SYNOPSIS
mia2dmyoperiodicnonrigid i <infile> o <outfile> [options]DESCRIPTION
mia2dmyoperiodicnonrigid This program runs the nonrigid registration of an perfusion image series preferable acquired letting the patient breath freely. The registration algorithm implementes G. Wollny, MJ LedesmaCabryo, P.Kellman, and A.Santos, "Exploiting Quasiperiodicity in Motion Correction of FreeBreathing," IEEE Transactions on Medical Imaging, 29(8), 2010
OPTIONS
FileIO

 i infile=(input, required); string
 input perfusion data set
 o outfile=(output, required); string
 output perfusion data set
 r registered=reg
 file name base for registered fiels
 savereferences
 Save synthetic references to files refXXXX.v
Preconditions

 k skip=0
 Skip images at the begin of the seriesSkip images at the begin of the series
 maxcandidates=20
 maximum number of candidates for global reference imagemaximum number of candidates for global reference image
 S costseries=image:cost=[ngf:eval=ds]
 Const function to use for the analysis of the seriesConst function to use for the analysis of the series For supported plugins see PLUGINS:2dimage/fullcost
 refidx=
 save reference index number to this file
 R globalreference=1
 save reference index number to this filesave reference index number to this file
 D maxsubsetdelta=0
 Maximum delta between two elements of the prealigned subsetMaximum delta between two elements of the prealigned subset
Registration

 O optimizer=gsl:opt=gd,step=0.01
 Optimizer used for minimizationOptimizer used for minimization For supported plugins see PLUGINS:minimizer/singlecost
 refiner=
 optimizer used for additional minimizationoptimizer used for additional minimization For supported plugins see PLUGINS:minimizer/singlecost
 l mrlevels=3
 multiresolution levelsmultiresolution levels
 f transForm=spline:rate=16,penalty=[divcurl:weight=0.01]
 transformation typetransformation type For supported plugins see PLUGINS:2dimage/transform
 1 costsubset=image:cost=[ngf:eval=ds]
 Cost function for registration during the subset registrationCost function for registration during the subset registration For supported plugins see PLUGINS:2dimage/fullcost
 2 costfinal=image:cost=ssd
 Cost function for registration during the final registrationCost function for registration during the final registration For supported plugins see PLUGINS:2dimage/fullcost
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
 Bspline kernel creation , supported parameters are:

d
= 3; int in [0, 5]

Spline degree.

Spline degree.
 omoms
 OMomsspline kernel creation, supported parameters are:

d
= 3; int in [3, 3]

Spline degree.

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.

half width of the window used for evaluating the localized cross correlation.
 lsd
 LeastSquares 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.

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.

Number of histogram bins used for the moving image.

mkernel
= [bspline:d=3]; factory

Spline kernel for moving image parzen hinstogram.
For supported plugins see PLUGINS:1d/splinekernel

Spline kernel for moving image parzen hinstogram.
For supported plugins see PLUGINS:1d/splinekernel

rbins
= 64; uint in [1, 256]

Number of histogram bins used for the reference image.

Number of histogram bins used for the reference image.

rkernel
= [bspline:d=0]; factory

Spline kernel for reference image parzen hinstogram.
For supported plugins see PLUGINS:1d/splinekernel

Spline kernel for reference image parzen hinstogram.
For supported plugins 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

plugin subtype.
Supported values are:
 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.

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.

Set whether the metric should be normalized by the number of image pixels.
 ssdautomask
 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.

Threshold intensity value for reference image.

sthresh
= 0; double

Threshold intensity value for source image.

Threshold intensity value for source image.
PLUGINS: 2dimage/fullcost
 image
 Generalized image similarity cost function that also handles multiresolution processing. The actual similarity measure is given es extra parameter., supported parameters are:

cost
= ssd; factory

Cost function kernel.
For supported plugins see PLUGINS:2dimage/cost

Cost function kernel.
For supported plugins see PLUGINS:2dimage/cost

debug
= 0; bool

Save intermediate resuts for debugging.

Save intermediate resuts for debugging.

ref
=(input, string)

Reference image.

Reference image.

src
=(input, string)

Study image.

Study image.

weight
= 1; float

weight of cost function.

weight of cost function.
 labelimage
 Similarity cost function that maps labels of two images and handles labelpreserving multiresolution processing., supported parameters are:

debug
= 0; int in [0, 1]

write the distance transforms to a 3D image.

write the distance transforms to a 3D image.

maxlabel
= 256; int in [2, 32000]

maximum number of labels to consider.

maximum number of labels to consider.

ref
=(input, string)

Reference image.

Reference image.

src
=(input, string)

Study image.

Study image.

weight
= 1; float

weight of cost function.

weight of cost function.
 maskedimage
 Generalized masked image similarity cost function that also handles multiresolution processing. The provided masks should be densly filled regions in multiresolution 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 plugins see PLUGINS:2dimage/maskedcost

Cost function kernel.
For supported plugins see PLUGINS:2dimage/maskedcost

ref
=(input, string)

Reference image.

Reference image.

refmask
=(input, string)

Reference image mask (binary).

Reference image mask (binary).

src
=(input, string)

Study image.

Study image.

srcmask
=(input, string)

Study image mask (binary).

Study image mask (binary).

weight
= 1; float

weight of cost function.

weight of cost function.
PLUGINS: 2dimage/io
 bmp
 BMP 2Dimage 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: [email protected]
 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 2Dimage 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 2Dimage 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.

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.

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.

Number of histogram bins used for the moving image.

mkernel
= [bspline:d=3]; factory

Spline kernel for moving image parzen hinstogram.
For supported plugins see PLUGINS:1d/splinekernel

Spline kernel for moving image parzen hinstogram.
For supported plugins see PLUGINS:1d/splinekernel

rbins
= 64; uint in [1, 256]

Number of histogram bins used for the reference image.

Number of histogram bins used for the reference image.

rkernel
= [bspline:d=0]; factory

Spline kernel for reference image parzen hinstogram.
For supported plugins see PLUGINS:1d/splinekernel

Spline kernel for reference image parzen hinstogram.
For supported plugins 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 plugins see PLUGINS:1d/splinebc

image interpolation boundary conditions.
For supported plugins see PLUGINS:1d/splinebc

imgkernel
= [bspline:d=3]; factory

image interpolator kernel.
For supported plugins see PLUGINS:1d/splinekernel

image interpolator kernel.
For supported plugins 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 plugins see PLUGINS:1d/splinebc

image interpolation boundary conditions.
For supported plugins see PLUGINS:1d/splinebc

imgkernel
= [bspline:d=3]; factory

image interpolator kernel.
For supported plugins see PLUGINS:1d/splinekernel

image interpolator kernel.
For supported plugins see PLUGINS:1d/splinekernel

rotcenter
= [[0,0]]; 2dfvector

Relative rotation center, i.e. <0.5,0.5> corresponds to the center of the support rectangle.

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 plugins see PLUGINS:1d/splinebc

image interpolation boundary conditions.
For supported plugins see PLUGINS:1d/splinebc

imgkernel
= [bspline:d=3]; factory

image interpolator kernel.
For supported plugins see PLUGINS:1d/splinekernel

image interpolator kernel.
For supported plugins see PLUGINS:1d/splinekernel

rotcenter
= [[0,0]]; 2dfvector

Relative rotation center, i.e. <0.5,0.5> corresponds to the center of the support rectangle.

Relative rotation center, i.e. <0.5,0.5> corresponds to the center of the support rectangle.
 spline
 Freeform transformation that can be described by a set of Bspline coefficients and an underlying Bspline kernel., supported parameters are:

anisorate
= [[0,0]]; 2dfvector

anisotropic coefficient rate in pixels, nonpositive values will be overwritten by the 'rate' value..

anisotropic coefficient rate in pixels, nonpositive values will be overwritten by the 'rate' value..

imgboundary
= mirror; factory

image interpolation boundary conditions.
For supported plugins see PLUGINS:1d/splinebc

image interpolation boundary conditions.
For supported plugins see PLUGINS:1d/splinebc

imgkernel
= [bspline:d=3]; factory

image interpolator kernel.
For supported plugins see PLUGINS:1d/splinekernel

image interpolator kernel.
For supported plugins see PLUGINS:1d/splinekernel

kernel
= [bspline:d=3]; factory

transformation spline kernel..
For supported plugins see PLUGINS:1d/splinekernel

transformation spline kernel..
For supported plugins see PLUGINS:1d/splinekernel

penalty
= ; factory

Transformation penalty term.
For supported plugins see PLUGINS:2dtransform/splinepenalty

Transformation penalty term.
For supported plugins see PLUGINS:2dtransform/splinepenalty

rate
= 10; float in [1, inf)

isotropic coefficient rate in pixels.

isotropic coefficient rate in pixels.
 translate
 Translation only (two degrees of freedom), supported parameters are:

imgboundary
= mirror; factory

image interpolation boundary conditions.
For supported plugins see PLUGINS:1d/splinebc

image interpolation boundary conditions.
For supported plugins see PLUGINS:1d/splinebc

imgkernel
= [bspline:d=3]; factory

image interpolator kernel.
For supported plugins see PLUGINS:1d/splinekernel

image interpolator kernel.
For supported plugins see PLUGINS:1d/splinekernel
 vf
 This plugin 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 plugins see PLUGINS:1d/splinebc

image interpolation boundary conditions.
For supported plugins see PLUGINS:1d/splinebc

imgkernel
= [bspline:d=3]; factory

image interpolator kernel.
For supported plugins see PLUGINS:1d/splinekernel

image interpolator kernel.
For supported plugins 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.

penalty weight on curl.

div
= 1; float in [0, inf)

penalty weight on divergence.

penalty weight on divergence.

norm
= 0; bool

Set to 1 if the penalty should be normalized with respect to the image size.

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.

weight of penalty energy.
PLUGINS: minimizer/singlecost
 gdas
 Gradient descent with automatic step size correction., supported parameters are:

ftolr
= 0; double in [0, inf)

Stop if the relative change of the criterion is below..

Stop if the relative change of the criterion is below..

maxstep
= 2; double in (0, inf)

Maximal absolute step size.

Maximal absolute step size.

maxiter
= 200; uint in [1, inf)

Stopping criterion: the maximum number of iterations.

Stopping criterion: the maximum number of iterations.

minstep
= 0.1; double in (0, inf)

Minimal absolute step size.

Minimal absolute step size.

xtola
= 0.01; double in [0, inf)

Stop if the infnorm of the change applied to x is below this value..

Stop if the infnorm of the change applied to x is below this value..
 gdsq
 Gradient descent with quadratic step estimation, supported parameters are:

ftolr
= 0; double in [0, inf)

Stop if the relative change of the criterion is below..

Stop if the relative change of the criterion is below..

gtola
= 0; double in [0, inf)

Stop if the infnorm of the gradient is below this value..

Stop if the infnorm of the gradient is below this value..

maxiter
= 100; uint in [1, inf)

Stopping criterion: the maximum number of iterations.

Stopping criterion: the maximum number of iterations.

scale
= 2; double in (1, inf)

Fallback fixed step size scaling.

Fallback fixed step size scaling.

step
= 0.1; double in (0, inf)

Initial step size.

Initial step size.

xtola
= 0; double in [0, inf)

Stop if the infnorm of xupdate is below this value..

Stop if the infnorm of xupdate is below this value..
 gsl
 optimizer plugin based on the multimin optimizers ofthe GNU Scientific Library (GSL) https://www.gnu.org/software/gsl/, supported parameters are:

eps
= 0.01; double in (0, inf)

gradient based optimizers: stop when grad < eps, simplex: stop when simplex size < eps..

gradient based optimizers: stop when grad < eps, simplex: stop when simplex size < eps..

iter
= 100; uint in [1, inf)

maximum number of iterations.

maximum number of iterations.

opt
= gd; dict

Specific optimizer to be used..
Supported values are:
 bfgs  BroydenFletcherGoldfarbShann
 bfgs2  BroydenFletcherGoldfarbShann (most efficient version)
 cgfr  FlecherReeves conjugate gradient algorithm
 gd  Gradient descent.
 simplex  Simplex algorithm of Nelder and Mead
 cgpr  PolakRibiere conjugate gradient algorithm

Specific optimizer to be used..
Supported values are:

step
= 0.001; double in (0, inf)

initial step size.

initial step size.

tol
= 0.1; double in (0, inf)

some tolerance parameter.

some tolerance parameter.
 nlopt
 Minimizer algorithms using the NLOPT library, for a description of the optimizers please see 'http://abinitio.mit.edu/wiki/index.php/NLopt_Algorithms', supported parameters are:

ftola
= 0; double in [0, inf)

Stopping criterion: the absolute change of the objective value is below this value.

Stopping criterion: the absolute change of the objective value is below this value.

ftolr
= 0; double in [0, inf)

Stopping criterion: the relative change of the objective value is below this value.

Stopping criterion: the relative change of the objective value is below this value.

higher
= inf; double

Higher boundary (equal for all parameters).

Higher boundary (equal for all parameters).

localopt
= none; dict

local minimization algorithm that may be required for the main minimization algorithm..
Supported values are:
 gnorigdirectl  Dividing Rectangles (original implementation, locally biased)
 gndirectlnoscal  Dividing Rectangles (unscaled, locally biased)
 gnisres  Improved Stochastic Ranking Evolution Strategy
 ldtnewton  Truncated Newton
 gndirectlrand  Dividing Rectangles (locally biased, randomized)
 lnnewuoa  Derivativefree Unconstrained Optimization by Iteratively Constructed Quadratic Approximation
 gndirectlrandnoscale  Dividing Rectangles (unscaled, locally biased, randomized)
 gnorigdirect  Dividing Rectangles (original implementation)
 ldtnewtonprecond  Preconditioned Truncated Newton
 ldtnewtonrestart  Truncated Newton with steepestdescent restarting
 gndirect  Dividing Rectangles
 lnneldermead  NelderMead simplex algorithm
 lncobyla  Constrained Optimization BY Linear Approximation
 gncrs2lm  Controlled Random Search with Local Mutation
 ldvar2  Shifted LimitedMemory VariableMetric, Rank 2
 ldvar1  Shifted LimitedMemory VariableMetric, Rank 1
 ldmma  Method of Moving Asymptotes
 ldlbfgsnocedal  None
 ldlbfgs  Lowstorage BFGS
 gndirectl  Dividing Rectangles (locally biased)
 none  don't specify algorithm
 lnbobyqa  Derivativefree Boundconstrained Optimization
 lnsbplx  Subplex variant of NelderMead
 lnnewuoabound  Derivativefree Boundconstrained Optimization by Iteratively Constructed Quadratic Approximation
 lnpraxis  Gradientfree Local Optimization via the PrincipalAxis Method
 gndirectnoscal  Dividing Rectangles (unscaled)
 ldtnewtonprecondrestart  Preconditioned Truncated Newton with steepestdescent restarting

local minimization algorithm that may be required for the main minimization algorithm..
Supported values are:

lower
= inf; double

Lower boundary (equal for all parameters).

Lower boundary (equal for all parameters).

maxiter
= 100; int in [1, inf)

Stopping criterion: the maximum number of iterations.

Stopping criterion: the maximum number of iterations.

opt
= ldlbfgs; dict

main minimization algorithm.
Supported values are:
 gnorigdirectl  Dividing Rectangles (original implementation, locally biased)
 gmlsllds  MultiLevel SingleLinkage (lowdiscrepancysequence, require local gradient based optimization and bounds)
 gndirectlnoscal  Dividing Rectangles (unscaled, locally biased)
 gnisres  Improved Stochastic Ranking Evolution Strategy
 ldtnewton  Truncated Newton
 gndirectlrand  Dividing Rectangles (locally biased, randomized)
 lnnewuoa  Derivativefree Unconstrained Optimization by Iteratively Constructed Quadratic Approximation
 gndirectlrandnoscale  Dividing Rectangles (unscaled, locally biased, randomized)
 gnorigdirect  Dividing Rectangles (original implementation)
 ldtnewtonprecond  Preconditioned Truncated Newton
 ldtnewtonrestart  Truncated Newton with steepestdescent restarting
 gndirect  Dividing Rectangles
 auglageq  Augmented Lagrangian algorithm with equality constraints only
 lnneldermead  NelderMead simplex algorithm
 lncobyla  Constrained Optimization BY Linear Approximation
 gncrs2lm  Controlled Random Search with Local Mutation
 ldvar2  Shifted LimitedMemory VariableMetric, Rank 2
 ldvar1  Shifted LimitedMemory VariableMetric, Rank 1
 ldmma  Method of Moving Asymptotes
 ldlbfgsnocedal  None
 gmlsl  MultiLevel SingleLinkage (require local optimization and bounds)
 ldlbfgs  Lowstorage BFGS
 gndirectl  Dividing Rectangles (locally biased)
 lnbobyqa  Derivativefree Boundconstrained Optimization
 lnsbplx  Subplex variant of NelderMead
 lnnewuoabound  Derivativefree Boundconstrained Optimization by Iteratively Constructed Quadratic Approximation
 auglag  Augmented Lagrangian algorithm
 lnpraxis  Gradientfree Local Optimization via the PrincipalAxis Method
 gndirectnoscal  Dividing Rectangles (unscaled)
 ldtnewtonprecondrestart  Preconditioned Truncated Newton with steepestdescent restarting
 ldslsqp  Sequential LeastSquares Quadratic Programming

main minimization algorithm.
Supported values are:

step
= 0; double in [0, inf)

Initial step size for gradient free methods.

Initial step size for gradient free methods.

stop
= inf; double

Stopping criterion: function value falls below this value.

Stopping criterion: function value falls below this value.

xtola
= 0; double in [0, inf)

Stopping criterion: the absolute change of all xvalues is below this value.

Stopping criterion: the absolute change of all xvalues is below this value.

xtolr
= 0; double in [0, inf)

Stopping criterion: the relative change of all xvalues is below this value.

Stopping criterion: the relative change of all xvalues is below this value.
EXAMPLE
Register the perfusion series given in 'segment.set'. Skip two images at the beginning, usa spline transformation of a knot rate 16 pixels, and penalize the transformation by divcurl with weight 5. Store the result in 'registered.set'.
 mia2dmyoperiodicnonrigid i segment.set o registered.set k 2 d 5 f spline:rate=16,penalty=[divcurl:weight=5]
AUTHOR(s)
Gert WollnyCOPYRIGHT
This software is Copyright (c) 19992015 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'.