I've read in the mailing list archives people have had issues with tkmedit and free view displaying control points differently. For me the first brain I've loaded up has a single control point in free view that does not show in tkmedit. Others have complained of free view showing points seemingly at random? Is this a user related issue perhaps?
Here are the contents of the control.dat file in question
55.000000 -60.000000 -41.000000 54.000000 -61.000000 -41.000000 53.000000 -62.000000 -41.000000 52.000000 -59.000000 -37.000000 52.000000 -63.000000 -40.000000 2.000000 48.000000 14.000000 2.000000 47.000000 13.000000 1.000000 46.000000 11.000000 1.000000 41.000000 8.000000 1.000000 40.000000 6.000000 0.000000 45.000000 10.000000 0.000000 44.000000 10.000000 0.000000 43.000000 10.000000 0.000000 39.000000 6.000000 0.000000 38.000000 6.000000 0.000000 37.000000 7.000000 -1.000000 42.000000 10.000000 info numpoints 17 useRealRAS 0
the errant control point is on slice 128 best viewed coronally.
jon