Checking skull stripping after autorecon1

In order to check the skull stripping, use

You can use the key combinations "CTRL 1" and "CTRL 2" to switch between views of your complete MRI and the skull-stripped MRI (not surprisingly, that's your MRI without the skull). The aim is to check whether the skull was completely removed, or whether some of it is still left.

You will see something like this:


Instructions on how to fix a bad skull strip are on the Freesurfer Wiki. Few data sets (if any) will need this type of editing.