Control points are used in surface construction. Every subject has an associated control.dat file in their tmp directory; this is the list of control points, in Talairach space, that is read in to TkMedit automatically upon start.
Control points appear as green cross hairs in the Display Window. They can be turned off by unchecking Views->Control Points.
Control points can be edited with the Edit Control Points tool, which can be activated by pushing the button on the Main Toolbar, by choosing Tools->Edit Control Points, or by pressing the 'c' key when the mouse is in the Display Window.
To make a new control point, click anywhere in the Display Window with mouse button 2. To remove a control point, click near it with mouse button 3. Button 3 will remove the closest control point to the voxel clicked, within 3 voxels.
Whenever a new control point is made, it is automatically written to the control.dat file. However, removed control points are not removed from the file until you choose File->Save Control Points or quit normally with the File->Quit command.
In normal cases, the control.dat file is saved in the subject's tmp directory, so the FreeSurfer programs that use the file know where to find it. However, if you used the -f option to load a volume file by name, not specifying a subject name and directory, you will see a warning when you try to write a control point, and the file will be saved in the current working directory. This file can then be moved to a subject's tmp directory later.