(From an earlier email reply)

Hello Yufeng,

Dear Sir,
I want to translate the freesurfer result to the AFNI by using SUMA. Now I want all the subjects to align to a Standard-Mesh Surfaces. My question is as followed:
1. If I need to use MapIcosahedron to produce the Standard-Mesh Surfaces for every subject or the @SUMA_Make_Spec_FS now generates standard-mesh surfaces by default.
You can use what @SUMA_Make_Spec_FS creates, or you can also create your own. The only reason to create your own is if you want to have higher or lower mesh density. The 141 surfaces are pretty dense (~200'000 nodes) and the 60 surfaces have ~36'000 nodes (see CreateIcosahedron -nums -ld 141). If you prefer different densities, you can use the -ld option to add more. For example, adding all three: -ld 141 -ld 60 -ld 121 would create std121 surfaces in addition to 141 and 60.

Also I recommend you start using the -GIFTI option for @SUMA_Make_Spec_FS

2. How can I set the -ld value in the MapIcosahedron?? Now I just set -1, and I am not sure if it is the best?
You should set it to be the same across all of your subjects. Using 141, you will get surfaces that are more dense than what comes out of FreeSurfer (distance between nodes, on average, will be smaller). You can get the average edge length by loading the surface in SUMA, then open the surface controller, and press 'more' to see information about the surface. Search for 'avg seg. length' . Or from the command line: SurfInfo -i std141.lh.smoothwm.asc -detail 1 | grep 'avg set.'

3. I want to check the result if the subjest has align to the Standard-Mesh Surfaces prefectly. I find suma can color the result by using Node index number in the suma.pdf( page:37 and 38). I want to know how can exam the result by using this way.

That requires a little work. You can of course just create a color file a load it on the surfaces and see how they compare. You can also put all the surfaces in one spec file (as I do in the demo script run_stdmesh_demo) and then click on one surface and see where the corresponding locations are in the remaining surfaces.

I hope this helps.
cheers,
Ziad