FA image, however, looks a little different from what it normally looks like. Could you please advise if I have missed any steps or did anything incorrectly? Also, could you please let me know if MD, AD, and RD images look ok?
From your code, I can’t decide whether there is a problem. The visualization results can be different because of a lot of things. You can check the view options in mrview to see if there is any difference, I think Intensity scaling may have some effects. Or maybe you should use other toolboxes(e.g. FSL) to generate metrics and directly check the voxel-vise values.
Still, some optimization can be applied.
First, from where I stand, the brain mask that HCP provided is not so good, so maybe you can generate a new mask for DWI image using MRtrix3.
Secendly, although HCP pipeline has preprocessed the data. It is suggested that mrdenoise and mrdegibbs should be used in the tutorial.
Lastly, the order of your command is a bit confusing, I prefer to type like this：
