chxc123 Wrote:
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> Hi Ziad,
>
> Thanks for your suggestion.
>
> I tried it and loaded the output file onto a
> inflated std.141 surface. It looked like a mesh
> covering the brain surface, but the locations and
> size of BA areas looked fine.
>
Do you mean the color pattern covered the whole surface? What are the values at the regions outside of BAs when you right click on them in SUMA?

> I then tried to use MapIcosahedron directly by
> editing the .spec file: replaced the LabelDset
> name (lh.aparc.a2009s.annot.niml.dset) with
> lh.BA.thred.annot.niml.dset (the file generated
> with FSread_annot) and only kept smoothwm and
> sphere.reg in "States" and "NewSurface" to save
> time. After running MapIcosahedron, I loaded the
> output file (std.141.lh.BA.thred.annot.niml.dset)
> onto a inflated std.141 surface and the BA areas
> looked the same as shown with tksurfer on the
> original surface (no "mesh" looking).

Well done. I should consider adding all the atlases to the default of @SUMA_Make_Spec_FS. Someday I hope.

>
> So, I guess for converting a surface into standard
> mesh, MapIcosahedron may do a bettter job than
> SurfToSurf with a M2M file. I am not sure if this
> is a disply / colormap issue. Please correct me if
> I am wrong here.

Most likely, see below.

>
> BTW, can MapIcosahedron only convert the data
> assigned with the option "-NN-dset_map" or
> "-dset_map" without converting all the surface
> data included in the .spec file?
>
Not at the moment, that is why I suggested SurfToSurf. But SurfToSurf does not label atlas data in any special way so SUMA does not know how to display it best. I will have to add this feature to SurfToSurf at some point.

> Thanks,
>
> Xiangchuan

cheers,
z