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