mia-3dfluid - Online in the Cloud

PROGRAM:

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'.

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