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

External Email - Use Caution 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.