Provided by: mia-tools_2.0.13-1_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 image(s) to be filtered For supported file types see PLUGINS:3dimage/io
-o --out-file=(required)
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)
output file type
--help-plugins
give some help about the filter plugins
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
warning ‐ Warnings
error ‐ Report errors
fail ‐ Report test failures
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
gauss spacial Gauss filter kernel, supported parameters are:
w = 1 (int)
half filter width. in [0, 2147483647]
PLUGINS: 1d/splinekernel
bspline B-spline kernel creation , supported parameters are:
d = 3 (int)
Spline degree. in [0, 5]
omoms OMoms-spline kernel creation, supported parameters are:
d = 3 (int)
Spline degree. in [3, 3]
PLUGINS: 3dimage/filter
bandpass intensity bandpass filter, supported parameters are:
max = 3.40282e+38 (float)
maximum of the band. in [-3.40282e+38, 3.40282e+38]
min = 0 (float)
minimum of the band. in [-3.40282e+38, 3.40282e+38]
binarize image binarize filter, supported parameters are:
max = 3.40282e+38 (float)
maximum of accepted range. in [0, 3.40282e+38]
min = 0 (float)
minimum of accepted range. in [0, 3.40282e+38]
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
convert image pixel format conversion filter, supported parameters are:
a = 1 (float)
linear conversion parameter a. in [-3.40282e+38, 3.40282e+38]
b = 0 (float)
linear conversion parameter b. in [-3.40282e+38, 3.40282e+38]
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:
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
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)
blocksize in x direction. in [1, 2147483647]
by = 1 (uint)
blocksize in y direction. in [1, 2147483647]
bz = 1 (uint)
blocksize in z direction. in [1, 2147483647]
kernel = gauss (factory)
smoothing filter kernel to be applied (filter width is determined based on the scaling
factor). 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)
filter width parameter. in [0, 2147483647]
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. in [-3.40282e+38, 3.40282e+38]
ref = (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)
isometric target voxel size. in [0.001, 1e+06]
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)
number of classes. in [0, 255]
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
load Load the input image from a file and use it to replace the current image in the pipeline.,
supported parameters are:
file = (required, io)
name of the input file to load from.. For supported file types see PLUGINS:3dimage/io
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, io)
second input image file name. For supported file types see PLUGINS:3dimage/io
median median 3d filter, supported parameters are:
w = 1 (int)
filter width parameter. in [0, 2147483647]
mlv Mean of Least Variance 3D image filter, supported parameters are:
w = 1 (int)
filter width parameter. in [0, 2147483647]
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:
yzx ‐ rotate x->z->y->x
yxz ‐ switch x-y
xyz ‐ keep orientation
xzy ‐ switch y-z
zxy ‐ rotate x->y->z->x
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)
thresh value. in [0, 3.40282e+38]
w = 1 (int)
filter width parameter. in [0, 2147483647]
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)
target size in x direction (0:use input image size). in [0, 4294967295]
sy = 0 (uint)
target size in y direction (0:use input image size). in [0, 4294967295]
sz = 0 (uint)
target size in y direction (0:use input image size). in [0, 4294967295]
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 = (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 = (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 = (required, io)
Name of the file containing the transformation.. For supported file types see
PLUGINS:3dtransform/io
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)
Relative gradient norm threshold. The actual value threshhold value is thresh * (max_grad
- min_grad) + min_grad. Bassins separated by gradients with a lower norm will be joined.
in [0, 1]
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:
unsigned 16 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
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)
sphere radius. in [0, 3.40282e+38]
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) 1999‐2013 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'.