.TH mia\-3dcost\-translatedgrad 1 "v2.4.6"  "USER COMMANDS"
.SH NAME
('mia\\-3dcost\\-translatedgrad',)
\- Evaluate the cost gradient between two images and convert it to a spline representation.
.SH SYNOPSIS
.B  mia\-3dcost\-translatedgrad \-i <in\-file> \-r <ref\-file> \-o <out\-file> [options]
.SH DESCRIPTION
.B mia\-3dcost\-translatedgrad
Evaluate the cost gradient between two images and evaluate the transformation related gradient for it based on the given transformation model.
.SH OPTIONS
.RS
.IP "\-i \-\-in-file=(input, required); io"
input image 
 For supported file types see PLUGINS:3dimage/io
.IP "\-r \-\-ref-file=(input, required); io"
reference image 
 For supported file types see PLUGINS:3dimage/io
.IP "\-o \-\-out-file=(output, required); io"
output vector field 
 For supported file types see PLUGINS:3dtransform/io
.IP "\-g \-\-gradimg-file=(output); io"
norm image of the spline transformed gradient
 For supported file types see PLUGINS:3dimage/io
.IP "\-C \-\-cost-gradimg-file=(output); io"
norm image of the cost gradient
 For supported file types see PLUGINS:3dimage/io
.IP "\-f \-\-transForm=spline:rate=5"
Transformation the gradient relates to
 For supported plugins see PLUGINS:3dimage/transform
.IP "\-c \-\-cost=ssd"
cost function to use
 For supported plugins see PLUGINS:3dimage/cost
.RE
.SS Help & Info
.RS
.IP "\-V \-\-verbose=warning"
verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

.RS 10
.I
info
\(hy Low level messages
.RE
.RS 10
.I
trace
\(hy Function call trace
.RE
.RS 10
.I
fail
\(hy Report test failures
.RE
.RS 10
.I
warning
\(hy Warnings
.RE
.RS 10
.I
error
\(hy Report errors
.RE
.RS 10
.I
debug
\(hy Debug output
.RE
.RS 10
.I
message
\(hy Normal messages
.RE
.RS 10
.I
fatal
\(hy Report only fatal errors
.RE
.IP "   \-\-copyright"
print copyright information

.IP "\-h \-\-help"
print this help

.IP "\-? \-\-usage"
print a short help

.IP "   \-\-version"
print the version number and exit

.RE
.SS Processing
.RS
.IP "   \-\-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).

.RE
.SH PLUGINS: 1d/splinebc
.TP 10
.B mirror
Spline interpolation boundary conditions that mirror on the boundary
.P
.RS 14
(no parameters)
.RE
.TP 10
.B repeat
Spline interpolation boundary conditions that repeats the value at the boundary
.P
.RS 14
(no parameters)
.RE
.TP 10
.B zero
Spline interpolation boundary conditions that assumes zero for values outside
.P
.RS 14
(no parameters)
.RE
.SH PLUGINS: 1d/splinekernel
.TP 10
.B bspline
B-spline kernel creation , supported parameters are: 
.P
.RS 14
.I
d
= 3; int in [0, 5] 
.RS 2
Spline degree.

.RE
.RE
.TP 10
.B omoms
OMoms-spline kernel creation, supported parameters are: 
.P
.RS 14
.I
d
= 3; int in [3, 3] 
.RS 2
Spline degree.

.RE
.RE
.SH PLUGINS: 3dimage/cost
.TP 10
.B lncc
local normalized cross correlation with masking support., supported parameters are: 
.P
.RS 14
.I
w
= 5; uint in [1, 256] 
.RS 2
half width of the window used for evaluating the localized cross correlation.

.RE
.RE
.TP 10
.B mi
Spline parzen based mutual information., supported parameters are: 
.P
.RS 14
.I
cut
= 0; float in [0, 40] 
.RS 2
Percentage of pixels to cut at high and low intensities to remove outliers.

.RE
.RE
.RS 14
.I
mbins
= 64; uint in [1, 256] 
.RS 2
Number of histogram bins used for the moving image.

.RE
.RE
.RS 14
.I
mkernel
= [bspline:d=3]; factory 
.RS 2
Spline kernel for moving image parzen hinstogram.
For supported plug-ins see PLUGINS:1d/splinekernel

.RE
.RE
.RS 14
.I
rbins
= 64; uint in [1, 256] 
.RS 2
Number of histogram bins used for the reference image.

.RE
.RE
.RS 14
.I
rkernel
= [bspline:d=0]; factory 
.RS 2
Spline kernel for reference image parzen hinstogram.
For supported plug-ins see PLUGINS:1d/splinekernel

.RE
.RE
.TP 10
.B ncc
normalized cross correlation.
.P
.RS 14
(no parameters)
.RE
.TP 10
.B 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: 
.P
.RS 14
.I
eval
= ds; dict 
.RS 2
plugin subtype (sq, ds,dot,cross).
Supported values are:
.RS 4
.I
ds
\(hy square of scaled difference
.RE
.RS 4
.I
dot
\(hy scalar product kernel
.RE
.RS 4
.I
cross
\(hy cross product kernel
.RE

.RE
.RE
.TP 10
.B ssd
3D image cost: sum of squared differences, supported parameters are: 
.P
.RS 14
.I
autothresh
= 0; float in [0, 1000] 
.RS 2
Use automatic masking of the moving image by only takeing intensity values into accound that are larger than the given threshold.

.RE
.RE
.RS 14
.I
norm
= 0; bool 
.RS 2
Set whether the metric should be normalized by the number of image pixels.

.RE
.RE
.TP 10
.B ssd-automask
3D image cost: sum of squared differences, with automasking based on given thresholds, supported parameters are: 
.P
.RS 14
.I
rthresh
= 0; double 
.RS 2
Threshold intensity value for reference image.

.RE
.RE
.RS 14
.I
sthresh
= 0; double 
.RS 2
Threshold intensity value for source image.

.RE
.RE
.SH PLUGINS: 3dimage/io
.TP 10
.B analyze
Analyze 7.5 image
.P
.RS 14
('Recognized file extensions: ', '.HDR, .hdr')
.RE
 
.RS 14
Supported element types: 
.RS 2
unsigned 8 bit, signed 16 bit, signed 32 bit, floating point 32 bit, floating point 64 bit
.RE
 
.RE
.TP 10
.B datapool
Virtual IO to and from the internal data pool
.P
.RS 14
('Recognized file extensions: ', '.@')
.RE
 
.TP 10
.B dicom
Dicom image series as 3D
.P
.RS 14
('Recognized file extensions: ', '.DCM, .dcm')
.RE
 
.RS 14
Supported element types: 
.RS 2
signed 16 bit, unsigned 16 bit
.RE
 
.RE
.TP 10
.B hdf5
HDF5 3D image IO
.P
.RS 14
('Recognized file extensions: ', '.H5, .h5')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B inria
INRIA image
.P
.RS 14
('Recognized file extensions: ', '.INR, .inr')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B mhd
MetaIO 3D image IO using the VTK implementation (experimental).
.P
.RS 14
('Recognized file extensions: ', '.MHA, .MHD, .mha, .mhd')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B nifti
NIFTI-1 3D image IO. The orientation is transformed in the same way like it is done with 'dicomtonifti --no-reorder' from the vtk-dicom package.
.P
.RS 14
('Recognized file extensions: ', '.NII, .nii')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B vff
VFF Sun raster format
.P
.RS 14
('Recognized file extensions: ', '.VFF, .vff')
.RE
 
.RS 14
Supported element types: 
.RS 2
unsigned 8 bit, signed 16 bit
.RE
 
.RE
.TP 10
.B vista
Vista 3D
.P
.RS 14
('Recognized file extensions: ', '.-, .V, .VISTA, .v, .vista')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B vti
3D image VTK-XML in- and output (experimental).
.P
.RS 14
('Recognized file extensions: ', '.VTI, .vti')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B vtk
3D VTK image legacy in- and output (experimental).
.P
.RS 14
('Recognized file extensions: ', '.VTK, .VTKIMAGE, .vtk, .vtkimage')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.SH PLUGINS: 3dimage/transform
.TP 10
.B affine
Affine transformation (12 degrees of freedom), supported parameters are: 
.P
.RS 14
.I
imgboundary
= mirror; factory 
.RS 2
image interpolation boundary conditions.
For supported plug-ins see PLUGINS:1d/splinebc

.RE
.RE
.RS 14
.I
imgkernel
= [bspline:d=3]; factory 
.RS 2
image interpolator kernel.
For supported plug-ins see PLUGINS:1d/splinekernel

.RE
.RE
.TP 10
.B 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: 
.P
.RS 14
.I
axis
=(required, 3dfvector)
.RS 2
rotation axis.

.RE
.RE
.RS 14
.I
imgboundary
= mirror; factory 
.RS 2
image interpolation boundary conditions.
For supported plug-ins see PLUGINS:1d/splinebc

.RE
.RE
.RS 14
.I
imgkernel
= [bspline:d=3]; factory 
.RS 2
image interpolator kernel.
For supported plug-ins see PLUGINS:1d/splinekernel

.RE
.RE
.RS 14
.I
origin
=(required, 3dfvector)
.RS 2
center of the transformation.

.RE
.RE
.TP 10
.B 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: 
.P
.RS 14
.I
axis
=(required, 3dfvector)
.RS 2
rotation axis.

.RE
.RE
.RS 14
.I
imgboundary
= mirror; factory 
.RS 2
image interpolation boundary conditions.
For supported plug-ins see PLUGINS:1d/splinebc

.RE
.RE
.RS 14
.I
imgkernel
= [bspline:d=3]; factory 
.RS 2
image interpolator kernel.
For supported plug-ins see PLUGINS:1d/splinekernel

.RE
.RE
.RS 14
.I
origin
=(required, 3dfvector)
.RS 2
center of the transformation.

.RE
.RE
.TP 10
.B rigid
Rigid transformation, i.e. rotation and translation (six degrees of freedom)., supported parameters are: 
.P
.RS 14
.I
imgboundary
= mirror; factory 
.RS 2
image interpolation boundary conditions.
For supported plug-ins see PLUGINS:1d/splinebc

.RE
.RE
.RS 14
.I
imgkernel
= [bspline:d=3]; factory 
.RS 2
image interpolator kernel.
For supported plug-ins see PLUGINS:1d/splinekernel

.RE
.RE
.RS 14
.I
origin
= [[0,0,0]]; 3dfvector 
.RS 2
Relative rotation center, i.e.  <0.5,0.5,0.5> corresponds to the center of the volume.

.RE
.RE
.TP 10
.B rotation
Rotation transformation (three degrees of freedom)., supported parameters are: 
.P
.RS 14
.I
imgboundary
= mirror; factory 
.RS 2
image interpolation boundary conditions.
For supported plug-ins see PLUGINS:1d/splinebc

.RE
.RE
.RS 14
.I
imgkernel
= [bspline:d=3]; factory 
.RS 2
image interpolator kernel.
For supported plug-ins see PLUGINS:1d/splinekernel

.RE
.RE
.RS 14
.I
origin
= [[0,0,0]]; 3dfvector 
.RS 2
Relative rotation center, i.e.  <0.5,0.5,0.5> corresponds to the center of the volume.

.RE
.RE
.TP 10
.B 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: 
.P
.RS 14
.I
imgboundary
= mirror; factory 
.RS 2
image interpolation boundary conditions.
For supported plug-ins see PLUGINS:1d/splinebc

.RE
.RE
.RS 14
.I
imgkernel
= [bspline:d=3]; factory 
.RS 2
image interpolator kernel.
For supported plug-ins see PLUGINS:1d/splinekernel

.RE
.RE
.RS 14
.I
norot
= 0; bool 
.RS 2
Don't optimize the rotation.

.RE
.RE
.RS 14
.I
origin
=(required, 3dfvector)
.RS 2
center of the transformation.

.RE
.RE
.TP 10
.B spline
Free-form transformation that can be described by a set of B-spline coefficients and an underlying B-spline kernel., supported parameters are: 
.P
.RS 14
.I
anisorate
= [[0,0,0]]; 3dfvector 
.RS 2
anisotropic coefficient rate in pixels, nonpositive values will be overwritten by the 'rate' value..

.RE
.RE
.RS 14
.I
debug
= 0; bool 
.RS 2
enable additional debugging output.

.RE
.RE
.RS 14
.I
imgboundary
= mirror; factory 
.RS 2
image interpolation boundary conditions.
For supported plug-ins see PLUGINS:1d/splinebc

.RE
.RE
.RS 14
.I
imgkernel
= [bspline:d=3]; factory 
.RS 2
image interpolator kernel.
For supported plug-ins see PLUGINS:1d/splinekernel

.RE
.RE
.RS 14
.I
kernel
= [bspline:d=3]; factory 
.RS 2
transformation spline kernel.
For supported plug-ins see PLUGINS:1d/splinekernel

.RE
.RE
.RS 14
.I
penalty
= ; factory 
.RS 2
transformation penalty energy term.
For supported plug-ins see PLUGINS:3dtransform/splinepenalty

.RE
.RE
.RS 14
.I
rate
= 10; float in [1, inf) 
.RS 2
isotropic coefficient rate in pixels.

.RE
.RE
.TP 10
.B translate
Translation (three degrees of freedom), supported parameters are: 
.P
.RS 14
.I
imgboundary
= mirror; factory 
.RS 2
image interpolation boundary conditions.
For supported plug-ins see PLUGINS:1d/splinebc

.RE
.RE
.RS 14
.I
imgkernel
= [bspline:d=3]; factory 
.RS 2
image interpolator kernel.
For supported plug-ins see PLUGINS:1d/splinekernel

.RE
.RE
.TP 10
.B 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: 
.P
.RS 14
.I
imgboundary
= mirror; factory 
.RS 2
image interpolation boundary conditions.
For supported plug-ins see PLUGINS:1d/splinebc

.RE
.RE
.RS 14
.I
imgkernel
= [bspline:d=3]; factory 
.RS 2
image interpolator kernel.
For supported plug-ins see PLUGINS:1d/splinekernel

.RE
.RE
.SH PLUGINS: 3dtransform/io
.TP 10
.B bbs
Binary (non-portable) serialized IO of 3D transformations
.P
.RS 14
('Recognized file extensions: ', '.bbs')
.RE
 
.TP 10
.B datapool
Virtual IO to and from the internal data pool
.P
.RS 14
('Recognized file extensions: ', '.@')
.RE
 
.TP 10
.B vista
Vista storage of 3D transformations
.P
.RS 14
('Recognized file extensions: ', '.v, .v3dt')
.RE
 
.TP 10
.B xml
XML serialized IO of 3D transformations
.P
.RS 14
('Recognized file extensions: ', '.x3dt')
.RE
 
.SH PLUGINS: 3dtransform/splinepenalty
.TP 10
.B divcurl
divcurl penalty on the transformation, supported parameters are: 
.P
.RS 14
.I
curl
= 1; float in [0, inf) 
.RS 2
penalty weight on curl.

.RE
.RE
.RS 14
.I
div
= 1; float in [0, inf) 
.RS 2
penalty weight on divergence.

.RE
.RE
.RS 14
.I
norm
= 0; bool 
.RS 2
Set to 1 if the penalty should be normalized with respect to the image size.

.RE
.RE
.RS 14
.I
weight
= 1; float in (0, inf) 
.RS 2
weight of penalty energy.

.RE
.RE
.SH EXAMPLE
Evaluate the SSD cost between src.v and ref.v and store the gradient gradient corresponding to a spline transformation in grad.v3dt.
.HP
mia\-3dcost\-translatedgrad \-i src.v \-o grad.v3dt \-f spline:rate=8 \-c ssd
.SH AUTHOR(s)
Gert Wollny
.SH COPYRIGHT
This software is Copyright (c) 1999\(hy2015 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'.