AFNI program: @NoisySkullStrip

Usage: @NoisySkullStrip <-input ANAT> 
                     [-keep_tmp] [-3dSkullStrip_opts OPTS]

Strips the skull of anatomical datasets with low SNR
You can recognize such dataset by the presence of relatively
elevated (grayish) signal values outside the skull.

This script does some pre-processing before running 3dSkullStrip
If you're intrigued, read the code.

This script is experimental and has only been tested on a dozen nasty
datasets. So use it ONLY when you need it, i.e. when 3dSkullStrip 
fails on its own and you have low SNR

Examples of use:
   For a normal anatomy with low SNR
   @NoisySkullStrip -input anat+orig

   For an anatomy with lots of CSF and low SNR
   Note how 3dSkullStrip options are passed after -3dSkullStrip_opts
@NoisySkullStrip  -input old_anat+orig \
               -3dSkullStrip_opts \
                  -use_skull -blur_fwhm 1 -shrink_fac_bot_lim 0.4


Mandatory parameters:
   -input ANAT : The anatomical dataset
Optional parameters:
   -3dSkullStrip_opts SSOPTS: Anything following this option is passed
                              to 3dSkullStrip
   -keep_tmp: Do not erase temporary files at the end.

The script outputs the following:
   ANAT.ns  : A skull stripped version of ANAT
   ANAT.air and ANAT.skl: A couple of special masks

Do send me feedback on this script's performance.

Ziad S. Saad, March 28 08.
saadz@mail.nih.gov