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):
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 <mysubjectname> -autorecon2-cp
Then check again.
Check White Matter
Using the same tkmedit command as above, you can check whether there is white matter not included in the segmentation, or whether voxels are assigned to white matter when they shouldn't.
See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits Freesurfer Wiki] on what to do in this case.
If you made edits, run
recon-all -subjid <mysubjectname> -autorecon2-wm