Hints
The following are some hints to help you identify the problem with the 5 troubleshooting subjects.
Subject 1
The trouble with this subject has occured in the skull stripping step, check the brainmask.mgz volume carefully, comparing it to the T1.mgz volume (loaded in aux) to make sure that the skull has been completely stripped away, leaving behind the complete cortex and the cerebellum.
Subject 2
The trouble with this subject has occured during the white matter segmentation step, check the surfaces to find the spot that they don't match the actual boundaries. If you load the wm.mgz volume in as the aux volume you will see a hole in this area. If you are looking in tksurfer you will see a hole or dimple in the inflated surface. You can use the "save point" "goto point" commands to find this spot in the volume.
Subject 3
The trouble with this subject has occured while making the final surfaces, check the final surfaces to make sure that they follow the actual boundaries and do not include anything that should not be included.
Subject 4