Sorry, lost track of the remaining questions. I believe the area is in mm2.
There is no simple tool for applying nonlinear warps to surfaces, but you can convert the surface to .asc or .ply and compute the new coordinates with 3dNwarpXYZ. Then you would have to save the new coordinates with the same triangles. Depending on the warp, it will likely make surfaces that flip inside-out and outside-in at various places, but you can try it. Moving surfaces with just an affine transformation can be accomplished with ConvertSurface.
quickspec takes type, name minimally, but you can add fun options like state, anatomical flag, domain parent and an associated label file if you like. You can also add a spec file name for the output; otherwise, it uses quick.spec for the output name.
# simplest example of quickspec
quickspec -tn gii mysurface.gii
IsoSurface is our tool for generating surfaces. You can compute a surface for every region in an atlas with a command like this one:
mkdir surfs
cd surfs
IsoSurface -isorois+dsets -input myatlas.nii.gz -o myatlassurfs.gii -Tsmooth 0.01 1500
suma -onestate -i *.gii
