Linda Wrote:
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> For anatomical data: I get the result from the
> freesurfer and translate the result by using
> @SUMA_Make_Spec_FS and then MapIcosahedron.

The new @SUMA_Make_Spec_FS will run MapIcosahedron for you. I also recommend the -GIFTI option which creates more convenient output.

> For functional data: I do the correlation between
> two condition (different eye watching the same
> stimulate) within each subject . And then align
> each subject's the correlation result to the
> T1.nii (getting from freesurfer) by using
> 3dAllineate.

I don't understand what is being done here.

>
> 1 If I need to do @SUMA_AlignToExperiment next for
> anatomical for surface? I am a little confuse
> about the different between
> MapIcosahedron and @SUMA_AlignToExperiment.

MapIcosahedron has little to do with @SUMA_AlignToExperiment.
MapIcosahedron is used to create standard mesh versions of the original freesurfer surfaces. This remeshing of the surfaces greatly simplifies the process for group analysis (see this SUMA paper for details)
@SUMA_AlignToExperiment is used to align the anatomical volume in the SUMA/ directory (importe from the FreeSurfer output) to the anatomical volume in register with your current data. Unless the two volumes are identical, and you used the -GIFTI option for @SUMA_Make_Spec_FS, you will need to run this script in order to map current volumetric data onto the surfaces.
Remember to always open afni and suma, make them talk, and verify the alignments.

>
> 2 If I need to align the correlation result to the
> freesurfer's by using 3dvol2surf next? For the
> raw functional data, it need to align the
> functional data to anatomical data by using
> 3dvol2surf.

To be clear, 3dVol2Surf is for mapping volumetric data onto the surface, and not for alignment. You should be in a position where you have functional volume (F), anatomical volume (A), and the result of @SUMA_AlignToExperiment (S2A) all in alignment.
Then to map F onto the sufaces, you use 3dVol2Surf, with -sv S2A .
If this is all too confusing, I highly recommend you go though the bootcamp class slides and demo material.

I hope this helps.

cheers,
Ziad

But for me, the functional result has
> align to the T1.nii properly by using 3dAllineate.
> So I am not sure what to do next. Or I just not
> to align the correlation result by using
> 3dAllineate but directly use the 3dvol2surf.
> Thanks very much!