Provided by: mia-tools_2.4.6-5build3_amd64 
NAME
mia-3dimagefilterstack - Filter a series of 3D images.
SYNOPSIS
mia-3dimagefilterstack -i <in-file> -o <out-file> -t <type> [options] <PLUGINS:3dimage/filter>
DESCRIPTION
mia-3dimagefilterstack This program is used to filter and convert a consecutive numbered series gray of
scale images. File names must follow the pattern 'dataXXXX.v' (X being digits), i.e. the numbering comes
right before the dot.
OPTIONS
-i --in-file=(required, input); io
input image(s) to be filtered
For supported file types see PLUGINS:3dimage/io
-o --out-file=(required, output); io
output file name base, numbers are added accorfing to the input file pattern, and the file
extension is added according to the 'type' option.
For supported file types see PLUGINS:3dimage/io
-t --type=(required); set
output file type
Supported values are:( analyze, datapool, dicom, hdf5, inria, mhd, nifti, vff, vista,
vti, vtk, )
Help & Info
-V --verbose=warning
verbosity of output, print messages of given level and higher priorities. Supported
priorities starting at lowest level are:
trace ‐ Function call trace
debug ‐ Debug output
info ‐ Low level messages
message ‐ Normal messages
warning ‐ Warnings
fail ‐ Report test failures
error ‐ Report errors
fatal ‐ Report only fatal errors
--copyright
print copyright information
-h --help
print this help
-? --usage
print a short help
--version
print the version number and exit
Processing
--threads=-1
Maxiumum number of threads to use for processing,This number should be lower or equal to
the number of logical processor cores in the machine. (-1: automatic estimation).
PLUGINS: 1d/spacialkernel
cdiff Central difference filter kernel, mirror boundary conditions are used.
(no parameters)
gauss spacial Gauss filter kernel, supported parameters are:
w = 1; uint in [0, inf)
half filter width.
scharr This plugin provides the 1D folding kernel for the Scharr gradient filter
(no parameters)
PLUGINS: 1d/splinebc
mirror Spline interpolation boundary conditions that mirror on the boundary
(no parameters)
repeat Spline interpolation boundary conditions that repeats the value at the boundary
(no parameters)
zero Spline interpolation boundary conditions that assumes zero for values outside
(no parameters)
PLUGINS: 1d/splinekernel
bspline B-spline kernel creation , supported parameters are:
d = 3; int in [0, 5]
Spline degree.
omoms OMoms-spline kernel creation, supported parameters are:
d = 3; int in [3, 3]
Spline degree.
PLUGINS: 3dimage/combiner
absdiff Image combiner 'absdiff'
(no parameters)
add Image combiner 'add'
(no parameters)
div Image combiner 'div'
(no parameters)
mul Image combiner 'mul'
(no parameters)
sub Image combiner 'sub'
(no parameters)
PLUGINS: 3dimage/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 =(required, input, io)
second image that is needed in the combiner. For supported file types see
PLUGINS:3dimage/io
op =(required, factory)
Image combiner to be applied to the images. For supported plug-ins see
PLUGINS:3dimage/combiner
reverse = 0; bool
reverse the order in which the images passed to the combiner.
convert image pixel format conversion filter, supported parameters are:
a = 1; float
linear conversion parameter a.
b = 0; float
linear conversion parameter b.
map = opt; dict
conversion mapping. Supported values are:
copy ‐ copy data when converting
linear ‐ apply linear transformation x -> a*x+b
range ‐ apply linear transformation that maps the input data type range to the output
data type range
opt ‐ apply a linear transformation that maps the real input range to the full output
range
optstat ‐ apply a linear transform that maps based on input mean and variation to the
full output range
repn = ubyte; dict
output pixel type. Supported values are:
bit ‐ binary data
sbyte ‐ signed 8 bit
ubyte ‐ unsigned 8 bit
sshort ‐ signed 16 bit
ushort ‐ unsigned 16 bit
sint ‐ signed 32 bit
uint ‐ unsigned 32 bit
slong ‐ signed 64 bit
ulong ‐ unsigned 64 bit
float ‐ floating point 32 bit
double ‐ floating point 64 bit
none ‐ no pixel type defined
crop Crop a region of an image, the region is always clamped to the original image size in the sense
that the given range is kept., supported parameters are:
end = [[4294967295,4294967295,4294967295]]; streamable
end of cropping range, maximum = (-1,-1,-1).
start = [[0,0,0]]; streamable
begin of cropping range.
dilate 3d image stack dilate filter, supported parameters are:
hint = black; string
a hint at the main image content (black|white).
shape = [sphere:r=2]; factory
structuring element. For supported plug-ins see PLUGINS:3dimage/shape
distance Evaluate the 3D distance transform of an image. If the image is a binary mask, then result of
the distance transform in each point corresponds to the Euclidian distance to the mask. If the
input image is of a scalar pixel value, then the this scalar is interpreted as heighfield and
the per pixel value adds to the distance.
(no parameters)
downscale Downscale the input image by using a given block size to define the downscale factor. Prior to
scaling the image is filtered by a smoothing filter to eliminate high frequency data and avoid
aliasing artifacts., supported parameters are:
b = [[1,1,1]]; 3dbounds
blocksize.
bx = 1; uint in [1, inf)
blocksize in x direction.
by = 1; uint in [1, inf)
blocksize in y direction.
bz = 1; uint in [1, inf)
blocksize in z direction.
kernel = gauss; factory
smoothing filter kernel to be applied, the size of the filter is estimated based on the
blocksize.. For supported plug-ins see PLUGINS:1d/spacialkernel
erode 3d image stack erode filter, supported parameters are:
hint = black; string
a hint at the main image content (black|white).
shape = [sphere:r=2]; factory
structuring element. For supported plug-ins see PLUGINS:3dimage/shape
gauss isotropic 3D gauss filter, supported parameters are:
w = 1; int in [0, inf)
filter width parameter.
gradnorm 3D image to gradient norm filter
(no parameters)
growmask Use an input binary mask and a reference gray scale image to do region growing by adding the
neighborhood pixels of an already added pixel if the have a lower intensity that is above the
given threshold., supported parameters are:
min = 1; float
lower threshold for mask growing.
ref =(required, input, 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 =(required, input, 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 =(required, input, 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 =(required, input, io)
second input image file name. For supported file types see PLUGINS:3dimage/io
mean 3D image mean filter, supported parameters are:
w = 1; int in [1, inf)
half filter width.
median median 3d filter, supported parameters are:
w = 1; int in [1, inf)
filter width parameter.
mlv Mean of Least Variance 3D image filter, supported parameters are:
w = 1; int in [1, inf)
filter width parameter.
msnormalizer
3D image mean-sigma normalizing filter, supported parameters are:
w = 1; int in [1, inf)
half filter width.
open morphological open, supported parameters are:
hint = black; string
a hint at the main image content (black|white).
shape = [sphere:r=2]; factory
structuring element. For supported plug-ins see PLUGINS:3dimage/shape
reorient 3D image reorientation filter, supported parameters are:
map = xyz; dict
oriantation mapping to be applied. Supported values are:
xyz ‐ keep orientation
p-yzx ‐ permutate x->z->y->x
p-zxy ‐ permutate x->y->z->x
f-yz ‐ flip y-z
f-xy ‐ flip x-y
f-xz ‐ flip x-z
r-x90 ‐ rotate around x-axis clockwise 90 degree
r-x180 ‐ rotate around x-axis clockwise 180 degree
r-x270 ‐ rotate around x-axis clockwise 270 degree
r-y90 ‐ rotate around y-axis clockwise 90 degree
r-y180 ‐ rotate around y-axis clockwise 180 degree
r-y270 ‐ rotate around y-axis clockwise 270 degree
r-z90 ‐ rotate around z-axis clockwise 90 degree
r-z180 ‐ rotate around z-axis clockwise 180 degree
r-z270 ‐ rotate around z-axis clockwise 270 degree
resize Resize an image. The original data is centered within the new sized image., supported
parameters are:
size = [[0,0,0]]; streamable
new size of the image a size 0 indicates to keep the size for the corresponding
dimension..
sandp salt and pepper 3d filter, supported parameters are:
thresh = 100; float in [0, inf)
thresh value.
w = 1; int in [1, inf)
filter width parameter.
scale 3D image filter that scales to a given target size , supported parameters are:
interp = [bspline:d=3]; factory
interpolation kernel to be used . For supported plug-ins see PLUGINS:1d/splinekernel
s = [[0,0,0]]; 3dbounds
target size to set all components at once (component 0:use input image size).
sx = 0; uint in [0, inf)
target size in x direction (0:use input image size).
sy = 0; uint in [0, inf)
target size in y direction (0:use input image size).
sz = 0; uint in [0, inf)
target size in y direction (0:use input image size).
scharr The 3D Scharr filter for gradient evaluation. Note that the output pixel type of the filtered
image is the same as the input pixel type, so converting the input beforehand to a floating
point valued image is recommendable., supported parameters are:
dir = x; dict
Gradient direction. Supported values are:
x ‐ gradient in x-direction
y ‐ gradient in y-direction
z ‐ gradient in z-direction
selectbig A filter that creats a binary mask representing the intensity with the highest pixel count.The
pixel value 0 will be ignored, and if two intensities have the same pixel count, then the
result is undefined. The input pixel must have an integral pixel type.
(no parameters)
sepconv 3D image intensity separaple convolution filter, supported parameters are:
kx = [gauss:w=1]; factory
filter kernel in x-direction. For supported plug-ins see PLUGINS:1d/spacialkernel
ky = [gauss:w=1]; factory
filter kernel in y-direction. For supported plug-ins see PLUGINS:1d/spacialkernel
kz = [gauss:w=1]; factory
filter kernel in z-direction. For supported plug-ins see PLUGINS:1d/spacialkernel
sobel The 2D Sobel filter for gradient evaluation. Note that the output pixel type of the filtered
image is the same as the input pixel type, so converting the input beforehand to a floating
point valued image is recommendable., supported parameters are:
dir = x; dict
Gradient direction. Supported values are:
x ‐ gradient in x-direction
y ‐ gradient in y-direction
z ‐ gradient in z-direction
sws seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given
in the seed image., supported parameters are:
grad = 0; bool
Interpret the input image as gradient. .
mark = 0; bool
Mark the segmented watersheds with a special gray scale value.
n = [sphere:r=1]; factory
Neighborhood for watershead region growing. For supported plug-ins see
PLUGINS:3dimage/shape
seed =(required, input, 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 =(required, output, 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 =(required, input, 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 a series of images that follow the numbering pattern imageXXXX.hdr
and store the output in images filteredXXXX.hdr
mia-3dimagefilterstack -i image0000.hdr -o filtered -t hdr mlv:w=2
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'.