Provided by: mia-tools_2.4.6-5build3_amd64 
NAME
mia-2dmyomilles - Run a registration of a series of 2D images.
SYNOPSIS
mia-2dmyomilles -i <in-file> -o <out-file> [options]
DESCRIPTION
mia-2dmyomilles This program is use to run a modified version of the ICA based registration approach
described in Milles et al. 'Fully Automated Motion Correction in First-Pass Myocardial Perfusion MR Image
Sequences', Trans. Med. Imaging., 27(11), 1611-1621, 2008. Changes include the extraction of the quasi-
periodic movement in free breathingly acquired data sets and the option to run affine or rigid
registration instead of the optimization of translations only.
OPTIONS
File-IO
-i --in-file=(required, input); string
input perfusion data set
-o --out-file=(required, output); string
output perfusion data set
-r --registered=
file name base for registered files
--save-references=
save synthetic reference images to this file base
--save-cropped=
save cropped image set to this file
--save-feature=
save the features images resulting from the ICA and some intermediate images used for the
RV-LV segmentation with the given file name base to PNG files. Also save the coefficients
of the initial best and the final IC mixing matrix.
Help & Info
-V --verbose=warning
verbosity of output, print messages of given level and higher priorities. Supported
priorities starting at lowest level are:
trace ‐ Function call trace
debug ‐ Debug output
info ‐ Low level messages
message ‐ Normal messages
warning ‐ Warnings
fail ‐ Report test failures
error ‐ Report errors
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
ICA
--fastica=internal
FastICA implementationto be used
For supported plugins see PLUGINS:fastica/implementation
-C --components=0
ICA components 0 = automatic estimation
--normalize
normalized ICs
--no-meanstrip
don't strip the mean from the mixing curves
-g --guess
use initial guess for myocardial perfusion
-s --segscale=1.4
segment and scale the crop box around the LV (0=no segmentation)
-k --skip=0
skip images at the beginning of the series as they are of other modalities
-m --max-ica-iter=400
maximum number of iterations in ICA
-E --segmethod=features
Segmentation method
delta-feature ‐ difference of the feature images
delta-peak ‐ difference of the peak enhancement images
features ‐ feature images
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).
Registration
-c --cost=ssd
registration criterion
-O --optimizer=gsl:opt=simplex,step=1.0
Optimizer used for minimization
For supported plugins see PLUGINS:minimizer/singlecost
-f --transForm=rigid
transformation type
For supported plugins see PLUGINS:2dimage/transform
-l --mg-levels=3
multi-resolution levels
-R --reference=-1
Global reference all image should be aligned to. If set to a non-negative value, the images
will be aligned to this references, and the cropped output image date will be injected into
the original images. Leave at -1 if you don't care. In this case all images with be
registered to a mean position of the movement
-P --passes=2
registration passes
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 in [0, 5]
Spline degree.
omoms OMoms-spline kernel creation, supported parameters are:
d = 3; int in [3, 3]
Spline degree.
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]]; 2dfvector
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]]; 2dfvector
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 in [1, inf)
isotropic coefficient rate in pixels.
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 in [0, inf)
penalty weight on curl.
div = 1; float in [0, inf)
penalty weight on divergence.
norm = 0; bool
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.
PLUGINS: fastica/implementation
internal This is the MIA implementation of the FastICA algorithm.
(no parameters)
itpp This is the IT++ implementation of the FastICA algorithm.
(no parameters)
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:
simplex ‐ Simplex algorithm of Nelder and Mead
cg-fr ‐ Flecher-Reeves conjugate gradient algorithm
cg-pr ‐ Polak-Ribiere conjugate gradient algorithm
bfgs ‐ Broyden-Fletcher-Goldfarb-Shann
bfgs2 ‐ Broyden-Fletcher-Goldfarb-Shann (most efficient version)
gd ‐ Gradient descent.
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-direct ‐ Dividing Rectangles
gn-direct-l ‐ Dividing Rectangles (locally biased)
gn-direct-l-rand ‐ Dividing Rectangles (locally biased, randomized)
gn-direct-noscal ‐ Dividing Rectangles (unscaled)
gn-direct-l-noscal ‐ Dividing Rectangles (unscaled, locally biased)
gn-direct-l-rand-noscale ‐ Dividing Rectangles (unscaled, locally biased, randomized)
gn-orig-direct ‐ Dividing Rectangles (original implementation)
gn-orig-direct-l ‐ Dividing Rectangles (original implementation, locally biased)
ld-lbfgs-nocedal ‐ None
ld-lbfgs ‐ Low-storage BFGS
ln-praxis ‐ Gradient-free Local Optimization via the Principal-Axis Method
ld-var1 ‐ Shifted Limited-Memory Variable-Metric, Rank 1
ld-var2 ‐ Shifted Limited-Memory Variable-Metric, Rank 2
ld-tnewton ‐ Truncated Newton
ld-tnewton-restart ‐ Truncated Newton with steepest-descent restarting
ld-tnewton-precond ‐ Preconditioned Truncated Newton
ld-tnewton-precond-restart ‐ Preconditioned Truncated Newton with steepest-descent
restarting
gn-crs2-lm ‐ Controlled Random Search with Local Mutation
ld-mma ‐ Method of Moving Asymptotes
ln-cobyla ‐ Constrained Optimization BY Linear Approximation
ln-newuoa ‐ Derivative-free Unconstrained Optimization by Iteratively Constructed
Quadratic Approximation
ln-newuoa-bound ‐ Derivative-free Bound-constrained Optimization by Iteratively
Constructed Quadratic Approximation
ln-neldermead ‐ Nelder-Mead simplex algorithm
ln-sbplx ‐ Subplex variant of Nelder-Mead
ln-bobyqa ‐ Derivative-free Bound-constrained Optimization
gn-isres ‐ Improved Stochastic Ranking Evolution Strategy
none ‐ don't specify algorithm
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-direct ‐ Dividing Rectangles
gn-direct-l ‐ Dividing Rectangles (locally biased)
gn-direct-l-rand ‐ Dividing Rectangles (locally biased, randomized)
gn-direct-noscal ‐ Dividing Rectangles (unscaled)
gn-direct-l-noscal ‐ Dividing Rectangles (unscaled, locally biased)
gn-direct-l-rand-noscale ‐ Dividing Rectangles (unscaled, locally biased, randomized)
gn-orig-direct ‐ Dividing Rectangles (original implementation)
gn-orig-direct-l ‐ Dividing Rectangles (original implementation, locally biased)
ld-lbfgs-nocedal ‐ None
ld-lbfgs ‐ Low-storage BFGS
ln-praxis ‐ Gradient-free Local Optimization via the Principal-Axis Method
ld-var1 ‐ Shifted Limited-Memory Variable-Metric, Rank 1
ld-var2 ‐ Shifted Limited-Memory Variable-Metric, Rank 2
ld-tnewton ‐ Truncated Newton
ld-tnewton-restart ‐ Truncated Newton with steepest-descent restarting
ld-tnewton-precond ‐ Preconditioned Truncated Newton
ld-tnewton-precond-restart ‐ Preconditioned Truncated Newton with steepest-descent
restarting
gn-crs2-lm ‐ Controlled Random Search with Local Mutation
ld-mma ‐ Method of Moving Asymptotes
ln-cobyla ‐ Constrained Optimization BY Linear Approximation
ln-newuoa ‐ Derivative-free Unconstrained Optimization by Iteratively Constructed
Quadratic Approximation
ln-newuoa-bound ‐ Derivative-free Bound-constrained Optimization by Iteratively
Constructed Quadratic Approximation
ln-neldermead ‐ Nelder-Mead simplex algorithm
ln-sbplx ‐ Subplex variant of Nelder-Mead
ln-bobyqa ‐ Derivative-free Bound-constrained Optimization
gn-isres ‐ Improved Stochastic Ranking Evolution Strategy
auglag ‐ Augmented Lagrangian algorithm
auglag-eq ‐ Augmented Lagrangian algorithm with equality constraints only
g-mlsl ‐ Multi-Level Single-Linkage (require local optimization and bounds)
g-mlsl-lds ‐ Multi-Level Single-Linkage (low-discrepancy-sequence, require local
gradient based optimization and bounds)
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 automatic ICA estimation. Skip two images
at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.
mia-2dmyomilles -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'.