Sorry for the late response. From dcm2nii you should be getting a nifti file, bvec and bval file for each series. If you are using a philips scanner with their stock sequences, you will have a dummy volume at the end and dcm2nii will output 6 files for each series. the 3 files mentioned and the same 3 files but starting with “x” where the dummy sequence is removed which is what you want to use.
You can find example files here: http://brainsuite.org/WebTutorialData/DWI_Feb15.zip
and explanations of file formats here: http://brainsuite.org/processing/diffusion/file-formats/