mia-3dcost - Online in the Cloud

PROGRAM:

NAME

mia-3dcost - Evaluate similarity of two 3D images.

SYNOPSIS

mia-3dcost [options] <PLUGINS:3dimage/fullcost>

DESCRIPTION

mia-3dcost This program evauates the cost function as given by the free parameters on the
command line.

OPTIONS

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: 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

mia-3dcost

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'.

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