Open a command line window in the directory containing raw2mzdb.exe (where archive file have been unzipped) 
Type:
raw2mzdb.exe -i <rawfilename> -o <outputfilename>

By default, the raw file will be converted in the “fitted” mode for the MS1 (MS2 is often in centroid mode and cannot be converted in fitted mode). If the MS2 (or superior) are acquired in high resolution (i.e in profile mode), you could specify that you want to convert several MSs in the required mode: 
raw2mzdb.exe -i <rawfilename> -o <outputfilename> -f 1-2 will try to convert MS1 to MS2 in fitted mode. 

There are two other available conversion modes: 

1. “profile”, the command line is then: raw2mzdb.exe -i <rawfilename> -o <outputfilename> -p 1 (means you want profile mode for MS1, others MS will be stored as they were stored in the raw file)
2. “centroid” : raw2mzdb.exe -i <rawfilename> -o <outputfilename> -c 1 (means you want centroid mode for MS1, others MS will be stored as they were stored in the raw file)

Ensure your regional settings parameters are '.' for the decimal symbol and ',' for the list separator