[Freesurfer] To what extend will brain.mgz affect final surfaces

Hi, FreeSurfer experts I apologize for so many questions, but I am fairly new to FreeSurfer and do need some help on reconstructing surfaces.

I noticed that in many areas, such as the subcortical regions with low signal intensity, even if they are filled in the wm.mgz and filled.mgz files, they are still excluded in the final surface files (see the attached file where the crossing hair is located).  So, I wonder which file actually decides a voxel will be included in the final surface or not, wm.mgz, filled.mgz, brain.mgz or all of them combined? Hope this will help when I modify the mgz files for fixing some topological defects.

Thank you in advance for the help. Leon