Dear Krik, 

Thank you so much for your reply,

I am a beginner in using this software, so I will be really grateful if you assist me additionally.

I understand we have to do averaging of B0 (which I did not do before), however, concerning the different number of directions, I created 2 separate txt files each corresponding to a b-value gradient, and then I opened a command line to insert my parameters (the ndir, indexes, bvals from my DKE_paramters file) but nothing is defined in the cmd.exe, is this the right way to run dke from command line?

The problem now is that even with another set of data (1 B0, 20 directions b=1000, and 20 directions B=2000), the program is assuming that I have 40 direction for each b-value (as you can see in the SAM_DKE_parameters), so I do not know how to solve this issue. I am simply inserting the bvec file (which have 20 directions for b1000 and 20 for b2000) into the user-defined gradient vectors. 

I attached the parameters, 4d nifti and bvecs for the dki data set (1b0, 20 dir b=1000, and 20 dir b=2000) and data for noddi which I am using to estimate kurtosis (9b0, 30 b=711, and 60 b=2855). 

Thank you so much in advance, 
Regards, 
Wafaa