Check intensity normalisation
With the following command you can check whether white matter was segmented correctly:
tkmedit <mysubjectname> brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white
Use the "TkMedit Tools" window to scroll through slices ("Slice +/-"), to change the views ("C, H, S") etc.
This is what you should look out for (rare in our data):
See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints Freesurfer Wiki] on how to fix such a problem.
If you made edits (i.e. added control points), run
recon-all -subjid <mysubjectname> -autorecon2-cp -autorecon3
Then check again.