Yes, all of the folders contain files - currently (after changing preprocess_options.navg to 1 as you suggested) there are 5 of the folders: dki_avg1_coreg, dki_avg1_nii, dki_b0_coreg, dki_b0_nii and combined. And the files inside are all *.nii files.

So in this moment, the co-registration, averaging images and reading input files are complete!
Now I have a problem with this:

Undefined function 'plus' for input arguments of type 'cell'.
Error in dke_estimate (line 183)
Error in dke (line 182)
MATLAB:UndefinedFunction
 
I thought it has something to do with the variables dti_method.b_value and dti_method.directions. I tried to write [1:30] instead of {1:30} and some other options, but nothing seems to be the right way... Currently it is like this:

dti_method.b_value = [300 600 900 1200 1500];
dti_method.directions{1} = {1:30};
dti_method.directions{2} = {1:30};
dti_method.directions{3} = {1:30};
dti_method.directions{4} = {1:30};
dti_method.directions{5} = {1:30};

Do you by any chance have an idea what to do with that?

Thank you!