Provided by: mia-tools_2.4.6-5build3_amd64 
NAME
mia-3dfluid-syn-registration - Non-linear registration of 3D images by using a diffeomorphic SyN
registration
SYNOPSIS
mia-3dfluid-syn-registration -i <in-image> -r <ref-image> -o <transform> -O <inverse-transform> [options]
DESCRIPTION
mia-3dfluid-syn-registration This program implements the registration of two gray scale 3D images. The
transformation applied is a symmeric diffeomorpic fluid dynamic registration. To work most efficiently,
this program makes a few assumptions about the imput data, i.e. the image must be of the same size, have
the same voxel spacing, and any intensity range normalization or equalization should also be done before
calling this program.
OPTIONS
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
IO
-i --in-image=(required, input); io
test image
For supported file types see PLUGINS:3dimage/io
-r --ref-image=(required, input); io
reference image
For supported file types see PLUGINS:3dimage/io
-o --transform=(required, output); io
output transformation
For supported file types see PLUGINS:3dtransform/io
-O --inverse-transform=(required, output); io
inverse output transformation
For supported file types see PLUGINS:3dtransform/io
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
-l --mg-levels=3
Number of multi-resolution levels to run the registration on. Not that some registration
parameters can be given as a coma seperated list to indicate per level values. In these
cases if the number of given values is smaller than the number of multi-resolution levels
(this parameter), the the last given value is used for all subsequest multi-resolution
levels.
-S --step=0.25; float in (0, 0.5]
Initial step size for all levels
-c --cost=ssd
Image similarity function to be minimized
For supported plugins see PLUGINS:3dimage/cost
-R --regularizer=sor:kernel=fluid,maxiter=50
Regularization for the force to transformation update
For supported plugins see PLUGINS:3dvf/regularizer
-T --conv-test-interval=; vuint in [4, 40]
Convergence test interations intervall: In order to measure convergence the cost function
value is averaged over this amount of iterations, and the decline rate is evaluated based
on the linare regression of the cost function values in this intervall. This parameter can
be given as a coma-seperated list with values corresponding to the multi-resolution levels,
see option --mg-levels for more information.
-D --stop-decline-rate=; vdouble in [0, inf)
Stopping criterium for registration based on the cost decline rate. If the rate below this
value, the iteration is stopped. This parameter can be given as a coma-seperated list with
values corresponding to the multi-resolution levels, see option --mg-levels for more
information.
-C --stop-cost=
Stopping criterium for registration based on the cost value. If the cost drops below this
value, the iteration is stopped. This parameter can be given as a coma-seperated list with
values corresponding to the multi-resolution levels, see option --mg-levels for more
information.
-I --iter=; vuint in [4, inf)
Naximum number if iterations done on each multi-resolution level. This parameter can be
given as a coma-seperated list with values corresponding to the multi-resolution levels,
see option --mg-levels for more information.
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/cost
lncc local normalized cross correlation with masking support., supported parameters are:
w = 5; uint in [1, 256]
half width of the window used for evaluating the localized cross correlation.
mi Spline parzen based mutual information., supported parameters are:
cut = 0; float in [0, 40]
Percentage of pixels to cut at high and low intensities to remove outliers.
mbins = 64; uint in [1, 256]
Number of histogram bins used for the moving image.
mkernel = [bspline:d=3]; factory
Spline kernel for moving image parzen hinstogram. For supported plug-ins see
PLUGINS:1d/splinekernel
rbins = 64; uint in [1, 256]
Number of histogram bins used for the reference image.
rkernel = [bspline:d=0]; factory
Spline kernel for reference image parzen hinstogram. For supported plug-ins see
PLUGINS:1d/splinekernel
ncc normalized cross correlation.
(no parameters)
ngf This function evaluates the image similarity based on normalized gradient fields. Given
normalized gradient fields $ _S$ of the src image and $ _R$ of the ref image various evaluators
are implemented., supported parameters are:
eval = ds; dict
plugin subtype (sq, ds,dot,cross). Supported values are:
ds ‐ square of scaled difference
dot ‐ scalar product kernel
cross ‐ cross product kernel
ssd 3D image cost: sum of squared differences, supported parameters are:
autothresh = 0; float in [0, 1000]
Use automatic masking of the moving image by only takeing intensity values into accound
that are larger than the given threshold.
norm = 0; bool
Set whether the metric should be normalized by the number of image pixels.
ssd-automask
3D image cost: sum of squared differences, with automasking based on given thresholds,
supported parameters are:
rthresh = 0; double
Threshold intensity value for reference image.
sthresh = 0; double
Threshold intensity value for source image.
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
PLUGINS: 3dvf/regularizer
sor This plugin implements successive (over-)relaxation as a solver to regularize the vector
field., supported parameters are:
abs_f = 0.01; float in [0, inf)
breaking condition: absolute residuum.
kernel = fluid; factory
solver kernel to be used. For supported plug-ins see PLUGINS:3dvf/regularizerkernel
maxiter = 100; uint in [0, inf)
maximum number of iterations.
rel_f = 1e-05; float in (0, 1)
breaking condition: relative residuum.
PLUGINS: 3dvf/regularizerkernel
fluid Evaluation kernel for the fluid-dynamics solver, either using successive (over-)relaxation, or
a Gauss-Southwell relaxation. This implementation is generic and doesn't implement any
architecture specific optimizations., supported parameters are:
lambda = 1; float in [0, 10000]
bulk viscosity (compressibility).
mu = 1; float in (0, 10000]
dynamic viscosity (shear).
relax = 1; float in [0.1, 2]
Relaxation parameter for the solver.
EXAMPLE
Register image test.v to image ref.v saving the transformation to transform.v and the inverse transform
to inverse-transform.v. Use three multiresolution levels, ssd as image cost function.
mia-3dfluid-syn-registration -i test.v -r ref.v -t transform.v -T inverse-transform.v -l 3 ssd
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'.