Provided by: ants_2.2.0-1ubuntu1_amd64

**NAME**

KellyKapowski - 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, 45:867--879.OPTIONS:-d,--image-dimensionality2/3 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.-s,--segmentation-imageimageFilename [imageFilename,<grayMatterLabel=2>,<whiteMatterLabel=3>] A segmentation image must be supplied labeling the grayand white matters. Ddefault values = 2 and 3, respectively.-g,--gray-matter-probability-imageimageFilename 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,--white-matter-probability-imageimageFilename 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,--thickness-prior-estimatethicknessPriorEstimate Provides a prior constraint on the final thickness measurement. Default = 10 mm.-a,--thickness-prior-imagethicknessPriorFileName An image containing spatially varying prior thickness values.-r,--gradient-stepstepSize Gradient step size for the optimization. Default = 0.025.-l,--smoothing-variancevariance Defines the Gaussian smoothing of the hit and total images. Default = 1.0.-m,--smoothing-velocity-field-parametervariance isotropicMeshSpacing 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).-b,--use-bspline-smoothing1/(0) Sets the option for B-spline smoothing of the velocity field.Default = false.-n,--number-of-integration-pointsnumberOfPoints Number of compositions of the diffeomorphism per iteration. Default = 10.-p,--maximum-number-of-invert-displacement-field-iterationsnumberOfIterations Maximum number of iterations for estimating the invert displacement field. Default = 20.-o,--outputimageFileName [imageFileName,warpedWhiteMatterImageFileName] The output consists of a thickness map defined in the segmented gray matter.-v,--verbose(0)/1 Verbose output.-hPrint the help menu (short version).--helpPrint the help menu. <VALUES>: 1