Knowing little about FreeSurfer, I'll jump in recklessly nonetheless. AFNI's +x coordinate is Left and +y is Posterior, but FreeSurfer's is probably +x=Right and +y=Anterior. So x and y need to be negated to transform from one to the other, probably.
It would be easy to try this out for Option 2. I don't recall,
are there "# comment lines" at the top of rh.IT.1D, or is it
all just numbers? If it is just numbers, you can try:
awk '{printf "%f %f %f\n", -$2, -$3, $4}' rh.IT.1D > rh.IT.RAI.1D
This will just extract those 3 columns, negating the first
two (note again that awk uses 1-based indexing for the
columns). Then you can just use rh.IT.RAI.1D in your
3dSurf2Vol command, without using the option,
'-sxyz_orient_as_gpar', and without any column indices.
Hopefully one of these two options will work out for you.
- rick
