yfh2013 Wrote:
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> Dear Sir,
> I have translated the freesurfer result to the
> SUMA by using @SUMA_Make_Spec_FS. 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.

@SUMA_Make_Spec_FS does generate standard meshes.

> 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 one.

By default it generates them ld values of 141 and 60. My personal preference is powers of two (with low values for testing, high values for publication-quality analyses), but that's up to you. For example, ld=128 gives pretty meshes but may also be overkill unless you are working with high-res functional data. But any value around 100 or more will do perfectly fine.

> 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.

in two terminal windows, run

1) afni -niml
2) suma -spec your_spec_file.spec -sv T1.nii.gz

then in suma press 't' to let them talk and check the alignment visually