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
@NoisySkullStrip -input anat+orig
For an anatomy with lots of CSF and low SNR Note how 3dSkullStrip options are passed after -3dSkullStrip_opts
Optional parameters:
- -3dSkullStrip_opts SSOPTS: Anything following this option is passed
- to 3dSkullStrip
-keep_tmp: Do not erase temporary files at the end.
ANAT.ns : A skull stripped version of ANAT ANAT.air and ANAT.skl: A couple of special masks ANAT.lsp : A volume that is used to threshold ‘air’
out of the volume to be stripped. @NoisySkullStrip tries to choose a threshold automatically but fails at times. You can set the threshold manually with -lspth and rerun the script to try and get a better result
Do send me feedback on this script’s performance.
-h_web: Open webpage with help for this program
-hweb: Same as -h_web
-h_view: Open -help output in a GUI editor
-hview: Same as -hview
-all_opts: List all of the options for this script
- -h_find WORD: Search for lines containing WORD in -help
- output. Seach is approximate.
Ziad S. Saad, March 28 08. saadz@mail.nih.gov