SYNOPSIS
mia-3dfluid -i <in-image> -r <ref-image> -o <out-transformation> [options]DESCRIPTION
mia-3dfluid This program is used for non-rigid registration based on fluid dynamics as described in: Wollny, G. and Kruggel, F., 'Computational cost of non-rigid registration algorithms based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002, doi:10.1109/TMI.2002.803113. It uses SSD as the sole registration criterion.OPTIONS
File-IO
-
- -i --in-image=(input, required); io
- input image For supported file types see PLUGINS:3dimage/io
- -r --ref-image=(input, required); io
- reference image For supported file types see PLUGINS:3dimage/io
- -o --out-transformation=(output, required); io
- output transformation comprising the registering transformation field For supported file types see PLUGINS:3dtransform/io
- -d --out-image=(output); io
- save deformed image For supported file types see PLUGINS:3dimage/io
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).
Registration parameters
-
- --disable-multigrid
- disable multi-grid processing
- --disable-fullres
- disable processing on the full resolution image
- --lambda=1
- elasticy constantelasticy constant
- --mu=1
- elasticy constantelasticy constant
- -s --start-size=16
- initial multigrided sizeinitial multigrided size
- -m --method=sora
-
method for solving PDE
- sor - succesive overrelaxation
- sora - Gauss Southwell relexation
- --step=0.8
- Initial stepsizeInitial stepsize
- -p --interpolator=bspline:d=3
- image interpolator kernelimage interpolator kernel For supported plugins see PLUGINS:1d/splinekernel
- --relax=1
- overrelaxation factor vor method soroverrelaxation factor vor method sor
- --maxiter=10
- maxium iterationsmaxium iterations
- --epsilon=0.01
- truncation conditiontruncation condition
- --matter=4
- intensity above which real matter is assumed (experimental)intensity above which real matter is assumed (experimental)
PLUGINS: 1d/splinekernel
- bspline
- B-spline kernel creation , supported parameters are:
-
d
= 3; int in [0, 5]
-
Spline degree.
-
Spline degree.
- omoms
- OMoms-spline kernel creation, supported parameters are:
-
d
= 3; int in [3, 3]
-
Spline degree.
-
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: 3dtransform/io
- bbs
- Binary (non-portable) serialized IO of 3D transformations
- Recognized file extensions: .bbs
- datapool
- Virtual IO to and from the internal data pool
- Recognized file extensions: .@
- vista
- Vista storage of 3D transformations
- Recognized file extensions: .v, .v3dt
- xml
- XML serialized IO of 3D transformations
- Recognized file extensions: .x3dt
EXAMPLE
Register image test.v to image ref.v and write the deformation vector field regfield.v. Start registration at the smallest size above 16 pixel.- mia-3dfluid -i test.v -r ref.v -o regfield.v -s 16
AUTHOR(s)
Gert WollnyCOPYRIGHT
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'.