Isabelle Wrote:
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> Hi Ziad,
>
> I ran mris_convert on the new .annot files. I get
> a .gii file and when I open it using this : suma
> -spec S001_lh.spec and then I load the .gii file,
> I can see my new ROIs. However, the names are a
> bit odd. It looks like SUMA is putting the name
> twice for a regions so you get something like
> wm_G_SuperiorTemporalG_Temporal_Superior.
I don't know why this is happening. If SUMA has two parcellation files loaded, it will show you the labels from both files. In your case, most nodes will have the same labels but they will appear in this form: LABEL|LABEL. For example: G_cuneus|G_cuneus
If that is not what is happening, then the problem may be in mris_convert.

I am
> guessing, I should make new spec files to
> accomodate the new parcellation.
You can replace the default parcellation file with the new one in the spec file if you like.
You probably want to make a copy of the original spec, should you choose to get back to it.
At the moment, you cannot specify two label datasets on the same hemisphere in the spec file.
Can I use
> @SUMA_make_spec_FS do to it? Or maybe I don't
> need to. My goal is to get a standardize
> annotation file that I can use to create a mask to
> extract ROIs.
I don't see why you need to. See 'NOTE II' in MapIcosahedron -help for an example on how to map your new parcellation file to the standard meshes you created earlier.
>
> Can I just standardize the .gii file and create a
> mask to extract the functional data?
Yes, see NOTE II reference above
>
> Thank you again for all of your help,
>
> Isabelle

cheers,
z