Hello-

I assume you are using my software on a Windows computer. This uses a special version of BET that we compiled for the Windows operating system. At the time, there were different versions of BET for different image precisions, so my software essentially creates a temporary image with a specific precision to generate a mask. With MRIcron you can save the final masked image using the File/SaveAsNIfTI command. This does mean that the BET software will not be particularly useful from the command line: it works in concert with MRIcron to set an appropriate brightness and mask. For using BET from the command line I would strongly suggest using a modern implementation of BET using an OSX or Unix computer. One solution would be to set up a neurodebian virtual box. I think you can set up a shared folder so BET will be able to process an image in a Windows folder. This will give you a much more modern variant of BET (the version we used did not have the terrific "robust" -R option). The modern versions of BET do preserve data precision.