KellyKapowski - part of ANTS registration suite

- 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.

**-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