[Freesurfer] missing brain

Hi,

I am currently in the process of reconstructing my brains after edits. However, the brains keep being reconstructed with large portions of brain missing/cerebellum missing; ie they are much worse than before I edited them. However, I am sure that I have only put control points in white matter areas; ie not partial volume, so I am very confused as to why this is happening; in one brain for example I had not put any cotnrol points (only made a very small white matter edit). Has this happened to anyone else before? Am i somehow running the wrong command somewhere? Could the watershed be wrong in the script, ie accidentally changed?

Grateful for help,

Regards Cathy