Skull Strip (-<no>skullstrip)

Removes the skull from mri/T1.mgz and stores the result in mri/ 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
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.


skullstrip (last edited 2010-04-01 20:13:03 by AllisonStevens)