Provided by: mia-tools_2.4.6-4ubuntu2_amd64 bug

NAME

       ('mia\-3dimagefilter',) - Filter a 3D images.

SYNOPSIS

       mia-3dimagefilter -i <in-file> -o <out-file> [options] <PLUGINS:3dimage/filter>

DESCRIPTION

       mia-3dimagefilter This program is used to filter and convert gray scale 3D images.

OPTIONS

              -i --in-file=(input, required); io
                     input image(s) to be filtered
                      For supported file types see PLUGINS:3dimage/io

              -o --out-file=(output, required); io
                     output image(s) that have been filtered
                      For supported file types see PLUGINS:3dimage/io

   Help & Info
              -V --verbose=warning
                     verbosity  of  output,  print messages of given level and higher priorities.
                     Supported priorities starting at lowest level are:

                        info ‐ Low level messages
                        trace ‐ Function call trace
                        fail ‐ Report test failures
                        warning ‐ Warnings
                        error ‐ Report errors
                        debug ‐ Debug output
                        message ‐ Normal messages
                        fatal ‐ Report only fatal errors

                 --copyright
                     print copyright information

              -h --help
                     print this help

              -? --usage
                     print a short help

                 --version
                     print the version number and exit

   Processing
                 --threads=-1
                     Maxiumum number of threads to use for processing,This number should be lower
                     or  equal  to  the  number  of  logical processor cores in the machine. (-1:
                     automatic estimation).

PLUGINS: 1d/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/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:
                           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; 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:
                           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).

       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:
                           y ‐ gradient in y-direction
                           x ‐ gradient in x-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:
                           y ‐ gradient in y-direction
                           x ‐ gradient in x-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 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, 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/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/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: 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')

EXAMPLE

       Run  a  mean-least-varaiance  filter on input.v, then run a 5-class k-means classification
       and binarize by selecting the 4th class.

       mia-3dimagefilter -i image.v -o filtered.v mlv:w=2 kmeans:c=5 binarize:min=4,max=4

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'.