Hi Russell,

Thank you very much for getting back to me.

I do supply nifty as inputs and I only run dke, not dke_ft. My understanding is that by running dke, I am not doing tractography. Is that right?

My output files consist of dax.nii, dmean.nii, drad.nii, DT.mat, fa.nii, kax.nii, kfa.nii, kmean.nii, krad.nii, KT.mat, and mkt.nii. When I view these nii output files in fsl, I only load these output files and no other images. Comparing to the input file (which I named dki.nii), the output files are all flipped in the A-P direction and also there is a tilt in saggital view (as if the slices were acquired at an oblique angle but in fact, they were axial).

Is there anything that I can check in the nifty header to see if there is a "flag" that is somehow accidentally set in the header and causes confusion to the dke code? Does it help if I provide you my dke_parameters.dat file?

Thank you!

Yi-Fen