mia-3ddeform - Online in the Cloud

PROGRAM:

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); io
input image For supported file types see PLUGINS:3dimage/io

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

-t --transformation=(input, required); io
transformation vector field For supported file types see PLUGINS:3dvf/io

-p --interpolator=bspline:d=3
image interpolator kernelimage 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).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 in [0, 5]
Spline degree.

omoms OMoms-spline kernel creation, supported parameters are:

d = 3; int in [3, 3]
Spline degree.

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) 1999‐2015 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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