KellyKapowski(1)
part of ANTS registration suite
DESCRIPTION
COMMAND:

KellyKapowski

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, 45:867879.
OPTIONS:

d, imagedimensionality 2/3

 This option forces the image to be treated as a specifieddimensional image. If
not specified, DiReCT tries to infer the dimensionality from the input image.
 s, segmentationimage imageFilename

[imageFilename,<grayMatterLabel=2>,<whiteMatterLabel=3>]

A segmentation image must be supplied labeling the grayand white matters.
Ddefault values = 2 and 3, respectively.

g, graymatterprobabilityimage imageFilename

 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.

w, whitematterprobabilityimage imageFilename

 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.

c, convergence [<numberOfIterations=50>,<convergenceThreshold=0.001>,<convergenceWindowSize=10>]

 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.

t, thicknesspriorestimate thicknessPriorEstimate

 Provides a prior constraint on the final thickness measurement. Default = 10 mm.

a, thicknesspriorimage thicknessPriorFileName

 An image containing spatially varying prior thickness values.

r, gradientstep stepSize

 Gradient step size for the optimization. Default = 0.025.

l, smoothingvariance variance

 Defines the Gaussian smoothing of the hit and total images. Default = 1.0.
 m, smoothingvelocityfieldparameter variance

isotropicMeshSpacing

Defines the Gaussian smoothing of the velocity field (default = 1.5).If the
bspline smoothing option is chosen, then this defines the isotropic mesh
spacing for the smoothing spline (default = 15).

b, usebsplinesmoothing 1/(0)

 Sets the option for Bspline smoothing of the velocity field.Default = false.

n, numberofintegrationpoints numberOfPoints

 Number of compositions of the diffeomorphism per iteration. Default = 10.

p, maximumnumberofinvertdisplacementfielditerations numberOfIterations

 Maximum number of iterations for estimating the invert displacement field.
Default = 20.

o, output imageFileName

[imageFileName,warpedWhiteMatterImageFileName]

 The output consists of a thickness map defined in the segmented gray matter.

v, verbose (0)/1

 Verbose output.

h

 Print the help menu (short version).

help

 Print the help menu.
<VALUES>: 1