AFNI program: 3dClipLevel
Output of -help
Usage: 3dClipLevel [options] dataset
Estimates the value at which to clip the anatomical dataset so
that background regions are set to zero.
The program's output is a single number sent to stdout. This
value can be 'captured' to a shell variable using the backward
single quote operator; a trivial csh/tcsh example is
set ccc = `3dClipLevel -mfrac 0.333 Elvis+orig`
3dcalc -a Elvis+orig -expr "step(a-$ccc)" -prefix Presley
(a) Set some initial clip value using wizardry (AKA 'variance').
(b) Find the median of all positive values >= clip value.
(c) Set the clip value to 0.50 of this median.
(d) Loop back to (b) until the clip value doesn't change.
This method was made up out of nothing, based on histogram gazing.
-mfrac ff = Use the number ff instead of 0.50 in the algorithm.
-doall = Apply the algorithm to each sub-brick separately.
[Cannot be combined with '-grad'!]
-grad ppp = In addition to using the 'one size fits all routine',
also compute a 'gradual' clip level as a function
of voxel position, and output that to a dataset with
[This is the same 'gradual' clip level that is now the
default in 3dAutomask - as of 24 Oct 2006.
You can use this option to see how 3dAutomask clips
the dataset as its first step. The algorithm above is
is used in each octant of the dataset, and then these
8 values are interpolated to cover the whole volume.]
* Use at your own risk! You might want to use the AFNI Histogram
plugin to see if the results are reasonable. This program is
likely to produce bad results on images gathered with local
RF coils, or with pulse sequences with unusual contrasts.
* For brain images, most brain voxels seem to be in the range from
the clip level (mfrac=0.5) to about 3-3.5 times the clip level.
- In T1-weighted images, voxels above that level are usually
blood vessels (e.g., inflow artifact brightens them).
* If the input dataset has more than 1 sub-brick, the data is
analyzed on the median volume -- at each voxel, the median
of all sub-bricks at that voxel is computed, and then this
median volume is used in the histogram algorithm.
* If the input dataset is short- or byte-valued, the output will
be an integer; otherwise, the output is a float value.
* Example -- Scaling a sequence of sub-bricks from a collection of
anatomicals from different sites to have about the
same numerical range (from 0 to 255):
3dTcat -prefix input anat_*+tlrc.HEAD
3dClipLevel -doall input+tlrc > clip.1D
3dcalc -datum byte -nscale -a input+tlrc -b clip.1D \
-expr '255*max(0,min(1,a/(3.2*b)))' -verb -prefix scaled
* Author: Emperor Zhark -- Sadistic Galactic Domination since 1994!
++ Compile date = May 22 2013
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Thu May 23 09:53:48 EDT 2013