The atlases used by samseg are very different from freesurfer GCAs, and the samseg-template creation is not an easily-accessible utility at the moment. Feel free to look through the GEMS code in the FS repository, but it might be some time before we have an easy-to-use samseg atlas building tool in freesurfer.

Best

Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alberto Del Cerro Leon <bertocerron@gmail.com>
Date: Wednesday, May 5, 2021 at 11:11 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] help with SAMSEG

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Hello Freesurfer team, my group is interested in using the SAMSEG tool to evaluate white matter lesions in MCI patients. We would like to use a personalized atlas for the measure. We suppose that we need to use the flag --atlas but we don`t know if we need a generic atlas or we need an atlas at each subject' spaces.

Thanks in advance for your help.