Hi Corinne,

Thank you for the prompt reply!


So first, the data was aquired on a Siemens scanner, 3 shells (0, 1000, 2500), in both AP and PA directions.

My pipline is as follows:

I convert my data from dicom to nifti using dcm2nii gui, then I denoise the data using dwidenoise function in MRTrix3. The denosied dwi data is then corrected for motion, eddy current and susceptibility artifacts using FSL topup and eddy. Then using fslmerge and fslroi, I arrange the corrected diffusion data in the format required by DKE, average b0 first, then the second shell (b=1000 in my case) and then the third (b=2500). As for the bvecs, they are transposed in matlab to put them in 3 colums (x,y,z), and then arranged in a txt file to correspond to the arrangement of shells.

Would it help if I attach an example of the DKE produced fa/kfa files?

Thank you so much for the help! Looking forward to your reply.

Best,
Shereif