I am currently trying to run FreeSurfer on a set of mouse brains and I have a few questions about it: 

1. Is it possible to generate 2D surfaces from a set of structural scans on mouse brain in FreeSurfer? 

2. Do the individual steps like Normalisation, Segmentation, Tessellation, etc rely on the Talairach space? 

3. Is there any way that I can replace the Talairach atlas that the steps use in the root directories or codes?

Thank you!

Best Regards, 

Heidi Foo