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PROGRAM:

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=(input, required); io
input image For supported file types see PLUGINS:3dimage/io

-r --ref-file=(input, required); io
reference image For supported file types see PLUGINS:3dimage/io

-o --out-file=(output, required); io
output vector field For supported file types see PLUGINS:3dtransform/io

-g --gradimg-file=(output); io
norm image of the spline transformed gradient For supported file types see
PLUGINS:3dimage/io

-C --cost-gradimg-file=(output); io
norm image of the cost gradient For supported file types see
PLUGINS:3dimage/io

-f --transForm=spline:rate=5
Transformation the gradient relates toTransformation the gradient relates to
For supported plugins see PLUGINS:3dimage/transform

-c --cost=ssd
cost function to usecost 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
trace ‐ Function call trace
fail ‐ Report test failures
warning ‐ Warnings
error ‐ Report errors
debug ‐ Debug output
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).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 in [0, 5]
Spline degree.

omoms OMoms-spline kernel creation, supported parameters are:

d = 3; int in [3, 3]
Spline degree.

PLUGINS: 3dimage/cost


lncc local normalized cross correlation with masking support., supported parameters
are:

w = 5; uint in [1, 256]
half width of the window used for evaluating the localized cross
correlation.

mi Spline parzen based mutual information., supported parameters are:

cut = 0; float in [0, 40]
Percentage of pixels to cut at high and low intensities to remove
outliers.

mbins = 64; uint in [1, 256]
Number of histogram bins used for the moving image.

mkernel = [bspline:d=3]; factory
Spline kernel for moving image parzen hinstogram. For supported plug-ins
see PLUGINS:1d/splinekernel

rbins = 64; uint in [1, 256]
Number of histogram bins used for the reference image.

rkernel = [bspline:d=0]; factory
Spline kernel for reference image parzen hinstogram. For supported plug-
ins see PLUGINS:1d/splinekernel

ncc normalized cross correlation.

(no parameters)

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; dict
plugin subtype (sq, ds,dot,cross). Supported values are:
ds ‐ square of scaled difference
dot ‐ scalar product kernel
cross ‐ cross product kernel

ssd 3D image cost: sum of squared differences, supported parameters are:

autothresh = 0; float in [0, 1000]
Use automatic masking of the moving image by only takeing intensity values
into accound that are larger than the given threshold.

norm = 0; bool
Set whether the metric should be normalized by the number of image pixels.

ssd-automask
3D image cost: sum of squared differences, with automasking based on given
thresholds, supported parameters are:

rthresh = 0; double
Threshold intensity value for reference image.

sthresh = 0; double
Threshold intensity value for source image.

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:
signed 16 bit, unsigned 16 bit

hdf5 HDF5 3D image IO

Recognized file extensions: .H5, .h5

Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit,
signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating
point 32 bit, floating point 64 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

nifti NIFTI-1 3D image IO

Recognized file extensions: .NII, .nii

Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32
bit, unsigned 32 bit, signed 64 bit, unsigned 64 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:
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

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

axisrot Restricted rotation transformation (1 degrees of freedom). The transformation is
restricted to the rotation around the given axis about the given rotation
center, supported parameters are:

axis =(required, 3dfvector)
rotation axis.

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

origin =(required, 3dfvector)
center of the transformation.

raffine Restricted affine transformation (3 degrees of freedom). The transformation is
restricted to the rotation around the given axis and shearing along the two axis
perpendicular to the given one, supported parameters are:

axis =(required, 3dfvector)
rotation axis.

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

origin =(required, 3dfvector)
center of the transformation.

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

origin = [[0,0,0]]; 3dfvector
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

origin = [[0,0,0]]; 3dfvector
Relative rotation center, i.e. <0.5,0.5,0.5> corresponds to the center of
the volume.

rotbend Restricted transformation (4 degrees of freedom). The transformation is
restricted to the rotation around the x and y axis and a bending along the x
axis, independedn in each direction, with the bending increasing with the
squared distance from the rotation axis., 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

norot = 0; bool
Don't optimize the rotation.

origin =(required, 3dfvector)
center of the transformation.

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 in [1, inf)
isotropic coefficient rate in pixels.

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 in [0, inf)
penalty weight on curl.

div = 1; float in [0, inf)
penalty weight on divergence.

norm = 0; bool
Set to 1 if the penalty should be normalized with respect to the image
size.

weight = 1; float in (0, inf)
weight of penalty energy.

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) 1999‐2015 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'.

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