Hi Amit,
The first thing that comes to (my) mind is an issue with the gradients orientation. Is it possible that you have a flipped sign in the x-direction (or y-direction)? You could try rerunning the analysis pipeline after flipping either the x- and/or y-component of the gradients and see if that makes any difference.
One way to spot this could be visualizing the spherical harmonics lobes from the CSD file you created along the way. Could you perhaps visualize them on an axial slice around the genu of the of corpus callosum? That would allow you to see if the orientation is fine.
Also, 20 diffusion encoding directions is not much. Are you trying to use the spherical harmonics approach rather than a diffusion tensor approach for modelling the data? Check out this page on the relation between number of diffusion directions and the maximal l_max you should be fitting to your data.
Best,
Roey
P.S.
There’s a very old thread about it (from the older version of mrtrix), mentioning gradient issues specific for GE scanners. Might be useful (might not).
See other gradient-direction issues here. Making sure you’re using the up-to-date versions of the various toolboxes might also be helpful.