Most of the time, your files are organized and handled by a BrainVISA database. However, this does not mean that BrainVISA is unable to work with files that do not come from its database(s). Some processes do not require data to be stored in a specific directory. Moreover, all the processes allow the user to select input or output files outside of the database. It all depends on what you want to do! If you are not sure, stay in the database to avoid scattering your data.