mia-3dfluid(1)
3dfluid
Description
mia-3dfluid
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:
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’.