Provided by: mia-tools_2.0.13-1_amd64 
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=(required)
input perfusion data set
-o --out-file=(required)
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 series
-O --optimizer=gsl:opt=gd,step=0.1
Optimizer used for minimization
-l --mg-levels=3
multi-resolution levels
-f --transForm=spline
transformation type For supported plugins see PLUGINS:2dimage/transform
-r --ref=-1
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
warning ‐ Warnings
error ‐ Report errors
fail ‐ Report test failures
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).
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)
Spline degree. in [0, 5]
omoms OMoms-spline kernel creation, supported parameters are:
d = 3 (int)
Spline degree. in [3, 3]
PLUGINS: 2dimage/cost
lsd Least-Squares Distance measure
(no parameters)
mi Spline parzen based mutual information., supported parameters are:
cut = 0 (float)
Percentage of pixels to cut at high and low intensities to remove outliers. in [0, 40]
mbins = 64 (uint)
Number of histogram bins used for the moving image. in [1, 256]
mkernel = [bspline:d=3] (factory)
Spline kernel for moving image parzen hinstogram. For supported plug-ins see
PLUGINS:1d/splinekernel
rbins = 64 (uint)
Number of histogram bins used for the reference image. in [1, 256]
rkernel = [bspline:d=0] (factory)
Spline kernel for reference image parzen hinstogram. For supported plug-ins see
PLUGINS:1d/splinekernel
ngf This function evaluates the image similarity based on normalized gradient fields. Various
evaluation kernels are availabe., supported parameters are:
eval = ds (string)
plugin subtype (sq, ds,dot,cross).
ssd 2D imaga cost: sum of squared differences, supported parameters are:
norm = 0 (bool)
Set whether the metric should be normalized by the number of image pixels.
PLUGINS: 2dimage/fullcost
divcurl divcurl penalty cost function, supported parameters are:
curl = 1 (float)
penalty weight on curl. in [0, 3.40282e+38]
div = 1 (float)
penalty weight on divergence. in [0, 3.40282e+38]
weight = 1 (float)
weight of cost function. in [-1e+10, 1e+10]
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 = ref.@ (io)
Reference image. For supported file types see PLUGINS:2dimage/io
src = src.@ (io)
Study image. For supported file types see PLUGINS:2dimage/io
weight = 1 (float)
weight of cost function. in [-1e+10, 1e+10]
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:
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/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]] (streamable)
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]] (streamable)
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)
isotropic coefficient rate in pixels. in [1, 3.40282e+38]
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)
penalty weight on curl. in [0, 3.40282e+38]
div = 1 (float)
penalty weight on divergence. in [0, 3.40282e+38]
weight = 1 (float)
weight of penalty energy. in [0, 3.40282e+38]
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) 1999‐2013 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'.