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. Control points are also used for editing subject's with intensity normalization problems. For example, if the white matter surface does not fully extend to include all the white matter voxels. In this case, control points can be added to increase the intensity of the voxels around the problem area to increase the intensity to 110. To better understand these edits, click here to go to the control points tutorial.
Control points appear as green dots in the Display Window. They can be turned off by choosing the Point Sets tab and unchecking control.dat.
Control points can be edited by choosing File->Load Point Set, a window will pop up, search for control.dat in the tmp directory as the file name and check Control Points and hit OK.
To make a new control point, choose the Point Set Edit button, now you can click anywhere in the Display Window where you would like to add a control point. To delete a control point, Shift+Left Click on the control point you would like to delete.
To save edits you have made to the control.dat file, choose File->Save Point Set.