Nina-

For this task I would recommend using Surf Ice rather than MRIcroGL. This script
    https://github.com/rordenlab/spmScripts/blob/master/nii_coord2spheres.m
will generate one sphere for each node in your array, so you can call it like so
  c=[0,0,0,1,1; 40,0,0,2,2]; %1st at origin, 2nd 40mm right of origin
  nii_coord2spheres(c);
For more details on scripting Surf Ice see
  https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Scripting_from_Matlab

If you really prefer MRIcroGL, you can modify this script for your needs
  https://github.com/rordenlab/spmScripts/blob/master/nii_makeseed.m