Hi Tanmay
DiffusionWeightedVolumeMasking is a 3D Slicer based brain masking tool. If you choose FSL for your masking, then you can safely disregard this warning (which just tells you that it could not find this particular brain masking tool).

If you look at your masking protocol, it says BRAINMASK_method 1 . By double clicking on that, a window pops up that lets you select the method (We should change the information displayed to a description, not a simple number).

Also, DTIPrep is pretty strict regarding the exact naming. Your BRAINMASK_bcheck is set to "yes", but it should be "Yes" (upper case Y). In your case, this meant that the masking was not run (Brain mask check NOT set)

Martin