== 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.

== Troubleshooting the Skull Strip ==
If you would like to quickly run several different watershed thresholds simultaneously, you can use the -multistrip flag which will create several orig, T1, and nu volumes stripped with the following preflood heights: 5, 10, 20, 30.

You can change which preflood heights it uses (instead of 5, 10, 20, 30) by first doing:
{{{
setenv SUBJECTS_DIR /path/to/your/data
setenv WATERSHED_PREFLOOD_HEIGHTS '20 30 40 50'
recon-all -multistrip -clean-bm -s <subjid> -no-isrunning
}}}

Note that it will launch mri_watershed for each one for each vol orig, nu and T1, so if you have 12 heights, for example there will be 36 processes.



=== Programs ===

 * [[mri_em_register]]
 * [[mri_watershed]]