I am still having issues getting all of my control points to be effective. When I load my original point set (control.dat) and add control points to the set (using the control points edit tool), the new control points are visible but are not taken into
account when I re-run recon-all (recon-all -autorecon2 -autorecon3 -s Subject1). I have also tried saving multiple control points (control2.dat, etc) and that does not seem to work either. It appears as though I am unable to add control points after saving
the first set during my first edit of a brain. This is problematic because one edit of a brain is rarely sufficient, and I typically need to edit my control point set. Yet there seems to be no way to do this. The only other thing that I think may be causing
the problem is that I am running freeview 5.3 and freesurfer 5.2 (to keep our data consistent with the same version). Any ideas how to resolve this issue?