Provided by: mia-tools_2.2.7-3_amd64 
NAME
mia-2dmyopgt-nonrigid - Run a registration of a series of 2D images.
SYNOPSIS
mia-2dmyopgt-nonrigid -i <in-file> -o <out-file> [options]
DESCRIPTION
mia-2dmyopgt-nonrigid This program implements the non-linear registration based on Pseudo
Ground Thruth for motion compensation of series of myocardial perfusion images given as a
data set as decribed in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial
Perfusion MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-
Assisted Intervention MICCAI 2009, 165-172, 2009. Note that for this nonlinear motion
correction a preceding linear registration step is usually required.
OPTIONS
File-IO
-i --in-file=(input, required); string
input perfusion data set
-o --out-file=(output, required); string
output perfusion data set
-r --registered=reg
file name base for registered files, the image file type is the same as
given in the input data set
Pseudo Ground Thruth estimation
-A --alpha=1
spacial neighborhood penalty weightspacial neighborhood penalty weight
-B --beta=1
temporal second derivative penalty weighttemporal second derivative penalty
weight
-R --rho-thresh=0.85
correlation threshold for neighborhood analysiscorrelation threshold for
neighborhood analysis
-k --skip=0
skip images at the beginning of the series e.g. because as they are of other
modalitiesskip images at the beginning of the series e.g. because as they
are of other modalities
Registration
-O --optimizer=gsl:opt=gd,step=0.1
Optimizer used for minimizationOptimizer used for minimization For
supported plugins see PLUGINS:minimizer/singlecost
-a --start-c-rate=32
start coefficinet rate in spines, gets divided by --c-rate-divider with
every passstart coefficinet rate in spines, gets divided by --c-rate-divider
with every pass
--c-rate-divider=4
cofficient rate divider for each passcofficient rate divider for each pass
-d --start-divcurl=20
start divcurl weight, gets divided by --divcurl-divider with every passstart
divcurl weight, gets divided by --divcurl-divider with every pass
--divcurl-divider=4
divcurl weight scaling with each new passdivcurl weight scaling with each
new pass
-w --imageweight=1
image cost weightimage cost weight
-l --mg-levels=3
multi-resolution levelsmulti-resolution levels
-P --passes=4
registration passesregistration passes
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: 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..
max-step = 2; double in (0, inf)
Maximal absolute step size.
maxiter = 200; uint in [1, inf)
Stopping criterion: the maximum number of iterations.
min-step = 0.1; double in (0, inf)
Minimal absolute step size.
xtola = 0.01; double in [0, inf)
Stop if the inf-norm 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..
gtola = 0; double in [0, inf)
Stop if the inf-norm of the gradient is below this value..
maxiter = 100; uint in [1, inf)
Stopping criterion: the maximum number of iterations.
scale = 2; double in (1, inf)
Fallback fixed step size scaling.
step = 0.1; double in (0, inf)
Initial step size.
xtola = 0; double in [0, inf)
Stop if the inf-norm of x-update 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..
iter = 100; uint in [1, inf)
maximum number of iterations.
opt = gd; dict
Specific optimizer to be used.. Supported values are:
bfgs ‐ Broyden-Fletcher-Goldfarb-Shann
bfgs2 ‐ Broyden-Fletcher-Goldfarb-Shann (most efficient version)
cg-fr ‐ Flecher-Reeves conjugate gradient algorithm
gd ‐ Gradient descent.
simplex ‐ Simplex algorithm of Nelder and Mead
cg-pr ‐ Polak-Ribiere conjugate gradient algorithm
step = 0.001; double in (0, inf)
initial step size.
tol = 0.1; double in (0, inf)
some tolerance parameter.
nlopt Minimizer algorithms using the NLOPT library, for a description of the
optimizers please see 'http://ab-
initio.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.
ftolr = 0; double in [0, inf)
Stopping criterion: the relative change of the objective value is below
this value.
higher = inf; double
Higher boundary (equal for all parameters).
local-opt = none; dict
local minimization algorithm that may be required for the main
minimization algorithm.. Supported values are:
gn-orig-direct-l ‐ Dividing Rectangles (original implementation,
locally biased)
gn-direct-l-noscal ‐ Dividing Rectangles (unscaled, locally biased)
gn-isres ‐ Improved Stochastic Ranking Evolution Strategy
ld-tnewton ‐ Truncated Newton
gn-direct-l-rand ‐ Dividing Rectangles (locally biased, randomized)
ln-newuoa ‐ Derivative-free Unconstrained Optimization by Iteratively
Constructed Quadratic Approximation
gn-direct-l-rand-noscale ‐ Dividing Rectangles (unscaled, locally
biased, randomized)
gn-orig-direct ‐ Dividing Rectangles (original implementation)
ld-tnewton-precond ‐ Preconditioned Truncated Newton
ld-tnewton-restart ‐ Truncated Newton with steepest-descent restarting
gn-direct ‐ Dividing Rectangles
ln-neldermead ‐ Nelder-Mead simplex algorithm
ln-cobyla ‐ Constrained Optimization BY Linear Approximation
gn-crs2-lm ‐ Controlled Random Search with Local Mutation
ld-var2 ‐ Shifted Limited-Memory Variable-Metric, Rank 2
ld-var1 ‐ Shifted Limited-Memory Variable-Metric, Rank 1
ld-mma ‐ Method of Moving Asymptotes
ld-lbfgs-nocedal ‐ None
ld-lbfgs ‐ Low-storage BFGS
gn-direct-l ‐ Dividing Rectangles (locally biased)
none ‐ don't specify algorithm
ln-bobyqa ‐ Derivative-free Bound-constrained Optimization
ln-sbplx ‐ Subplex variant of Nelder-Mead
ln-newuoa-bound ‐ Derivative-free Bound-constrained Optimization by
Iteratively Constructed Quadratic Approximation
ln-praxis ‐ Gradient-free Local Optimization via the Principal-Axis
Method
gn-direct-noscal ‐ Dividing Rectangles (unscaled)
ld-tnewton-precond-restart ‐ Preconditioned Truncated Newton with
steepest-descent restarting
lower = -inf; double
Lower boundary (equal for all parameters).
maxiter = 100; int in [1, inf)
Stopping criterion: the maximum number of iterations.
opt = ld-lbfgs; dict
main minimization algorithm. Supported values are:
gn-orig-direct-l ‐ Dividing Rectangles (original implementation,
locally biased)
g-mlsl-lds ‐ Multi-Level Single-Linkage (low-discrepancy-sequence,
require local gradient based optimization and bounds)
gn-direct-l-noscal ‐ Dividing Rectangles (unscaled, locally biased)
gn-isres ‐ Improved Stochastic Ranking Evolution Strategy
ld-tnewton ‐ Truncated Newton
gn-direct-l-rand ‐ Dividing Rectangles (locally biased, randomized)
ln-newuoa ‐ Derivative-free Unconstrained Optimization by Iteratively
Constructed Quadratic Approximation
gn-direct-l-rand-noscale ‐ Dividing Rectangles (unscaled, locally
biased, randomized)
gn-orig-direct ‐ Dividing Rectangles (original implementation)
ld-tnewton-precond ‐ Preconditioned Truncated Newton
ld-tnewton-restart ‐ Truncated Newton with steepest-descent restarting
gn-direct ‐ Dividing Rectangles
auglag-eq ‐ Augmented Lagrangian algorithm with equality constraints
only
ln-neldermead ‐ Nelder-Mead simplex algorithm
ln-cobyla ‐ Constrained Optimization BY Linear Approximation
gn-crs2-lm ‐ Controlled Random Search with Local Mutation
ld-var2 ‐ Shifted Limited-Memory Variable-Metric, Rank 2
ld-var1 ‐ Shifted Limited-Memory Variable-Metric, Rank 1
ld-mma ‐ Method of Moving Asymptotes
ld-lbfgs-nocedal ‐ None
g-mlsl ‐ Multi-Level Single-Linkage (require local optimization and
bounds)
ld-lbfgs ‐ Low-storage BFGS
gn-direct-l ‐ Dividing Rectangles (locally biased)
ln-bobyqa ‐ Derivative-free Bound-constrained Optimization
ln-sbplx ‐ Subplex variant of Nelder-Mead
ln-newuoa-bound ‐ Derivative-free Bound-constrained Optimization by
Iteratively Constructed Quadratic Approximation
auglag ‐ Augmented Lagrangian algorithm
ln-praxis ‐ Gradient-free Local Optimization via the Principal-Axis
Method
gn-direct-noscal ‐ Dividing Rectangles (unscaled)
ld-tnewton-precond-restart ‐ Preconditioned Truncated Newton with
steepest-descent restarting
ld-slsqp ‐ Sequential Least-Squares Quadratic Programming
step = 0; double in [0, inf)
Initial step size for gradient free methods.
stop = -inf; double
Stopping criterion: function value falls below this value.
xtola = 0; double in [0, inf)
Stopping criterion: the absolute change of all x-values is below this
value.
xtolr = 0; double in [0, inf)
Stopping criterion: the relative change of all x-values is below this
value.
EXAMPLE
Register the perfusion series given in 'segment.set' by using Pseudo Ground Truth
estimation. Skip two images at the beginning and otherwiese use the default parameters.
Store the result in 'registered.set'.
mia-2dmyopgt-nonrigid -i segment.set -o registered.set -k 2
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'.