Josephine -
  The name of the file you want to convert is always the LAST parameter provided. The rationale for this is that it supports operating systems where you drag and drop the file you want to convert onto the application. Therefore, your command should be
  dcm2niix -o $outdir $datadir/filename.PAR.gz
run dcm2niix with no parameters 
  dcm2niix
to get more help on proper usage. I would also recommend updating to the latest version.

-chrs