# init-dof¶

## Synopsis¶

init-dof <dofout> [output option] [options]


## Description¶

This tool either creates a new affine transformation with the given parameters or approximates an affine transformation or non-rigid deformation given a set of corresponding landmarks or point displacements (see init-dof -displacements).

The output transformation is by default an affine transformation. One of the output options below can be used to request a different type of output transformation. This option should be given right after the output transformation name as it may be altered using one of the other output related options (e.g. disable init-dof -shearing).

An affine transformation is the composition of a shearing followed by a scaling, a rotation, and a translation. The homogeneous transformation matrix, A, is given by the matrix product:

$A = Translate * Rotate * Scale * Shear, where Rotate = (Rz Ry Rx)^T$

## Output options¶

-rigid

Output rigid transformation.

-similarity

Output similarity transformation.

-affine

Output affine transformation.

-affine-mffd

Output affine transformation as global component of MFFD.

-mffd

Output multi-level free-form deformation (MFFD).

-ffd

Output free-form deformation (FFD).

-svffd

Output diffeomorphic free-form deformation (SV FFD).

-translations, -notranslations

Allow/disallow translations.

-rotations, -norotations

Allow/disallow rotations.

-scaling, -noscaling

Allow/disallow scaling.

-shearing, -noshearing

Allow/disallow shearing.

## Command options¶

-dofin <dof>

Read affine parameters from input transformation.

-orientation <x1> <x2> <x3> <y1> <y2> <y3> <z1> <z2> <z3>

Set upper 3x3 (rotation) matrix entries (e.g., image orientation from image info output).

-image-reset <file>

Set transformation to difference between spatial image to world mapping of given image and the default lattice with axes parallel to the axes of the world coordinate system and image center at the origin. The affine output transformation maps points of the unoriented world system with origin at the image center to the world coordinates of the input image.

-image-rotation <file>

Set transformation to difference between spatial image to world mapping of given image and an image lattice with axes parallel to the axes of the world coordinate system. The affine output transformation maps points of the unoriented world system to the world coordinates of the input image. Hence, the domain of the map is the same as the world domain of the image, except that the orientation matrix is equal the identity matrix.

-tx <tx>

Translation along x axis in mm. (default: 0)

-ty <ty>

Translation along y axis in mm. (default: 0)

-tz <tz>

Translation along z axis in mm. (default: 0)

-rx <rx>

Rotation around x axis in degrees. (default: 0)

-ry <ry>

Rotation around x axis in degrees. (default: 0)

-rz <rz>

Rotation around x axis in degrees. (default: 0)

-sx <sx>

Scaling of x axis in percentage. (default: 100)

-sy <sy>

Scaling of y axis in percentage. (default: 100)

-sz <sz>

Scaling of z axis in percentage. (default: 100)

-s <s>

Isotropic scaling in percentage. (default: 100)

-sxy <sxy>

Skew angle between x and y axis in degrees. (default: 0)

-sxz <sxz>

Skew angle between x and z axis in degrees. (default: 0)

-syz <syz>

Skew angle between y and z axis in degrees. (default: 0)

-target <image>

Target image. Required when output is a FFD. (default: none)

-source <image>

Source image. Used to initialize translation. (default: none)

-Tp <value>

Target background value. (default: none)

-Sp <value>

Source background value. (default: none)

-align-top

Align top-most slices of -target and -source image. (default: center)

-displacements, -disp <pset1> <pset2> [<cor12>]

Create transformation which minimizes the mean squared distance between pairs of fiducial point sets <pset1> and <pset2>. When a single <pset> is given, it creates a transformation which approximates the displacement vectors stored in the “vectors” point set attributes array. Option can be used multiple times.

-approximate <dofin>

Create transformation which approximates another given transformation. Option can be used multiple times.

## Free-form deformation options¶

-dx <dx>

Control point spacing of FFD in x. (default: target voxel size)

-dy <dy>

Control point spacing of FFD in y. (default: target voxel size)

-dz <dz>

Control point spacing of FFD in z. (default: target voxel size)

-ds <ds>

Control point spacing of FFD. (default: target voxel size)

-subdiv <n>

Number of subdivisions to use for approximating a non-rigid deformation from input -displacements. (default: 4)

## Standard options¶

-v, -verbose [n]

Increase/Set verbosity of output messages. (default: 0)

-debug [level]

Increase/Set debug level for output of intermediate results. (default: 0)

-version [major.minor]

Print version and exit or set version to emulate.

-revision

Print revision (or version) number only and exit.

-h, -help

Print help and exit.