NAME
mia-3dfluid - Fluid dynamic 3D registration
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. ⟨https://doi.org/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:
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).
Registration parameters
- --disable-multigrid
-
disable multi-grid processing
- --disable-fullres
-
disable processing on the full resolution image
- --lambda=1
-
elasticy constant
- --mu=1
-
elasticy constant
- -s --start-size=16
-
initial multigrided size
- -m --method=sora
-
method for solving PDE
sor ‐ successive overrelaxation
sora ‐ Gauss Southwell relexation
- --step=0.8
-
Initial stepsize
- -p --interpolator=bspline:d=3
-
image interpolator kernel
For supported plugins see PLUGINS:1d/splinekernel
- --relax=1
-
overrelaxation factor vor method sor
- --maxiter=10
-
maximum iterations
- --epsilon=0.01
-
truncation condition
- --matter=4
-
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:
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 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'.