The Time Course is displayed in a separate graph window. The graph will only be shown if the Time Course volume has more than one time point. Clicking on a vertex in the Display Window finds the corresponding functional voxel based on the registration and displays the values at that voxel for all time points in the graph window.
If there are multiple conditions defined in the header file, each condition will show up as a separate line in the graph. The legend on the right side of the graph window displays what line corresponds to what condition. By moving the mouse over a condition label in the legend, the corresponding line in the graph will be highlighted. This is useful for picking out one condition in a crowded graph.
You can also zoom into the graph. Click and drag with button 2 to draw a box around the area of interest. The graph will be resized around that box. Click with button 3 to zoom back out.
You can specify an average area to graph in two ways. You can click the vertices you want, marking them, and then choose Tools->Graph Marked Vertices Avg to graph the average. (Note that loading a patch marks vertices, so you can also graph the average of a path this way.) You can also load a label and graph the average of it with the Tools->Graph Label Avg.
The contents of the graph window can be written to a Postscript file with the Tools->Save Graph to Postscript File... command. It can then be included in another document or printed.