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