Hi @zeydabadi,
No worries about those zeros, that’s entirely expected (and should even be like that). See also @jdtournier’s reply to your other post here: Contents of response_*.txt , which may help you to understand these zeros. The first line of your response_wm.txt is essentially the b=0 part of the WM response function. We don’t expect ( / want) any anisotropy at b=0, so only the lmax=0 term is non-zero. The non-zero lmax=0 term encodes the overall size of that shell of the response, whereas the lmax=2,4,6,8,10 terms encode the shape. If the latter are all zero, you’ve got an isotropic shell, which is exactly what the b=0 shell is.
That’s entirely separate to your second issue, the chopped WM FOD image. I don’t know for sure what happened there, but it appears either your dwi2fod step crashed or otherwise stopped prematurely, or the result has not been written to disk yet. The latter may be the case if you work with a remote storage, under certain circumstances. Did you get an error / crash from dwi2fod? Are you sure it wasn’t still running at the time you opened that image in mrview? If it all finished successfully, and you subsequently open the WM FOD file (again), you shouldn’t get this. (the only other explanation would be that your brain mask stops right there, but that’d be weird in its own right)
Cheers,
Thijs