.
  • Page 23 NIRStar 14.1 - User Manual Right new to the drop-down menu, one may find the option “Perform Hyperscanning”, which allows the user to expand the chosen configuration for two subjects if the number of sources and detectors required are available (please refer to section 19 for more information on Hyperscanning requirements). Figure 7.
  • Page 24 NIRStar 14.1 - User Manual Figure 9. GUI interface successfully loaded and Cortex figures (Subject 1 and 2) displayed. In other words, only using the Predefined Montage tab, the user is able to completely configure the system for the experiment (given that the Hardware Specification tab has been previously set), select whether one or two subjects will be measured and also to load and display the Cortex plot(s) to be used to plot in real-time the data collected by the measurement.
  • Page 25 NIRStar 14.1 - User Manual Figure 10. “Create new Montage” form that appears by clicking “New…”. Here, the user may enter the desired montage name, the number of sources and detectors, and which additional files (TopoLayout, Probe Setup and head models) they would like to add to this montage. Please note that “Standard TopoLayout (.tpl)”...

  • Page 26: Channel Setup

    NIRStar 14.1 - User Manual Figure 11. Upon completion, the Montage drop-down menu list is updated and now shows Empathy_8x8. This message will also be displayed in the case that “Customized” Montage is chosen, which may happen either manually or when the user changes any setting of the Hardware Configuration, because this will result on a different configuration than the previously selected Montage.
  • Page 27 NIRStar 14.1 - User Manual Illumination Pattern The NIRStar software provides the user with the ability to specify illumination sequences. illumination pattern graphic identified under the Channel Setup tab indicates the illumination sequence used in the experiment, i.e., the order in which the sources are turned on during each scan. Each column of the matrix represents a source (in consecutive order from left to right, starting with source no.
  • Page 28 NIRStar 14.1 - User Manual The Scan Rate display on the right is automatically updated when the illumination pattern is changed. For EARLIER SOFTWARE VERSIONS (up to NIRStar 12.4) the scan rate was given as: = 62.5 Hz / (no. of steps + 2) scan Starting with Vers.
  • Page 29 NIRStar 14.1 - User Manual Parallel Illumination For a given number of sources, the number of steps may be reduced, and the scan rate increased, by turning on more than one source per step (i.e., highlight more than one dot per row). Figure 13 shows the case of a scan sequence in which two LEDs are switched on at the same time, i.e., 1 &...
  • Page 30 NIRStar 14.1 - User Manual Parallel illumination considerations Per LED driver card a maximum number of four sources may be used for simultaneous (parallel) illumination; this satisfies the most commonly encountered experimental situations. Trying to use a larger number of sources within the same cycle will cause an alert: Figure 14.

  • Page 31: Topographic Layout Editor ('Topo Layout')

    NIRStar 14.1 - User Manual Topographic Layout Editor (‘Topo Layout’) NIRStar 14.1 offers different ways of topographic data mapping. The ‘Topo Layout’ editor described here and shown in Figure 15 offers simplified, schematic mapping of the channels onto a geometric, rectilinear pattern.
  • Page 32 NIRStar 14.1 - User Manual The Layout Editor offers a convenient way of specifying the spatial arrangement of specific source- detector-combinations (‘channels’). As illustrated in Figure 15 and in Figure 16, the physical layout on the head (in this example, referenced to the international 10-10 system) is transferred to a tabular rectilinear view.
  • Page 33 NIRStar 14.1 - User Manual The Topo Layout matrix can have up to 20 rows and 15 columns, for a maximum of 300 cells. However, the largest array that the real-time Block Average display function can display is 15×10, so a maximum of 150 channels can be simultaneously viewed during the data collection process.

  • Page 34: Save Or Load A Topographic Layout

    NIRStar 14.1 - User Manual 5.4.1 Save or Load a Topographic Layout A specified topographic map may be saved for later use. Likewise, a saved layout may be loaded for use or re-editing. Both Save and Load functions are available in the Topo Layout tab. Clicking on either button (upper right corner of the user interface) brings up a navigator window, in which the user selects a desired location and specifies a filename (Figure 18).

  • Page 35: Channel Masking

    NIRStar 14.1 - User Manual Channel Masking The Channel Masking tab is used for selection of specific source-detector-combinations (i.e., measurement channels) for display in the time-series plots (see Section 10.1). Typically, these will be channels that are expected to yield good data quality based on the sensor separation distance being less than ~3.5 cm.

  • Page 36: Data Streaming

    The NIRStar 14.1 software includes a real-time data streaming facility, which allows the software to act as a server for transmitting the acquired NIRS data in real time to another computer via TCP/IP (see Figure 20). NIRx provides an optional software development kit (SDK) that enables users to build client software for receiving the data.
  • Page 37 NIRStar 14.1 - User Manual Please note that zero streaming latency is achieved for No. of Sources ≥ 8 Fewer Sources require internal data buffering, resulting in data latency on the order of 0.8 sec (4...7 sources) and 2 seconds (1...3 sources). Stream Data Pushing this button enables NIRStar’s function as a server to publish data over the network.
  • Page 38 NIRStar 14.1 - User Manual Buffer Depth In case the available bandwidth for the TCP/IP connection is severely limited, the data may be buffered to improve the streaming performance. Buffer Depth specifies the number of scans that are buffered before being transmitted. The minimum number and default for this parameter is ‘1’, i.e., each scan is transmitted immediately after acquisition.

  • Page 39: Advanced Setup

    NIRStar 14.1 - User Manual Advanced Setup The Advanced Setup tab allows the user to change basic instrument parameters affecting timing, LED modulation, etc. These should be changed only by developers and professional staff, and are password- protected to prevent users from inadvertently changing parameters. Figure 23.

  • Page 40: Additional Menu Bar Items

    One particular example is the use of a pulsed laser source for combined optogenetics/NIRS studies. In this case, the TTL trigger input of a diode laser module (optional equipment NIRx DL-473, 473 nm 0...100mW optical power, fiber-coupled output) is connected to one of the NIRScoutX digital output lines.
  • Page 41 NIRStar 14.1 - User Manual may be initiated in the target tissue. This particular example demonstrates the measurement of NIRS activation following optogenetic stimulation. Other forms of tissue stimulation (magnetic, electric, thermal, etc.) may be considered. The NIRStar digital I/O interface (Figure 24) provides programmable control of the timing and output states of the NIRScoutX system’s digital output port (for details of the hardware, connections, and signal specifications please refer to the NIRScoutX user manual).
  • Page 42 NIRStar 14.1 - User Manual 2) Pulse Sequence This digital I/O mode allows the user to generate finite pulse sequences. Available parameters are: Use: Activate this channel to generate a pulse sequence. If activated, any Start Marker in this channel will be deactivated.

  • Page 43: Diagnostics

    0.1 mV for Gains 0-5, and below 1.0 mV for Gain 6. For Gain 7, less than 10 mV of noise is to be expected. Please see Section 16.1.4 for NIRSport considerations. When performing a dark-noise test, it is CRITICAL that stray light be prevented from entering the optical detector fibers or the fiber ports on the detector cards.

  • Page 44: File Options

    Data Root directory All data files are organized within root_directory\... where the location of root_directory can be specified by the user. By default, data are located under C:\NIRx\Data\. Date directory All data recorded on a specific day are collected in a subdirectory of root_directory\..., which is named according to the format root_directory\yyyy-mm-dd.
  • Page 45 NIRStar 14.1 - User Manual Experiment directory For each recorded experiment, a subdirectory is generated, within the appropriate date directory, whose name contains a date identifier and the running number for that day: yyyy-mm-dd_xxx\. File name For each experiment, different files are generated (see section 13), all of which have identical filenames consisting of a prefix, a date identifier, and the running number of experiments recorded on that day.

  • Page 46: About

    NIRStar 14.1 - User Manual It is necessary to access the information from the Probe Setup (*_probeInfo.mat) file corresponding to the measurement, as explained on the alert message that pops up for the user once this option is enabled (Figure 29). If the user has set up the probes and prepared the display for Topographic Rendering (see section 18) before starting the measurement, the *.nirs file (format expected by Homer2) will be automatically generated and saved along with the other files in the dataset folder.

  • Page 47: Operating Panel

    In this step the instrument determines the optimum gain (or signal amplification) for each source-detector combination. Gain levels are numbered from 0 to 7 (NIRScout Systems) or from 0 to 2 (NIRSport), with each step representing a 10-fold amplification factor. During calibration, the Signal Quality (see Section 8.1) will be updated to reflect the current...

  • Page 48: Record

    NIRStar 14.1 - User Manual Record The Record button initiates a scan for which the data, gain settings, trigger events and various system settings get recorded. If first a test scan is initiated with the Preview button, and at some point afterwards during the scan the Record button is clicked, all data (i.e., both preceding and following the instant that the Record button was pressed) will be saved.

  • Page 49: System Setup

    NIRStar 14.1 - User Manual System Setup The System Setup tab is displayed when NIRStar is started. In a typical experiment and data recording setup, the user would first place the sources and detectors on the subject’s head, then calibrate the instrument, and then perform the data recording.
  • Page 50 NIRx imagers. This classification is a combined metric that takes into account all features of the traditional setup display (Gain, Level, Noise: please see definitions on section 8.2) at all wavelengths according to the table below.
  • Page 51 NIRStar 14.1 - User Manual Refresh The Refresh function serves to update the quality measures without having to perform a full calibration procedure. When the user clicks on the Refresh button, another brief measurement will be performed, consisting of the number of scans specified in the Scans: field. The data recorded during these scans are used to update the Signal Quality map according to the new Level and Noise indicators (but NOT the gain settings).

  • Page 52: Gain Map, Level And Noise Displays

    NIRStar 14.1 - User Manual Show Topo Labels If the Show Topo Labels option is selected, in General Display Options at the bottom of the software GUI, a source-detector identifier will be overlaid onto all topographic displays, as illustrated in Figure 34. Please note that this option is only enabled when “Use Topo View”...
  • Page 53 This can occur when with short source-detector separations, measures performed on the static phantom supplied with the NIRx imagers, or with measures performed on the forehead. Channels for which the maximum gain level of 7 does not provide sufficient signal strength to reach the recommended signal level are marked red.
  • Page 54 NIRStar 14.1 - User Manual Figure 36. Gain (top), Level (mid) and Noise (bottom) maps are displayed on new (left) and old (right) style Page 54 of 124...

  • Page 55: Navigating The Quality Display

    NIRStar 14.1 - User Manual 8.2.1 Navigating the Quality Display There are several buttons available on the Quality Scale window, as shown in Figure 37. Figure 37. Further buttons available on the Quality Scale window. Refresh: May be used to refresh the results depicted from the current calibration setup, similar to the Refresh button on the NIRStar main screen: the system will perform a brief measurement in order to update only the Level and Noise results.
  • Page 56 (a damaged emitter for the second wavelength) seemed most likely to be the cause. Please note that NIRx recommends its customers running periodical static phantom tests in order to make sure that the hardware is working correctly. The Quality Scale itself is not enough to evaluate it and should be used only as a first indicator of some problem.

  • Page 57: Experiment Notes And System Status History

    NIRStar 14.1 - User Manual Experiment Notes and System Status History Instrument in Use: Instrument type detected by the software Source Type: Indicates whether LED or Laser source is used (Laser is only available for NIRScoutX systems with optional equipment) Modulation Amplitude: Indicates the LED power level, ‘Human subject’...

  • Page 58: Data Visualization And Recording

    NIRStar 14.1 - User Manual 10 Data Visualization and Recording Following the proper System Setup steps, data may be previewed or recorded. The real-time data visualization capability of the NIRStar 14.1 software in the Data Visualization tab is automatically opened. Two basic ways of data display are presented side-by-side: A traces display, and topographic maps.

  • Page 59: Trace Plot Display

    NIRStar 14.1 - User Manual Trace Plot Display The time series data of the estimated oxy- and deoxy-hemoglobin concentration changes for each channel selected in the Channel Mask (see Section 5.5) are represented in a trace plot on the left side of the Data Visualization tab (see Figure 41).

  • Page 60: Topographic Display

    NIRStar 14.1 - User Manual 10.2 Topographic Display In addition to the trace displays, the relative Hb concentration changes in the measurement channels are presented as 2-D color maps in a topographic view (see Figure 41 and Figure 43). Depending on whether or not the Use Topo View box is checked, the map represents either the channel arrangement defined in the Topo Layout tab of the Hardware Configuration user interface (see Section 5.4), or all channels as a ‘Sources ×...
  • Page 61 PC extension card) or, alternatively, over third-party hardware interfaces communicating with the USB bus (2). These trigger signals are transmitted over a cable to the Trigger Input of the NIRScout(X) / NIRsport instrument where they are recorded, digitized, and transmitted to NIRStar for display and storage on the recording PC (3).

  • Page 62: Triggers And Timestamps

    Typically, event markers may signify the start or the cessation of a task, or a subject response. To this end, all NIRx imaging devices have digital signal inputs that accept trigger signals from other equipment such as stimulus presentation computers. These inputs are...
  • Page 63 NIRStar 14.1 - User Manual The Frame counter (Figure 46) displays the number of completed scans, or frames, which is defined as the number of full illumination steps. The n illumination scan (frame) is completed when all illumination points (LEDs) have blinked n times during the measurement. Figure 46.

  • Page 64: Subject Demographics

    NIRStar 14.1 - User Manual 11 Subject Demographics NIRStar offers a convenient way of recording the subject’s demographic and other information relevant to the statistical analysis of the experiment. Whenever the ‘Preview’ or ‘Record’ button is clicked, a dialog form will appear that allows entering information about the subject (identity, gender, age, etc), the experiment, and general notes.

  • Page 65: Integrated Stimulus Presentation

    Nevertheless its capabilities are sufficient to allow the control and timing of many basic psychophysiological experimental paradigms. NIRStim is particularly well suited to operate in wearable settings with NIRSport: Running NIRStim on the portable acquisition PC allows auditory stimulus or instruction presentation to the subject through headphones while trigger signals are transmitted to NIRStar through software without the requirement trigger generating hardware or trigger cabling.

  • Page 66: Nirstim Event Synchronization

    (LPT) port or through the StimTracker™ USB interface, a proprietary 3 party device made by Cedrus Corp. (http://cedrus.com/stimtracker), available through NIRx. Alternatively, if NIRStim is running on the same computer as NIRStar, the triggers may be sent internally, via software (Shared Variable), without requiring any additional hardware communication;...

  • Page 67: Data File Formats

    NIRStar 14.1 - User Manual 13 Data File Formats 13.1 File Naming and Organization By default, the NIRStar software organizes and names files automatically, using to the date and time of acquisition to define the target directory name and the common root of the file names. Alternatively, the user may specify a directory and/or a file-name prefix (see Section 6.3).

  • Page 68: Header File: *.Hdr

    NIRStar 14.1 - User Manual Parallel source Illumination It is important to note that even when more than one source is active per scan step (e.g., ‘bilateral’ setup), or the sequence in which the sources are illuminated, NIRStar will still save the data channels in the format outlined above.
  • Page 69 NIRStar 14.1 - User Manual TrigOuts=0 No. of trigger outputs (only available for NIRScoutX) AnIns=0 No. of auxiliary analog inputs (future option) SamplingRate=3.906250 Sampling rate in Hz Mod Amp="0.40 0.40" Modulation amplitude used for illumination Threshold=”0.00 0.00” Modulation threshold used (≠0 only for Laser) Paradigm Information Records details about the experimental paradigm.
  • Page 70 By using combinations of trigger inputs, as many as 15 conditions can be encoded by NIRScout and NIRSport systems, while NIRScoutX receives up to 255 conditions (8 inputs). Column 3: The number of the scan frame during which the trigger event was received.

  • Page 71: Other Files: *.Set, *.Evt, *._Config.txt, *.Inf, *.Nirs, *.Tpl, *_Probeinfo.mat

    *.hdr file. 13.4.2 filename.evt This file records the event marker channel code and frame number in a format compatible with the NIRx NIRS imaging systems. Each row of the tab-separated table corresponds to a recorded trigger event. The first column contains the frame number at which the trigger was received.

  • Page 72: Filename_Config.txt

    NIRStar 14.1 - User Manual 13.4.3 filename_config.txt This file is required by the NIRx NAVI analysis software and provides general information about the measurement parameters. raw_data_name='NIRS-2010-08-27_001'; Filename SamplingRate=6.25; Sampling rate in Hz waveLength_N=2; No. of wavelengths Wavelengths=[760 850]; Wavelengths used source_N=8;...

  • Page 73: Topo Layout File: Filename.tpl

    NIRStar 14.1 - User Manual 13.4.6 Topo Layout file: filename.tpl This file records the topographic layout information as it is entered in the topo layout editor of the Configure Hardware dialog (see section 5.4). The information is recorded in a tabular layout identical to the row and column structure in the Topo Layout editor.

  • Page 74: Quick Start Guide

    NIRStar 14.1 - User Manual 14 Quick Start Guide 14.1 Turning on the System 1. Make sure all system components are plugged in and that the host PC is turned on. 2. If using a NIRScout system, make sure that a valid USB link is established between the devices, by noting that the green Status LED on the USB controller front panel is blinking continuously.

  • Page 75: Perform Scan (Measurement)

    NIRStar 14.1 - User Manual 14.6 Perform Scan (Measurement) The measurement is initiated by pressing the RECORD button. Adjust viewing options as desired. 14.7 Stop Scan (Measurement) Use the STOP button to terminate the data recording. 14.8 Shut Down System 1.

  • Page 76: Data Review

    NIRStar 14.1 - User Manual 15 Data Review 15.1 Online/Offline Mode NEW FEATURE NIRStar14-1 can be run on two different operating modes: online (acquisition) or offline (review). The online mode is used to acquire data and to which almost all the functions described on the previous chapters refer.
  • Page 77 NIRStar 14.1 - User Manual On Offline mode, all the buttons on NIRStar main screen concerning hardware configuration, diagnostics and online measurement will be disabled and grayed out (Figure 52), because this mode is only expected to be used for data reviewing purposes. Figure 52.

  • Page 78: Reviewer Function

    Block Average – see section 17.2) will now represent the chosen dataset (Figure 55). For example, if you had a NIRSport originally in use and you load a dataset recorded using NIRScoutX, the Instrument in Use will now display the information concerning the loaded file, because it is on Offline mode.
  • Page 79 NIRStar 14.1 - User Manual Figure 55. NIRStar screens after dataset is correctly loaded. Top: System Setup; Bottom: Data Visualization. Page 79 of 124...

  • Page 80: Device-Specific Information

    (e.g., for a NIRSport 8×8, No. of Source = No. of Detectors = 8). Instead, an Instrument Type drop-down menu is displayed, in which the appropriate device or model must be selected.

  • Page 81: Setup Screen

    4-6 of a NIRScout device, to which these roughly correspond. Battery Charge Indicator When connecting to a NIRSport device, a ‘Battery Charge’ indicator will appear in the Timing area of the user interface. The indicator will probe and update the battery’s charge level every 10 seconds, in 25%- steps.

  • Page 82: Dynamic Range Consideration: Detector Gain And Source Amplitude

    Figure 58. Low levels of battery charge and alert messages. Left: Level <= 50%; Right: Level <= 25%. 16.1.3 Dynamic Range Consideration: Detector Gain and Source Amplitude In addition to the detector gain switching mechanism, by which NIRSport achieves a dynamic measuring range of approximately 1:10 , a new LED intensity adjustment was implemented to prevent situations of detector saturation.
  • Page 83 Figure 61 shows the resulting gain setup. For both the prefrontal and the motor cortex, valid gain values are reached, and no signal saturation is observed. In this example, the LED amplitude of the NIRSport imaging the prefrontal area was set to 0.018 V for optimal, non-saturated readings while the more absorbing motor region required the full intensity setting of 0.4 V.
  • Page 84 Figure 61. Gain setup for the layout example above (screenshot from an earlier version of NIRStar). In Tandem mode, each NIRSport is set to the optimal illumination strength individually. The final illumination setting is recorded in the *.hdr file, as shown below.

  • Page 85: Diagnostics/Dark Noise Test

    Figure 62. The illumination setting (amplitude in Volts) is recorded in the *.hdr file (parameter ‘Mod Amp’). 16.1.4 Diagnostics/Dark Noise Test For NIRSport devices, the dark-noise test window shows a scale with Gains 0-2, according to the specifics of the detection hardware (Figure 63). For expected noise levels, please refer to the hardware manual.

  • Page 86: Channel Setup

    Figure 64. Illumination Pattern is disabled and grayed out for NIRSport device. 16.2 Tandem Operation When two identical NIRx NIRS imager models are connected to the control PC, NIRStar offers the option of operating both instruments in Tandem Mode, i.e., as one imaging system with twice the channel capacity of either unit by itself.

  • Page 87: Master And Slave Concept

    NIRStar 14.1 - User Manual Figure 65. Specification of Tandem Mode in the Hardware Configuration dialog 16.2.1 Master and Slave Concept The software will automatically designate one instrument ‘Master’ and the other ‘Slave’. The assignment of Master and Slave is relevant for the channel numbering and the connection of event-trigger cables. Whenever a new NIRS instrument is connected to the control computer, the NIRStar instrument drivers will automatically assign it an internal device number that will be permanently retained for this particular instrument.

  • Page 88: Channel Numbering Scheme

    NIRStar 14.1 - User Manual Cross-talk between devices must be avoided by all means because sources from one device can cause signal distortion in the other device’s detector channels. Measurements are possible only between sources and detectors of the same (i.e., Master or Slave) device.

  • Page 89: Channel Masking

    NIRStar 14.1 - User Manual Figure 66. Channel Setup in Tandem Mode 16.2.4 Channel Masking Two separate channel masks are defined, one per device. Similar to the Channel Setup, use the Master/Slave selector radio button to toggle between the Channel Masking corresponding to each device.

  • Page 90: Advanced Displays Capabilities

    NIRStar 14.1 - User Manual 17 Advanced Displays Capabilities NIRStar 14.1 provides advanced real-time display features including topographic rendering and event- related averaging. These features are available under the Displays Setup tab in Hardware Configuration (Figure 67). Starting on NIRStar14, the rendering functions in NIRStar do not require a Matlab license to be installed on the same computer.

  • Page 91: Topographic Display

    NIRStar 14.1 - User Manual 17.1 Topographic Display This function provides rendering of the topographic hemoglobin data onto realistic coordinate spaces in 2D or 3D (Figure 68). This functionality is implemented in a separate module distributed with NIRStar, and requires separate installation (see section 3). Figure 68.

  • Page 92: Preparing The Block Average Display

    For each condition, a unique event trigger marker is expected to be received by NIRStar. Trigger Marker: Specify the event marker code associated with each condition (1-15 for NIRScout or NIRsport, 1-255 for NIRScoutX). Block averaging is performed only if at least one of the fields is assigned a non-zero value.

  • Page 93: Channels Distance

    NIRStar 14.1 - User Manual 17.2.2 Channels Distance NIRStar 14 allows the user to enter individual source-detector pair distances for the channels enabled in the Channel Masking tab (Figure 71) in the case that non-equidistant source-detector separation values should be considered. These values will be considered in the calculation of the Hb/HbO concentration changes performed by NIRStar.

  • Page 94: Displaying Real-Time Block Average Plots

    NIRStar 14.1 - User Manual Figure 72. Block Average control. 17.2.3 Displaying Real-Time Block Average Plots The Block Average plot is activated and controlled in the ‘Block Average’ tab of the NIRStar main screen (Figure 72), under ‘Block Average Setup’. The ‘Block Average’ tab also contains an enlarged plot of one channel, which may be selected with the vertical scroll bar to the right of the plot.

  • Page 95: Block Average Display

    NIRStar 14.1 - User Manual Figure 73. Block Average Display in action Open: If at least one marker has been set to a non-zero value, the Open button is enabled as soon as the user clicks on Preview or Scan. Clicking this button will launch a separate Block Average Display window (Figure 73).
  • Page 96 NIRStar 14.1 - User Manual Please note that the numbers of rows and columns in Topo Layout determine the size of each graph in the Block Average Display. Therefore, we advise you not to insert any blank rows/columns. The label in each graph gives the source- and detector-optode numbers for the corresponding channel. For example, 5-7 displays block-averaged data for the channel defined by Source 5 and Detector 7.
  • Page 97 NIRStar 14.1 - User Manual If the time interval between two consecutive triggers for the same marker is less than the user-defined upper limit for the display time period, then the upper limit will automatically be adjusted downward to the lower value (see Figure 74). Low-Pass Filter The ‘General Display Options’...
  • Page 98 NIRStar 14.1 - User Manual Figure 77. Deselecting two channels (3-2 and 7-6) in Hardware Configuration Masking of Noisy Channels Channel masking affects the block-average display and may be used to deactivate noisy channels. After a calibration is performed, one may infer from the Gain, Level and SNR values that some channels are noisy and may, therefore, want to exclude them from real-time visualization.

  • Page 99: Topographic Rendering

    Figure 78. Error message example if Topographic Rendering capability is not installed Please make sure to install NIRStar in its default location. In case of the need for specific, non-default file locations please consult with NIRx Support. 18.2 Use of Topographic Rendering Displays To use Topographic Rendering please go to the Display Setup tab in the Hardware Configuration dialog.
  • Page 100 Some examples are shown in Figure 80. A newly generated layout may be saved for later use in NIRx standard ‘probeInfo’ format (*_probeInfo.mat). If a pre-defined layout is available it only needs to be loaded for use. A library of standard cap configurations (source- detector arrangements) for a host of applications together with the appropriate probeInfo files are available from NIRx.
  • Page 101 NIRStar 14.1 - User Manual For detailed information about the use of the ‘3D Probe Setup’ tool, please refer to the separate nirsLAB User Manual. Please note that the Probe Setup should be coherent to the configuration from NIRStar, i.e. the number of sources, the number of detectors and channels chosen should be the same.

  • Page 102: Real-Time Display

    NIRStar 14.1 - User Manual Plot Mode After a ProbeInfo file has been loaded, use the Plot Mode area to select one of three available rendering views (for examples, please see Figure 68). Prepare Display Clicking this button will bring up a topographic display window with a blank head plot of the selected mode (Figure 81).

  • Page 103: Quick Guide

    NIRStar 14.1 - User Manual Data Type: Select the Hb-state to be shown in the MATLAB display (HbO: Oxy-Hemoglobin; Hb: Deoxy-Hemoglobin; Total: Total Hemoglobin, i.e. the sum of Hb and HbO). Scale Factor: This slider may be used to adjust the amplitude scale of the topographic plot. Data Points Average: The time average (specified in data points) determines the number of scans that the software averages between successive display updates.

  • Page 104: Faq

    NIRStar 14.1 - User Manual 18.2.3 FAQ The plots won’t work as described! Please make sure that: 1. you have the standalone rendering program installed 2. the ‘Prepared’ indicator light is on (initially red color changes to green) 3. your measurement configuration (no. of sources, no. of detectors and channel masking) is correct and does not conflict with the advanced display settings 4.

  • Page 105: Hyperscanning

    NIRStar 14.1 - User Manual Figure 82. Hyperscanning example 19 Hyperscanning 19.1 Setting up Hyperscanning NIRStar offers a Hyperscanning mode to study functional neurovascular activation on two people simultaneously (see Figure 82). The Hyperscanning mode is accessible in Channel Setup tab of the Hardware Configuration GUI, provided that valid numbers of sources and detectors are available.
  • Page 106 NIRStar 14.1 - User Manual Figure 84. Hardware Configuration → Channels Setup: Perform Hyperscanning Hyperscanning is available only if an even multiple of four detector optodes and an even multiple of eight source optodes are available in the system. In Channel Setup, make sure to set the numbers of sources and detectors accordingly.

  • Page 107: Hyperscanning 3D Display

    NIRStar 14.1 - User Manual subjects. In Channel Masking, any change made for one subject will automatically be applied to the other, i.e., both subjects will always have the same Channel Masking. The recorded data are saved in two different folders, ‘Subject1’ and ‘Subject2’, that are located in the experiment-specific main directory (see Section 6.3).

  • Page 108: Laser Operation

    NIRStar 14.1 - User Manual Figure 86. Optional 4-Wavelength laser operation of NIRScoutX device. 20 Laser Operation NIRScout extended devices allow the substitution of the regular dual-wavelength LED light sources with laser diode based 4-wavelength illumination sources (Figure 86). 20.1 Hardware Specification Figure 87.
  • Page 109 NIRStar 14.1 - User Manual In order to operate the laser sources on a NIRScoutX device, the ‘Source Type’ selector under Hardware Specification needs to be set to ‘Laser’. This option will only be available for NIRScoutX devices, and only if at least one Laser Driver Card is installed in the system (for details, see NIRScoutX Laser Module Manual).
  • Page 110 NIRStar 14.1 - User Manual Lasers must NOT be operated with LED modulation amplitudes. Mishandling this operation may permanently damage the system! When the Laser option is selected as Study Type, the checkbox “Laser Splitter Box?” will appear (Figure 89). Figure 89.

  • Page 111: Saved Files

    NIRStar 14.1 - User Manual When ‘Laser Splitter Box’ is checked, the Number of Sources field under the Channel Setup tab will be kept an even number i.e. each time the user increases or decreases the number of sources by clicking on the corresponding arrow up or down, a pair of sources will be respectively added or removed from the illumination pattern.

  • Page 112: Appendix A. How To Use A 'Simulated Device' For Testing And Training

    NIRScoutX systems: NI USB-6259 iii) NIRSport systems: NI USB-6216 Using the same codes listed above, with NIRStar14-1 one is also able to simulate these devices. In order to create a new device, right-click “Devices and Interfaces” and select “New”. A new window will pop up, as depicted below.
  • Page 113 NIRStar 14.1 - User Manual Figure 93. Create new NI device Select the option “Simulated NI-DAQmx Device or Modular Instrument”, as chosen on Figure 93. On the new window, you may use the search field to look for the desired instrument. Following the example below, one may find the simulated device corresponding for NIRScout systems: Figure 94.
  • Page 114 NIRStar 14.1 - User Manual Figure 95. The simulated device (yellow) is now listed under Devices and Interfaces If your computer has more than one device installed, you may identify the simulated device marked in yellow. Real devices will be either green (connected) or white (installed, but not connected). When launching NIRStar, the software will connect to the first device from this list (alphabetic order).

  • Page 115: Appendix B. How To Generate A Channel-Layout Grid For An Arbitrary Optode Array

    (and a strong point of NIRScout and NIRSport systems is the flexibility they afford users in the positioning of optodes). For concreteness, here we consider a specific example that came from a research group interested in collecting data from a region in the back of the subject’s head,...
  • Page 116 NIRStar 14.1 - User Manual 1. Draw line segments connecting all pairs of adjacent source and detector optodes (see Higher-Order Considerations, p. 78). Each line segment represents one measurement channel: Figure 98: Measurement channels (nearest source-detector neighbors). 2. Place a mark in the middle of each line segment. These marks indicate the approximate locations of the centers of the volumes of tissue that the channels are sensitive to: Figure 99: Indication of channel positions.
  • Page 117 NIRStar 14.1 - User Manual 3. Count the number of distinct channel locations in the vertical dimension. This will tell you how many rows to specify in your channel layout: Figure 100: Horizontal Channel locations = number of rows in your layout. 4.
  • Page 118 NIRStar 14.1 - User Manual 5. Give each channel a numerical label, m-n, where m is the source number and n is the detector number: 6-11 6-11 6-11 7-11 7-11 7-11 7-10 7-10 7-10 2-10 2-10 2-10 2-12 2-12 2-12 8-12 8-12 8-12...
  • Page 119 NIRStar 14.1 - User Manual The 6-step method for generating a channel layout is straightforward to implement for nearly any optode array. A possible downside is that it can lead you to generate a grid containing large numbers of rows and columns (10 and 14 for the example above), with only a small percentage of the grid cells occupied by channels (26 out of 140, or ~19%).
  • Page 120 NIRStar 14.1 - User Manual Higher-Order Considerations Implicit in the instructions presented above is the idea that you will want to define channels for all pairs of nearest-neighbor sources and detectors, and only for these pairs. In our experience the assumption usually is correct, but you may find that for a particular analysis you either do not want to include every possible nearest-neighbor pair, and/or that you do want to include channels defined by optode pairs that are not nearest neighbors.
  • Page 121 NIRStar 14.1 - User Manual This change does not call for any modification to the sequence of steps given above. However, the number of rows in the channel grid will increase by 2, and the number of columns by 1, as shown next: 131415 131415 1314...
  • Page 122 NIRStar 14.1 - User Manual Likewise, the grid can be collapsed into a 9×5 one, by merging pairs of adjacent rows and columns: Figure 108: a more compact grid with nearest and non-nearest channels. So the new channels can be incorporated into the method presented here for specifying a channel layout.

  • Page 123: Index

    Configure Hardware, 39 Masking, Block Average, 98 Curve Display, 58 Master and Slave, 87 dark noise, 43 Menu Bar, 19, 20, 40 Dark Noise Test, NIRSport, 85 NIRSport, 80 Data Review, 76 NIRStim, 65 Data Streaming, 36 normalize, 59 Data Visualization, 58...
  • Page 124 NIRStar 14.1 - User Manual Start Marker, 41 Topo View, 33, 51, 60 Status and Options Bar, 19 Topographic display, 91, 99 Stimulus, 65 Topographic Display, 60 Stop, 42, 48, 75 topographic map, 34 System Setup, 49 Trace Plot Display, 59 System Setup Tab, 19 Trigger, 70 System Status History, 57...

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