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This is the command landmark_warp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



landmark_warp - warp an image using point landmarks


landmark_warp [options]


The landmark_warp executable performs registration by matching fiducials on reference and
test images. The list of possible options can be seen by typing:

landmark_warp --help

The command line usage is given as follows:

Usage: landmark_warp [options]
-a, --algorithm <arg> RBF warping algorithm {tps,gauss,
-d, --default-value <arg> Value to set for pixels with unknown
--dim <arg> Size of output image
in voxels "x [y z]"
-F, --fixed <arg> Fixed image (match output size to this
-f, --fixed-landmarks <arg> Input fixed landmarks
-h, --help Display this help message
-I, --input-image <arg> Input image to warp
-v, --input-vf <arg> Input vector field (applied prior to
landmark warping)
-m, --moving-landmarks <arg>
Output moving landmarks
-N, --numclusters <arg> Number of clusters of landmarks
--origin <arg> Location of first image voxel
in mm "x y z"
-O, --output-image <arg> Output warped image
-L, --output-landmarks <arg>
Output warped landmarks
-V, --output-vf <arg> Output vector field
-r, --radius <arg> Radius of radial basis function
(in mm)
--spacing <arg> Voxel spacing in mm "x [y z]"
-Y, --stiffness <arg> Young modulus (default = 0.0)

Options "-a", "-r", "-Y", "-d" are set by default to:

-a=gauss Gaussian RBFs with infinite support
-r=50.0 Gaussian width 50 mm
-Y=0.0 No regularization of vector field
-d=-1000 Air

You may want to choose different algorithm:

-a=tps Thin-plate splines (for global registration)
-a=wendland Wendland RBFs with compact support (for
local registration)

In the case of Wendland RBFs "-r" option sets the radius of support.

Regularization of vector field is available for "gauss" and "wendland" algorithms. To
regularize the output vector field increase "-Y" to '0.1' and up with increment '0.1'.

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