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mia-2dseriestovolume - Online in the Cloud

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PROGRAM:

NAME


mia-2dseriestovolume - Create a 3D volume from a segmentation series.

SYNOPSIS


mia-2dseriestovolume -i <in-file> -o <out-file> [options]

DESCRIPTION


mia-2dseriestovolume Obtaines a 3D volume image by combining the images of the
segmentation set.

OPTIONS


-i --in-file=(input, required); string
input segmentation set

-o --out-file=(output, required); io
output 3D image For supported file types see PLUGINS:3dimage/io

-k --skip=0
number of frames to skip at the beginning of the series.number of frames to
skip at the beginning of the series.

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: 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

EXAMPLE


Create the volume volume.v from the series series.set but skip the first two images.

mia-2dseriestovolume -i series.set -k 2 -o volume.v

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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