Hi Oori,
I have added an option to SurfClust called -prepend_node_index that should solve your problem.
In general, I recommend that you do not bother interpreting .niml files unless you are using afni's i/o routines. For parsing purposes, you can also use ConvertDset to write datasets in the simplest of 1D forms. With the -prepend_node_index option, now also in ConvertDset, you can force the node index to be part of the output dataset.
Binaries containing these changes should be available this evening.
cheers,
ziad
