Okay I found the problem.
set nums = ( `awk -F= '/LC/ {print $2 * 10000}' 3dD.nodata.${iter}` )
This line looks for the string "LC" in the 3dD.nodata file, but how many lines of LC you have depends on how many general linear tests you do.
So the 3 glts is 3 nums.
Sorry for the confusion!
