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tyler
2026-09-10 11:52:24 -07:00
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Home.md
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@@ -23,7 +23,7 @@ Once FLARES opens, you will be greeted with a welcome popup that will contain al
These names will be reused throughout the Wiki to refer to content present in these physical locations. These names will be reused throughout the Wiki to refer to content present in these physical locations.
## Navigation Bar ## ## Navigation Bar ##
The navigation bar stores most of the actions that you will want to use. There are 7 buttons available and all of them have submenus. Here is a high level overview of the buttons and what they do: The navigation bar stores most of the actions that you will want to use. There are 7 buttons available and all of them have submenus. Here is a high-level overview of the buttons and what they do:
- File - File
- Open File... - Opens a singular .snirf file into the application and loads adjacent metadata (if applicable) - Open File... - Opens a singular .snirf file into the application and loads adjacent metadata (if applicable)
- Open Folder... - Opens all .snirf files from a singular folder into the application and loads adjacent metadata (if applicable). This supports the BIDS structure for storing .snirf files. - Open Folder... - Opens all .snirf files from a singular folder into the application and loads adjacent metadata (if applicable). This supports the BIDS structure for storing .snirf files.
@@ -61,7 +61,7 @@ The navigation bar stores most of the actions that you will want to use. There a
- Plugins - Plugins
- Manage Plugins... - Opens the plugin manager window to allow for downloading plugins - Manage Plugins... - Opens the plugin manager window to allow for downloading plugins
- Terminal - Terminal
- New Terminal... - Opens a text based terminal to interact with the software using commands - New Terminal... - Opens a text-based terminal to interact with the software using commands
## File Information ## ## 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, File > Open Folder, or via dragging and dropping a file/folder onto this area. 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: 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, File > Open Folder, or via dragging and dropping a file/folder onto this area. 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:
@@ -73,7 +73,7 @@ This area is designated to providing information about a singular file. For info
- Full file path - Full path of the file that was loaded - 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: 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 - Annotations - Onset time, Duration, and Description of an event that occurred in the file
- Digitization Points - Kind, ID, and Coordinates (Location) of optodes - Digitization Points - Kind, ID, and Coordinates (Location) of optodes
- Measurement Date - Date that the data was written into the .snirf file - Measurement Date - Date that the data was written into the .snirf file
- 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 - 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
@@ -83,14 +83,14 @@ If the data loaded was in the BIDS structure and does contain metadata about the
There are four parameters that are added to the right of the File information area that can be changed once a file has been selected. None of these additional parameters are required to be set for the analysis to function. These parameters will be automatically populated from the adjacent metadata, but can be modified here unlike in the view-only File Information panel. These parameters are: There are four parameters that are added to the right of the File information area that can be changed once a file has been selected. None of these additional parameters are required to be set for the analysis to function. These parameters will be automatically populated from the adjacent metadata, but can be modified here unlike in the view-only File Information panel. 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 to create a generic DPF value - Age - Used to calculate the DPF of the participant. If Age is not specified, the value will be set to `25` automatically to create a generic DPF value
- Sex - Used to assist in the generation of groups based on the participants sex - Sex - Used to assist in the generation of groups based on the participant's sex
- Hand - Used to assist in the generation of groups based on the participants dominant hand - Hand - Used to assist in the generation of groups based on the participant's dominant hand
- Group- Used as a filter option once results have been generated at the end of the analysis. If Group is not specified, the value will be set to `Default` - Group- Used as a filter option once results have been generated 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. A "Why are these useful?" button can be found below this area and when clicked, will restate this information in a popup window.
## Loaded files ## ## 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, Sex, Handiness, 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: 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, Sex, Handiness, and Group. When processing is occurring, 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 the default file browser navigated to the location that this file is stored on disk - Reveal - Opens the default file browser navigated 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 a participant is removed after they have been fully processed, their data will still be included in the analysis. To get an analysis without this file, currently all participants will have to be processed again. - Remove - Unloads and removes the file, preventing it from being processed. This does not modify the file on disk. If a participant is removed after they have been fully processed, their data will still be included in the analysis. To get an analysis without this file, currently all participants will have to be processed again.
@@ -129,13 +129,13 @@ When performing a fNIRS analysis, these parameters are some of the most importan
## Buttons ## ## Buttons ##
At the bottom of all the parameters, there will be buttons visible that can be pushed that will perform various actions. These buttons include: At the bottom of all the parameters, there will be buttons visible that can be pushed that will perform various actions. These buttons include:
- Clear - Will clear all loaded files and any processing that has occured. - Clear - Will clear all loaded files and any processing that has occurred.
- Process - Will only be available once a file has been loaded. Will start the processing of all loaded files. - 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. - Cancel - Will only be available when processing is occurring, and takes place of the Process button. Will cancel processing immediately.
- Analysis - Will ony be available once processing has been completed, or when loading a saved project file that has already completed processing. Clicking this will launch the analysis viewer launcher window. - Analysis - Will only be available once processing has been completed, or when loading a saved project file that has already completed processing. Clicking this will launch the analysis viewer launcher window.
## Status Bar ## ## Status Bar ##
The status bar can be found at the bottom of the application and takes the entire 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. The status bar can be found at the bottom of the application and takes the entire width. It displays information throughout normal use of the application to denote successes, 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 # What's Next
Congratulations! You now should understand the application layout and some of the features that FLARES provides. See the [Understanding Parameters](https://git.research.dezeeuw.ca/tyler/flares/wiki/Understanding-Parameters) Wiki page to continue your journey. Congratulations! You now should understand the application layout and some of the features that FLARES provides. See the [Understanding Parameters](https://git.research.dezeeuw.ca/tyler/flares/wiki/Understanding-Parameters) Wiki page to continue your journey.