| mia-3ddeform(1) | General Commands Manual | 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); io
- input image
For supported file types see PLUGINS:3dimage/io - -o --out-image=(required, output); 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 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:
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: 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. 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
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'.
| v2.4.7 | USER COMMANDS |