I would recommend that you adjust the watershed values in freesurfer's skullstrip and then continue running the rest of the freesurfer recon-all pipeline. There are details on the Freesurfer wiki
Fixing a Freesurfer Skull-strip.
Another option (though I've never tried it), is you can tell recon-all to not do skull-stripping using the -noskullstrip option. I believe you can then take the last file created in autorecon1 and then skull-strip that using your choice of tools (3dSkullStrip, bet, etc). Then continue on with autorecon2 and autorecon3.
Skull Strip (-<no>skullstrip)
Removes the skull from mri/T1.mgz and stores the result in
mri/brainmask.auto.mgz and mri/brainmask.mgz.
Runs the mri_watershed program. If the strip fails, users can specify
seed points (-wsseed) or change the threshold (-wsthresh, -wsmore, -wsless).
The -autorecon1 stage ends here.
When in doubt, I find the
Freesurfer Mailing List to be excellent.
