Put a control on the GUI that will get the user input. This control could take the form of a edit text box, a slider, a popup menu, a listbox, a checkbox, or whatever you want. To get the values from any function or callback function that has access to handles, do this:
userValue = handles.slider1.Value;
userValue = handles.popup1.Value;
userValue = handles.editText1.String;
userValue = handles.checkbox1.Value;
userValue = handles.listbox1.Value;
