Welcome to the Wiki for FLARES (fNIRS Lightweight, Analysis, Research, & Evaluation Suite). Here will be the home of all the information that you will need to use this software.
Getting Started
In order to use FLARES, you will need a device with the following hardware specifications:
- OS: Windows 10/11 (64-Bit), Ubuntu 22.04/24.04 (64-Bit), MacOS Ventura/Sonoma/Sequoia/Tahoe (x64/ARM64) or newer
- Processor: Intel Core i7 Skylake, Ryzen 7 2nd Gen, Apple M1 or newer
- Memory: 16 GB RAM or more
- Storage: 4 GB of available space, SSD recommended
Download the appropriate version from the Releases tab and extract the zip file once it has completed downloading. Once the folder has been extracted, run the "flares" executable. The first launch of FLARES will take some time, so please be patient. FLARES will automatically check and download available updates every time the application starts. If you do not want FLARES to perform this action, you can block the app in your devices firewall or set your internet options to be a metered connection. FLARES does not currently run on ARM powered Windows devices.
Getting used to FLARES
Once FLARES opens, you will be greeted with a welcome popup that will contain all of the new features in your version of FLARES. Once this popup has been dismissed, you will encounter many options visible on the screen. To remain simple, this guide will break down what is visible on the screen into five distinct sections:
- Navigation Bar (Top of screen)
- File Information (Top left area)
- Loaded Files (Bottom left area)
- Parameters (Right area)
- Buttons (Bottom right area)
- Status Bar (Bottom bar)
These names will be reused throughout the Wiki to refer to content present in these physical locations.
Navigation Bar
The navigation bar stores most of the actions that you will want to use. There are 6 buttons available and all of them have submenus. Here is a high level overview of the buttons and what they do:
- File
- Open File... - Opens a singular .snirf file into the application
- Open Folder... - Opens all .snirf files from a singular folder into the application
- Recent Files - Contains a list of the 10 most recent files opened by the application
- Load Project... - Loads an existing saved project created by FLARES
- Recent Projects - Contains a list of the 10 most recent projects opened by the application
- Save Project... - Saves all loaded files, parameters, and results into a single file that can be opened at a later time by FLARES
- Save Project As... - Same as above, but asks for the destination to save the project every time
- Exit - Exits the application
- Edit
- Cut - Cuts the highlighted text
- Copy - Copies the highlighted text
- Paste - Pastes text from the clipboard
- View
- Toggle Status Bar - Turns on or off visibility of text notifications at the bottom of the application
- Reset Window Layout - Resets the dimensions of the File Information, Loaded Files, & Parameters to their default layout
- Options
- User Guide - Opens a pop-up window containing some information about processing stages
- Check for updates... - Checks the Git repository for any available updates. If an update is found, it is downloaded and extracted automatically
- Show Update Changelog - Pops out the update changelog in a new window
- Update events in snirf file (BORIS)... - See Updating Events in SNIRF File (BORIS)
- Update events in snirf file (BLAZES)... - See Updating Events in SNIRF File (BLAZES)
- Update optodes in snirf file... - See Updating Optodes in SNIRF File
- Reset to Default Configuration - Resets all saved Preferences, Window Layout, and Recent Files / Projects back to their original values
- About - Pops out information about the application in a new window
- Preferences
- 2D Data Bypass - TBD
- Incompatible Save Bypass - TBD
- Missing Events Bypass - TBD
- Analysis Clearing Bypass - TBD
- Folding Bypass - TBD
- Terminal
- New Terminal... - Opens a text based terminal to interact with the software using commands
File Information
This area is designated to providing information about a singular file. For information to be visible here, a file has to be loaded using File > Open File or File > Open Folder. Once a file has been opened and finishes initial processing, it will be visible in the Loaded files area. Selecting this file with a left click will cause generic information to be visible in the File Information area. This includes:
- File name - Name of the loaded file
- File size - Size of the file in bytes
- Creation date - Date the file was created
- Modified date - Date the file was last modified
- Full file path - Full path of the file that was loaded
On top of this generic information, there is also some data that is unique to SNIRF files:
- Annotations - Onset time, Duration, and Description of an event that occured in the file
- Digitization Points - Kind, ID, and Coordinates (Location) of optodes
- Measurement Date - Date that the data was written into the snirf
- Short Channels - Likely if short channel exists, Unlikely if a short channel does not exist. This is an educated guess based on distance, and may not be accurate
- Source-Detector Distances - Distances of channels in metres
This information panel is purely for validation purposes and it is not possible to change any of the values from this area since this is data from inside the file that was made when the file was created. There are three parameters that do get added to the File Information area once a file has been selected that can be changed. None of these additional parameters need to be set for the analysis to function. These parameters are:
- Age - Used to calculate the DPF of the participant. If Age is not specified, the value will be set to 25 automatically
- Gender - Used as a filter option to filter results at the end of the analysis. This is not implemented and currently will have no effect.
- Group - Used as a filter option to filter results at the end of the analysis.. If Group is not specified, the value will be set to "Default"
A "Why are these useful?" button can be found below this area and when clicked, will restate this information in a popup window. This is not implemented and currently will have no effect.
Loaded files
When files are loaded either from opening a singular file or opening a whole folder, all valid files will be shown in this area, along with a 28-stage progress bar. Clicking on a file will bring up its information in the File Information area and will allow for changes to be made to the participants Age, Gender, and Group. When processing is occuring, the 28-stage progress bar will update based on how far the participant has been processed. Each participant will have their own progress bar denoting how far their file has been processed. It is also possible to hover over any stage of the 28-stage progress bar to see which stage it represents. Right clicking a file in the Loaded Files area will bring up two buttons:
- Reveal - Opens a file browser set to the location that this file is stored on disk
- Remove - Unloads and removes the file, preventing it from being processed. This does not modify the file on disk. If the participant is removes after they have been fully processed, their data will still be included in the analysis. To get an analyis without this file, all participants will have to be processed again.
Parameters
When performing a fNIRS analysis, these parameters are some of the most important settings and it is crucial that they are correct for the study that is being performed. FLARES exposes most of the parameters needed for an analysis allowing for immense customizability. These parameters have been broken down into subcategories in an attempt to keep them simple. These parameters are also shown in the order that they will be applied, and logical values have been applied by default. Due to the length of describing each parameter, their decsriptions are provided on their own Wiki page that can be found by clicking this link, or by clicking one of their links. Information about the individual parameters can also be found in summary form inside the app by clicking the "?" icon next to the respective parameter. Below is the complete list of parameter sections:
- Preprocessing
- Trimming
- Verify Optode Placement
- Short/Long Channels
- Heart Rate
- Scalp Coupling Index
- Signal to Noise Ratio
- Peak Spectral Power
- Coefficient of Variation
- Median Absolute Deviation
- Power Spectral Density Noise
- Channel Variance
- Bad Channels Handling
- Optical Density
- Temporal Derivative Distribution Repair filtering
- Wavelet filtering
- Haemoglobin Concentration
- Enhance Negative Correlation
- Filtering
- Extracting Events
- Epoch Calculations
- Design Matrix
- General Linear Model
- Finishing Touches
- Other
Buttons
At the bottom of all the parameters, there will be buttons visible that can be pushed. These buttons include:
- Clear - Will clear all loaded files and any processing that has occured.
- Process - Will only be available once a file has been loaded. Will start the processing of all loaded files.
- Cancel - Will only be available when processing is occuring, and takes place of the Process button. Will cancel processing immediately.
- Analysis - Will ony be available once processing has been completed, on when loading a saved project file that has already completed processing. Will launch the analysis options window.
Status Bar
The status bar can be found at the bottom of the application and takes the whole width. It displays information throughout normal use of the application to denote sucesses, updates, or failures. It is recommended to keep the Status Bar enabled, however is can be disabled to get more real estate for other areas.
What's Next
Congratulations! You now should understand the application layout and some of the features that FLARES provides. See the Understanding Parameters Wiki page to continue your journey.
FLARES is distributed under the GPL-3.0 license.
Copyright (C) 2025-2026 Tyler de Zeeuw