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’.