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.
Method:
Find the median of all positive values >= clip value.
Set the clip value to 0.50 of this median.
Repeat until the clip value doesn't change.
Options:
-mfrac ff = Use the number ff instead of 0.50 in the algorithm.
-verb = The clip value is always printed to stdout. If
this option is used to select verbose output,
progress reports are printed to stderr as well.
N.B.: This program only works with byte- and short-valued
datasets, and prints a warning message if any input
voxels are negative. If the dataset has more than one
sub-brick, all sub-bricks are used to build the histogram.
N.B.: 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.
A csh command line for the truly adventurous:
afni -dset "v1:time+orig<`3dClipLevel 'v1:time+orig[4]'` .. 10000>"
(the dataset is from the 'sample96.tgz' data samples). Can you
figure out what this does?
(Hint: each type of quote "'` means something different to csh.)
This page generated on
Tue Aug 3 16:42:44 EDT 2004