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Manpage of voxelclassify
voxelclassify
Section: User Commands (1)
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NAME
voxelclassify - Classifies voxels according to the lowest-order spherical
harmonic series needed to fit the data adequately.
SYNOPSIS
voxelclassify
[-bgthresh <value>] [-csfthresh <maxA0>] [-order <maxOrder>]
[-ftest <thresholds>]
DESCRIPTION
Computes the spherical harmonic expansion of log(A(q)) in each voxel
and uses an F-test to determine the simplest model that gives a good
fit to the data.
If F-test thresholds are specified, the program performs the F-Test
and outputs the highest spherical harmonic order required to fit the
data: 0 for isotropic data, 2 for anisotropic Gaussian, and 4 or more
(up to the maximum) for anisotropic non-Gaussian data. Voxels
classified as background (see OPTIONS) have order -1.
If no f-test thresholds are specified on the command line, the program
outputs all the f-statistics in each voxel for independent processing.
These results are suitable for reading into the vcthreshselect program
for interactive model selection. The format of the output for each
voxel is:
exit code
log b=0 intensity estimate
f statistic comparing order 0 and order 2 models
f for order 0 and 4
:
f for order 0 and n where n is the maximum order specified
f for order 2 and 4
:
f for order 2 and n
:
f for order n-2 and n
OPTIONS
- -ftest <thresholds>
-
Specifies the F-test thresholds for adopting higher order models. A
threshold must be provided for every order between 0 and the
maximum order. The program will not consider a higher order model
unless the result of the F-test is smaller than the relevant threshold.
- -bgthresh <minA0>
-
Classifies all voxels with A(0) < minA0 as background, without
performing the F-test on the voxel. Ignored if -ftest is not
specified.
- -csfthresh <maxA0>
-
Classifies all voxels with A(0) > maxA0 as isotropic, without
performing the F-Test on the voxel. Ignored if -ftest is not
specified.
- -bgmask <image>
-
Set an explicit brain / background mask. Overrides -bgthresh.
- -order <maxOrder>
-
Set the maximum even spherical harmonic order that will be considered
by the program. Must be a positive even number. Default is 4.
EXAMPLES
Classify the data in image SubjectA.Bfloat, using no csf
threshold. Classify all voxels with A(0) < 50.0 as background. The
threshold for selecting an order 2 model is 1E-20, the thresholds for
the order 4 and 6 model are 1E-6.
voxelclassify -inputfile SubjectA.Bfloat -bgthresh 50.0 -schemefile
A.scheme -order 6 -ftest 1E-20 1E-6 1E-6 > SubjectA.VC.Bint
The next example does the same thing, but because no -ftest is
specified, the program outputs the raw F-Test data for later analysis
(eg with vcthreshselect(1)).
voxelclassify -inputfile SubjectA.Bfloat -schemefile
A.scheme -order 6 > SubjectA.VCthresholds.Bdouble
AUTHORS
Daniel Alexander <camino@cs.ucl.ac.uk>
SEE ALSO
vcthreshselect(1)
BUGS
Index
- NAME
-
- SYNOPSIS
-
- DESCRIPTION
-
- OPTIONS
-
- EXAMPLES
-
- AUTHORS
-
- SEE ALSO
-
- BUGS
-
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