.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH KELLYKAPOWSKI "1" "September 2017" "KellyKapowski 2.1.0" "User Commands"
.SH NAME
KellyKapowski \- part of ANTS registration suite
.SH DESCRIPTION
.SS "COMMAND:"
.IP
KellyKapowski
.IP
DiReCT is a registration based estimate of cortical thickness. It was published
in S. R. Das, B. B. Avants, M. Grossman, and J. C. Gee, Registration based
cortical thickness measurement, Neuroimage 2009, 45:867\-\-879.
.SS "OPTIONS:"
.HP
\fB\-d\fR, \fB\-\-image\-dimensionality\fR 2/3
.IP
This option forces the image to be treated as a specified\-dimensional image. If
not specified, DiReCT tries to infer the dimensionality from the input image.
.TP
\fB\-s\fR, \fB\-\-segmentation\-image\fR imageFilename
[imageFilename,<grayMatterLabel=2>,<whiteMatterLabel=3>]
.IP
A segmentation image must be supplied labeling the grayand white matters.
Ddefault values = 2 and 3, respectively.
.HP
\fB\-g\fR, \fB\-\-gray\-matter\-probability\-image\fR imageFilename
.IP
In addition to the segmentation image, a gray matter probability image can be
used. If no such image is supplied, one is created using the segmentation image
and a variance of 1.0 mm.
.HP
\fB\-w\fR, \fB\-\-white\-matter\-probability\-image\fR imageFilename
.IP
In addition to the segmentation image, a white matter probability image can be
used. If no such image is supplied, one is created using the segmentation image
and a variance of 1.0 mm.
.HP
\fB\-c\fR, \fB\-\-convergence\fR [<numberOfIterations=50>,<convergenceThreshold=0.001>,<convergenceWindowSize=10>]
.IP
Convergence is determined by fitting a line to the normalized energy profile of
the last N iterations (where N is specified by the window size) and determining
the slope which is then compared with the convergence threshold.
.HP
\fB\-t\fR, \fB\-\-thickness\-prior\-estimate\fR thicknessPriorEstimate
.IP
Provides a prior constraint on the final thickness measurement. Default = 10 mm.
.HP
\fB\-a\fR, \fB\-\-thickness\-prior\-image\fR thicknessPriorFileName
.IP
An image containing spatially varying prior thickness values.
.HP
\fB\-r\fR, \fB\-\-gradient\-step\fR stepSize
.IP
Gradient step size for the optimization. Default = 0.025.
.HP
\fB\-l\fR, \fB\-\-smoothing\-variance\fR variance
.IP
Defines the Gaussian smoothing of the hit and total images. Default = 1.0.
.TP
\fB\-m\fR, \fB\-\-smoothing\-velocity\-field\-parameter\fR variance
isotropicMeshSpacing
.IP
Defines the Gaussian smoothing of the velocity field (default = 1.5).If the
b\-spline smoothing option is chosen, then this defines the isotropic mesh
spacing for the smoothing spline (default = 15).
.HP
\fB\-b\fR, \fB\-\-use\-bspline\-smoothing\fR 1/(0)
.IP
Sets the option for B\-spline smoothing of the velocity field.Default = false.
.HP
\fB\-n\fR, \fB\-\-number\-of\-integration\-points\fR numberOfPoints
.IP
Number of compositions of the diffeomorphism per iteration. Default = 10.
.HP
\fB\-p\fR, \fB\-\-maximum\-number\-of\-invert\-displacement\-field\-iterations\fR numberOfIterations
.IP
Maximum number of iterations for estimating the invert displacement field.
Default = 20.
.HP
\fB\-o\fR, \fB\-\-output\fR imageFileName
.IP
[imageFileName,warpedWhiteMatterImageFileName]
.IP
The output consists of a thickness map defined in the segmented gray matter.
.HP
\fB\-h\fR
.IP
Print the help menu (short version).
.HP
\fB\-\-help\fR
.IP
Print the help menu.
<VALUES>: 1