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PROGRAM:

NAME


mia-2dmyoset-all2one-nonrigid - Non-linear registration of a series of 2D images.

SYNOPSIS


mia-2dmyoset-all2one-nonrigid -i <in-file> -o <out-file> [options]
<PLUGINS:2dimage/fullcost>

DESCRIPTION


mia-2dmyoset-all2one-nonrigid This program runs non-rigid registration of a series of
images given in an image set. All images are registered to one user defined reference
image.

OPTIONS


File-IO
-i --in-file=(input, required); string
input perfusion data set

-o --out-file=(output, required); string
output perfusion data set

--out-filebase=reg
file name basae for registered files, file type is deducted from the image
file type in the input data set.

Registration
-k --skip=0
Skip images at the beginning of the seriesSkip images at the beginning of
the series

-O --optimizer=gsl:opt=gd,step=0.1
Optimizer used for minimization

-l --mg-levels=3
multi-resolution levelsmulti-resolution levels

-f --transForm=spline
transformation typetransformation type For supported plugins see
PLUGINS:2dimage/transform

-r --ref=-1
reference frame (-1 == use image in the middle)reference frame (-1 == use
image in the middle)

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).

PLUGINS: 1d/splinebc


mirror Spline interpolation boundary conditions that mirror on the boundary

(no parameters)

repeat Spline interpolation boundary conditions that repeats the value at the boundary

(no parameters)

zero Spline interpolation boundary conditions that assumes zero for values outside

(no parameters)

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: 2dimage/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.

lsd Least-Squares Distance measure

(no parameters)

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. Various evaluation kernels are availabe., supported parameters are:

eval = ds; dict
plugin subtype. Supported values are:
sq ‐ square of difference
ds ‐ square of scaled difference
dot ‐ scalar product kernel
cross ‐ cross product kernel

ssd 2D imaga 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
2D 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: 2dimage/fullcost


image Generalized image similarity cost function that also handles multi-resolution
processing. The actual similarity measure is given es extra parameter.,
supported parameters are:

cost = ssd; factory
Cost function kernel. For supported plug-ins see PLUGINS:2dimage/cost

debug = 0; bool
Save intermediate resuts for debugging.

ref =(input, string)
Reference image.

src =(input, string)
Study image.

weight = 1; float
weight of cost function.

labelimage
Similarity cost function that maps labels of two images and handles label-
preserving multi-resolution processing., supported parameters are:

debug = 0; int in [0, 1]
write the distance transforms to a 3D image.

maxlabel = 256; int in [2, 32000]
maximum number of labels to consider.

ref =(input, string)
Reference image.

src =(input, string)
Study image.

weight = 1; float
weight of cost function.

maskedimage
Generalized masked image similarity cost function that also handles multi-
resolution processing. The provided masks should be densly filled regions in
multi-resolution procesing because otherwise the mask information may get lost
when downscaling the image. The reference mask and the transformed mask of the
study image are combined by binary AND. The actual similarity measure is given
es extra parameter., supported parameters are:

cost = ssd; factory
Cost function kernel. For supported plug-ins see
PLUGINS:2dimage/maskedcost

ref =(input, string)
Reference image.

ref-mask =(input, string)
Reference image mask (binary).

src =(input, string)
Study image.

src-mask =(input, string)
Study image mask (binary).

weight = 1; float
weight of cost function.

PLUGINS: 2dimage/io


bmp BMP 2D-image input/output support

Recognized file extensions: .BMP, .bmp

Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit

datapool Virtual IO to and from the internal data pool

Recognized file extensions: .@

dicom 2D image io for DICOM

Recognized file extensions: .DCM, .dcm

Supported element types:
signed 16 bit, unsigned 16 bit

exr a 2dimage io plugin for OpenEXR images

Recognized file extensions: .EXR, .exr

Supported element types:
unsigned 32 bit, floating point 32 bit

jpg a 2dimage io plugin for jpeg gray scale images

Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg

Supported element types:
unsigned 8 bit

png a 2dimage io plugin for png images

Recognized file extensions: .PNG, .png

Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit

raw RAW 2D-image output support

Recognized file extensions: .RAW, .raw

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

tif TIFF 2D-image input/output support

Recognized file extensions: .TIF, .TIFF, .tif, .tiff

Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit

vista a 2dimage io plugin for vista images

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

PLUGINS: 2dimage/maskedcost


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 with masking., 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 with masking support.

(no parameters)

ssd Sum of squared differences with masking.

(no parameters)

PLUGINS: 2dimage/transform


affine Affine transformation (six degrees of freedom)., supported parameters are:

imgboundary = mirror; factory
image interpolation boundary conditions. For supported plug-ins see
PLUGINS:1d/splinebc

imgkernel = [bspline:d=3]; factory
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel

rigid Rigid transformations (i.e. rotation and translation, three degrees of
freedom)., supported parameters are:

imgboundary = mirror; factory
image interpolation boundary conditions. For supported plug-ins see
PLUGINS:1d/splinebc

imgkernel = [bspline:d=3]; factory
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel

rot-center = [[0,0]]; 2dfvector
Relative rotation center, i.e. <0.5,0.5> corresponds to the center of the
support rectangle.

rotation Rotation transformations (i.e. rotation about a given center, one degree of
freedom)., supported parameters are:

imgboundary = mirror; factory
image interpolation boundary conditions. For supported plug-ins see
PLUGINS:1d/splinebc

imgkernel = [bspline:d=3]; factory
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel

rot-center = [[0,0]]; 2dfvector
Relative rotation center, i.e. <0.5,0.5> corresponds to the center of the
support rectangle.

spline Free-form transformation that can be described by a set of B-spline coefficients
and an underlying B-spline kernel., supported parameters are:

anisorate = [[0,0]]; 2dfvector
anisotropic coefficient rate in pixels, nonpositive values will be
overwritten by the 'rate' value..

imgboundary = mirror; factory
image interpolation boundary conditions. For supported plug-ins see
PLUGINS:1d/splinebc

imgkernel = [bspline:d=3]; factory
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel

kernel = [bspline:d=3]; factory
transformation spline kernel.. For supported plug-ins see
PLUGINS:1d/splinekernel

penalty = ; factory
Transformation penalty term. For supported plug-ins see
PLUGINS:2dtransform/splinepenalty

rate = 10; float in [1, inf)
isotropic coefficient rate in pixels.

translate Translation only (two degrees of freedom), supported parameters are:

imgboundary = mirror; factory
image interpolation boundary conditions. For supported plug-ins see
PLUGINS:1d/splinebc

imgkernel = [bspline:d=3]; factory
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel

vf This plug-in implements a transformation that defines a translation for each
point of the grid defining the domain of the transformation., supported
parameters are:

imgboundary = mirror; factory
image interpolation boundary conditions. For supported plug-ins see
PLUGINS:1d/splinebc

imgkernel = [bspline:d=3]; factory
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel

PLUGINS: 2dtransform/splinepenalty


divcurl divcurl penalty on the transformation, supported parameters are:

curl = 1; float in [0, inf)
penalty weight on curl.

div = 1; float in [0, inf)
penalty weight on divergence.

norm = 0; bool
Set to 1 if the penalty should be normalized with respect to the image
size.

weight = 1; float in (0, inf)
weight of penalty energy.

EXAMPLE


Register the perfusion series given in segment.set by optimizing a spline based
transformation with a coefficient rate of 16 pixel using Mutual Information and penalize
the transformation by using divcurl with aweight of 2.0.

mia-2dmyoset-all2one-nonrigid -i segment.set -o registered.set
-f spline:rate=16,penalty=[divcurl:weight=2.0] image:cost=mi,weight=2.0

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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