= Check intensity normalisation = With the following command you can check whether white matter was segmented correctly: '''tkmedit 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.