Scroll to navigation

mia-3ddeform(1) USER COMMANDS mia-3ddeform(1)

NAME

mia-3ddeform - Transform a 3D image by means of a vector field.

SYNOPSIS

mia-3ddeform -i <in-image> -o <out-image> -t <transformation> [options]

DESCRIPTION

mia-3ddeform Transform a 3D image by applying a given 3D transformation that is defined by a 3D vector field v according to x:=x-v(x)

OPTIONS

-i --in-image=(input,required)
input image For supported file types see PLUGINS:3dimage/io
-o --out-image=(output,required)
transformed image For supported file types see PLUGINS:3dimage/io
-t --transformation=(input,required)
transformation vector field For supported file types see PLUGINS:3dvf/io
-p --interpolator=bspline:d=3
image interpolator kernel For supported plugins see PLUGINS:1d/splinekernel

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: 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/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

PLUGINS: 3dvf/io

cvista
obsolete 3d vector field io plugin for range compressend vista (saving not supported)
Recognized file extensions: .CVF, .cvf
Supported element types:
floating point 32 bit
datapool
Virtual IO to and from the internal data pool
Recognized file extensions: .@
vista
a 3d vector field io plugin for vista
Recognized file extensions: .V, .VF, .v, .vf
Supported element types:
floating point 32 bit
vtk
3D Vector field in- and output (experimental). No attributes are stored or read.
Recognized file extensions: .VTK, .VTKVF, .vtk, .vtkvf
Supported element types:
floating point 32 bit

EXAMPLE

Transform an image input.v by the transformation defined by the vector field field.v by using bspline interpolation of degree 4 and store the result in output.v
mia-3ddeform -i input.v -t field.v -o output.v -p bspline:d=4

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'.
17 October 2014 2.0.10