NAME
mia-3dcombine-imageseries - Combine images.
SYNOPSIS
mia-3dcombine-imageseries -o <out-file> [options] <PLUGINS:3dimage/io>
DESCRIPTION
mia-3dcombine-imageseries This programs takes various input images of the same dimensions and creates a combined output images that uses the define operation for the combination.
OPTIONS
- -o --out-file=(output, required); io
-
output file that contains the combined image.
For supported file types see PLUGINS:3dimage/io
- -p --operation=mean
-
Operation to be applied when combining the images
mean ‐ mean image intensities
max ‐ select max per pixel intensity
add ‐ add pixel intensities
- -r --repn=none
-
Output pixel representation (if not given, then the representation of the first input image will be used
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
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: 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
mia-3dcombine-imageseries
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'.