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-dimensionality 2/3

              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-image imageFilename
              [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-image 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, --white-matter-probability-image 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, --thickness-prior-estimate thicknessPriorEstimate

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

       -a, --thickness-prior-image thicknessPriorFileName

              An image containing spatially varying prior thickness values.

       -r, --gradient-step stepSize

              Gradient step size for the optimization. Default = 0.025.

       -l, --smoothing-variance variance

              Defines the Gaussian smoothing of the hit and total images. Default = 1.0.

       -m, --smoothing-velocity-field-parameter variance
              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-smoothing 1/(0)

              Sets the option for B-spline smoothing of the velocity field.Default = false.

       -n, --number-of-integration-points numberOfPoints

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

       -p, --maximum-number-of-invert-displacement-field-iterations 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