AnalyzingData/check_autorecon2 - Meg Wiki

Revision 4 as of 2010-06-09 13:52:55

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location: AnalyzingData / check_autorecon2

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 [ 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

Then check again.