Hi all,

     I need ROIs of SC(Superior Colliculus). Can freesurfer distinguish it from other brainstem structures in segmentation?

     I also need to see responses of distinct layers of SC. Can freesurfer do layers segmentation according to the distance between each voxel and SC surface layer? 

That is, I need ROIs of different depth in the SC. The depth should be calculated by the distance from the voxel to SC surface.  

How to modify the 'recon-all -all' code if I just need the segmentation function mentioned above?

Please forgive the ignorance of a freesurfer beginner. 

Thank you in advance!

                                                                                         Chen He