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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>

BUGS

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Time: 02:07:11 GMT, December 04, 2017

Voxelclassify