Hi Chenxi,

I am not exactly sure, but I think you would have to modify the SeriesDescription in each of the extra b0 images manually for DKE's preprocessing to recognize them. Perhaps someone else can answer?

Alternatively, it looks like you've used the dcm2nii gui from MRIcron to generate the .bval and .bvec files. In this case you can use the dki_preprocessing script attached which will coregister and average nifti images in a folder with the .bval and .bvec files and generate outputs for DKE including a 4D nifti and a gradient table for DKE. The coregistration uses SPM, so you would add these scripts and SPM to the matlab path for everything to run. 

I hope that helps,

Russell