Hi again @isAarya,
Just to briefly let you know: the actual bug has been fixed by @bjeurissen in the mean time. Coincidentally, a more major MRtrix release (candidate) was scheduled to happen today, and this bug fix has just made it in in time (thanks to you drawing our attention to the bug)!
Click here for more information about the bigger update that happened minutes ago.
(there’s some kudos for you in there 
)
If you update your MRtrix installation via git pull and ./build, you get all the new features as well as the bug fix for the -shell option to dwi2fod msmt_csd! 