Dear Ehsan, 

Every processing software works a little different. DKE expects the gradient table to be structured as a Ndir x 3 matrix. Specifically, this is a matrix with 3 columns and the number of rows equal to the number of gradient directions (only one set). Do not add any zero rows corresponding to your b0 image, this will result in errors.  If you have different gradient directions for each b-value you can create several text files and refer to them in the DKEparameters.dat file under :

fn_gradients = 'gradient_vectors_siemens30.dat'; % text file containing the gradient vectors; each row corresponds to a gradient vector; if a different gradient set was used for each b-value, a 1-by-(nbval-1) cell array of file names should be specified, with each cell specifying the gradient file name for the corresponding nonzero b-value

The 4D nifti you need to upload will exist of 1 b0 image (this can be an average of all your b0s) followed by your diffusion weighted images (e.g 30 B1000, 30 B2000) in the same order as your gradient table. 

Hope this makes sense, 
Best 
Emilie