SYNOPSIS
mia-mesh-deformable-model -i <in-file> -o <out-file> -r <ref-file> [options]DESCRIPTION
mia-mesh-deformable-model This program runs a deformable model to adapt a mesh to an iso-value within a given image. <FIXME: Reference>OPTIONS
File I/O
-
- -i --in-file=(input, required); io
- input mesh to be adapted For supported file types see PLUGINS:mesh/io
- -o --out-file=(output, required); io
- output mesh that has been deformed For supported file types see PLUGINS:mesh/io
- -r --ref-file=(input, required); io
- reference image 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
Model parameters
-
- --smoothing-weight=0.04; float in [0, inf)
- Weight of the inner force used to smooth the mesh
- --gradient-weight=0.04
- Weight of the gradient force drive the mesh deformation. Use a negative value to invert the search direction.Weight of the gradient force drive the mesh deformation. Use a negative value to invert the search direction.
- --intensity-weight=0.02; float in [0, inf)
- Weight of the force resulting from the intensity difference at the vertex position versus the reference intensity 'iso'.
- --intensity-scaling=1; float in (0, inf)
- Scaling of the raw intensity difference.
- -s --iso=64
- Intensity value the mesh verices should adapt to.Intensity value the mesh verices should adapt to.
Preprocessing
-
- --image-smoothing=gauss:w=2
- Prefilter to smooth the reference image.Prefilter to smooth the reference image. For supported plugins see PLUGINS:3dimage/filter
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).
- -m --maxiter=200; uint in (0, inf)
- Maximum number of iterations.
- -e --epsilon=0.001; float in (0, inf)
- Stop iteration when the maximum shift of the vertices falls below this value
- --reorient
- Reorientate the mesh triangles
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.
-
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.
-
Spline degree.
- omoms
- OMoms-spline kernel creation, supported parameters are:
-
d
= 3; int in [3, 3]
-
Spline degree.
-
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.
-
maximum of the band.
-
min
= 0; float
-
minimum of the band.
-
minimum of the band.
- binarize
- image binarize filter, supported parameters are:
-
max
= 3.40282e+38; float
-
maximum of accepted range.
-
maximum of accepted range.
-
min
= 0; float
-
minimum of accepted range.
-
minimum of accepted range.
- close
- morphological close, supported parameters are:
-
hint
= black; string
-
a hint at the main image content (black|white).
-
a hint at the main image content (black|white).
-
shape
= [sphere:r=2]; factory
-
structuring element.
For supported plug-ins see PLUGINS:3dimage/shape
-
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.
-
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
-
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.
-
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.
-
linear conversion parameter a.
-
b
= 0; float
-
linear conversion parameter b.
-
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
-
conversion mapping.
Supported values are:
-
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
-
output pixel type.
Supported values are:
- 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).
-
end of cropping range, maximum = (-1,-1,-1).
-
start
= [[0,0,0]]; streamable
-
begin of cropping range.
-
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).
-
a hint at the main image content (black|white).
-
shape
= [sphere:r=2]; factory
-
structuring element.
For supported plug-ins see PLUGINS:3dimage/shape
-
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.
-
blocksize.
-
bx
= 1; uint in [1, inf)
-
blocksize in x direction.
-
blocksize in x direction.
-
by
= 1; uint in [1, inf)
-
blocksize in y direction.
-
blocksize in y direction.
-
bz
= 1; uint in [1, inf)
-
blocksize in z direction.
-
blocksize in z direction.
-
kernel
= gauss; string
-
smoothing filter kernel to be applied, the size of the filter is estimated based on the blocksize..
-
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).
-
a hint at the main image content (black|white).
-
shape
= [sphere:r=2]; factory
-
structuring element.
For supported plug-ins see PLUGINS:3dimage/shape
-
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.
-
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.
-
lower threshold for mask growing.
-
ref
=(input, required, string)
-
reference image for mask region growing.
-
reference image for mask region growing.
-
shape
= 6n; factory
-
neighborhood mask.
For supported plug-ins see PLUGINS:3dimage/shape
-
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
-
interpolation kernel to be used .
For supported plug-ins see PLUGINS:1d/splinekernel
-
size
= 1; float in (0, inf)
-
isometric target voxel size.
-
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.
-
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
-
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.
-
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.
-
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..
-
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..
-
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.
-
second input image file name.
- mean
- 3D image mean filter, supported parameters are:
-
w
= 1; int in [1, inf)
-
half filter width.
-
half filter width.
- median
- median 3d filter, supported parameters are:
-
w
= 1; int in [1, inf)
-
filter width parameter.
-
filter width parameter.
- mlv
- Mean of Least Variance 3D image filter, supported parameters are:
-
w
= 1; int in [1, inf)
-
filter width parameter.
-
filter width parameter.
- msnormalizer
- 3D image mean-sigma normalizing filter, supported parameters are:
-
w
= 1; int in [1, inf)
-
half filter width.
-
half filter width.
- open
- morphological open, supported parameters are:
-
hint
= black; string
-
a hint at the main image content (black|white).
-
a hint at the main image content (black|white).
-
shape
= [sphere:r=2]; factory
-
structuring element.
For supported plug-ins see PLUGINS:3dimage/shape
-
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
-
oriantation mapping to be applied.
Supported values are:
- 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..
-
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.
-
thresh value.
-
w
= 1; int in [1, inf)
-
filter width parameter.
-
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
-
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).
-
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).
-
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).
-
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).
-
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
-
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
-
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
-
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. .
-
Interpret the input image as gradient. .
-
mark
= 0; bool
-
Mark the segmented watersheds with a special gray scale value.
-
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
-
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.
-
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..
-
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..
-
Name of the file containing the transformation..
-
imgboundary
= ; string
-
override image interpolation boundary conditions.
-
override image interpolation boundary conditions.
-
imgkernel
= ; string
-
override image interpolator kernel.
-
override image interpolator kernel.
- variance
- 3D image variance filter, supported parameters are:
-
w
= 1; int in [1, inf)
-
half filter width.
-
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.
-
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.
-
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
-
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.
-
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
- 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/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.
-
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
PLUGINS: mesh/io
- datapool
- Virtual IO to and from the internal data pool
- Recognized file extensions: .@
- off
- plugin to load/store some Geomview OFF Files
- Recognized file extensions: .OFF, .off
- ply
- Ply triangle mesh input/output support
- Recognized file extensions: .PLY, .ply
- stl
- STL mesh io plugin
- Recognized file extensions: .STL, .stl
- vista
- Vista/Simbio triangle mesh input/output support
- Recognized file extensions: .V, .VMESH, .v, .vmesh
- vtk
- A subset of VTK mesh in-and output: Triangle meshes are written, and triangle meshes and triangle strips are read. Additional per-vertex attributes are supported: 'normals', 'colors' for three component colors, and 'scale' for a scalar value attached to each vertex. The data is written by the vtkPolyDataWriter in binary format.
- Recognized file extensions: .VTK, .VTKMESH, .vtk, .vtkmesh
EXAMPLE
Run the deforemable model on input.vmesh with 200 iterations adapting to a value of 128 in the image ref.v and save the result to deformed.vmesh- mia-mesh-deformable-model -i input.vmesh -o deformed.vmesh --iso 128 --maxiter 200
AUTHOR(s)
Gert WollnyCOPYRIGHT
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'.