---
name: "mia-3dcost-translatedgrad"
section: "1"
platform: "linux"
package: "mia-tools"
version: "2.4.7-11+b1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/mia-3dcost-translatedgrad"
---

# mia-3dcost-translatedgrad(1)

Evaluate the cost gradient between two images and convert it to a spline representation.

## 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); io

  input image \
    For supported file types see PLUGINS:3dimage/io

- \-r --ref-file=(required, input); 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:

  *trace* ‐ Function call trace

  *debug* ‐ Debug output

  *info* ‐ Low level messages

  *message* ‐ Normal messages

  *warning* ‐ Warnings

  *fail* ‐ Report test failures

  *error* ‐ Report errors

  *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 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'.