mia-2dmyopgt-nonrigid {-i string} {-o string} [ options ...]


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.



-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

-r, --registered=reg; stringSTRING

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; double

spacial neighborhood penalty weight

-B, --beta=1; double

temporal second derivative penalty weight

-R, --rho-thresh=0.85; double

crorrelation threshhold for neighborhood analysis

-k, --skip=0; ulong

skip images at the beginning of the series e.g. because as they are of other modalities


-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=32; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass

--c-rate-divider=4; double

cofficient rate divider for each pass

-d, --start-divcurl=20; double

start divcurl weight, gets divided by --divcurl-divider with every pass

--divcurl-divider=4; double

divcurl weight scaling with each new pass

-w, --imageweight=1; double

image cost weight

-l, --mg-levels=3; ulong

multi-resolution levels

-P, --passes=4; ulong

registration passes

Help & Info

-V, --verbose=warning; dict

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
error:Report errors
debug:Debug output
message:Normal messages
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit


--threads=-1; int

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).


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


Gert Wollny