Usage: 3dClipLevel [options] dataset Estimates the value at which to clip the anatomical dataset so
that background regions are set to zero.
set ccc = 3dClipLevel **-mfrac** 0.333 Elvis+orig 3dcalc -a Elvis+orig -expr “step(a-$ccc)” -prefix Presley
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 prefix ‘ppp’.
- [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.]
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.
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).
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.
be an integer; otherwise, the output is a float value.
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
++ Compile date = Dec 16 2015