The surfaces we generate do not include subcortical nor extratentorial structures.
You can generate surfaces from any mask or label.
If you have the svreg.label.nii.gz file loaded, open up the tools–> mask tool–> label mask tool
then click “update list”
you can then select any ROI (subcortical structures are in the 600s) and then click “make surfaces for each label”
These surfaces can be saved using the surface display toolbox (hit “s” and it will appear or Surface->Show Surface Display Properties Toolbox)
Your question on saving views was answered here: http://forums.brainsuite.org/forums/topic/bci-dni_brain_atlas-how2-save-retrieve-different-views/
you can remove the slices from the surface viewer by hitting ctrl+v or cmd+v
you can also unclick “slow slices” option in the surface display toolbox. Specific orientations can also optionally be turned off.
You can view your surface as a solid color by going to the surface display toolbox.
select your surface then select “solid color”
unclick that and your colorized surfaces will be reappear
Good luck. Glad you’re enjoying our interface