mia-3dmany2one-nonrigid(1)

NAME
mia-3dmany2one-nonrigid - Registration of series of 3D images

SYNOPSIS
mia-3dmany2one-nonrigid -i <in-file> [options] <PLUGINS:3dimage/fullcost>

DESCRIPTION
mia-3dmany2one-nonrigid This program runs the non-rigid registration of an image series by registereing all images to a user-selected reference.

OPTIONS

  File-IO

    -i --in-file=(input, required); io
        input perfusion data set
         For supported file types see PLUGINS:3dimage/io

    -o --out-file=(output); io
        file name for registered files
         For supported file types see PLUGINS:3dimage/io

  Registration

    -O --optimizer=gsl:opt=gd,step=0.1
        Optimizer used for minimization

    -l --mg-levels=3
        multi-resolution levels

    -f --transForm=spline
        transformation type
         For supported plugins see PLUGINS:3dimage/transform

    -r --ref=-1
        reference frame (-1 == use image in the middle)

  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/spacialkernel

cdiff
    Central difference filter kernel, mirror boundary conditions are used.

    (no parameters)

gauss
    spacial Gauss filter kernel, supported parameters are:

    w = 1; uint in [0, inf)
        half filter width.

scharr
    This plugin provides the 1D folding kernel for the Scharr gradient filter

    (no parameters)

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/combiner

absdiff
    Image combiner 'absdiff'

    (no parameters)

add Image combiner 'add'

    (no parameters)

div Image combiner 'div'

    (no parameters)

mul Image combiner 'mul'

    (no parameters)

sub Image combiner 'sub'

    (no parameters)

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/filter

bandpass
    intensity bandpass filter, supported parameters are:

    max = 3.40282e+38; float
        maximum of the band.

    min = 0; float
        minimum of the band.

binarize
    image binarize filter, supported parameters are:

    max = 3.40282e+38; float
        maximum of accepted range.

    min = 0; float
        minimum of accepted range.

close
    morphological close, supported parameters are:

    hint = black; string
        a hint at the main image content (black|white).

    shape = [sphere:r=2]; factory
        structuring element. For supported plug-ins see PLUGINS:3dimage/shape

combiner
    Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are:

    image =(input, required, io)
        second image that is needed in the combiner. For supported file types see PLUGINS:3dimage/io

    op =(required, factory)
        Image combiner to be applied to the images. For supported plug-ins see PLUGINS:3dimage/combiner

    reverse = 0; bool
        reverse the order in which the images passed to the combiner.

convert
    image pixel format conversion filter, supported parameters are:

    a = 1; float
        linear conversion parameter a.

    b = 0; float
        linear conversion parameter b.

    map = opt; dict
        conversion mapping. Supported values are:
            copy - copy data when converting
            linear - apply linear transformation x -> a*x+b
            range - apply linear transformation that maps the input data type range to the output data type range
            opt - apply a linear transformation that maps the real input range to the full output range
            optstat - apply a linear transform that maps based on input mean and variation to the full output range

    repn = ubyte; dict
        output pixel type. Supported values are:
            bit - binary data
            sbyte - signed 8 bit
            ubyte - unsigned 8 bit
            sshort - signed 16 bit
            ushort - unsigned 16 bit
            sint - signed 32 bit
            uint - unsigned 32 bit
            slong - signed 64 bit
            ulong - unsigned 64 bit
            float - floating point 32 bit
            double - floating point 64 bit
            none - no pixel type defined

crop
    Crop a region of an image, the region is always clamped to the original image size in the sense that the given range is kept., supported parameters are:

    end = [[4294967295,4294967295,4294967295]]; streamable
        end of cropping range, maximum = (-1,-1,-1).

    start = [[0,0,0]]; streamable
        begin of cropping range.

dilate
    3d image stack dilate filter, supported parameters are:

    hint = black; string
        a hint at the main image content (black|white).

    shape = [sphere:r=2]; factory
        structuring element. For supported plug-ins see PLUGINS:3dimage/shape

distance
    Evaluate the 3D distance transform of an image. If the image is a binary mask, then result of the distance transform in each point corresponds to the Euclidian distance to the mask. If the input image is of a scalar pixel value, then the this scalar is interpreted as heighfield and the per pixel value adds to the distance.

    (no parameters)

downscale
    Downscale the input image by using a given block size to define the downscale factor. Prior to scaling the image is filtered by a smoothing filter to eliminate high frequency data and avoid aliasing artifacts., supported parameters are:

    b = [[1,1,1]]; 3dbounds
        blocksize.

    bx = 1; uint in [1, inf)
        blocksize in x direction.

    by = 1; uint in [1, inf)
        blocksize in y direction.

    bz = 1; uint in [1, inf)
        blocksize in z direction.

    kernel = gauss; factory
        smoothing filter kernel to be applied, the size of the filter is estimated based on the blocksize.. For supported plug-ins see PLUGINS:1d/spacialkernel

erode
    3d image stack erode filter, supported parameters are:

    hint = black; string
        a hint at the main image content (black|white).

    shape = [sphere:r=2]; factory
        structuring element. For supported plug-ins see PLUGINS:3dimage/shape

gauss
    isotropic 3D gauss filter, supported parameters are:

    w = 1; int in [0, inf)
        filter width parameter.

gradnorm
    3D image to gradient norm filter

    (no parameters)

growmask
    Use an input binary mask and a reference gray scale image to do region growing by adding the neighborhood pixels of an already added pixel if the have a lower intensity that is above the given threshold., supported parameters are:

    min = 1; float
        lower threshold for mask growing.

    ref =(input, required, io)
        reference image for mask region growing. For supported file types see PLUGINS:3dimage/io

    shape = 6n; factory
        neighborhood mask. For supported plug-ins see PLUGINS:3dimage/shape

invert
    intensity invert filter

    (no parameters)

isovoxel
    This filter scales an image to make the voxel size isometric and its size to correspond to the given value, supported parameters are:

    interp = [bspline:d=3]; factory
        interpolation kernel to be used . For supported plug-ins see PLUGINS:1d/splinekernel

    size = 1; float in (0, inf)
        isometric target voxel size.

kmeans
    3D image k-means filter. In the output image the pixel value represents the class membership and the class centers are stored as attribute in the image., supported parameters are:

    c = 3; int in [2, inf)
        number of classes.

label
    A filter to label the connected components of a binary image., supported parameters are:

    n = 6n; factory
        neighborhood mask. For supported plug-ins see PLUGINS:3dimage/shape

labelmap
    Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are:

    map =(input, required, string)
        Label mapping file.

labelscale
    A filter that only creates output voxels that are already created in the input image. Scaling is done by using a voting algorithms that selects the target pixel value based on the highest pixel count of a certain label in the corresponding source region. If the region comprises two labels with the same count, the one with the lower number wins., supported parameters are:

    out-size =(required, 3dbounds)
        target size given as two coma separated values.

load
    Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are:

    file =(input, required, io)
        name of the input file to load from.. For supported file types see PLUGINS:3dimage/io

lvdownscale
    This is a label voting downscale filter. It adownscales a 3D image by blocks. For each block the (non-zero) label that appears most times in the block is issued as output pixel in the target image. If two labels appear the same number of times, the one with the lower absolute value wins., supported parameters are:

    b = [[1,1,1]]; 3dbounds
        blocksize for the downscaling. Each block will be represented by one pixel in the target image..

mask
    Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary., supported parameters are:

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

mean
    3D image mean filter, supported parameters are:

    w = 1; int in [1, inf)
        half filter width.

median
    median 3d filter, supported parameters are:

    w = 1; int in [1, inf)
        filter width parameter.

mlv Mean of Least Variance 3D image filter, supported parameters are:

    w = 1; int in [1, inf)
        filter width parameter.

msnormalizer
    3D image mean-sigma normalizing filter, supported parameters are:

    w = 1; int in [1, inf)
        half filter width.

open
    morphological open, supported parameters are:

    hint = black; string
        a hint at the main image content (black|white).

    shape = [sphere:r=2]; factory
        structuring element. For supported plug-ins see PLUGINS:3dimage/shape

reorient
    3D image reorientation filter, supported parameters are:

    map = xyz; dict
        oriantation mapping to be applied. Supported values are:
            xyz - keep orientation
            p-yzx - permutate x->z->y->x
            p-zxy - permutate x->y->z->x
            f-yz - flip y-z
            f-xy - flip x-y
            f-xz - flip x-z
            r-x90 - rotate around x-axis clockwise 90 degree
            r-x180 - rotate around x-axis clockwise 180 degree
            r-x270 - rotate around x-axis clockwise 270 degree
            r-y90 - rotate around y-axis clockwise 90 degree
            r-y180 - rotate around y-axis clockwise 180 degree
            r-y270 - rotate around y-axis clockwise 270 degree
            r-z90 - rotate around z-axis clockwise 90 degree
            r-z180 - rotate around z-axis clockwise 180 degree
            r-z270 - rotate around z-axis clockwise 270 degree

resize
    Resize an image. The original data is centered within the new sized image., supported parameters are:

    size = [[0,0,0]]; streamable
        new size of the image a size 0 indicates to keep the size for the corresponding dimension..

sandp
    salt and pepper 3d filter, supported parameters are:

    thresh = 100; float in [0, inf)
        thresh value.

    w = 1; int in [1, inf)
        filter width parameter.

scale
    3D image filter that scales to a given target size , supported parameters are:

    interp = [bspline:d=3]; factory
        interpolation kernel to be used . For supported plug-ins see PLUGINS:1d/splinekernel

    s = [[0,0,0]]; 3dbounds
        target size to set all components at once (component 0:use input image size).

    sx = 0; uint in [0, inf)
        target size in x direction (0:use input image size).

    sy = 0; uint in [0, inf)
        target size in y direction (0:use input image size).

    sz = 0; uint in [0, inf)
        target size in y direction (0:use input image size).

scharr
    The 3D Scharr filter for gradient evaluation. Note that the output pixel type of the filtered image is the same as the input pixel type, so converting the input beforehand to a floating point valued image is recommendable., supported parameters are:

    dir = x; dict
        Gradient direction. Supported values are:
            x - gradient in x-direction
            y - gradient in y-direction
            z - gradient in z-direction

selectbig
    A filter that creats a binary mask representing the intensity with the highest pixel count.The pixel value 0 will be ignored, and if two intensities have the same pixel count, then the result is undefined. The input pixel must have an integral pixel type.

    (no parameters)

sepconv
    3D image intensity separaple convolution filter, supported parameters are:

    kx = [gauss:w=1]; factory
        filter kernel in x-direction. For supported plug-ins see PLUGINS:1d/spacialkernel

    ky = [gauss:w=1]; factory
        filter kernel in y-direction. For supported plug-ins see PLUGINS:1d/spacialkernel

    kz = [gauss:w=1]; factory
        filter kernel in z-direction. For supported plug-ins see PLUGINS:1d/spacialkernel

sobel
    The 2D Sobel filter for gradient evaluation. Note that the output pixel type of the filtered image is the same as the input pixel type, so converting the input beforehand to a floating point valued image is recommendable., supported parameters are:

    dir = x; dict
        Gradient direction. Supported values are:
            x - gradient in x-direction
            y - gradient in y-direction
            z - gradient in z-direction

sws seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image., supported parameters are:

    grad = 0; bool
        Interpret the input image as gradient. .

    mark = 0; bool
        Mark the segmented watersheds with a special gray scale value.

    n = [sphere:r=1]; factory
        Neighborhood for watershead region growing. For supported plug-ins see PLUGINS:3dimage/shape

    seed =(input, required, string)
        seed input image containing the labels for the initial regions.

tee Save the input image to a file and also pass it through to the next filter, supported parameters are:

    file =(output, required, io)
        name of the output file to save the image too.. For supported file types see PLUGINS:3dimage/io

thinning
    3D morphological thinning, based on: Lee and Kashyap, 'Building Skeleton Models via 3-D Medial Surface/Axis Thinning Algorithms', Graphical Models and Image Processing, 56(6):462-478, 1994. This implementation only supports the 26 neighbourhood.

    (no parameters)

transform
    Transform the input image with the given transformation., supported parameters are:

    file =(input, required, io)
        Name of the file containing the transformation.. For supported file types see PLUGINS:3dtransform/io

    imgboundary = ; factory
        override image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc

    imgkernel = ; factory
        override image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel

variance
    3D image variance filter, supported parameters are:

    w = 1; int in [1, inf)
        half filter width.

ws  basic watershead segmentation., supported parameters are:

    evalgrad = 0; bool
        Set to 1 if the input image does not represent a gradient norm image.

    mark = 0; bool
        Mark the segmented watersheds with a special gray scale value.

    n = [sphere:r=1]; factory
        Neighborhood for watershead region growing. For supported plug-ins see PLUGINS:3dimage/shape

    thresh = 0; float in [0, 1)
        Relative gradient norm threshold. The actual value threshold value is thresh * (max_grad - min_grad) + min_grad. Bassins separated by gradients with a lower norm will be joined.

PLUGINS: 3dimage/fullcost

image
    Generalized image similarity cost function that also handles multi-resolution processing. The actual similarity measure is given es extra parameter., supported parameters are:

    cost = ssd; factory
        Cost function kernel. For supported plug-ins see PLUGINS:3dimage/cost

    debug = 0; bool
        Save intermediate resuts for debugging.

    ref =(input, io)
        Reference image. For supported file types see PLUGINS:3dimage/io

    src =(input, io)
        Study image. For supported file types see PLUGINS:3dimage/io

    weight = 1; float
        weight of cost function.

labelimage
    Similarity cost function that maps labels of two images and handles label-preserving multi-resolution processing., supported parameters are:

    maxlabel = 256; int in [2, 32000]
        maximum number of labels to consider.

    ref =(input, io)
        Reference image. For supported file types see PLUGINS:3dimage/io

    src =(input, io)
        Study image. For supported file types see PLUGINS:3dimage/io

    weight = 1; float
        weight of cost function.

maskedimage
    Generalized masked image similarity cost function that also handles multi-resolution processing. The provided masks should be densly filled regions in multi-resolution procesing because otherwise the mask information may get lost when downscaling the image. The mask may be pre-filtered - after pre-filtering the masks must be of bit-type.The reference mask and the transformed mask of the study image are combined by binary AND. The actual similarity measure is given es extra parameter., supported parameters are:

    cost = ssd; factory
        Cost function kernel. For supported plug-ins see PLUGINS:3dimage/maskedcost

    ref =(input, io)
        Reference image. For supported file types see PLUGINS:3dimage/io

    ref-mask =(input, io)
        Reference image mask (binary). For supported file types see PLUGINS:3dimage/io

    ref-mask-filter = ; factory
        Filter to prepare the reference mask image, the output must be a binary image.. For supported plug-ins see PLUGINS:3dimage/filter

    src =(input, io)
        Study image. For supported file types see PLUGINS:3dimage/io

    src-mask =(input, io)
        Study image mask (binary). For supported file types see PLUGINS:3dimage/io

    src-mask-filter = ; factory
        Filter to prepare the study mask image, the output must be a binary image.. For supported plug-ins see PLUGINS:3dimage/filter

    weight = 1; float
        weight of cost function.

taggedssd
    Evaluates the Sum of Squared Differences similarity measure by using three tagged image pairs. The cost function value is evaluated based on all image pairs, but the gradient is composed by composing its component based on the tag direction., supported parameters are:

    refx =(input, io)
        Reference image X-tag. For supported file types see PLUGINS:3dimage/io

    refy =(input, io)
        Reference image Y-tag. For supported file types see PLUGINS:3dimage/io

    refz =(input, io)
        Reference image Z-tag. For supported file types see PLUGINS:3dimage/io

    srcx =(input, io)
        Study image X-tag. For supported file types see PLUGINS:3dimage/io

    srcy =(input, io)
        Study image Y-tag. For supported file types see PLUGINS:3dimage/io

    srcz =(input, io)
        Study image Z-tag. For supported file types see PLUGINS:3dimage/io

    weight = 1; float
        weight of cost function.

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/maskedcost

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 with masking., 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 with masking support.

    (no parameters)

ssd Sum of squared differences with masking.

    (no parameters)

PLUGINS: 3dimage/shape

18n 18n neighborhood 3D shape creator

    (no parameters)

26n 26n neighborhood 3D shape creator

    (no parameters)

6n  6n neighborhood 3D shape creator

    (no parameters)

sphere
    Closed spherical shape neighborhood including the pixels within a given radius r., supported parameters are:

    r = 2; float in (0, inf)
        sphere radius.

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
Register the images given as numbered files imagesXXXX.v by optimizing a spline based transformation with a coefficient rate of 16 pixel using a weighted combination of normalized gradient fields and SSD as cost measure, and penalize the transformation by using divcurl with aweight of 2.0. Store the resultsing images in registeredXXXX.v.

mia-3dmany2one-nonrigid -i images0000.v -o registered%04d.v -F spline:rate=16 image:cost=[ngf:eval=ds],weight=2.0 image:cost=ssd,weight=0.1 divcurl:weight=2.0

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'.