Opensuse 11.4 : Freesurfer 5.3 :QAtools_v1.1

I am trying to generate QC data from data generated using Freesurfer ver 5.3 and I'm getting the following error

"   Checking if all files exist...PASSED

     Checking actual file order...FAILED
     (read ../1006454_20216_2_0/scripts/recon_checker.log)
     ERROR: Actual file order disagrees with common file order for subject 1006454_20216_2_0"

On checking the recon_checker.log it states

     This subject may have been
     processed with a different version of FreeSurfer other than the version
     used to create the common file order file (based on v5.1 by default if not
     specified by the user).  Consider generating an output file order file for
     your specific dataset using the 'genoutputorderfile' flag.

     See the '-help' flag for details.

I cannot find any details of this flag in any help file or any online help as to how to correct his problem

Dave Liewald