ELASTIX(1) User Commands ELASTIX(1)NAME
elastix - perform image registration
SYNOPSIS
elastix mandatory-args [optional-args]
DESCRIPTION
elastix registers a moving image to a fixed image. The registration-process is specified in the parameter file.
OPTIONS
Call elastix from the command line with mandatory arguments:
-f fixed image
-m moving image
-out output directory
-p parameter file, elastix handles 1 or more "-p"
Optional extra commands:
-fMask mask for fixed image
-mMask mask for moving image
-t0 parameter file for initial transform
-priority set the process priority to high or belownormal (Windows only)
-threads set the maximum number of threads of elastix
The parameter-file must contain all the information necessary for elastix to run properly. That includes which metric to use, which opti-
mizer, which transform, etc. It must also contain information specific for the metric, optimizer, transform, ... For a usable parame-
ter-file, see the website.
SEE ALSO transformix(1)
Check the website http://elastix.isi.uu.nl, or mail elastix.support@gmail.com.
elastix version: 4.400 December 2010 ELASTIX(1)
Check Out this Related Man Page
LANDMARK_WARP(1) Plastimatch LANDMARK_WARP(1)NAME
landmark_warp - warp an image using point landmarks
SYNOPSIS
landmark_warp [options]
DESCRIPTION
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]
Options:
-a, --algorithm <arg> RBF warping algorithm {tps,gauss,
wendland}
-d, --default-value <arg> Value to set for pixels with unknown
value
--dim <arg> Size of output image in voxels "x [y z]"
-F, --fixed <arg> Fixed image (match output size to this
image)
-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 cm
-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'.
AUTHOR
Plastimatch is a collaborative project. For more documentation, please visit http://plastimatch.org. For questions, comments, and bug
reports, please visit http://groups.google.com/group/plastimatch.
COPYRIGHT
Plastimatch development team (C) 2010-2011. You are free to use, modify, and distribute plastimatch according to a BSD-style license.
Please see LICENSE.TXT for details.
Plastimatch 1.5 June 11, 2011 LANDMARK_WARP(1)