Hi Kevin,

Note that deleting one and restarting suma may not be enough, since
afni already has the surfaces. You would actually have to re-start
afni to remove them. I will ponder this.


Prepare for more details than you want, but let me just start with
the short answer. :)

Choose the coloring you want via the Vol2Surf plugin. Please see
just a few lines of the plugin Help for basic usage.

Anyway, these messages are the result of some of the changes that I
have just added to afni. Please see this message for the basic details:

[afni.nimh.nih.gov]
in text: [afni.nimh.nih.gov]

----
For now, I wil just address the first message: "warning, found too
many surfaces for LDP"... I will follow this up with a post about
the "surfaces do not contain the same number of nodes" message soon.

In SUMA, Ziad has now implemented the idea of Local Domain Parents.
Every surfaces sharing an LDP has a node by node correspondence.
Basically as freesurfer "added air" to the balloon that is the white
matter surface (creating the pial, inflated and sphere surfaces), a
single node from the basic white matter surface could be tracked to
the other surfaces. This group of surfaces would then share an LDP
(where the LDP would be any of them, but one that had geometrically
accurate coordintates, such as the smoothwm surface).

----
When suma and afni talk together, suma sends all of the "geometrically
correct" surfaces to afni for display, and for afni to "color". But
now (through the changes Ziad and I have made), only one set of colors
is sent to suma per LDP, as all surfaces sharing an LDP will get the
same display in suma.

Also, since afni now uses vol2surf to colorize the surfaces, it only
makes sense to use (some combination of) 2 surfaces.

So currently, afni will complain if one LDP has more than 2 surfaces.
To avoid such a case, please select the 2 surfaces that you DO want to
match with the Vol2Surf plugin (or remove the surface you are not
interested in from the spec file).

Please let me know if some of this is not clear.

- rick