.TH mia\-3dcombine\-mr\-segmentations 1 "v2.4.6"  "USER COMMANDS"
.SH NAME
('mia\\-3dcombine\\-mr\\-segmentations',)
\- Combine segmentations.
.SH SYNOPSIS
.B  mia\-3dcombine\-mr\-segmentations \-i <in\-file> \-o <out\-file> [options] <PLUGINS:3dimage/io>
.SH DESCRIPTION
.B mia\-3dcombine\-mr\-segmentations
This programs takes various segmentation masks of the same data and a tissue probability image set and combines them into one labeled image. The masks are translated to labels according to the position on the command line. If a voxel is set as belonging to more then one mask, the probabilities are consulted.
.SH OPTIONS
.RS
.IP "\-i \-\-in-file=(input, required); io"
input probability images. The number of mask images must correspond to the number of probability images given here.
 For supported file types see PLUGINS:3dimage/io
.IP "\-o \-\-out-file=(output, required); io"
output image that contains the labeling.
 For supported file types see PLUGINS:3dimage/io
.RE
.SS Help & Info
.RS
.IP "\-V \-\-verbose=warning"
verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

.RS 10
.I
info
\(hy Low level messages
.RE
.RS 10
.I
trace
\(hy Function call trace
.RE
.RS 10
.I
fail
\(hy Report test failures
.RE
.RS 10
.I
warning
\(hy Warnings
.RE
.RS 10
.I
error
\(hy Report errors
.RE
.RS 10
.I
debug
\(hy Debug output
.RE
.RS 10
.I
message
\(hy Normal messages
.RE
.RS 10
.I
fatal
\(hy Report only fatal errors
.RE
.IP "   \-\-copyright"
print copyright information

.IP "\-h \-\-help"
print this help

.IP "\-? \-\-usage"
print a short help

.IP "   \-\-version"
print the version number and exit

.RE
.SS Processing
.RS
.IP "   \-\-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).

.RE
.SH PLUGINS: 3dimage/io
.TP 10
.B analyze
Analyze 7.5 image
.P
.RS 14
('Recognized file extensions: ', '.HDR, .hdr')
.RE
 
.RS 14
Supported element types: 
.RS 2
unsigned 8 bit, signed 16 bit, signed 32 bit, floating point 32 bit, floating point 64 bit
.RE
 
.RE
.TP 10
.B datapool
Virtual IO to and from the internal data pool
.P
.RS 14
('Recognized file extensions: ', '.@')
.RE
 
.TP 10
.B dicom
Dicom image series as 3D
.P
.RS 14
('Recognized file extensions: ', '.DCM, .dcm')
.RE
 
.RS 14
Supported element types: 
.RS 2
signed 16 bit, unsigned 16 bit
.RE
 
.RE
.TP 10
.B hdf5
HDF5 3D image IO
.P
.RS 14
('Recognized file extensions: ', '.H5, .h5')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B inria
INRIA image
.P
.RS 14
('Recognized file extensions: ', '.INR, .inr')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B mhd
MetaIO 3D image IO using the VTK implementation (experimental).
.P
.RS 14
('Recognized file extensions: ', '.MHA, .MHD, .mha, .mhd')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B 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.
.P
.RS 14
('Recognized file extensions: ', '.NII, .nii')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B vff
VFF Sun raster format
.P
.RS 14
('Recognized file extensions: ', '.VFF, .vff')
.RE
 
.RS 14
Supported element types: 
.RS 2
unsigned 8 bit, signed 16 bit
.RE
 
.RE
.TP 10
.B vista
Vista 3D
.P
.RS 14
('Recognized file extensions: ', '.-, .V, .VISTA, .v, .vista')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B vti
3D image VTK-XML in- and output (experimental).
.P
.RS 14
('Recognized file extensions: ', '.VTI, .vti')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B vtk
3D VTK image legacy in- and output (experimental).
.P
.RS 14
('Recognized file extensions: ', '.VTK, .VTKIMAGE, .vtk, .vtkimage')
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.SH EXAMPLE

    
.HP
mia\-3dcombine\-mr\-segmentations 
.SH AUTHOR(s)
Gert Wollny
.SH COPYRIGHT
This software is Copyright (c) 1999\(hy2015 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'.