Hi, Emilie,
So I check both folders. The folder with which I can run DKE successfully contains 3 folders, named "combined", "dki_avg_coreg" and "dki_avg_nii" persepctively. And each folder contains NII files like rdki_0.nii, rdki_1000_1-30.nii and rdki_2000_1-30.nii, and in dki_avg1_nii contains one more named meandki_0.nii
While in the folder that fails to run DKE, in the intermediate_processing folder there is only one folder named "dki_avg1_nii", and then it also contains rdki_0.nii, rdki_1000_1-42.nii and rdki_2000_1-42.nii, without meandki_0.nii
Do you know what's wrong with that? Looking forward to your reply. 
Best regards,
Xinman