xenial (1) mia-3dmany2one-nonrigid.1.gz

Provided by: mia-tools_2.2.7-3_amd64 bug

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 levelsmulti-resolution levels

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

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

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, string)
                       second image that is needed in the combiner.

                     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:
                           opt ‐ apply a linear transformation that maps the real input range to the full output
                           range
                           range ‐ apply linear transformation that maps the input data type range to the output
                           data type range
                           copy ‐ copy data when converting
                           linear ‐ apply linear transformation x -> a*x+b
                           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:
                           none ‐ no pixel type defined
                           float ‐ floating point 32 bit
                           sbyte ‐ signed 8 bit
                           ulong ‐ unsigned 64 bit
                           double ‐ floating point 64 bit
                           sint ‐ signed 32 bit
                           ushort ‐ unsigned 16 bit
                           sshort ‐ signed 16 bit
                           uint ‐ unsigned 32 bit
                           slong ‐ signed 64 bit
                           bit ‐ binary data
                           ubyte ‐ unsigned 8 bit

       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; string
                       smoothing filter kernel to be applied, the size of the filter is estimated based  on  the
                       blocksize..

       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, string)
                       reference image for mask region growing.

                     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, string)
                       name of the input file to load from..

       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, string)
                       second input image file name.

       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:
                           p-zxy ‐ permutate x->y->z->x
                           r-x180 ‐ rotate around x-axis clockwise 180 degree
                           xyz ‐ keep orientation
                           p-yzx ‐ permutate x->z->y->x
                           r-z180 ‐ rotate around z-axis clockwise 180 degree
                           r-y270 ‐ rotate around y-axis clockwise 270 degree
                           f-xz ‐ flip x-z
                           f-yz ‐ flip y-z
                           r-x90 ‐ rotate around x-axis clockwise 90 degree
                           r-y90 ‐ rotate around y-axis clockwise 90 degree
                           r-x270 ‐ rotate around x-axis clockwise 270 degree
                           r-z270 ‐ rotate around z-axis clockwise 270 degree
                           r-z90 ‐ rotate around z-axis clockwise 90 degree
                           f-xy ‐ flip x-y
                           r-y180 ‐ rotate around y-axis clockwise 180 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).

       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

       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 lables 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, string)
                       name of the output file to save the image too..

       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, string)
                       Name of the file containing the transformation..

                     imgboundary = ; string
                       override image interpolation boundary conditions.

                     imgkernel = ; string
                       override image interpolator kernel.

       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, string)
                       Reference image.

                     src =(input, string)
                       Study image.

                     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, string)
                       Reference image.

                     src =(input, string)
                       Study image.

                     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, string)
                       Reference image.

                     ref-mask =(input, string)
                       Reference image mask  (binary).

                     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, string)
                       Study image.

                     src-mask =(input, string)
                       Study image mask (binary).

                     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, string)
                       Reference image  X-tag.

                     refy =(input, string)
                       Reference image  Y-tag.

                     refz =(input, string)
                       Reference image  Z-tag.

                     srcx =(input, string)
                       Study image X-tag.

                     srcy =(input, string)
                       Study image Y-tag.

                     srcz =(input, string)
                       Study image Z-tag.

                     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

                     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:
                       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

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 debuging 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

       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'.