mia-3dfluid(1) | General Commands Manual | mia-3dfluid(1) |
NAME¶
mia-3dfluid - Fluid dynamic 3D registrationSYNOPSIS¶
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 ‐ successive 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
- maximum iterationsmaximum 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.
- 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:
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'.v2.4.3 | USER COMMANDS |