Hi Rick,
Thank you so much for the explanation.
So essentially if I use @SUMA_MAKE_SPEC_FS it will automatically call the Mapicosaohedron which will take your standard icosahedron shape and AFFINELY warp it to the native brain subject, correct?
1)Are all surface tools such as SurftoSurf and 3dVol2surf affine transforms (based on your response above), and if so are there any tools external to AFNI that use nonlinear that you are aware of?
2) In looking at the SUMA_AligntoExperiement command it uses 3dWarpDrive and 3dAllineate for warping my native brain surface to MNI. Do you see any issues if I replaced these command lines with nonlinear afni tools (ie 3dQwarp) to perform the nonlinear warp instead or is this not valid for surface based analyses?
Thanks,
Ajay