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mia-3dimagecombine(1) General Commands Manual mia-3dimagecombine(1)

NAME

('mia\-3dimagecombine',) - Combine two 3D images.

SYNOPSIS

mia-3dimagecombine -1 <image1> -2 <image2> -c <combiner> -o <out-file> [options]

DESCRIPTION

mia-3dimagecombine This program is used to combine two images using a given image combiner.

OPTIONS

-1 --image1=(input, required); io
input image 1 to be combined For supported file types see PLUGINS:3dimage/io
-2 --image2=(input, required); io
input image 2 to be combined For supported file types see PLUGINS:3dimage/io
-c --combiner=(required); factory
combiner operation For supported plugins see PLUGINS:3dimage/combiner
-o --out-file=(output, required); io
output image file 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: 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/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

EXAMPLE

Take two images l1.v and l2.v and evaluate the per-voxel sum.

mia-3dimagecombine -1 l1.v -2 l2.v -c sum.v -c add

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'.
v2.4.6 USER COMMANDS