diff --git a/Home.md b/Home.md index 5b4c395..b8e835f 100644 --- a/Home.md +++ b/Home.md @@ -25,8 +25,8 @@ These names will be reused throughout the Wiki to refer to content present in th ## 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 + - 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. - 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 @@ -39,9 +39,10 @@ The navigation bar stores most of the actions that you will want to use. There a - 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 + - Reset Window Layout - Resets the dimensions of the File Information, Loaded Files, and Parameters areas to their default layout - Options - User Guide - Opens a pop-up window containing some information about processing stages + - Regroup Files from Metadata - Opens a pop-up window that allow for abatch assignment of groups based on other metadata such as age or sex - 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) @@ -74,20 +75,23 @@ On top of this generic information, there is also some data that is unique to SN - 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" +If the data loaded was in the BIDS structure and does contain metadata about the .snirf files such as age, sex, or handiness, this will also be present to view under BIDS - (value). 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, or parsed from the adjacent metadata. -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. +There are four parameters that are added to the right of the File information area once a file has been selected that can be changed. 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 +- Sex - Used to assist in the generation of groups based on the participants sex +- Hand - Used to assist in the generation of groups based on the participants 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` + +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 ## -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. +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: +- 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. ## 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](https://git.research.dezeeuw.ca/tyler/flares/wiki/Parameters), 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: +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. By default, FLARES exposes most of the parameters needed for an analysis allowing for immense customizability, with some more advanced parameters being hidden behind the `Show Advanced Parameters` preference. 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 descriptions are provided on their own Wiki page that can be found by [clicking this link](https://git.research.dezeeuw.ca/tyler/flares/wiki/Parameters), or by clicking one of their categorical links. Information about the individual parameters can also be found in summary form inside FLARES by clicking the "?" icon next to the respective parameter. Below is the complete list of parameter sections, with sections that have all their parameters marked as advanced or no parameters being labeled with a ⚠️ symbol. This does not mean that the step itself is advanced, but rather that it is simply not visible by default: - [Preprocessing](#preprocessing) - [Trimming](#trimming) @@ -100,30 +104,34 @@ When performing a fNIRS analysis, these parameters are some of the most importan - [Coefficient of Variation](#coefficient-of-variation) - [Median Absolute Deviation](#median-absolute-deviation) - [Power Spectral Density Noise](#power-spectral-density-noise) -- [Channel Variance](#channel-variance) +- [Sensor Dropout](#sensor-dropout) - [Bad Channels Handling](#bad-channels-handling) -- [Optical Density](#optical-density) +- [⚠️ Optical Density](#optical-density) - [Temporal Derivative Distribution Repair filtering](#temporal-derivative-distribution-repair-filtering) - [Wavelet filtering](#wavelet-filtering) -- [Haemoglobin Concentration](#haemoglobin-concentration) +- [⚠️ Haemoglobin Concentration](#haemoglobin-concentration) - [Enhance Negative Correlation](#enhance-negative-correlation) - [Filtering](#filtering) - [Extracting Events](#extracting-events) - [Epoch Calculations](#epoch-calculations) - [Design Matrix](#design-matrix) - [General Linear Model](#general-linear-model) -- [Finishing Touches](#finishing-touches) +- [⚠️ Generate GLM Results] +- [⚠️ Generate Channel Results] +- [Region of Interest](#finishing-touches) +- [⚠️ Generate Contrast Results] +- [⚠️ Finishing Up] - [Other](#other) ## Buttons ## -At the bottom of all the parameters, there will be buttons visible that can be pushed. 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. - 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. +- 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. ## 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. +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. # 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. \ No newline at end of file