Hi Anne

I suspect that if you removed enough manually it would change. The atlas-based registration will change if the skull-stripping changes significantly, which will change the resulting segmentation.

cheers Bruce

On Sun, 20 Mar 2011, Hendrikx, A.A.E.M. (Anne) wrote:

Dear all,

We, members from the Donders Institute Nijmegen (The Netherlands), are using FreeSurfer to calculate amygdala volumes on MRI's. After a couple of tests we are suprised about the following:

We are wondering why the amygdala volume changes, after changing the watershed threshold. Besides, if we should nog change the ws-treshold, but manually remove remaining skull, the amygdala volume will not change.

We don't understand this. Can anyone explane this to us? And besides, what consequences are there for the accuracy of the calculations?

Best wishes,

Anne Hendrikx _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer