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Hi Dusan, Volumes are computed from soft segmentations, which ameliorates the problems with partial voluming with the surrounding CSF. Kind regards, /Eugenio

-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Dusan Hirjak dusanhirjak@hotmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, 16 May 2019 at 16:21 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, "freesurfer-request@nmr.mgh.harvard.edu" freesurfer-request@nmr.mgh.harvard.edu Subject: [Freesurfer] brainstem - partial volume effects

External Email - Use Caution Dear Freesurfer experts,

I have one question regarding the partial volume effects on brainstem volume when using Freesurfer 6.0 brainstem tool: Could partial volume effects in a comparatively small sample (n=92) have an influence on the results (group difference in SCP volumes)? How should I deal with this effect? Any suggestions are welcome.

best regards

Dusan