A few of my brains were excessively skull stripped and I used watershedding to correct them by adjusting the h-values. After that I ran 

recon-all -autorecon-pial -subjid <subject name>

I observe that the brainmask and aseg are remade but not the wm.mgz. Why is that so? Aseg is missing those parts of the brain which were initially excessively stripped (even after setting the brain mask alright and it looking perfect). I am attaching some pics here . Anyone have any solutions?