Hi Dov,

Are you using standard meshes? i.e. do the surfaces for
your subjects have the same number of nodes to begin with?
If not, please see Ziad's page for this:
<[afni.nimh.nih.gov];

Is so then there are two reasons for which a node might not
be displayed. One is that all of the voxels that are used for
that node's value are excluded from your mask implied from the
-cmask command line option.

The other possibility is that the xyz location for the node in
question is outside the space of the AFNI volume that you are
getting data values from.

If you wish voxels for either of these cases to be included in
the output, you can use the '-oom_value' option to specify a
default value for a node which is obscured by your -cmask, or
you can include either '-oob_index' or '-oob_value' to specify
a default index and/or value for those nodes that lie outside
the AFNI volume.

Please see '3dVol2Surf' for more details about these options.

Please let me know if you have further questions.

- rick