Provided by: mia-tools_2.0.13-1_amd64 
NAME
mia-2dmyoica-nonrigid2 - Run a registration of a series of 2D images.
SYNOPSIS
mia-2dmyoica-nonrigid2 -i <in-file> -o <out-file> [options]
DESCRIPTION
mia-2dmyoica-nonrigid2 This program runs the non-rigid registration of an perfusion image
series.In each pass, first an ICA analysis is run to estimate and eliminate the periodic
movement and create reference images with intensities similar to the corresponding
original image. Then non-rigid registration is run using the an "ssd + divcurl" cost
model. The B-spline c-rate and the divcurl cost weight are changed in each pass according
to given parameters.In the first pass a bounding box around the LV myocardium may be
extractedto speed up computation Special note to this implemnentation: the registration is
always run from the original images to avoid the accumulation of interpolation errors.
OPTIONS
File-IO
-i --in-file=(required)
input perfusion data set
-o --out-file=(required)
output perfusion data set
-r --registered=reg
file name base for registered fiels
--save-cropped=
save cropped set to this file
--save-feature=
save segmentation feature images and initial ICA mixing matrix
ICA
-C --components=0
ICA components 0 = automatic estimation
--normalize
don't normalized ICs
--no-meanstrip
don't strip the mean from the mixing curves
-s --segscale=0
segment and scale the crop box around the LV (0=no segmentation)
-k --skip=0
skip images at the beginning of the series e.g. because as they are of other
modalities
-m --max-ica-iter=400
maximum number of iterations in ICA
-E --segmethod=features
Segmentation method
delta-peak ‐ difference of the peak enhancement images
features ‐ feature images
delta-feature ‐ difference of the feature images
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
-p --interpolator=bspline:d=3
image interpolator kernel For supported plugins see PLUGINS:1d/splinekernel
-l --mg-levels=3
multi-resolution levels
-P --passes=3
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
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/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: minimizer/singlecost
gdsq Gradient descent with quadratic step estimation, supported parameters are:
ftolr = 0 (double)
Stop if the relative change of the criterion is below.. in [0, INF]
gtola = 0 (double)
Stop if the inf-norm of the gradient is below this value.. in [0, INF]
maxiter = 100 (uint)
Stopping criterion: the maximum number of iterations. in [1, 2147483647]
scale = 2 (double)
Fallback fixed step size scaling. in [1, INF]
step = 0.1 (double)
Initial step size. in [0, INF]
xtola = 0 (double)
Stop if the inf-norm of x-update is below this value.. in [0, INF]
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)
gradient based optimizers: stop when |grad| < eps, simplex: stop when
simplex size < eps.. in [1e-10, 10]
iter = 100 (int)
maximum number of iterations. in [1, 2147483647]
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)
initial step size. in [0, 10]
tol = 0.1 (double)
some tolerance parameter. in [0.001, 10]
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)
Stopping criterion: the absolute change of the objective value is below
this value. in [0, INF]
ftolr = 0 (double)
Stopping criterion: the relative change of the objective value is below
this value. in [0, INF]
higher = inf (double)
Higher boundary (equal for all parameters). in [INF, INF]
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). in [INF, INF]
maxiter = 100 (int)
Stopping criterion: the maximum number of iterations. in [1, 2147483647]
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)
Initial step size for gradient free methods. in [0, INF]
stop = -inf (double)
Stopping criterion: function value falls below this value. in [INF, INF]
xtola = 0 (double)
Stopping criterion: the absolute change of all x-values is below this
value. in [0, INF]
xtolr = 0 (double)
Stopping criterion: the relative change of all x-values is below this
value. in [0, INF]
EXAMPLE
Register the perfusion series given in 'segment.set' by using automatic ICA estimation.
Skip two images at the beginning and otherwiese use the default parameters. Store the
result in 'registered.set'.
mia-2dmyoica-nonrigid2 -i segment.set -o registered.set -k 2
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'.