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mia-2dmyopgt-nonrigid(1) | General Commands Manual | mia-2dmyopgt-nonrigid(1) |
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 described 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 weight
- -B --beta=1
- temporal second derivative penalty weight
- -R --rho-thresh=0.85
- correlation threshold for neighborhood analysis
- -k --skip=0
- skip 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 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 pass
- --c-rate-divider=4
- cofficient rate divider for each pass
- -d --start-divcurl=20
- start divcurl weight, gets divided by --divcurl-divider with every pass
- --divcurl-divider=4
- divcurl weight scaling with each new pass
- -w --imageweight=1
- image cost weight
- -l --mg-levels=3
- multi-resolution levels
- -P --passes=4
- registration 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).
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 of the 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 WollnyCOPYRIGHT¶
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'.v2.4.6 | USER COMMANDS |