Hi Ajay,
1) Our tools do not do any surface alignment at all.
MapIcosahedron can work on top of FreeSurfer's surface
based (non-linear) registration. It users the spherical
registration to create standard mesh surfaces in the
space of the original surface.
The surface coordinates are in the same space at the
input anatomy, except there is node correspondence
across subjects (not xyz coordinate correspondence).
2) They do not warp to standard space. The intention
is to align the anatomy of a subject, possibly acquired
months ago, to the anatomy of the SAME subject, acquired
in the current scanning session. There is no reason to
use a non-linear program for this step.
3) I would have to look into SurftoSurf. But 3dVol2Surf
is used to map between volume and surface domains, not
to perform any coordinate transformations.
- rick