I've just created two new env variables to help manage setting overlay thresholds in tkmedit and tksurfer. If you just:
setenv FS_TKFTHRESH 3 setenv FS_TKFMAX 5
then the threshold will be set to 3 and the max/sat will be set to 5 in both tkmedit and tksurfer (so they will be consistent). You can still override them at the cmd line.
I've just checked these changes in, so they will be live in dev on the next update.
doug
freesurfer@nmr.mgh.harvard.edu