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Voxelclassify

Content-type: text/html Manpage of voxelclassify

voxelclassify

Section: User Commands (1)
Index Return to Main Contents
 

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

This document was created by man2html, using the manual pages.
Time: 02:07:11 GMT, December 04, 2017

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Page last modified on October 26, 2009, at 03:09 PM