User-Manual.md

+[[_TOC_]]
+# Open data set
+Click on the toolbar button to open a data set   
+
+![image](uploads/4497e89faa7348be698ad253911f29b0/image.png)
+
+You can also use the File Menu  
+
+# Open BIDS folder
+
+Use the File Menu->Open BIDS option.   Note that you can also open a BIDS data set if you manually open a data file which is within a BIDS folder. AnyWave will detect the file is part of a BIDS and then will open the BIDS folder.
+
+# [Basic features](basic-features)
+
+# [Montages](montage)
+
+# [Markers](markers)
+
+# AnyWave Folders
+
+The application will create several folders in the Home directory of the user:
+
+* _Documents\\AnyWave_ on Windows
+* _/Users/username/AnyWave_ on macOS
+* _/home/username/AnyWave_ on Linux
+
+They are several folders created by AnyWave but only some are usefull to know for the user.
+
+## Settings
+
+This is the folder where AnyWave will put configuration and settings files. Do not delete or modify them.
+
+However, this is also the place to create a **user.json** file to specify particular parameters AnyWave will use.
+
+See Customise settings section.
+
+# Customise settings
+
+AnyWave allows the user to change preferences using the Edit->Preferences menu.\
+However, it is possible to customise some features using a user.json file that the user can put in the HOMEDIR/AnyWave/Settings folder.
+
+## MATLAB
+On Linux and macOS AnyWave expects MATLAB to be installed on /usr/local and /Applications respectively.   
+If you have installed MATLAB and MATLAB Runtime in another location, please add a user.json file in AnyWave Settings folder:   
+````json
+{
+"matlab_path" : "/path/to/MATLAB/including/Release folder",
+"matlab_runtime_path" : "/path to RUNTIME including the Release foder"
+}
+````
+Restart AnyWave.    
+
+This is not needed on Windows as MATLAB and MATLAB Runtime should be in the PATH environment variable, allowing AnyWave to detect them.   
+