So in that case if I need to run the script in Windows then how should I frame the command. I am following the http://mrtrix.readthedocs.io/en/0.3.16/tutorials/hcp_connectome.html link* to generate the connectome mtrix. Nothing else is mentioned in the doc about how to run in Windows. The script was not executing without FSL or Freesurfer as I posted in separate thread.
*now located at: Processing of HCP data