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If you made edits (i.e. added control points), run

   '''recon-all -subjid <mysubjectname> -autorecon2-cp -autorecon3'''

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):


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

CbuMeg: AnalyzingData/check_autorecon2 (last edited 2016-10-25 09:57:42 by OlafHauk)