---
name: "KellyKapowski"
section: "1"
platform: "linux"
package: "ants"
version: "2.1.0-5"
release: "Debian 9 (Stretch)"
platforms: ["linux"]
url: "https://new.carta.tech/KellyKapowski"
---

# KellyKapowski(1)

part of ANTS registration suite

## 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.

**-h**

-

  Print the help menu (short version).

**--help**

-

  Print the help menu. \<VALUES\>: 1