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@@ -10,7 +10,7 @@ In order to use FLARES, you will need a device with the following hardware speci
 
 Download the appropriate version from the [Releases](https://git.research.dezeeuw.ca/tyler/flares/releases) tab and extract the zip file once it has completed downloading. Once the folder has been extractes, 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.
 
-# App Layout #
+# Getting used to the app and its layout #
 Once FLARES opens, you will be greeted with many options on the screen. To remain simple this guide will break down what is visible on the screen into four sections:
 
 - Navigation Bar (Top of screen)
@@ -20,7 +20,7 @@ Once FLARES opens, you will be greeted with many options on the screen. To remai
 
 These names will be reused throughout the Wiki to refer to content in these physical locations.
 
-# Navigation Bar #
+## Navigation Bar ##
 The navigation bar stores most of the actions that you will want to use. There are 5 buttons availabe 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 file into the application
@@ -43,25 +43,55 @@ The navigation bar stores most of the actions that you will want to use. There a
 - Terminal 
   - New Terminal... - Opens a text based terminal
 
-# File Information #
+## File Information ##
 This area is designated to providing information about a singular file. Once a file has been opened and selected from the Loaded files area, generic information will be visible. This includes:
 - File name
 - File size
 - Creation date
 - Modifies date
 - Full file path
-\nOn 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:
 - Measurement date
 - Short channels (this is a guess based on distance)
 - Source-Detector distances
 - Digitization points
 - Annotations
+
 This information panel is purely for validation purposes, and it is not possible to change any of the values from this area. There is three parameters that do get added when a file is selected that can be changed. None of these values need to be set for the analysis to function. These parameters are:
-- Age - Needed to calculate the DPF of the participant. If Age is not specified, the value will be set to 25
+- Age - Used to calculate the DPF of the participant. If Age is not specified, the value will be set to 25
 - Gender - Used as a filter option to filter results at the end of the analysis. Not currently implemented.
 - 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"
 
-# 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 progress bar. Clicking on a file will bring up its information in the File Information area and allow for changes to the participants Age, Gender, and Group. When the analysis is running, the progress bar will update based on how far the participant has been processed. Right clicking the file will bring up two buttons:
 - Reveal - Opens a file browser 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 an analysis, their data will be still included in the analysis. To get data without this file, the analysis will have to be run again
+
+The analysis will finish when all progress bars have completed. If the analysis completes and a progress bar has not finished, then something went wrong processing that file. Checking the logs could provide insight into what went wrong.
+
+## 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. Below is a list of the submenus:
+- Preprocessing
+- Trimming
+- Verify Optode Placement
+- Heart Rate
+- Scalp Coupling Index
+- Signal to Noise Ratio
+- Peak Spectral Power
+- Bad Channels Handling
+- Optical Density
+- Temporal Dericative Distribution Repair filtering
+- Wavelet filtering
+- Haemoglobin Concentration
+- Enhance Negative Correlation
+- Filtering
+- Short/Long Channels
+- Extracting Events
+- Epoch Calculations
+- Design Matrix
+- General Linear Model
+- Finishing Touches
+- Other
+
+Information about the individual parameters can be found by chicking the "?" icon next to the respective parameter. There are more popups and menus that will appear after the analysis has completed. They will be discussed further down in the Analysis section.