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

This is what you should look out for (rare in our data:

attachment:checkintensity.jpg

See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints Freesurfer Wiki] on how to fix such a problem.