Sorry, I didn't see the most recent posts. The command you would use is:

dke.sh /Applications/MATLAB/MATLAB_Runtime/v90/ /Applications/MATLAB/MATLAB_Runtime/v90/dke_parameter.dat

And the first parts of your dke_parameters.dat file would be the following:

studydir = 'Volumes/sifnosspace/ReesWork/dki_example_data_nifti'; % root folder for data from all study subjects
subject_list = {''}; % cell array of subject sub-folders within the root folder studydir
...
preprocess_options_fn_nii='4Drdki_0.nii';


NOTE that I added an ellipsis for the other parameters which must still be included, they just were not relevant here.