Are you using the same gradient directions for each b value?
how many gradient directions are in fn_gradient.dat

The structure you need is the following:
fn_gradients = 'gradient_vectors_siemens30.dat'; = path where DKE can find your gradient table
bval = [ 0 300 600 900 1200 1500]; = your b values , you should have acquired 0 too
ndir = 30;
idx_gradients = {1:ndir 1:ndir 1:ndir 1:ndir 1:ndir}; = for your non zero b-values write down which lines in your gradient table correspond to the correct gradient directions. If in fn_gradient.dat there are only 30 gradients this is the right set up.
If you have a different gradient table for each bvalue the set up is different.
I noticed below you copied something about dti_method ? Unless you are interested in pure DTI calculations you can just keep that part turned off. The DKI output will include FA, MD etc.
You should be able to follow the manual more closely now that your bruker data is coverted to nifti. From this point on any error will not be related to the bruker data but to the way you set up your .dat file.
Hope this helped.
Emilie