Provided by: mia-tools_2.0.13-1_amd64 
NAME
mia-3dcost-translatedgrad - Evaluate the cost gradient between two images and convert it
to a spline representation.
SYNOPSIS
mia-3dcost-translatedgrad -i <in-file> -r <ref-file> -o <out-file> [options]
DESCRIPTION
mia-3dcost-translatedgrad Evaluate the cost gradient between two images and evaluate the
transformation related gradient for it based on the given transformation model.
OPTIONS
-i --in-file=(required)
input image For supported file types see PLUGINS:3dimage/io
-r --ref-file=(required)
reference image For supported file types see PLUGINS:3dimage/io
-o --out-file=(required)
output vector field For supported file types see PLUGINS:3dtransform/io
-g --gradimg-file=
norm image of the spline transformed gradient For supported file types see
PLUGINS:3dimage/io
-C --cost-gradimg-file=
norm image of the cost gradient For supported file types see
PLUGINS:3dimage/io
-f --transForm=spline:rate=5
Transformation the gradient relates to For supported plugins see
PLUGINS:3dimage/transform
-c --cost=ssd
cost function to use For supported plugins see PLUGINS:3dimage/cost
Help & Info
-V --verbose=warning
verbosity of output, print messages of given level and higher priorities.
Supported priorities starting at lowest level are:
info ‐ Low level messages
warning ‐ Warnings
error ‐ Report errors
fail ‐ Report test failures
message ‐ Normal messages
fatal ‐ Report only fatal errors
--copyright
print copyright information
-h --help
print this help
-? --usage
print a short help
--version
print the version number and exit
Processing
--threads=-1
Maxiumum number of threads to use for processing,This number should be lower
or equal to the number of logical processor cores in the machine. (-1:
automatic estimation).
PLUGINS: 1d/splinebc
mirror Spline interpolation boundary conditions that mirror on the boundary
(no parameters)
repeat Spline interpolation boundary conditions that repeats the value at the boundary
(no parameters)
zero Spline interpolation boundary conditions that assumes zero for values outside
(no parameters)
PLUGINS: 1d/splinekernel
bspline B-spline kernel creation , supported parameters are:
d = 3 (int)
Spline degree. in [0, 5]
omoms OMoms-spline kernel creation, supported parameters are:
d = 3 (int)
Spline degree. in [3, 3]
PLUGINS: 3dimage/cost
mi Spline parzen based mutual information., supported parameters are:
cut = 0 (float)
Percentage of pixels to cut at high and low intensities to remove
outliers. in [0, 40]
mbins = 64 (uint)
Number of histogram bins used for the moving image. in [1, 256]
mkernel = [bspline:d=3] (factory)
Spline kernel for moving image parzen hinstogram. For supported plug-ins
see PLUGINS:1d/splinekernel
rbins = 64 (uint)
Number of histogram bins used for the reference image. in [1, 256]
rkernel = [bspline:d=0] (factory)
Spline kernel for reference image parzen hinstogram. For supported plug-
ins see PLUGINS:1d/splinekernel
ngf This function evaluates the image similarity based on normalized gradient
fields. Given normalized gradient fields $ _S$ of the src image and $ _R$ of the
ref image various evaluators are implemented., supported parameters are:
eval = ds (string)
plugin subtype (sq, ds,dot,cross).
ssd 3D image cost: sum of squared differences, supported parameters are:
norm = 0 (bool)
Set whether the metric should be normalized by the number of image pixels.
PLUGINS: 3dimage/io
analyze Analyze 7.5 image
Recognized file extensions: .HDR, .hdr
Supported element types:
unsigned 8 bit, signed 16 bit, signed 32 bit, floating point 32 bit,
floating point 64 bit
datapool Virtual IO to and from the internal data pool
Recognized file extensions: .@
dicom Dicom image series as 3D
Recognized file extensions: .DCM, .dcm
Supported element types:
unsigned 16 bit
inria INRIA image
Recognized file extensions: .INR, .inr
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32
bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit
mhd MetaIO 3D image IO using the VTK implementation (experimental).
Recognized file extensions: .MHA, .MHD, .mha, .mhd
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32
bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit
vff VFF Sun raster format
Recognized file extensions: .VFF, .vff
Supported element types:
unsigned 8 bit, signed 16 bit
vista Vista 3D
Recognized file extensions: .V, .VISTA, .v, .vista
Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit,
signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64
bit
vti 3D image VTK-XML in- and output (experimental).
Recognized file extensions: .VTI, .vti
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32
bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit
vtk 3D VTK image legacy in- and output (experimental).
Recognized file extensions: .VTK, .VTKIMAGE, .vtk, .vtkimage
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32
bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit
PLUGINS: 3dimage/transform
affine Affine transformation (12 degrees of freedom), supported parameters are:
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported plug-ins see
PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
rigid Rigid transformation, i.e. rotation and translation (six degrees of freedom).,
supported parameters are:
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported plug-ins see
PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
rot-center = [[0,0,0]] (streamable)
Relative rotation center, i.e. <0.5,0.5,0.5> corresponds to the center of
the volume.
rotation Rotation transformation (three degrees of freedom)., supported parameters are:
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported plug-ins see
PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
rot-center = [[0,0,0]] (streamable)
Relative rotation center, i.e. <0.5,0.5,0.5> corresponds to the center of
the volume.
spline Free-form transformation that can be described by a set of B-spline coefficients
and an underlying B-spline kernel., supported parameters are:
anisorate = [[0,0,0]] (3dfvector)
anisotropic coefficient rate in pixels, nonpositive values will be
overwritten by the 'rate' value..
debug = 0 (bool)
enable additional debuging output.
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported plug-ins see
PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
kernel = [bspline:d=3] (factory)
transformation spline kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
penalty = (factory)
transformation penalty energy term. For supported plug-ins see
PLUGINS:3dtransform/splinepenalty
rate = 10 (float)
isotropic coefficient rate in pixels. in [1, 3.40282e+38]
translate Translation (three degrees of freedom), supported parameters are:
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported plug-ins see
PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
vf This plug-in implements a transformation that defines a translation for each
point of the grid defining the domain of the transformation., supported
parameters are:
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported plug-ins see
PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
PLUGINS: 3dtransform/io
bbs Binary (non-portable) serialized IO of 3D transformations
Recognized file extensions: .bbs
datapool Virtual IO to and from the internal data pool
Recognized file extensions: .@
vista Vista storage of 3D transformations
Recognized file extensions: .v, .v3dt
xml XML serialized IO of 3D transformations
Recognized file extensions: .x3dt
PLUGINS: 3dtransform/splinepenalty
divcurl divcurl penalty on the transformation, supported parameters are:
curl = 1 (float)
penalty weight on curl. in [0, 3.40282e+38]
div = 1 (float)
penalty weight on divergence. in [0, 3.40282e+38]
weight = 1 (float)
weight of penalty energy. in [0, 3.40282e+38]
EXAMPLE
Evaluate the SSD cost between src.v and ref.v and store the gradient gradient
corresponding to a spline transformation in grad.v3dt.
mia-3dcost-translatedgrad -i src.v -o grad.v3dt -f spline:rate=8 -c ssd
AUTHOR(s)
Gert Wollny
COPYRIGHT
This software is Copyright (c) 1999‐2013 Leipzig, Germany and Madrid, Spain. It comes
with ABSOLUTELY NO WARRANTY and you may redistribute it under the terms of the GNU
GENERAL PUBLIC LICENSE Version 3 (or later). For more information run the program with the
option '--copyright'.