Provided by: mia-tools_2.2.7-3_amd64 
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, 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'.