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mia-3dcost-translatedgrad(1) | General Commands Manual | mia-3dcost-translatedgrad(1) |
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 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
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).
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. The orientation is transformed in the same way like it is done with 'dicomtonifti --no-reorder' from the vtk-dicom package.
('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:
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 debugging 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 WollnyCOPYRIGHT¶
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'.v2.4.6 | USER COMMANDS |