= 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. If you made edits (i.e. added control points), run '''recon-all -subjid -autorecon2-cp -autorecon3''' Then check again.