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.

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: 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'.