Hi @ZahirSid!
It’s great that you improved the resolution of your refined map by adjusting the parameters!
As you effectively disabled masking during NU Refinement by setting Dynamic mask start resolution (A) to 1, in your customised NU Refinement, the output refinement mask will encompass the entire box. Using this mask in 3DVA means that it will not be focussing on the region that contains your target volume, and this could explain the appearance of the job outputs that you show.
To run 3DVA with the particles from your customised NU Refinement in 3DVA, we suggest either using a mask from one of the NU Refinement jobs run with masking, or a custom mask created using Volume Tools.