Hi Rutvik,

A node is "out of bounds" if its coordinates are outside of
the box defined by the '-grid_parent' AFNI dataset. Since
the intention of the program is to output the AFNI volume
data in the surface domain, it made sense to only output
values for those nodes within the bounds to the data source.

However, I had originally considered adding an '-oob_value'
option (to specify the output value for nodes considered out
of bounds), and am still willing to do that. There just hasn't
been much interest in it.

At any rate, I will do this. My plan is to add 2 new options:

-oob_value VALUE : specify the value output for oob nodes
-oob_index INDEX : specify the indices for oob nodes

The reason for the second option is to fill in the index columns
in those same rows. Values of 0 or -1 both make sense to me.
These will default to 0, in the case where one is specified, but
not the other.

---

An option for the meantime would be to write a little script to
fix the output. You could just use awk to grab the 2 columns
that you want, pipe the output through sort, and send that to
another awk script that filled in any missing lines with:
NODE_INDEX 0

So if you wrote fillin.awk for the final step (and removed the '#'
comment lines from the top of the 3dVol2Surf output), you could
do something like:

awk '{printf "%07d\t%f\n", $1, $7}' 3ds2v.out | sort

The output of this would have the nodes sorted, so you could
pipe that through your fillin.awk script to fill in the gaps.

If you are in deparate need of this soon (either the program, or
more info on an awk script), please send me email.

Thanks,

- rick