AFNI program: @NoisySkullStrip
Output of -help
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 \
-use_skull -blur_fwhm 1 -shrink_fac_bot_lim 0.4
-input ANAT : The anatomical dataset
-3dSkullStrip_opts SSOPTS: Anything following this option is passed
-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
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.
Global Help Options:
-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.
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Fri Dec 2 21:09:19 EST 2022