## table of contents

- unstable 2.1.0-5+b1
- experimental 2.2.0-1+b2

KELLYKAPOWSKI(1) | User Commands | KELLYKAPOWSKI(1) |

# 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

September 2017 | KellyKapowski 2.1.0 |